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Pocket guide to clinical microbiology 4th Edition
Christopher D. Doern Digital Instant Download
Author(s): Christopher D. Doern
ISBN(s): 9781683670063, 168367006X
Edition: 4
File Details: PDF, 3.75 MB
Year: 2018
Language: english
 4 TH EDITION

Pocket Guide to
Clinical
Microbiology

Christopher D. Doern
 4 TH EDITION

POCKET GUIDE TO

Clinical
Microbiology
 4 TH EDITION

POCKET GUIDE TO

Clinical
Microbiology
Christopher D. Doern, PhD, D(ABMM)
Assistant Professor, Pathology
Director of Clinical Microbiology
Virginia Commonwealth University Health System
Medical College of Virginia Campus

Washington, DC
Copyright © 2018 Amer­i­can Society for Microbiology. All rights re­served.
No part of this pub­li­ca­tion may be re­pro­duced or trans­mit­ted in whole or
in part or re­used in any form or by any means, elec­tronic or me­chan­i­cal,
in­clud­ing pho­to­copy­ing and re­cord­ing, or by any in­for­ma­tion stor­age and
re­trieval sys­tem, with­out­ per­mis­sion in writ­ing from the pub­lish­er.

Disclaimer: To the best of the pub­lish­er’s knowl­edge, this pub­li­ca­tion pro­

vi­des in­for­ma­tion con­cern­ing the sub­ject mat­ter cov­ered that is ac­cu­rate as
of the date of pub­li­ca­tion. The pub­lisher is not pro­vid­ing le­gal, med­i­cal, or
other pro­fes­sional ser­vices. Any ref­er­ence herein to any spe­cific com­mer­cial
prod­ucts, pro­ce­dures, or ser­vices by trade name, trade­mark, man­u­fac­turer,
or oth­er­wise does not con­sti­tute or im­ply en­dorse­ment, rec­om­men­da­tion, or
fa­vored sta­tus by the Amer­i­can Society for Microbiology (ASM). The views
and opin­ions of the au­thor(s) ex­pressed in this pub­li­ca­tion do not nec­es­sar­ily
state or re­flect those of ASM, and they shall not be used to ad­ver­tise or en­
dorse any prod­uct.

Library of Congress Cataloging-in-Publication Data

Names: Doern, Chris­to­pher D., au­thor.

Title: Pocket guide to clin­i­cal mi­cro­bi­ol­ogy / Chris­to­pher D. Doern.
Description: Fourth edi­tion. | Wash­ing­ton, DC : ASM Press, 2018.
Identifiers: LCCN 2018008388 | ISBN 9781683670063 (pbk. : alk. pa­per)
Subjects: LCSH: Medical mi­cro­bi­ol­o­gy—Handbooks, man­u­als, etc.
Classification: LCC QR46 .M92 2018 | DDC 616.9/041—dc23 LC re­cord
avail­­able at https://​lccn.​loc.​gov/​2018008388

doi:10.1128/9781683670070

All Rights Reserved

Printed in the United States of Amer­i­ca

10 9 8 7 6 5 4 3 2 1

Address ed­i­to­r ial cor ­re­spon­dence to

ASM Press, 1752 N St., N.W.,
Wash­ing­ton, DC 20036-2904, USA

Send or­ders to ASM Press, P.O. Box 605, Hern­don, VA 20172, USA
Phone: 800-546-2416; 703-661-1593
Fax: 703-661-1501
E-mail: books@asmusa.​org
Online: http://​www.​asmscience.​org
To Drs. Carey-Ann Burnham, Mike Dunne, and
Betz Forbes: invaluable mentors and dear friends.
Contents

Preface xiii
About the Author xv

SECTION 1
Taxonomic Classification of Medically Important
Microorganisms 1
Ge­ne­ral Comments 2
Taxonomic Classification of Bacteria 2
Taxonomic Classification of Human Viruses 9
Taxonomic Classification of Fungi 13
Taxonomic Classification of Parasites 13

SECTION 2
Indigenous and Pathogenic Microbes of Humans 19
Ge­ne­ral Comments 20
Table 2.1 Human Indigenous Flora 22
Microbes Responsible for Human Disease 34
Summary of Notifiable Infectious Diseases:
United States, 2015 54
Table 2.2 Arthropod Vectors of Medically Important
Diseases 58
Table 2.3 Fungal Pathogens and Geographic Distribution 61
Table 2.4 Parasitic Pathogens and Geographic Distribution 71

SECTION 3
Specimen Collection and Transport 81
Ge­ne­ral Comments 82
Table 3.1 Bacteriology: Collection and
Transport Guidelines 84
viii Contents
Table 3.2 Specimen Collection and Transport Guidelines
for Infrequently Encountered Bacteria 105
Table 3.3 Guidelines for Collection of Specimens
for Anaerobic Culture 107
Virology: Ge­ne­ral Specimen Guidelines 107
Virology: Specific Specimen Guidelines 108
Table 3.4 Recommended Blood Volumes to
Collect for Blood Cultures 111
Table 3.5 Mycology: Collection and Transport Guidelines 112
Table 3.6 Parasitology: Specimen Guidelines 117
Table 3.7 Guidelines for Processing Stool Specimens
for Parasites 124

SECTION 4 127
Bacterial Diagnosis 127
Ge­ne­ral Comments 128
Table 4.1 Detection Methods for Bacteria 129
Table 4.2 Recommendations for Gram Stain and
Plating Media 133
Table 4.3 Screening Specimens for Routine Bacterial
Culture 137
Table 4.4 Processing Specimens for Mycobacterial
Identification 138
Microscopy 139
Primary Plating Media: Bacteria 141
Primary Plating Media: Mycobacteria 154
Specific Diagnostic Tests 157
Aerobic Gram-Positive Cocci 157
Aerobic Gram-Positive Rods 158
Acid-Fast and Partially Acid-Fast Gram-Positive Rods 160
Aerobic Gram-Negative Cocci 161
Aerobic Gram-Negative Rods 161
Anaerobic Bacteria 168
Curved and Spiral-Shaped Bacteria 170
Mycoplasma spp. and Obligate Intracellular
Bacteria 172
Identification Tables 175
 Contents ix
SECTION 5
Viral Diagnosis 219
Ge­ne­ral Comments 220
Table 5.1 Detection Methods for Viruses 221
Table 5.2 Cells Used for Viral Isolation 224
RNA Viruses 225
DNA Viruses 232
Transmissible Spongiform Encephalopathies 239

SECTION 6
Fungal Diagnosis 241
Mycology Specimen Collection and Transport
Guidelines 242
Table 6.1 Methods for the Identification of Fungi 245
Microscopy 246
Table 6.2 Characteristic Fungal Elements Seen by Direct
Examination of Clinical Specimens 248
Primary Plating Media 254
Table 6.3 Mycology Plating Guide 256
Specific Diagnostic Tests 258
Aspergillus Species 258
Blastomyces dermatitidis 258
Candida Species 259
Coccidioides Species 259
Cryptococcus Species 260
Histoplasma capsulatum 260
Malassezia Species 261
Paracoccidioides brasiliensis 261
Talaromyces (Penicillium) marneffei 262
Pneu­mo­cys­tis jiroveci 262
Sporothrix schenckii 262
Zygomycetes 262
Identification Tables 264
x Contents
SECTION 7
Parasitic Diagnosis 285
Ge­ne­ral Comments 286
Table 7.1 Detection Methods for Parasites 287
Microscopy 290
Specific Diagnostic Tests 291
Free-Living Amebae 291
Intestinal and Urogenital Protozoa 292
Blood and Tissue Protozoa 294
Microsporidia 297
Helminths: Nematodes 297
Helminths: Trematodes 299
Helminths: Cestodes 300
Identification Tables and Figures 302
Table 7.2 Trophozoites of Common Intestinal Amebae 302
Table 7.3 Cysts of Common Intestinal Amebae 305
Figure 7.1 Intestinal Amebae of Humans 308
Table 7.4 Trophozoites of Flagellates 309
Table 7.5 Cysts of Flagellates 311
Figure 7.2 Intestinal and Urogenital Flagellates
of Humans 312
Table 7.6 Morphological Characteristics of
Ciliates, Coccidia, Microsporidia, and Tissue
Protozoa 313
Table 7.7 Morphological Characteristics of
Protozoa Found in Blood 315
Table 7.8 Morphological Characteristics of
Blood and Tissue Nematodes 317
Table 7.9 Morphological Characteristics
of Helminths 318
Figure 7.3 Relative Sizes of Helminth Eggs 320

SECTION 8
Vaccines, Susceptibility Testing, and Methods
of Organism Identification 323
Ge­ne­ral Comments 324
Table 8.1 Recommended pe­di­at­ric im­mu­ni­za­tion sched­ule 325
 Contents xi
Table 8.2 Recommended adult im­mu­ni­za­tion sched­ule 328
Table 8.3 Clinical and Laboratory Standards Institute (CLSI)
doc­u­ments re­lated to an­ti­mi­cro­bial sus­cep­ti­bil­ity
test­ing from hu­mans 330
Table 8.4 Summary of CLSI an­ti­mi­cro­bial sus­cep­ti­bil­ity
test meth­ods for se­lect bac­te­ria, my­co­bac­te­ria, and fun­gi 332
Table 8.5 Routes of ad­min­is­tra­tion and drug class
for se­lect an­ti­mi­cro­bial agents 337
Table 8.6 Routes of ad­min­is­tra­tion and drug class
for se­lect an­ti­fun­gal agents 342
Table 8.7 Routes of ad­min­is­tra­tion and drug class
for se­lect an­ti­par­a­sitic agents 343
Table 8.8 Antibacterial agents for spe­cific bac­te­ria 345
Table 8.9 Intrinsic re­sis­tance of se­lected Gram-negative
bac­te­ria 354
Table 8.10 Intrinsic re­sis­tance of se­lected Gram
pos­i­tive bac­te­ria 356
Table 8.11 Important mech­a­nisms of mul­ti­drug re­sis­tance
in bac­te­ria. 358
Table 8.12 Organisms in­cluded in CLSI and EUCAST breakpoint
ta­bles 361
Table 8.13 Guide to in­ter­pre­tive cri­te­ria for se­lect or­gan­isms
for com­monly tested an­ti­mi­cro­bi­als 364
Table 8.14 Summary of MALDI-TOF MS iden­ti­fi­ca­tion
of bac­te­ria, my­co­bac­te­ria, and fun­gi 374
Table 8.15 Gene se­quenc­ing tar­gets for or­gan­ism
iden­ti­fi­ca­tion 380

