
Pocket Guide to Clinical Microbiology
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User-friendly, quick clinical microbiology reference
Stay ahead in clinical practice with the latest edition of Pocket Guide to Clinical Microbiology. This essential companion for clinical microbiology professionals delivers concise, up-to-date information on microbial identification, diagnostics, and treatment options, tailored for quick reference at the bench and in the clinic. Featuring the latest advancements, quick-reference tables, and practical insights, it is the go-to