Index 383
Preface

The Pocket Guide to Clinical Microbiology is unique among ref­er­

ence texts in that its pri­mary pur­pose is to pres­ent us­able in­for­ma­
tion in a con­cise and ac­ces­si­ble man­ner. Now in its fourth edi­tion,
this iconic text has re­mained pop­u­lar over the years be­cause it has
suc­cess­fully con­densed most of the in­for­ma­tion needed by the prac­
tic­ing clin­i­cal mi­cro­bi­ol­o­gist into a pock­et-sized guide. As Dr. Pat­
rick Mur­ray ar­tic­u­lated in the pref­ace of the third edi­tion, with
each it­er­a­tion of this text the for­mat has been honed to en­hance its
us­abil­ity. Although the over­all for­mat of the fourth edi­tion re­
mains true to the tem­plate of pre­vi­ous edi­tions, this edi­tion re­flects
the tre­men­dous evo­lu­tion that has oc­curred in clin­i­cal mi­cro­bi­ol­ogy
over the past de­cade. In par­tic­u­lar, three key ad­vances have re­shaped
the prac­tice of clin­i­cal mi­cro­bi­ol­ogy, and have there­fore, re­shaped
this edi­tion.
First, the wide­spread adop­tion of ma­trix-assisted la­ser de­sorp­tion/
ionization time-of-flight mass spec­trom­e­try (MALDI-TOF MS)
for or­gan­ism iden­ti­fi­ca­tion has al­tered the way many lab­o­ra­to­ries
prac­tice clin­i­cal mi­cro­bi­ol­ogy. Despite the fact that those us­ing
MALDI-TOF MS are less de­pen­dent on bio­chem­i­cal re­ac­tions to
iden­tify or­gan­isms, un­der­stand­ing bio­chem­i­cal pro­files is still re­
quired for the trou­ble­shoot­ing of failed or am­big­u­ous MALDI-TOF
MS iden­ti­fi­ca­tions. As such, this text has up­dated, but main­tained,
much of the bio­chem­i­cal re­ac­tions re­quired to iden­tify or­gan­isms
the “old school” way. It is my be­lief that un­der­stand­ing and us­ing
these re­ac­t ions to con­fi rm or­gan­ism iden­t i­fi­ca­t ions, re­mains one
of the foun­da­tions of good clin­i­cal mi­cro­bi­ol­ogy. This pocket guide
should pro­vide quick ref­er­ence to ev­ery­t hing the mi­cro­bi­ol­o­gist
needs to con­fi­dently iden­tify most or­gan­isms en­coun­tered in the
clin­i­cal lab­o­ra­tory. In ad­di­tion, new in­for­ma­tion has been added in
Section 8 that out­­lines the spe­cif­ics of MALDI-TOF MS per­for­
mance for in­di­vid­ual bac­te­ria, my­co­bac­te­r ia, and fun­gi.
Second, the de­vel­op­ment of mo­lec­u­lar tech­niques has rev­o­lu­
tion­ized the di­ag­no­sis of in­fec­tious dis­eases. Most no­ta­bly, nu­cleic
acid am­pli­fi­ca­tion test­ing (NAATs), also re­ferred to as po­ly­mer­ase
chain re­ac­tion (PCR), has dras­ti­cally changed the prac­tice of clin­i­cal
xiii
xiv Preface
vi­rol­ogy to the ex­tent that many lab­o­ra­to­r ies no lon­ger per­form
vi­ral cul­ture. Information re­gard­ing vi­ral cul­ture has been re­tained
in this guide for labs still per­form­ing those tech­niques, but sig­nif­
i­cant ad­di­tions have been made through­out­this edi­tion to re­flect
the use of mo­lec­u­lar di­ag­nos­tics. Also, be­cause gene se­quenc­ing is
now a com­mon tech­nique used to iden­tify bac­te­ria and fungi, Sec­
tion 8 con­tains new in­for­ma­tion to help in­ter­pret these re­sults.
Third, the con­tin­ued emer­gence of an­ti­mi­cro­bial re­sis­tance poses
sig­nif­i­cant chal­lenges to clin­i­cal mi­cro­bi­ol­o­gists as we strug­gle to
pro­vide treat­ment op­tions for in­creas­ingly dif­fi­cult-to-treat or­gan­
isms. To re­flect this re­al­ity, sig­nif­i­cant changes have been made to
this pocket guide to help the mi­cro­bi­ol­o­gist bet­ter per­form and in­
ter­pret an­ti­mi­cro­bial sus­cep­ti­bil­ity test­ing in the era of mul­ti­drug
re­sis­t ance. Acknowledging the in­ter­na­t ional ap­p eal of this text,
I added new ta­bles out­lin­ing guid­ance pro­vided by both the Clini­
cal and Laboratory Standards Institute (CLSI) and the Eu­ro­pean
Committee on Antimicrobial Susceptibility Testing (EUCAST).
The goal of these ta­bles is to help the reader eas­ily un­der­stand what
meth­ods can be used, and what in­ter­pre­tive cri­te­r ia ex­ist, for most
or­gan­ism/antibiotic com­bi­na­tions. Also in­cluded are ta­bles with im­
por­tant in­trin­sic re­sis­tance pro­files for com­monly en­coun­tered or­
gan­isms, as well as key mech­a­nisms of re­sis­tance.
Sir Isaac Newton once said, “If I have seen fur­ther than oth­ers,
it is by stand­ing on the shoul­ders of gi­ants.” Although I have no
il­lu­sions that I have “seen fur­ther” than any­one else, the hu­m il­ity
ex­pressed in this quote res­o­nates with me as I have un­der­taken the
task of up­dat­ing a text that was con­ceived and au­thored by Dr. Pat­
rick Mur­ray, one of the true gi­ants of clin­i­cal mi­cro­bi­ol­ogy. So first
and fore­most, I thank him for his work mak­ing this pocket guide
the re­spected re­source that it is. I hope that the fourth edi­tion will
do jus­tice to the tra­di­tion of this text. In ad­di­tion, I want to thank
the tal­ented, and pa­tient, pro­fes­sion­als at ASM Press. Specifically,
Chris­tine Charlip and Larry Klein, along with what I’m sure are
count­less oth­ers at ASM, war­rant spe­cial thanks for all­their work.
And last, I thank my wife Kelli, who pro­vided sup­port and un­der­
stand­ing through the many late nights and week­ends it took to
com­plete this pro­ject. I could not have fin­ished this pro­ject were it
not for her sup­port.
The prac­tice of clin­i­cal mi­cro­bi­ol­ogy is a won­der­ful dis­ci­pline,
re­quir­ing judge­ment, in­ves­ti­ga­tion, and crit­i­cal de­ci­sion-making
to pro­duce qual­ity re­sults. It is my hope that you will find this pocket
guide to be a us­er-friendly ref­er­ence that en­hances your abil­ity to
do all­of these things, and ul­ti­mately pro­vide the best pa­tient care
pos­si­ble.
Chris­to­pher D. Doern
About the Author

Christopher Doern, PhD, D(ABMM), is an Assistant Professor of

Pathology and the Director of Clinical Microbiology at the V
­ irginia
Commonwealth University Health System, Richmond, ­Virginia.
He earned his undergraduate and doctoral degrees from Wake Forest
University in Winston-­Salem, North Carolina. Doern went on to
a fellowship in Medical and Public Health Microbiology at the
Washington University School of Medicine, St. Louis, Missouri,
and is certified by the American Board of Medical Microbiology
(ABMM).

Doern is an active member of the clinical microbiology community

and serves on the ABMM, ASM Clinical Laboratory Practices Com­
mittee, Clinical Chemistry Trainee Council, and several Clinical
and Laboratory Standards Institute document development and
revision committees. He is an editor for the Clinical Microbiology
Newsletter and serves on the Journal of Clinical Microbiology and
Pediatric Infectious Diseases Journal editorial boards.

Doern is involved in educational programs that reach an interna­

tional audience. Among ­these is the Medical Microbiology Question
of the Day (www​.­pathquestions​.­com), for which he has been an edi­
tor since 2011. This ser­vice provides freely accessible educational
material to participants in more than 60 countries

xv
SECTION 1

Taxonomic Classification
of Medically Important
Microorganisms
Ge­ne­ral Comments 2
Taxonomic Classification of Bacteria 2
Taxonomic Classification of Human Viruses 9
Taxonomic Classification of Fungi 13
Taxonomic Classification of Parasites 13

doi:10.1128/9781683670070.ch1
 2 SECTION 1
In or­der to re­main true to the tra­di­tion set forth by the first three
edi­tions of this pocket guide, the first sec­tion will be de­voted to de­
Taxonomic Classification

scrib­ing the tax­on­omy of com­mon (and some un­com­mon) or­gan­

isms which are as­so­ci­ated with hu­mans and may be iso­lated by the
Clinical Microbiology Laboratory. Unfortunately, in the 13 or so
years that have passed since the third edi­tion of the Pocket Guide
was pub­lished, the rate of tax­o­nomic changes has con­tin­ued to in­
crease such that pub­lish­ing a tax­o­nomic list of or­gan­isms would be
out­of date be­fore this book goes to pub­li­ca­tion. This is a prod­uct
of con­tin­ued pro­lif­er­a­tion of new spe­cies of or­gan­isms which are
be­ing iden­ti­fied by in­creas­ingly so­phis­ti­cated ge­no­mic an­a­ly­ses. As
such, the re­vi­sed goal of this sec­tion will be to out­­line some high-
level tax­o­nomic group­i ngs and pro­vide the re­sources and ref­er­
ences one would need to iden­tify the most up-to-date tax­o­nomic
clas­si­fi­ca­tions.
It should be ap­pre­ci­ated that de­spite ap­pear­ances, changes in no­
men­cla­ture are reg­u­lated by a sys­tem of rules with over­sight gov­
erned by the International Code of Biological Nomenclature (www​
.​biosis.​org.​uk/​zrdocs/​codes/​codes.​htm). The International Code of
Nomenclature of Bacteria gov­erns bac­te­rial tax­on­omy, and all­bac­
te­r ia named af­ter 1980 must be val­idly pub­lished in the Interna-
tional Journal of Systematic and Evolutionary Microbiology. A
cur­rent list­ing of bac­te­r ia can be found at http://​www.​bacterio.​net,
http://​www.​bacterio.​cict.​fr/​, and https://​www.​dsmz.​de/​.​ The Inter­
national Committee on Taxonomy of Viruses (ICTV) governs viral
taxonomy, and all currently recognized viruses can be found at
https://​talk.​ictvonline.​org//​.​ The International Code of Botanical
Nomenclature gov­erns fun­gal clas­si­fi­ca­tion, and ad­di­tional in­for­ma­
tion can be found at http://​www.​iapt-​taxon.​org/​nomen/​main.​php/.

Taxonomic Classification of Bacteria

Classification and tax­on­omy of pro­kary­otes (bac­te­r ia) is com­pli­
cated and is gov­erned by the International Code of Nomenclature
of Bacteria (last re­vi­sed in 1990). By def­i­ni­tion, each pro­kary­otic
spe­cies must in­clude a ge­nus-level name that is in­cluded within a
hi­er­a r­chy or ranks, which in­cludes (from high­est to low­est rank)
sub­tribe, tribe, sub­fam­ily, fam­ily, sub­or­der, or­der, sub­class, class,
di­vi­sion (or phy­lum), and do­main (or em­pire). To fur­ther com­pli­cate
mat­ters, the tribe and sub­tribe do not ac­tu­ally in­clude names and
are there­fore not used.
Most im­por­tantly, there is no such thing as an of­fi­cial clas­si­fi­
ca­tion of pro­kary­otes. This is be­cause in con­trast to eu­kary­otes, the
pro­kary­otic des­ig­na­tions are a mat­ter of sci­en­tific judg­ment. There­
fore, the clos­est things that we have to “of­fi­cial” tax­o­nomic des­ig­
na­tions are those names that are gen­ er­a lly ac­ cepted by the
mi­cro­bi­ol­ogy com ­mu­n ity. Despite this fact, mi­cro­bi­ol­o­gists have
 Taxonomic Classification of Important Microorganisms 3
achieved some amount of con­sen­sus by re­ly­ing on re­sources such
as the International Journal of Systematic and Evolutionary Micro­

Taxonomic Classification
biology and Bergey’s Manual of Systematic Bacteriology.
As of the writ­ing of this fourth edi­tion Pocket Guide, the pro­
kary­otes were di­vided into 2 do­mains, 35 phyla, 80 clas­ses, 1 sub­
class, 178 or­ders, 20 sub­or­ders, 402 fam­i­lies, and 2,552 gen­era. The
fol­low­ing is a con­sol­i­dated tax­o­nomic out­­line, which will fo­cus on
the tax­o­nomic or­ga­ni­za­tion or those or­gan­isms that are most likely
to be en­coun­tered in the clin­i­cal mi­cro­bi­ol­ogy lab­o­ra­tory. This is not
meant to be an ex­haus­tive list of all­bac­te­ria. Rather, it is in­tended to
pro­vide some con­text to the re­la­tion­ships be­tween some of the most
com­monly en­coun­tered or­gan­isms in hu­man clin­i­cal spec­i­mens.
The tax­on­omy of bac­te­rial clas­si­fi­ca­tion is ar­ranged in the fol­
low­ing way. . .

Domain
Phyla
Class
Subclass
Order
Suborder
Family
Genera

Domain: Bacteria
Class. Actinobacteria
Family. Actinomycetaceae
Genus. Actinobaculum
Genus. Actinomyces
Genus. Arcanobacterium
Genus. Mobiluncus
Genus. Trueperella
Family. Corynebacteriaceae
Genus. Corynebacterium
Genus. Turicella
Family. Dietziaceae
Genus. Dietzia
Family. Mycobacteriaceae
Genus. Mycobacterium
Family. Nocardiaceae
Genus. Gordonia
Genus. Nocardia
Genus. Rhodococcus
Family. Tsukamurellaceae
Genus. Tsukamurella
Family. Propionibacteriaceae
Genus. Propionibacterium
 4 SECTION 1
Family. Streptocmycetaceae
Genus. Streptomyces
Taxonomic Classification

Family. Nocardiopsaceae
Genus. Nocardiopsis
Family. Bifidobacteriaceae
Genus. Alloscardovia
Genus. Bifidobacterium
Genus. Gardnerella
Family. Brevibacteriaceae
Genus. Brevibacterium
Family. Cellulomonadaceae
Genus. Cellulomonas
Genus. Oerskovia
Genus. Tropheryma
Family. Dermabacteraceae
Genus. Dermabacter
Genus. Helcobacillus
Family. Dermacoccaceae
Genus. Dermacocccus
Genus. Kytococcus
Family. Microbacteriaceae
Genus. Leifsonia
Genus. Microbacterium
Family. Micrococcaceae
Genus. Arthrobacter
Genus. Kocuria
Genus. Micrococcus
Genus. Rothia
Genus. Stomatococcus
Class. Coriobacteriia
Family. Atopobiaceae
Genus. Atopobium
Family. Eggerthellaceae
Genus. Eggerthella
Genus. Slackia
Class. Bacteroidia
Family. Bacteroidaceae
Genus. Bacteroides
Family. Porphyromonadaceae
Genus. Dysgonomonas
Genus. Microbacter
Genus. Parabacteroides
Genus. Porphyromonas
Genus. Tannerella
Family. Prevotellaceae
Genus. Prevotella
 Taxonomic Classification of Important Microorganisms 5
Class. Flavobacteriia
Family. Flavobacteriaceae

Taxonomic Classification
Genus. Bergeyella
Genus. Capnocytophaga
Genus. Chryseobacterium
Genus. Elizabethkingia
Genus. Empedobacter
Genus. Flavobacterium
Genus. Weeksella
Class. Sphingobacteriia
Family. Sphingobacteriaceae
Genus. Sphingobacterium
Class. Chlamydiae
Family. Chlamydiaceae
Genus. Chlamydia
Genus. Chlamydophila
Class. Bacilli or Fibribacteria
Family. Bacillaceae
Genus. Bacillus
Family. Listeriaceae
Genus. Listeria
Family. Paenibacillaceae
Genus. Paenibacillus
Family. Staphylococcaceae
Genus. Staphylococcus
Family. Unassigned
Genus. Gemella
Family. Aerococcaceae
Genus. Abiotrophia
Genus. Aerococcus
Genus. Dolosicoccus
Genus. Facklamia
Genus. Globicatella
Family. Carnobactericeae
Genus. Alloiococcus
Genus. Dolosigranulum
Genus. Granulicatella
Family. Enterococcaceae
Genus. Enterococcus
Genus. Vagococcus
Family. Lactobacillaceae
Genus. Lactobacillus
Genus. Pediococcus
Family. Leuconostocaceae
Genus. Leuconostoc
Genus. Weissella
 6 SECTION 1
Family. Streptococcaceae
Genus. Lactococcus
Taxonomic Classification

Genus. Streptococcus
Class. Clostridia
Family. Clostridiaceae
Genus. Clostridium
Genus. Sarcinia
Family. Peptococcaceae
Genus. Peptococcus
Family. Peptostreptococcaceae
Genus. Peptostreptococcus
Family. Unassigned
Genus. Anaerococcus
Genus. Finegoldia
Genus. Helcococcus
Genus. Peptoniphilus
Class. Erysipelotrichia
Family. Erysipelotrichaceae
Genus. Erysipelothrix
Class. Negativicutes
Family. Veillonellaceae
Genus. Veillonella
Class. Fusobacteriia
Family. Fusobacteriaceae
Genus. Fusobacterium
Family. Leptotrichiaceae
Genus. Leptotrichia
Genus. Sneathia
Genus. Streptobacillus
Class. Alphaproteobcteria
Family. Caulobacteraceae
Genus. Brevundimonas
Family. Bartonellaceae
Genus. Bartonella
Family. Brucellaceae
Genus. Brucella
Genus. Ochrabactrum
Family. Rhizobiaceae
Genus. Agrobacterium
Genus. Rhizobium
Family. Rhodobacteraceae
Genus. Paracoccus
Family. Acetobacteraceae
Genus. Roseomonas
Family. Rhodospirllaceae
Genus. Inquilinus
Family. Anaplasmataceae
 Taxonomic Classification of Important Microorganisms 7
Genus. Anaplasma
Genus. Ehrlichia

Taxonomic Classification
Genus. Wolbachia
Family. Rickettsiaceae
Genus. Orientia
Genus. Rickettsia
Family. Sphingomonadaceae
Genus. Sphingomonas
Class. Betaproteobacteria
Family. Alcaligenaceae
Genus. Achoromobacter
Genus. Alcaligenes
Genus. Bordetella
Genus. Oligella
Family. Burkholderiaceae
Genus. Burkholderia
Genus. Cupriavidis
Genus. Pandoraea
Genus. Ralstonia
Family. Comamonadaceae
Genus. Acidovorax
Genus. Comamonas
Genus. Defltia
Family. Oxalobacteraceae
Genus. Herbaspirillum
Family. Neisseriaceae
Genus. Eikenella
Genus. Kingella
Genus. Neisseria
Family. Sprillaceae
Genus. Genera
Genus. Sprillium
Class. Epsilonproteobacteria
Family. Campylobacteraceae
Genus. Arcobacter
Genus. Campylobacter
Family. Helicobacteraceae
Genus. Helicobacter
Class. Gammaproteobacteria
Family. Enterobacteriaceae
Genus. Cedecea
Genus. Citrobacter
Genus. Cronobacter
Genus. Edwardsiella
Genus. Enterobacter
Genus. Erwinia
Genus. Escherichia
 8 SECTION 1
Genus. Hafnia
Genus. Klebsiella
Taxonomic Classification

Genus. Kluybera
Genus. Leclercia
Genus. Morganella
Genus. Pantoea
Genus. Plesiomonas
Genus. Pro­teus
Genus. Providencia
Genus. Raoltella
Genus. Salmonella
Genus. Serratia
Genus. Shigella
Genus. Yersinia
Genus. Yokenella
Family. Vibrionaceae
Genus. Vibrio
Family. Aeromonadaceae
Genus. Aeromonas
Family. Shewanellaceae
Genus. Shewanella
Family. Cardiobacteriaceae
Genus. Cardiobacterium
Genus. Suttonella
Family. Coxiellaceae
Genus. Coxiella
Family. Legionellaceae
Genus. Legionella
Family. Pasteurellaceae
Genus. Actinobacillus
Genus. Aggregatibacter
Genus. Haemophilus
Genus. Pasteurella
Family. Moraxelaceae
Genus. Acinetobacter
Genus. Branhamella
Genus. Moraxella
Family. Pseudomonadaceae
Genus. Chryseomonas
Genus. Flavimonas
Genus. Pseudomonas
Family. Francisellaceae
Genus. Francisella
Class. Spirochaetes
Family. Brachyspiraceae
Genus. Brachyspira
 Taxonomic Classification of Important Microorganisms 9
Family. Leptospiraceae
Genus. Leptospira

Taxonomic Classification
Family. Borreliaceae
Genus. Borrelia
Family. Spirochaetaceae
Genus. Treponema
Class. Mollicutes
Family. Mycoplasmataceae
Genus. Mycoplasma
Genus. Ureaplasma

Taxonomic Classification of Human Viruses

The tax­on­omy of vi­ral clas­si­fi­ca­tion is ar­ranged in the fol­low­ing
way. . .
Order
Family
Subfamily
Genus
Species
Practically speak­ing, most clin­i­cal mi­cro­bi­ol­o­gists or­ga­nize vi­
ruses in terms of ge­nome struc­ture, fam­ily, and ge­nus, and only
rarely are the sub­fam­ily or spe­cies des­ig­na­tions uti­lized. As such,
the fol­low­ing tax­o­nomic struc­ture is pre­sented in terms of what
would be most use­ful to the prac­tic­ing clin­i­cal mi­cro­bi­ol­o­gist.

Single-stranded, nonenveloped DNA vi­rus­es

Family. Parvoviridae
Genus. Erythrovirus
Species. Human par­vo­vi­r us B19 vi­r us

Double-stranded, nonenveloped DNA vi­rus­es

Family. Polyomaviridae
Genus. Polyomavirus
Species. JC poly­oma­vi­r us, BK poly­oma­vi­r us
Family. Papillomaviridae
Genus. Papillomavirus
Species. Human pap­il­lo­ma­vi­r us
Family. Adenoviridae
Genus. Mastadenovirus
Species. Human ad­e­no­vi­r uses (spe­cies A to G)

Double-stranded, en­vel­oped DNA vi­rus­es

Family. Poxviridae
Genus. Orthopoxvirus
 10 SECTION 1
Species. Vaccinia vi­r us, va­r i­ola vi­r us small­pox vi­r us,
cow­pox vi­r us, mon­key­pox vi­r us
Taxonomic Classification

Genus. Molluscipoxvirus
Species. Molluscum contagiosum vi­r us
Genus. Parapoxvirus
Species. Orf vi­r us
Family. Hepadnaviridae
Genus. Orthohepadnavirus
Species. Hepatitis B vi­r us
Family. Herpesviridae
Genus. Simplexvirus
Species. Human her­pes­vi­r us 1 (her­pes sim­plex vi­r us
type 1; HHV-1), hu­man her­pes­vi­r us 2 (her­pes
sim­plex vi­r us type 2; HHV-2)
Genus. Varicellovirus
Species. Human her­pes­vi­r us 3 (var­i­cel­la-zoster vi­r us
[VZV]; HHV-3)
Genus. Lymphocryptovirus
Species. Human her­pes­vi­r us 4 (Ep­stein-Barr vi­r us
[EBV]; HHV-4)
Genus. Cytomegalovirus
Species. Human her­pes­vi­r us 5 (CMV; HHV-5)
Genus. Roseolovirus
Species. Human her­pes­vi­r us 6 (ro­se­ola vi­r us;
HHV-6), hu­man her­pes­vi­r us 7 (HHV-7)
Genus. Rhadinovirus
Species. Human her­pes­vi­r us 8 (HHV-8)

Single-stranded, pos­i­tive-sense, nonenveloped RNA vi­rus­es

Family. Picornaviridae
Genus. Enterovirus
Species. Enterovirus A (hu­man coxsackievirus A2,
hu­man en­tero­vi­r us 71) Enterovirus B (hu­man
coxsackievirus B1, hu­man echo­vi­r us), Enterovi-
rus C (hu­man po­lio­vi­r us 1 to 3, hu­man coxsacki­
evirus A1), Enterovirus D (hu­man en­tero­vi­r us
68, 70, and 94), Rhinovirus A, B, and C.
Genus. Aphthovirus
Species. Foot-and-mouth dis­ease vi­r us
Genus. Hepatovirus
Species. Human hep­a­ti­tis A vi­r us (HHAV)
Family. Caliciviridae
Genus. Norovirus
Species. Nor­walk vi­r us
Genus. Sapovirus
Species. Sap­poro vi­r us
Family. Astroviridae
 Taxonomic Classification of Important Microorganisms 11
Genus. Astrovirus
Species. Human astrovirus

Taxonomic Classification
Single-stranded, pos­i­tive-sense, en­vel­oped RNA vi­rus­es
Family. Coronaviridae
Genus. Coronavirus
Species. Human co­ro­na­vi­rus, Severe acute re­spi­ra­tory
syn­drome (SARS) vi­r us, Middle east­ern
re­spi­ra­tory syn­drome (MERS) vi­r us
Genus. Torovirus
Species. Human torovirus
Family. Togaviridae
Genus. Alphavirus
Species. Sindbis vi­r us, Eastern equine en­ceph­a­li­tis
(EEE) vi­r us, Western equine en­ceph­a­li­tis
(WEE) vi­r us, Ven­e­zu­e­lan equine en­ceph­a­li­tis
(VEE) vi­r us, Chickungunya vi­r us, many other
vi­r us­es
Genus. Rubivirus
Species. Rubella vi­r us
Family. Flaviviridae
Genus. Flavivirus
Species. Yellow fe­ver vi­r us, West Nile vi­r us,
St. Louis en­ceph­a­li­tis (SLE) vi­r us, Jap­a­nese
en­ceph­a­li­tis (JE) vi­r us, Dengue vi­r us (types 1
through 4), Zika vi­r us, many other vi­r us­es
Genus. Hepacivirus
Species. Hepatitis C vi­r us (HCV)

Single-stranded, neg­a­tive-sense, en­vel­oped RNA vi­rus­es

Family. Rhabdoviridae
Genus. Lyssavirus
Species. Rabies vi­r us
Family. Filoviridae
Genus. “Mar­burg-like vi­r us­es”
Species. Mar­burg vi­r us
Genus. “Ebo­la-like vi­r us­es”
Species. Ebo­la vi­r us
Family. Orthomyxoviridae
Genus. Influenzavirus A
Species. Influenza A vi­r us
Genus. Influenzavirus B
Species. Influenza B vi­r us
Genus. Influenzavirus C
Species. Influenza C vi­r us
Family. Paramyxoviridae
Genus. Respirovirus
 12 SECTION 1
Species. Sen­dai vi­r us, Human para­in­flu­enza vi­r us
(types 1 and 3)
Taxonomic Classification

Genus. Rubulavirus
Species. Mumps vi­r us, Human para­in­flu­enza vi­r us
(types 2 and 4)
Genus. Morbillivirus
Species. Measles vi­r us
Genus. Henipavirus
Species. Hendra vi­r us, Nipah vi­r us
Genus. Pneumovirus
Species. Human re­spi­ra­tory syn­cy­tial vi­r us (RSV)
Genus. Metapneumovirus
Species. hu­man metapneumovirus
Family. Bunyaviridae
Genus. Orthobunyavirus
Species. Bunyamwera vi­r us, Cal­i­for­nia en­ceph­a­li­tis
vi­r us, La Crosse vi­r us, many other vi­r us­es
Genus. Hantavirus
Species. Hantaan vi­r us, Sin Nombre vi­r us, other
vi­r us­es
Genus. Nairovirus
Species. Cri­me­an-Congo hem­or­rhagic fe­ver vi­r us
(CCFV), other vi­r us­es
Genus. Phlebovirus
Species. Rift Valley fe­ver vi­r us, other vi­r us­es
Family. Arenaviridae
Genus. Arenavirus
Species. Lymphocytic cho­rio­men­in­gi­tis (LCM) vi­rus,
Lassa vi­r us, Junin vi­r us, Machupo vi­r us, Sabia
vi­r us, other vi­r us­es

Double-stranded, en­vel­oped RNA vi­rus­es

Family. Retroviridae
Genus. Deltaretrovirus
Species. Human T-lymphotropic vi­r us type 1
(HTLV-1), hu­man T-lymphotropic vi­r us type 2
(HTLV-2)
Genus. Lentivirus
Species. Human im­mu­no­de­fi­ciency vi­r us type 1
(HIV-1), hu­man im­mu­no­de­fi­ciency vi­r us type 2
(HIV-2)
Family. Reoviridae
Genus. Rotavirus
Species. Rotavirus (types A, B, and C)
Genus. Coltivirus
Species. Col­o­rado tick fe­ver vi­r us
 Taxonomic Classification of Important Microorganisms 13
Taxonomic Classification of Fungi

Taxonomic Classification
The tax­o­nomic clas­si­fi­ca­tion of fun­gal or­gan­isms is com­plex be­cause
fungi can be clas­si­fied by dif­fer­ent meth­ods. The phylogentic tax­
on­omy for fungi is rep­re­sented in this chap­ter and is sub­ject to the
International Code of Nomenclature (ICN) for al­gae, fungi, and
plants (http://​www.​iapt-​taxon.​org). This or­ga­ni­za­tion was for­mally
known as the International Code of Botanical Nomenclature (ICBN).
Fungi are di­vided into four di­vi­sions (phy­lum or sub­phy­lum):
Mucormycotina, Entomophthoromycotina, Ascomycota, and Basid­
iomycota. The Protozoa and Chromista king­doms in­clude some
mem­bers that pos­sess a fun­gus-like ap­pear­ance and are clin­i­cally
rel­e­vant, such as Rhinosporidium and Pythium.
The tax­on­omy of fun­gal clas­si­fi­ca­tion is ar­ranged in the fol­low­
ing way. . .

Phylum
Subphylum
Class
Order
Family
Genus
Species

Since the last writ­ing of this Pocket Guide, a sig­nif­i­cant change

has oc­curred in the world of fun­gal tax­on­omy. As of Jan­u­a ry 1,
2013, only one name will be used to iden­tify fungi, and the “cor­
rect” name will be that which was first iden­ti­fied. Why has this oc­
curred? Most sci­ en­tists agree that the con­ ven­tion of hav­ ing
mul­ti­ple names for fungi to rep­re­sent the dif­fer­ing states of a fun­
gus is no lon­ger nec­es­sary with the use of DNA se­quence an­a­ly­ses.
The mul­ti-name con­ven­tion is con­fus­ing, and is es­pe­cially so for
the clin­i­cal mi­cro­bi­ol­o­gist who is try­ing to com ­mu­n i­cate un­der­
stand­able and ac­tion­able in­for­ma­tion to those car­ing for pa­tients.
Because fun­gal tax­o­nomic nam ­ing con­ven­tions are chang­ing
more quickly than for bac­te­r ia, par­a­sites, and vi­r uses, pub­lish­ing
an ex­ten­sive list of fun­gal tax­on­omy would be ren­dered in­ac­cu­rate
as soon as this Pocket Guide was pub­lished. In fact, many of the
names that would be in­cluded as of the writ­ing of this book will
likely cease to ex­ist.

Taxonomic Classification of Parasitesa

The term “par­a­site” re­fers to a group of eu­kary­otic or­gan­isms, about
200 of which are med­i­cally rel­e­vant hel­minths, and 80 of which are
med­i­cally rel­e­vant pro­to­zoan spe­cies. Within this sub­set of nearly
 14 SECTION 1
300 par­a­sites, about 100 spe­cies are com­monly found in hu­mans,
and an even smaller num­ber within that cause a dis­pro­por­tion­ate
Taxonomic Classification

num­ber of im­por­tant dis­eases. Presented in the fol­low­ing ta­ble are

the tax­o­nomic clas­si­fi­ca­tions of some of the most im­por­tant hu­man
par­a­sites.
Since the last edi­tion of this Pocket Guide was pub­lished, some
sig­nif­i­cant tax­o­nomic changes have oc­curred. The two most clin­i­
cally rel­e­vant changes re­late to the Microsporidia and Blastocystis
hominis. Due to re­cent ge­nome-wide an­a­ly­ses, Microsporidia now
be­long to the king­dom Fungi. The tax­on­omy of Blastocystis hom-
inis has been con­tro­ver­sial, and it has pre­vi­ously been con­sid­ered
a fun­g us and also as pro­to­zoa. Recent ge­nome an­a ­ly­ses sug­gest it
is most closely re­lated to Proteromonas, though this or­gan­ism is
a flag­el­late and B. hominis does pos­sess a fla­gel­lum and is not
mo­tile. It is now part of the king­dom Chromista rather than the
Protozoa.

Kingdom. Protozoa
Phylum. Metamonada (flag­el­lates)
Class. Trepomonadea (in­tes­ti­nal flag­el­lates)
Order. Diplomonadida
Genus. Giardia duodenalis
Class. Retortamonadea (in­tes­ti­nal flag­el­lates)
Order. Retortamonadida
Genus. Chilomastix mesnili,
Genus. Retortamonas intestinalis
Class. Trichomonadea (in­tes­ti­nal and re­lated flag­el­lates)
Order. Trichomonadida
Genus. Dientamoeba fragilis
Genus. Trichomonas va­gi­na/is
Genus. Trichomonas tenax
Genus. Pentatrichomonas hominis
Phylum. Percolozoa
Class. Heterolobosea (flag­el­lated amoe­bae)
Order. Schizopyrenida
Genus. Naegleria fowleri
Phylum. Euglenozoa
Class. Kinetoplastea (blood and tis­sue flag­el­lates)
Order. Trypanosomatida
Genus. Leishmania Don­o­van
Genus. Leishmania in­fan­tum (= L. chagasi)
Genus. Leishmania ma­jor
Genus. Leishmania tropica
Genus. Leishmania braziliensis
Genus. Leishmania mexicana
Genus. Trypanosoma cruzi
Genus. Trypanosoma brucei gambiense
 Taxonomic Classification of Important Microorganisms 15
Genus. Trypanosoma brucei rhodesiense
Genus. Trypanosoma rangeli

Taxonomic Classification
Phylum. Amoebozoa
Class. Amoebaea
Order. Acanthopodida
Genus. Acanthamoeba spp.
Genus. Balamuthia mandrillaris
Class. Archamoebea (in­tes­ti­nal amoe­bae)
Order. Euamoebida
Genus. Entamoeba histolytica
Genus. Entamoeba coli
Genus. Entamoeba dispar
Genus. Entamoeba hartmanni
Genus. Entamoeba gingivalis
Genus. Entamoeba polecki
Genus. Endolimax nana
Genus. Iodamoeba buetschlii
Phylum. Sporozoa (spo­ro­zo­ans)
Class. Coccidea
Order. Eimeriida
Genus. Cryptosporidium parvum
Genus. Toxoplasma gondii
Genus. Cyclospora cayetanensis
Genus. Cystoisospora (Isospora) bel­li
Genus. Sarcocystis hominis
Order. Piroplasmida
Genus. Babesia microti
Genus. Babesia divergens
Genus. Babesia gibsoni
Order. Haemosporida
Genus. Plasmodium fal­cip­a­rum
Genus. Plasmodium malariae
Genus. Plasmodium ova­le
Genus. Plasmodium vi­vax
Genus. Plasmodium knowlesi
Phylum. Ciliophora (cil­i­ates)
Class. Litostomatea
Order. Trichostomatia
Genus. Balantidium coli

Kingdom. Chromista
Phylum. Bigyra
Class. Blastocystea
Genus. Blastocystis hominis

Kingdom. Animalia
Phylum. Nemathelminthes (Nematodes, Roundworms)
 16 SECTION 1
Class. Adenophorea (Asphasmidea)
Family. Trichinellidae (Trichuridae)
Taxonomic Classification

Genus. Trichinella spiralis

Genus. Trichuris trichiura
Genus. Capillaria spp.
Class. Secernentea (Phasmidea)
Family. Ancylostomatidae
Genus. Ancylostoma duodenale
Genus. Necator americanus
Family. Angiostrongylidae
Genus. Parastrongylus (Angiostrongylus)
cantonensis
Genus. Parastrongylus (Angiostrongylus)
costaricensis
Family. Ascarididae
Genus. Ascaris lumbrioides
Genus. Toxocara canis
Genus. Toxocara cati
Genus. Bayliascaris procyonis
Family. Dracunculidae
Genus. Dracunculus medinensis
Family. Onchocercidae
Genus. Brugia malayi
Genus. Loa loa
Genus. Wuchereria bancrofii
Genus. Onchocerca vol­vu­lus
Genus. Brugia timori
Genus. Dirofilaria immitis
Genus. Mansonella ozzardi
Genus. Mansonella perstans
Family. Oxyuridae
Genus. Enterobius vermicularis
Family. Strongyloididae
Genus. Strongyloides stercoralis
Genus. Strongyloides fuelleborni
Family. Gnathostomatidae
Genus. Gnathostoma spinigerum

Phylum. Platyhelminthes
Class. Trematoda (flukes)
Order. Diplostomida
Family. Schistosomatidae
Genus. Schistosoma haematobium
Genus. Schistosoma japonicum
Genus. Schistosoma mansoni
Genus. Schistosoma mekongi
Genus. Schistosoma intercalatum
 Taxonomic Classification of Important Microorganisms 17
Order. Plagiorchiida
Family. Fasciolidae

Taxonomic Classification
Genus. Fasciola he­pat­i­ca
Genus. Fasciola gigantica
Genus. Fasciolopsis buski
Family. Heterophyidae
Genus. Heterophyes heterophyes
Family. Opisthorchidae
Genus. Clonorchis sinensis
Genus. Opisthorchis felineus
Genus. Opisthorchis viverrini
Family. Paragonimidae
Genus. Paragonimus westermani
Genus. Paragonimus kellicotti
Family. Paragonimidae
Genus. Dicrocoelium dentriticum
Class. Cestoda (tape­worms)
Order. Pseudophyllidea
Family. Diphyllobothriidae
Genus. Diphyllobothrium latum
Order. Cyclophyllidea
Family. Dipylidiidae
Genus. Dipylidium caninum
Family. Hymenolepididae
Genus. Hymenolepis nana
Genus. Hymenolepis diminuta
Family. Taeniidae
Genus. Taenia saginata
Genus. Taenia solium
Genus. Echinococcus granulosus
Genus. Echinococcus multilocularis
a
Adapted from J. H. Jorgensen, M. A. Pfaller, K. C. Car­roll, G. Funke, M. L.
Landry, S. S. Rich­ter, D. W. Warnock (ed.), Manual of Clinical Microbiology, 11th
ed., ASM Press, Wash­ing­ton, D.C., 2015.
SECTION 2

Indigenous and
Pathogenic Microbes
of Humans
Ge­ne­ral Comments 20
Table 2.1 Human Indigenous Flora 22
Microbes Responsible for Human Disease 34
Summary of Notifiable Infectious Diseases:
United States, 2015 54
Table 2.2 Arthropod Vectors of Medically Important
Diseases 58
Table 2.3 Fungal Pathogens and Geographic
Distribution 61
Table 2.4 Parasitic Pathogens and Geographic
Distribution 71

doi:10.1128/9781683670070.ch2
 20 SECTION 2
The re­la­tion­ship be­tween hu­mans and mi­crobes can be de­fined in
one of three ways: 1) tran­sient col­o­ni­za­tion, 2) per­sis­tent col­o­ni­za­
tion, 3) or path­o­genic in­fec­tion. The ma­jor­ity of or­gan­isms are un­
able to es­t ab­l ish per­ma­nent col­o­n i­za­tion/infection on the skin or
mu­co­sal sur­faces and are con­sid­ered an in­sig­nif­i­cant find­ing when
re­cov­ered in clin­i­cal spec­i­mens. Examples in­clude the molds and
many of the nonfermentative Gram-negative ba­cilli that can be iso­
Microbes of Humans

lated in soil, veg­e­t a­t ion, wa­t er, and food prod­ucts. These or­gan­
isms are un­able to com­pete with the nor­mal mi­cro­bial pop­u­la­tion
of the body or can­not sur­vive on the skin sur­face.
Other or­gan­isms are a­ ble to es­tab­lish long-term res­i­dency on or
in the hu­man body. The suc­cesses of these in­ter­ac­tions are influ­
enced by com­plex mi­cro­bial and host fac­tors (e.g., fa­vor­able en­vi­
ron­ment [pH, at­mo­sphere, mois­ture, avail­­able nu­tri­ents], abil­ity to
ad­here to sur ­faces, re­sis­t ance to bac­te­r io­cins, an­ti­bi­ot­ics, and
phago­cytic cells). These mi­crobes gen­er­ally ex­ist in a sym­bi­otic re­
la­tion­ship with their hu­man host and pro­duce dis­ease only when
they in­vade nor­mally ster­ile body sites such as tis­sues and body flu­
ids. Table 2.1 is a list­ing of the or­gan­isms most com­monly re­cov­
ered from the body sur­faces of healthy in­d i­vid­u­a ls. This ta­ble is
in­tended to serve as an in­ter­pre­tive guide­l ine for cul­t ured spec­i­
mens. It should be re­mem­bered that many or­gan­isms can­not be
de­tected when pres­ent in a mixed pop­u­la­tion (typ­i­cal of many body
sites). With the emer­gence of next gen­er­a­tion se­quenc­ing microbi­
ome ex­per­i­men­ta­tion, our un­der­stand­ing of the hu­man microbiome
has ex­panded sig­nif­i­cantly and dem­on­strated a greater di­ver­sity of
com­men­sal or­gan­isms than had been pre­vi­ously ap­pre­ci­at­ed.
Additionally, re­cent ad­vances in di­ag­nos­t ic tech­nol­ogy have
changed the prac­tice of clin­i­cal mi­cro­bi­ol­ogy for­ever. In par­tic­u­lar,
the use of ma­trix-assisted la­ser de­sorp­tion/ionization time-of-flight
mass spec­trom­e­try (MALDI-TOF MS) has al­lowed mi­cro­bi­ol­o­gists
to iden­tify or­gan­isms rap­idly and with more ac­cu­racy than ever be­
fore. Consequently, the mi­cro­bi­ol­o­gist must un­der­stand a greater
depth of or­gan­isms than ever be­fore, and it re­mains crit­i­cal that
only those or­gan­isms which are clin­i­cally sig­n if­i­cant be re­port­ed.
MALDI-TOF MS is a pow­er­ful tool that has greatly im­proved our
abil­ity to di­ag­nose in­fec­tious dis­eases. However, if used in­cor­rectly,
MALDI-TOF MS can lead to mis­di­ag­noses, pro­vider con­fu­sion,
and un­nec­es­sary an­ti­mi­cro­bial ther­a­py.
The quan­ti­ta­tive and qual­i­ta­tive pres­ence of spe­cific mi­crobes
will also vary with the in­di­vid­ual host, in­clud­ing dra­matic changes
in the in­dig­e­nous flora in hos­pi­tal­ized pa­tients. Thus, only qual­i­ta­
tive data (pres­ence or ab­sence of the or­gan­isms) are pre­sented. Data
for vi­r uses are not listed be­cause rep­li­ca­tion of vi­r uses gen­er­ally is
as­so­ci­ated with host tis­sue de­struc­tion or an im­mu­no­logic re­sponse
(al­though this can range from a clin­i­cally asymp­tom­atic in­fec­tion
to host death).
 Indigenous and Pathogenic Microbes of Humans 21
Most dis­eases in hu­mans are caused by in­fec­tions with en­dog­e­
nous bac­te­ria and yeasts or ex­po­sure to op­por­tu­nis­tic molds, par­a­
sites, and vi­ruses. However, some in­ter­ac­tions be­tween mi­crobes
and hu­mans com­monly lead to dis­ease. The most com­mon mi­crobes
re­spon­si­ble for hu­man dis­ease are sum­ma­rized in this sec­tion.
Selected path­o­gens are mon­i­tored rou­tinely, with all­ clin­i­cal lab­
o­ra­to­r ies re­quired to re­port spe­cific or­gan­isms or dis­eases to their

Microbes of Humans
state pub­lic health de­part­ment. This group of or­gan­isms and the dis­
eases as­so­ci­ated with them are re­ported weekly in Morbidity and
Mortality Weekly Report. Data for 2015 are sum­ma­rized in this sec­
tion. In ad­di­tion, the Department of Health and Human Services
(HHS) and the U.S. Department of Agriculture (USDA) have pub­
lished a list of se­lect agents and tox­ins. This list is pre­sented in this
sec­tion and can be found at this web­site (https://​www.​selectagents​
.​gov/​selectagentsandtoxinslist.​html).
Arthropods, par­a­sites in their own right, can also serve as vec­
tors for hu­man dis­ease. A list­ing of the most com­mon ar­thro­pod
vec­tors and their as­so­ci­ated dis­eases is in­cluded in Table 2.2.
Tables 2.3 and 2.4 are list­ings of fungi and par­a­sites iso­lated from
hu­mans and their geo­graphic dis­tri­bu­tion. For ad­di­tional in­for­ma­
tion about in­dig­e­nous and path­o­genic mi­crobes, please con­sult the
ref­er­ence texts listed in the Bibliography.
 Microbes of Humans

22 SECTION 2
Table 2.1 Human in­dig­e­nous flo­raa
Prevalence of car­riage inb:
Organism Resp tract GI tract GU tract Skin, ear, and eye
Abiotrophia defectiva + 0 0 0
Acholeplasma laidlawii + 0 0 0
Acidaminococcus fermentans + + 0 0
Acinetobacter baumannii 0 0 0 +
Acinetobacter junii + 0 0 +
Acinetobacter lwoffii + 0 0 +
Acinetobacter radioresistens 0 0 0 +
Actinomyces spp. + + + +
Aggregatibacter actinomycetemcomitans + 0 0 0
Aerococcus christensenii 0 0 + 0
Aerococcus viridans 0 0 0 +
Aerococcus urinae 0 0 + 0
Aeromonas spp. 0 + 0 0
Alistipes spp. + + + +
Alloiococcus oti­tis 0 0 0 +
Anaerococcus hydrogenalis 0 + + +
Anaerococcus lactolyticus 0 + + 0
Anaerococcus prevotii 0 + + 0
Anaerorhabdus forcosus 0 + 0 0
Arcanobacterium spp. + 0 0 +
Atopobium spp. + 0 0 0
Bacillus spp. 0 + 0 +
Bacteroides caccae + + + +
Bacteroides distasonis 0 + 0 0
Bacteroides eggerthii 0 + 0 0
Bacteroides fragilis + + + 0
Bacteroides merdae 0 + 0 0
Bacteroides ovatus 0 + 0 0
Bacteroides splanchnicus 0 + 0 0

Indigenous and Pathogenic Microbes of Humans 23

Bacteroides thetaiotaomicron + + 0 +
Bacteroides vulgatus + + + +
Bifidobacterium adolescentis 0 + 0 0
Bifidobacterium bifidum 0 + + 0
Bifidobacterium breve 0 + + 0
Bifidobacterium catenulatum 0 + + 0
Bifidobacterium dentium + + + 0
Bifidobacterium longum 0 + + 0
Bilophila wadsworthia + + + 0
Blastocystis hominis 0 + 0 0
Blastoschizomyces capitatus 0 0 0 +
Brevibacterium casei 0 0 0 +
Brevibacterium epidermidis 0 0 0 +
Burkholderia cepacia com­plex + 0 + +
Butyrivibrio fibrisolvens 0 + 0 0
Campylobacter concisus + + 0 +
Campylobacter curvus + + 0 0
Campylobacter gracilis + + 0 0
Campylobacter jejuni 0 + 0 0
(continued)

Microbes of Humans
Exploring the Variety of Random
Documents with Different Content
seeing himself threatened with the rack, went with the pirates to
show them; but the Spaniards perceiving their enemies to range
everywhere up and down the woods, were already fled thence
farther off into the thickest of the woods, where they built
themselves huts, to preserve from the weather those few goods they
had. The pirates judged themselves deceived by the peasant, and
hereupon, to revenge themselves, notwithstanding all his excuses
and supplication, they hanged him on a tree.
Then they divided into parties to search the plantations; for they
knew the Spaniards that were absconded could not live on what the
woods afforded, without coming now and then for provisions to their
country houses. Here they found a slave, to whom they promised
mountains of gold and his liberty, by transporting him to Jamaica, if
he would show them where the inhabitants of Gibraltar lay hid. This
fellow conducted them to a party of Spaniards, whom they instantly
made prisoners, commanding this slave to kill some before the eyes
of the rest; that by this perpetrated crime, he might never be able to
leave their wicked company. The negro, according to their orders,
committed many murders and insolencies upon the Spaniards, and
followed the unfortunate traces of the pirates; who eight days after
returned to Gibraltar with many prisoners, and some mules laden
with riches. They examined every prisoner by himself (who were in
all about two hundred and fifty persons), where they had hid the
rest of their goods, and if they knew of their fellow-townsmen. Such
as would not confess were tormented after a most inhuman manner.
Among the rest, there happened to be a Portuguese, who by a
negro was reported, though falsely, to be very rich; this man was
commanded to produce his riches. His answer was, he had no more
than one hundred pieces of eight in the world, and these had been
stolen from him two days before by his servant; which words,
though he sealed with many oaths and protestations, yet they would
not believe him, but dragging him to the rack, without any regard to
his age of sixty years, they stretched him with cords, breaking both
his arms behind his shoulders.
 This cruelty went not alone; for he not being able or willing to
make any other declaration, they put him to another sort of torment
more barbarous; they tied him with small cords by his two thumbs
and great toes to four stakes fixed in the ground, at a convenient
distance, the whole weight of his body hanging on those cords. Not
satisfied yet with this cruel torture, they took a stone of above two
hundred pounds, and laid it upon his belly, as if they intended to
press him to death; they also kindled palm leaves, and applied the
flame to the face of this unfortunate Portuguese, burning with them
the whole skin, beard, and hair. At last, seeing that neither with
these tortures, nor others, they could get anything out of him, they
untied the cords, and carried him half dead to the church, where
was their corps du garde; here they tied him anew to one of the
pillars thereof, leaving him in that condition, without giving him
either to eat or drink, unless very sparingly, and so little that would
scarce sustain life for some days; four or five being past, he desired
one of the prisoners might come to him, by whose means he
promised he would endeavour to raise some money to satisfy their
demands. The prisoner whom he required was brought to him, and
he ordered him to promise the pirates five hundred pieces of eight
for his ransom; but they were deaf and obstinate at such a small
sum, and instead of accepting it, beat him cruelly with cudgels,
saying, “Old fellow, instead of five hundred, you must say five
hundred thousand pieces of eight; otherwise you shall here end your
life.” Finally, after a thousand protestations that he was but a
miserable man, and kept a poor tavern for his living, he agreed with
them for one thousand pieces of eight. These he raised, and having
paid them, got his liberty; though so horribly maimed, that it is
scarce to be believed he could survive many weeks.
Other tortures, besides these, were exercised upon others, which
this Portuguese endured not: some were hanged up by the testicles,
or privy-members, and left till they fell to the ground, those parts
being torn from their bodies: if with this they minded to show mercy
to those wretches, thus lacerated in the most tender parts, their
mercy was, to run them through with their swords; otherwise they
used to lie four or five days under the agonies of death, before they
died. Others were crucified by these tyrants, and with kindled
matches burnt between the joints of their fingers and toes: others
had their feet put into the fire, and thus were left to be roasted
alive. Having used these and other cruelties with the white men,
they began to practise the same with the negroes, their slaves, who
were treated with no less inhumanity than their masters.
Among these slaves was one who promised Captain Morgan to
conduct him to a river of the lake, where he should find a ship and
four boats, richly laden with goods of the inhabitants of Maracaibo:
the same discovered likewise where the governor of Gibraltar lay
hid, with the greatest part of the women of the town; but all this he
revealed, upon great menaces to hang him, if he told not what he
knew. Captain Morgan sent away presently two hundred men in two
settees, or great boats, to this river, to seek for what the slave had
discovered; but he himself, with two hundred and fifty more,
undertook to go and take the governor. This gentleman was retired
to a small island in the middle of the river, where he had built a little
fort, as well as he could, for his defence; but hearing that Captain
Morgan came in person with great forces to seek him, he retired to
the top of a mountain not far off, to which there was no ascent but
by a very narrow passage, so straight, that whosoever did attempt
to gain the ascent, must march his men one by one. Captain Morgan
spent two days before he arrived at this little island, whence he
designed to proceed to the mountain where the governor was
posted, had he not been told of the impossibility of ascent, not only
for the narrowness of the way, but because the governor was well
provided with all sorts of ammunition: beside, there was fallen a
huge rain, whereby all the pirates’ baggage and powder was wet. By
this rain, also, they lost many men at the passage over a river that
was overflown: here perished, likewise, some women and children,
and many mules laden with plate and goods, which they had taken
from the fugitive inhabitants; so that things were in a very bad
condition with Captain Morgan, and his men much harassed, as may
be inferred from this relation: whereby, if the Spaniards, in that
juncture, had had but fifty men well armed, they might have entirely
destroyed the pirates. But the fears the Spaniards had at first
conceived were so great, that the leaves stirring on the trees they
often fancied to be pirates. Finally, Captain Morgan and his people,
having upon this march sometimes waded up to their middles in
water for half, or whole miles together, they at last escaped, for the
greatest part; but the women and children for the major part died.
Thus twelve days after they set forth to seek the governor they
returned to Gibraltar, with many prisoners: two days after arrived
also the two settees that went to the river, bringing with them four
boats, and some prisoners; but the greatest part of the merchandise
in the said boats they found not, the Spaniards having unladed and
secured it, having intelligence of their coming; who designed also,
when the merchandise was taken out, to burn the boats: yet the
Spaniards made not so much haste to unlade these vessels, but that
they left in the ship and boats great parcels of goods, which the
pirates seized, and brought a considerable booty to Gibraltar. Thus,
after they had been in possession of the place five entire weeks, and
committed an infinite number of murders, robberies, rapes, and
such-like insolencies, they concluded to depart; but first they
ordered some prisoners to go forth into the woods and fields, and
collect a ransom for the town, otherwise they would certainly burn it
down to the ground. These poor afflicted men went as they were
sent, and having searched the adjoining fields and woods, returned
to Captain Morgan, telling him they had scarce been able to find
anybody, but that to such as they had found they had proposed his
demands; to which they had answered, that the governor had
prohibited them to give any ransom for the town, but they
beseeched him to have a little patience, and among themselves they
would collect five thousand pieces of eight; and for the rest, they
would give some of their own townsmen as hostages, whom he
might carry to Maracaibo, till he had received full satisfaction.
Captain Morgan having now been long absent from Maracaibo,
and knowing the Spaniards had had sufficient time to fortify
themselves, and hinder his departure out of the lake, granted their
proposition, and made as much haste as he could for his departure:
he gave liberty to all the prisoners, first putting every one to a
ransom; yet he detained the slaves. They delivered him four persons
agreed on for hostages of what money more he was to receive, and
they desired to have the slave mentioned above, intending to punish
him according to his deserts; but Captain Morgan would not deliver
him, lest they should burn him alive. At last, they weighed anchor,
and set sail in all haste for Maracaibo: here they arrived in four days,
and found all things as they had left them; yet here they received
news from a poor distressed old man, whom alone they found sick in
the town, that three Spanish men-of-war were arrived at the entry of
the lake, waiting the return of the pirates: moreover, that the castle
at the entry thereof was again put into a good posture of defence,
well provided with guns and men, and all sorts of ammunition.
This relation could not choose but disturb the mind of Captain
Morgan, who now was careful how to get away through the narrow
entry of the lake: hereupon he sent his swiftest boat to view the
entry, and see if things were as they had been related. Next day the
boat came back, confirming what was said; assuring him, they had
viewed the ships so nigh, that they had been in great danger of their
shot: hereunto they added, that the biggest ship was mounted with
forty guns, the second with thirty, and the smallest with twenty-four.
These forces being much beyond those of Captain Morgan, caused a
general consternation in the pirates, whose biggest vessel had not
above fourteen small guns. Every one judged Captain Morgan to
despond, and to be hopeless, considering the difficulty of passing
safe with his little fleet amidst those great ships and the fort, or he
must perish. How to escape any other way, by sea or land, they saw
no way. Under these necessities, Captain Morgan resumed new
courage, and resolving to show himself still undaunted, he boldly
sent a Spaniard to the admiral of those three ships, demanding of
him a considerable ransom for not putting the city of Maracaibo to
the flames. This man (who was received by the Spaniards with great
admiration of the boldness of those pirates) returned two days after,
bringing to Captain Morgan a letter from the said admiral, as follows:
—
The Letter of Don Alonso del Campo y Espinosa, Admiral of the Spanish
Fleet, to Captain Morgan, Commander of the Pirates.

“Having understood by all our friends and neighbours, the

unexpected news that you have dared to attempt and commit
hostilities in the countries, cities, towns, and villages
belonging to the dominions of his Catholic Majesty, my
sovereign lord and master; I let you understand by these
lines, that I am come to this place, according to my
obligation, near that castle which you took out of the hands
of a parcel of cowards; where I have put things into a very
good posture of defence, and mounted again the artillery
which you had nailed and dismounted. My intent is, to dispute
with you your passage out of the lake, and follow and pursue
you everywhere, to the end you may see the performance of
my duty. Notwithstanding, if you be contented to surrender
with humility all that you have taken, together with the slaves
and all other prisoners, I will let you freely pass, without
trouble or molestation; on condition that you retire home
presently to your own country. But if you make any resistance
or opposition to what I offer you, I assure you I will
command boats to come from Caraccas, wherein I will put my
troops, and coming to Maracaibo, will put you every man to
the sword. This is my last and absolute resolution. Be
prudent, therefore, and do not abuse my bounty with
ingratitude. I have with me very good soldiers, who desire
nothing more ardently than to revenge on you, and your
people, all the cruelties, and base infamous actions, you have
committed upon the Spanish nation in America. Dated on
board the royal ship named the Magdalen, lying at anchor at
the entry of the lake of Maracaibo, this 24th of April, 1669.
“Don Alonso del Campo y Espinosa.”
 As soon as Captain Morgan received this letter, he called all his
men together in the market-place of Maracaibo, and after reading
the contents thereof, both in French and English, asked their advice
and resolution on the whole matter, and whether they had rather
surrender all they had got to obtain their liberty, than fight for it.
They answered all, unanimously, they had rather fight to the last
drop of blood, than surrender so easily the booty they had got with
so much danger of their lives. Among the rest, one said to Captain
Morgan, “Take you care for the rest, and I will undertake to destroy
the biggest of those ships with only twelve men: the manner shall
be, by making a brulot, or fire-ship, of that vessel we took in the
river of Gibraltar; which, to the intent she may not be known for a
fire-ship, we will fill her decks with logs of wood, standing with hats
and montera caps, to deceive their sight with the representation of
men. The same we will do at the port-holes that serve for the guns,
which shall be filled with counterfeit cannon. At the stern we will
hang out English colours, and persuade the enemy she is one of our
best men-of-war going to fight them.” This proposition was admitted
and approved by every one; howbeit, their fears were not quite
dispersed.
For, notwithstanding what had been concluded there, they
endeavoured the next day to come to an accommodation with Don
Alonso. To this effect, Captain Morgan sent to him two persons, with
these propositions: First, that he would quit Maracaibo, without
doing any damage to the town, or exacting any ransom for the firing
thereof. Secondly, that he would set at liberty one half of the slaves,
and all the prisoners, without ransom. Thirdly, that he would send
home freely the four chief inhabitants of Gibraltar, which he had in
his custody as hostages for the contributions those people had
promised to pay. These propositions were instantly rejected by Don
Alonso, as dishonourable: neither would he hear of any other
accommodation, but sent back this message: “That if they
surrendered not themselves voluntarily into his hands, within two
days, under the conditions which he had offered them by his letter,
he would immediately come, and force them to do it.”
 No sooner had Captain Morgan received this message from Don
Alonso, than he put all things in order to fight, resolving to get out
of the lake by main force, without surrendering anything. First, he
commanded all the slaves and prisoners to be tied, and guarded
very well, and gathered all the pitch, tar, and brimstone, they could
find in the whole town, for the fire-ship above-mentioned: then they
made several inventions of powder and brimstone with palm leaves,
well anointed with tar. They covered very well their counterfeit
cannon, laying under every piece many pounds of powder; besides,
they cut down many outworks of the ship, that the powder might
exert its strength the better; breaking open, also, new port-holes,
where, instead of guns, they placed little drums used by the
negroes. Finally, the decks were handsomely beset with many pieces
of wood, dressed up like men with hats, or monteras, and armed
with swords, muskets, and bandeleers.
The fire-ship being thus fitted, they prepared to go to the entry of
the port. All the prisoners were put into one great boat, and in
another of the biggest they placed all the women, plate, jewels, and
other rich things: into others they put the bales of goods and
merchandise, and other things of bulk: each of these boats had
twelve men aboard, very well armed; the brulot had orders to go
before the rest of the vessels, and presently to fall foul with the
great ship. All things being ready, Captain Morgan exacted an oath
of all his comrades, protesting to defend themselves to the last drop
of blood, without demanding quarter; promising withal, that
whosoever behaved himself thus, should be very well rewarded.
With this courageous resolution they set sail to seek the
Spaniards. On April 30, 1669, they found the Spanish fleet riding at
anchor in the middle of the entry of the lake. Captain Morgan, it
being now late and almost dark, commanded all his vessels to an
anchor, designing to fight even all night if they forced him to it. He
ordered a careful watch to be kept aboard every vessel till morning,
they being almost within shot, as well as within sight of the enemy.
The day dawning, they weighed anchor, and sailed again, steering
directly towards the Spaniards; who seeing them move, did instantly
the same. The fire-ship sailing before the rest fell presently upon the
great ship, and grappled her; which the Spaniards (too late)
perceiving to be a fire-ship, they attempted to put her off, but in
vain: for the flame seizing her timber and tackling, soon consumed
all the stern, the fore part sinking into the sea, where she perished.
The second Spanish ship perceiving the admiral to burn, not by
accident, but by industry of the enemy, escaped towards the castle,
where the Spaniards themselves sunk her, choosing to lose their ship
rather than to fall into the hands of those pirates. The third, having
no opportunity to escape, was taken by the pirates. The seamen that
sunk the second ship near the castle, perceiving the pirates come
towards them to take what remains they could find of their
shipwreck (for some part was yet above water), set fire also to this
vessel, that the pirates might enjoy nothing of that spoil. The first
ship being set on fire, some of the persons in her swam towards the
shore; these the pirates would have taken up in their boats, but they
would not ask or take quarter, choosing rather to lose their lives than
receive them from their hands, for reasons which I shall relate.
The pirates being extremely glad at this signal victory so soon
obtained, and with so great an inequality of forces, conceived
greater pride than they had before, and all presently ran ashore,
intending to take the castle. This they found well provided with men,
cannon, and ammunition, they having no other arms than muskets,
and a few hand granadoes: their own artillery they thought
incapable, for its smallness, of making any considerable breach in
the walls. Thus they spent the rest of the day, firing at the garrison
with their muskets, till the dusk of the evening, when they
attempted to advance nearer the walls, to throw in their fire-balls:
but the Spaniards resolving to sell their lives as dear as they could,
fired so furiously at them, that they having experimented the
obstinacy of the enemy, and seeing thirty of their men dead, and as
many more wounded, they retired to their ships.
The Spaniards believing the pirates would next day renew the
attack with their own cannon, laboured hard all night to put things in
order for their coming; particularly, they dug down, and made plain,
some little hills and eminences, when possibly the castle might be
offended.
 JOHAN MORGAN,
gebooren in de Provincie van Walles, in Engelandt
Generaal van der Roovere of Iamaica.
 HENRY MORGAN.
(From the Portrait in “De Americaensche Roovers.”)]

But Captain Morgan intended not to come again, busying himself

next day in taking prisoners some of the men who still swam alive,
hoping to get part of the riches lost in the two ships that perished.
Among the rest, he took a pilot, who was a stranger, and who
belonged to the lesser ship of the two, of whom he inquired several
things; as, What number of people those three ships had in them?
Whether they expected any more ships to come? From what port
they set forth last, when they came to seek them out? He answered,
in Spanish, “Noble sir, be pleased to pardon and spare me, that no
evil be done to me, being a stranger to this nation I have served,
and I shall sincerely inform you of all that passed till our arrival at
this lake. We were sent by orders from the Supreme Council of State
in Spain, being six men-of-war well equipped, into these seas, with
instructions to cruise upon the English pirates, and root them out
from these parts by destroying as many of them as we could.
“These orders were given, upon the news brought to the court of
Spain of the loss and ruin of Puerto Bello, and other places; of all
which damages and hostilities committed here by the English, dismal
lamentations have often been made to the catholic king and council,
to whom belongs the care and preservation of this new world. And
though the Spanish court hath many times by their ambassadors
complained hereof to the king of England; yet it hath been the
constant answer of his Majesty of Great Britain, that he never gave
any letters patent, nor commissions, for acting any hostility against
the subjects of the king of Spain. Hereupon the catholic king
resolved to revenge his subjects, and punish these proceedings:
commanded six men-of-war to be equipped, which he sent under
the command of Don Augustine de Bustos, admiral of the said fleet.
He commanded the biggest ship, named N. S. de la Soleda, of forty-
eight great guns, and eight small ones. The vice-admiral was Don
Alonso del Campo y Espinosa, who commanded the second ship
called La Conception, of forty-four great guns, and eight small ones;
beside four vessels more, whereof the first was named the
Magdalen, of thirty-six great guns, and twelve small ones, with two
hundred and fifty men. The second was called St. Lewis, with
twenty-six great guns, twelve small ones, and two hundred men.
The third was called La Marquesa, of sixteen great guns, eight small
ones, and one hundred and fifty men. The fourth and last, N. S. del
Carmen, with eighteen great guns, eight small ones, and one
hundred and fifty men.
“Being arrived at Carthagena, the two greatest ships received
orders to return to Spain, being judged too big for cruising on these
coasts. With the four ships remaining, Don Alonso del Campo y
Espinosa departed towards Campechy to seek the English: we
arrived at the port there, where, being surprised by a huge storm
from the north, we lost one of our ships, being that which I named
last. Hence we sailed for Hispaniola, in sight of which we came in a
few days, and steered for Santo Domingo: here we heard that there
had passed that way a fleet from Jamaica, and that some men
thereof had landed at Alta Gracia; the inhabitants had taken one
prisoner, who confessed their design was to go and pillage the city of
Caraccas. On this news, Don Alonso instantly weighed anchor, and,
crossing over to the continent, we came in sight of the Caraccas:
here we found them not, but met with a boat, which certified us
they were in the lake of Maracaibo, and that the fleet consisted of
seven small ships, and one boat.
“Upon this we came here, and arriving at the entry of the lake,
we shot off a gun for a pilot from the shore. Those on land
perceiving we were Spaniards, came willingly to us with a pilot, and
told us the English had taken Maracaibo, and that they were now at
the pillage of Gibraltar. Don Alonso, on this news, made a handsome
speech to his soldiers and mariners, encouraging them to their duty,
and promising to divide among them all they should take from the
English: he ordered the guns we had taken out of the ship that was
lost to be put into the castle, and mounted for its defence, with two
eighteen-pounders more, out of his own ship. The pilots conducted
us into the port, and Don Alonso commanded the people on shore to
come before him, whom he ordered to repossess the castle, and
reinforce it with one hundred men more than it had before its being
taken. Soon after, we heard of your return from Gibraltar to
Maracaibo, whither Don Alonso wrote you a letter, giving you an
account of his arrival and design, and exhorting you to restore what
you had taken. This you refusing, he renewed his promises to his
soldiers and seamen, and having given a very good supper to all his
people, he ordered them not to take or give any quarter, which was
the occasion of so many being drowned, who dared not to crave
quarter, knowing themselves must give none. Two days before you
came against us, a negro came aboard Don Alonso’s ship, telling
him, ‘Sir, be pleased to have great care of yourself; for the English
have prepared a fire-ship, with design to burn your fleet.’ But Don
Alonso not believing this, answered, ‘How can that be? Have they,
peradventure, wit enough to build a fire-ship? Or what instruments
have they to do it withal?’”
This pilot having related so distinctly these things to Captain
Morgan, was very well used by him, and, after some kind proffers
made to him, remained in his service. He told Captain Morgan, that,
in the ship which was sunk, there was a great quantity of plate, to
the value of forty thousand pieces of eight; which occasioned the
Spaniards to be often seen in boats about it. Hereupon, Captain
Morgan ordered one of his ships to remain there, to find ways of
getting out of it what plate they could; meanwhile, himself, with all
his fleet, returned to Maracaibo, where he refitted the great ship he
had taken, and chose it for himself, giving his own bottom to one of
his captains.
Then he sent again a messenger to the admiral, who was
escaped ashore, and got into the castle, demanding of him a ransom
of fire for Maracaibo; which being denied, he threatened entirely to
consume and destroy it. The Spaniards considering the ill-luck they
had all along with those pirates, and not knowing how to get rid of
them, concluded to pay the said ransom, though Don Alonso would
not consent.
 Hereupon, they sent to Captain Morgan, to know what sum he
demanded. He answered, that on payment of 30,000 pieces of eight,
and five hundred beeves, he would release the prisoners and do no
damage to the town. At last they agreed on 20,000 pieces of eight,
and five hundred beeves to victual his fleet. The cattle were brought
the next day, with one part of the money; and, while the pirates
were busied in salting the flesh, they made up the whole 20,000
pieces of eight, as was agreed.
But Captain Morgan would not presently deliver the prisoners, as
he had promised, fearing the shot of the castle at his going forth out
of the lake. Hereupon he told them he intended not to deliver them
till he was out of that danger, hoping thus to obtain a free passage.
Then he set sail with his fleet in quest of the ship he had left, to
seek for the plate of the vessel that was burnt. He found her on the
place, with 15,000 pieces of eight got out of the work, beside many
pieces of plate, as hilts of swords, and the like; also a great quantity
of pieces of eight melted and run together, by the force of the fire.
Captain Morgan scarce thought himself secure, nor could he
contrive how to avoid the shot of the castle: hereupon he wished the
prisoners to agree with the governor to permit a safe passage to his
fleet, which, if he should not allow, he would certainly hang them all
up in his ships. Upon this the prisoners met, and appointed some of
their fellow-messengers to go to the said governor, Don Alonso:
these went to him, beseeching and supplicating him to have
compassion on those afflicted prisoners, who were, with their wives
and children, in the hands of Captain Morgan; and that to this effect
he would be pleased to give his word to let the fleet of pirates freely
pass, this being the only way to save both the lives of them that
came with this petition, as also of those who remained in captivity;
all being equally menaced with the sword and gallows, if he granted
them not this humble request. But Don Alonso gave them for answer
a sharp reprehension of their cowardice, telling them, “If you had
been as loyal to your king in hindering the entry of these pirates, as
I shall do their going out, you had never caused these troubles
neither to yourselves nor to our whole nation, which hath suffered
so much through your pusillanimity. In a word, I shall never grant
your request, but shall endeavour to maintain that respect which is
due to my king, according to my duty.”
Thus the Spaniards returned with much consternation, and no
hopes of obtaining their request, telling Captain Morgan what
answer they had received: his reply was, “If Don Alonso will not let
me pass, I will find means how to do it without him.” Hereupon he
presently made a dividend of all they had taken, fearing he might
not have an opportunity to do it in another place, if any tempest
should rise and separate the ships, as also being jealous that any of
the commanders might run away with the best part of the spoil,
which then lay much more in one vessel than another. Thus they all
brought in according to their laws, and declared what they had, first
making oath not to conceal the least thing. The accounts being cast
up, they found to the value of 25,000 pieces of eight, in money and
jewels, beside the huge quantity of merchandise and slaves, all
which purchase was divided to every ship or boat, according to their
share.
The dividend being made, the question still remained how they
should pass the castle, and get out of the lake. To this effect they
made use of a stratagem, as follows: the day before the night
wherein they determined to get forth, they embarked many of their
men in canoes, and rowed towards the shore, as if they designed to
land: here they hid themselves under branches of trees that hang
over the coast awhile, laying themselves down in the boats; then the
canoes returned to the ships, with the appearance of only two or
three men rowing them back, the rest being unseen at the bottom of
the canoes: thus much only could be perceived from the castle, and
this false landing of men, for so we may call it, was repeated that
day several times: this made the Spaniards think the pirates
intended at night to force the castle by scaling it. This fear caused
them to place most of their great guns on the land side, together
with their main force, leaving the side towards the sea almost
destitute of defence.
 Night being come, they weighed anchor, and by moonlight,
without setting sail, committed themselves to the ebbing tide, which
gently brought them down the river, till they were near the castle;
being almost over against it, they spread their sails with all possible
haste. The Spaniards perceiving this, transported with all speed their
guns from the other side, and began to fire very furiously at them;
but these having a very favourable wind, were almost past danger
before those of the castle could hurt them; so that they lost few of
their men, and received no considerable damage in their ships.
Being out of the reach of the guns, Captain Morgan sent a canoe to
the castle with some of the prisoners, and the governor thereof gave
them a boat to return to their own homes; but he detained the
hostages from Gibraltar, because the rest of the ransom for not firing
the place was yet unpaid. Just as he departed, Captain Morgan
ordered seven great guns with bullets to be fired against the castle,
as it were to take his leave of them, but they answered not so much
as with a musket shot.
Next day after, they were surprised with a great tempest, which
forced them to cast anchor in five or six fathom water: but the storm
increasing, compelled them to weigh again, and put to sea, where
they were in great danger of being lost; for if they should have been
cast on shore, either into the hands of the Spaniards or Indians,
they would certainly have obtained no mercy: at last, the tempest
being spent, the wind ceased, to the great joy of the whole fleet.
While Captain Morgan made his fortune by these pillagings, his
companions, who were separated from his fleet at the Cape de
Lobos, to take the ship spoken of before, endured much misery, and
were unfortunate in all their attempts. Being arrived at Savona, they
found not Captain Morgan there, nor any of their companions, nor
had they the fortune to find a letter which Captain Morgan at his
departure left behind him in a place where in all probability they
would meet with it. Thus, not knowing what course to steer, they
concluded to pillage some town or other. They were in all about four
hundred men, divided into four ships and one boat: being ready to
set forth, they constituted an admiral among themselves, being one
who had behaved himself very courageously at the taking of Puerto
Bello, named Captain Hansel. This commander attempted the taking
of the town of Commana, on the continent of Caraccas, nigh sixty
leagues to the west of the Isle de la Trinidad. Being arrived there,
they landed their men, and killed some few Indians near the coast;
but approaching the town, the Spaniards having in their company
many Indians, disputed the entry so briskly, that, with great loss and
confusion, they were forced to retire to the ships. At last they arrived
at Jamaica, where the rest of their companions, who came with
Captain Morgan, mocked and jeered them for their ill success at
Commana, often telling them, “Let us see what money you brought
from Commana, and if it be as good silver as that which we bring
from Maracaibo.”
 CHAPTER XIII.
Captain Morgan goes to Hispaniola to equip a new fleet, with intent to pillage
again on the coast of the West Indies.

C aptainMorgan perceived now that Fortune favoured him, by

giving success to all his enterprises, which occasioned him, as is
usual in human affairs, to aspire to greater things, trusting she
would always be constant to him.
Such was the burning of Panama, wherein Fortune failed not to
assist him, as she had done before, though she had led him thereto
through a thousand difficulties. The history hereof I shall now relate,
being so remarkable in all its circumstances, as peradventure
nothing more deserving memory will be read by future ages.
Captain Morgan arriving at Jamaica, found many of his officers
and soldiers reduced to their former indigency, by their vices and
debaucheries. Hence they perpetually importuned him for new
exploits, thereby to get something to expend still in wine and
strumpets, as they had already done what they got before.
Captain Morgan, willing to follow Fortune’s call, stopped the
mouths of many inhabitants of Jamaica, who were creditors to his
men for large sums, with the hopes and promises of greater
achievements than ever, by a new expedition. This done, he could
easily levy men for any enterprise, his name being so famous
through all those islands as that alone would readily bring him in
more men than he could well employ. He undertook therefore to
equip a new fleet, for which he assigned the south side of Tortuga
as a place of rendezvous, writing letters to all the expert pirates
there inhabiting, as also to the governor, and to the planters and
hunters of Hispaniola, informing them of his intentions, and desiring
their appearance, if they intended to go with him. These people
upon this notice flocked to the place assigned, in huge numbers,
with ships, canoes, and boats, being desirous to follow him. Many,
who had not the convenience of coming by sea, traversed the woods
of Hispaniola, and with no small difficulties arrived there by land.
Thus all were present at the place assigned, and ready against
October 24, 1670.
Captain Morgan was not wanting to be there punctually, coming
in his ship to Port Couillon, over against the island De la Vaca, the
place assigned. Having gathered the greatest part of his fleet, he
called a council to deliberate about finding provisions for so many
people. Here they concluded to send four ships and one boat, with
four hundred men, to the continent, in order to rifle some country
towns and villages for all the corn or maize they could gather. They
set sail for the continent towards the river De la Hacha, designing to
assault the village called La Rancheria, usually best stored with
maize of all the parts thereabouts. Meanwhile Captain Morgan sent
another party to hunt in the woods, who killed a huge number of
beasts, and salted them: the rest remained in the ships, to clean, fit,
and rig them, that, at the return of their fellows, all things might be
in a readiness to weigh anchor and follow their designs.
 CHAPTER XIV.
What happened in the river De la Hacha.

T hese four ships setting sail from Hispaniola, steered for the river
De la Hacha, where they were suddenly overtaken with a tedious
calm. Being within sight of land becalmed for some days, the
Spaniards inhabiting along the coasts, who had perceived them to
be enemies, had sufficient time to prepare themselves, at least to
hide the best of their goods, that, without any care of preserving
them, they might be ready to retire, if they proved unable to resist
the pirates, by whose frequent attempts on those coasts they had
already learned what to do in such cases. There was then in the
river a good ship, come from Carthagena to lade with maize, and
now almost ready to depart. The men of this ship endeavoured to
escape; but, not being able to do it, both they and the vessel fell
into their hands. This was a fit purchase for them, being good part
of what they came for. Next morning, about break of day, they came
with their ships ashore, and landed their men, though the Spaniards
made good resistance from a battery they had raised on that side,
where, of necessity, they were to land; but they were forced to retire
to a village, whither the pirates followed them. Here the Spaniards
rallying, fell upon them with great fury, and maintained a strong
combat, which lasted till night; but then, perceiving they had lost a
great number of men, which was no less on the pirates’ side, they
retired to secret places in the woods.
Next day the pirates seeing them all fled, and the town left empty
of people, they pursued them as far as they could, and overtook a
party of Spaniards, whom they made prisoners, and exercised with
most cruel torments, to discover their goods. Some were forced, by
intolerable tortures, to confess; but others, who would not, were
used more barbarously. Thus, in fifteen days that they remained
there, they took many prisoners, much plate and movables, with
which booty they resolved to return to Hispaniola: yet, not content
with what they had got, they dispatched some prisoners into the
woods to seek for the rest of the inhabitants, and to demand a
ransom for not burning the town. They answered, they had no
money nor plate; but if they would be satisfied with a quantity of
maize, they would give as much as they could. The pirates accepted
this, it being then more useful to them than ready money, and
agreed they should pay four thousand hanegs, or bushels of maize.
These were brought in three days after, the Spaniards being desirous
to rid themselves of that inhuman sort of people. Having laded them
on board with the rest of their purchase, they returned to
Hispaniola, to give account to their leader, Captain Morgan, of all
they had performed.
They had now been absent five weeks on this commission, which
long delay occasioned Captain Morgan almost to despair of their
return, fearing lest they were fallen into the hands of the Spaniards;
especially considering the place whereto they went could easily be
relieved from Carthagena and Santa Maria, if the inhabitants were
careful to alarm the country. On the other side, he feared lest they
should have made some great fortune in that voyage, and with it
have escaped to some other place. But seeing his ships return in
greater numbers than they departed, he resumed new courage, this
sight causing both in him and his companions infinite joy, especially
when they found them full laden with maize, which they much
wanted for the maintenance of so many people, from whom they
expected great matters under such a commander.
Captain Morgan having divided the said, maize, as also the flesh
which the hunters brought, among his ships, according to the
number of men, he concluded to depart; having viewed beforehand
every ship, and observed their being well equipped and clean. Thus
he set sail, and stood for Cape Tiburon, where he determined to
resolve what enterprise he should take in hand. No sooner were they
arrived, but they met some other ships newly come to join them
from Jamaica; so that now their fleet consisted of thirty-seven ships,
wherein were two thousand fighting men, beside mariners and boys.
The admiral hereof was mounted with twenty-two great guns, and
six small ones of brass; the rest carried some twenty, some sixteen,
some eighteen, and the smallest vessel at least four; besides which,
they had great quantities of ammunition and fire-balls, with other
inventions of powder.
Captain Morgan having such a number of ships, divided the whole
fleet into two squadrons, constituting a vice-admiral, and other
officers of the second squadron, distinct from the former. To these
he gave letters patent, or commissions to act all manner of hostilities
against the Spanish nation, and take of them what ships they could,
either abroad at sea, or in the harbours, as if they were open and
declared enemies (as he termed it) of the king of England, his
pretended master. This done, he called all his captains and other
officers together, and caused them to sign some articles of
agreement betwixt them, and in the name of all. Herein it was
stipulated, that he should have the hundredth part of all that was
gotten to himself: that every captain should draw the shares of eight
men for the expenses of his ship, besides his own. To the surgeon,
beside his pay, two hundred pieces of eight for his chest of
medicaments. To every carpenter, above his salary, one hundred
pieces of eight. The rewards were settled in this voyage much higher
than before: as, for the loss of both legs, fifteen hundred pieces of
eight, or fifteen slaves, the choice left to the party: for the loss of
both hands, eighteen hundred pieces of eight, or eighteen slaves:
for one leg, whether right or left, six hundred pieces of eight, or six
slaves: for a hand, as much as for a leg; and for the loss of an eye,
one hundred pieces of eight, or one slave. Lastly, to him that in any
battle should signalize himself, either by entering first any castle, or
taking down the Spanish colours, and setting up the English, they
allotted fifty pieces of eight for a reward. All which extraordinary
salaries and rewards to be paid out of the first spoil they should
take, as every one should occur to be either rewarded or paid.
This contract being signed, Captain Morgan commanded his vice-
admirals and captains to put all things in order, to attempt one of
these three places; either Carthagena, Panama, or Vera Cruz. But
the lot fell on Panama, as the richest of all three; though this city
being situate at such a distance from the North Sea as they knew
not well the approaches to it, they judged it necessary to go
beforehand to the isle of St. Catherine, there to find some persons
for guides in this enterprise; for in the garrison there are commonly
many banditti and outlaws belonging to Panama and the
neighbouring places, who are very expert in the knowledge of that
country. But before they proceeded, they published an act through
the whole fleet, promising, if they met with any Spanish vessel, the
first captain who should take it should have for his reward the tenth
part of what should be found in her.
 CHAPTER XV.
Captain Morgan leaves Hispaniola, and goes to St. Catherine’s, which he takes.

C aptain Morgan and his companions weighed anchor from the Cape
of Tiburon, December 16, 1670. Four days after they arrived in
sight of St. Catherine’s, now in possession of the Spaniards again, as
was said before, to which they commonly banish the malefactors of
the Spanish dominions in the West Indies. Here are huge quantities
of pigeons at certain seasons. It is watered by four rivulets, whereof
two are always dry in summer. Here is no trade or commerce
exercised by the inhabitants; neither do they plant more fruits than
what are necessary for human life, though the country would make
very good plantations of tobacco of considerable profit, were it
cultivated.
As soon as Captain Morgan came near the island with his fleet, he
sent one of his best sailing vessels to view the entry of the river, and
see if any other ships were there, who might hinder him from
landing; as also fearing lest they should give intelligence of his
arrival to the inhabitants, and prevent his designs.
Next day, before sunrise, all the fleet anchored near the island, in
a bay called Aguade Grande. On this bay the Spaniards had built a
battery, mounted with four pieces of cannon. Captain Morgan landed
about one thousand men in divers squadrons, marching through the
woods, though they had no other guides than a few of his own men,
who had been there before, under Mansvelt. The same day they
came to a place where the governor sometimes resided: here they
found a battery called the Platform, but nobody in it, the Spaniards
having retired to the lesser island, which, as was said before, is so
near the great one, that a short bridge only may conjoin them.
 This lesser island was so well fortified with forts and batteries
round it, as might seem impregnable. Hereupon, as soon as the
Spaniards perceived the pirates approach, they fired on them so
furiously, that they could advance nothing that day, but were content
to retreat, and take up their rest in the open fields, which was not
strange to these people, being sufficiently used to such kind of
repose. What most afflicted them was hunger, having not eaten
anything that whole day. About midnight it rained so hard, that they
had much ado to bear it, the greatest part of them having no other
clothes than a pair of seaman’s trousers or breeches, and a shirt,
without shoes or stockings. In this great extremity they pulled down
a few thatched houses to make fires withal; in a word, they were in
such a condition, that one hundred men, indifferently well armed,
might easily that night have torn them all in pieces. Next morning,
about break of day, the rain ceased, and they dried their arms and
marched on: but soon after it rained afresh, rather harder than
before, as if the skies were melted into waters; which kept them
from advancing towards the forts, whence the Spaniards continually
fired at them.
The pirates were now reduced to great affliction and danger,
through the hardness of the weather, their own nakedness, and
great hunger; for a small relief hereof, they found in the fields an old
horse, lean, and full of scabs and blotches, with galled back and
sides: this they instantly killed and flayed, and divided in small
pieces among themselves, as far as it would reach (for many could
not get a morsel) which they roasted and devoured without salt or
bread, more like ravenous wolves than men. The rain not ceasing,
Captain Morgan perceived their minds to relent, hearing many of
them say they would return on board. Among these fatigues of mind
and body, he thought convenient to use some sudden remedy: to
this effect, he commanded a canoe to be rigged in haste, and
colours of truce to be hanged out. This canoe he sent to the Spanish
governor, with this message: “That if within a few hours he delivered
not himself and all his men into his hands, he did by that messenger
swear to him, and all those that were in his company, he would most
certainly put them to the sword, without granting quarter to any.”
In the afternoon the canoe returned with this answer: “That the
governor desired two hours’ time to deliberate with his officers about
it, which being past, he would give his positive answer.” The time
being elapsed, the governor sent two canoes with white colours, and
two persons to treat with Captain Morgan; but, before they landed,
they demanded of the pirates two persons as hostages. These were
readily granted by Captain Morgan, who delivered them two of his
captains for a pledge of the security required. With this the
Spaniards propounded to Captain Morgan, that the governor, in a full
assembly, had resolved to deliver up the island, not being provided
with sufficient forces to defend it against such an armada. But
withal, he desired Captain Morgan would be pleased to use a certain
stratagem of war, for the better saving of his own credit, and the
reputation of his officers both abroad and at home, which should be
as follows:—That Captain Morgan would come with his troops by
night to the bridge that joined the lesser island to the great one, and
there attack the fort of St. Jerome: that at the same time all his fleet
would draw near the castle of Santa Teresa, and attack it by land,
landing, in the meanwhile, more troops near the battery of St.
Matthew: that these troops being newly landed, should by this
means intercept the governor as he endeavoured to pass to St.
Jerome’s fort, and then take him prisoner; using the formality, as if
they forced him to deliver the castle; and that he would lead the
English into it, under colour of being his own troops. That on both
sides there should be continual firing, but without bullets, or at least
into the air, so that no side might be hurt. That thus having obtained
two such considerable forts, the chiefest of the isle, he need not
take care for the rest, which must fall of course into his hands.
These propositions were granted by Captain Morgan, on condition
they should see them faithfully observed; otherwise they should be
used with the utmost rigour: this they promised to do, and took their
leave, to give account of their negotiation to the governor. Presently
after, Captain Morgan commanded the whole fleet to enter the port,
and his men to be ready to assault, that night, the castle of St.
Jerome. Thus the false battle began, with incessant firing from both
the castles, against the ships, but without bullets, as was agreed.
Then the pirates landed, and assaulted by night the lesser island,
which they took, as also both the fortresses; forcing the Spaniards,
in appearance, to fly to the church. Before this assault, Captain
Morgan sent word to the governor, that he should keep all his men
together in a body; otherwise, if the pirates met any straggling
Spaniards in the streets, they should certainly shoot them.
This island being taken by this unusual stratagem, and all things
put in order, the pirates made a new war against the poultry, cattle,
and all sorts of victuals they could find, for some days; scarce
thinking of anything else than to kill, roast, and eat, and make what
good cheer they could. If wood was wanting, they pulled down the
houses, and made fires with the timber, as had been done before in
the field. Next day they numbered all the prisoners they had taken
upon the island, which were found to be in all four hundred and
fifty-nine persons, men, women, and children; viz., one hundred and
ninety soldiers of the garrison; forty inhabitants, who were married:
forty-three children, thirty-four slaves, belonging to the king; with
eight children, eight banditti, thirty-nine negroes belonging to private
persons; with twenty-seven female blacks, and thirty-four children.
The pirates disarmed all the Spaniards, and sent them out
immediately to the plantations to seek for provisions, leaving the
women in the church to exercise their devotions.
Soon after they reviewed the whole island, and all the fortresses
thereof, which they found to be nine in all, viz., the fort of St.
Jerome, next the bridge, had eight great guns, of twelve, six, and
eight pounds carriage; with six pipes of muskets, every pipe
containing ten muskets. Here they found still sixty muskets, with
sufficient powder and other ammunition. The second fortress, called
St. Matthew, had three guns, of eight pounds each. The third, and
chiefest, named Santa Teresa, had twenty great guns, of eighteen,
twelve, eight, and six pounds; with ten pipes of muskets, like those
before, and ninety muskets remaining, besides other ammunition.
This castle was built with stone and mortar, with very thick walls,
and a large ditch round it, twenty feet deep, which, though it was
dry, yet was very hard to get over. Here was no entry, but through
one door, to the middle of the castle. Within it was a mount, almost
inaccessible, with four pieces of cannon at the top; whence they
could shoot directly into the port. On the sea side it was
impregnable, by reason of the rocks round it, and the sea beating
furiously upon them. To the land it was so commodiously seated on
a mountain, as there was no access to it but by a path three or four
feet broad. The fourth fortress was named St. Augustine, having
three guns of eight and six pounds. The fifth, named La Plattaforma
de la Conception, had only two guns, of eight pounds. The sixth, by
name San Salvador, had likewise no more than two guns. The
seventh, called Plattaforma de los Artilleros, had also two guns. The
eighth, called Santa Cruz, had three guns. The ninth, called St.
Joseph’s Fort, had six guns, of twelve and eight pounds, besides two
pipes of muskets, and sufficient ammunition.
In the storehouses were above thirty thousand pounds of powder,
with all other ammunition, which was carried by the pirates on
board. All the guns were stopped and nailed, and the fortresses
demolished, except that of St. Jerome, where the pirates kept guard
and resistance. Captain Morgan inquired for any banditti from
Panama or Puerto Bello, and three were brought him, who
pretended to be very expert in the avenues of those parts. He asked
them to be his guides, and show him the securest ways to Panama,
which, if they performed, he promised them equal shares in the
plunder of that expedition, and their liberty when they arrived in
Jamaica. These propositions the banditti readily accepted, promising
to serve him very faithfully, especially one of the three, who was the
greatest rogue, thief, and assassin among them, who had deserved
rather to be broken alive on the wheel, than punished with serving
in a garrison. This wicked fellow had a great ascendant over the
other two, and domineered over them as he pleased, they not daring
to disobey his orders.
 Captain Morgan commanded four ships and one boat to be
equipped, and provided with necessaries, to go and take the castle
of Chagre, on the river of that name; neither would he go himself
with his whole fleet, lest the Spaniards should be jealous of his
farther design on Panama. In these vessels he embarked four
hundred men, to put in execution these his orders. Meanwhile,
himself remained in St. Catherine’s with the rest of the fleet,
expecting to hear of their success.
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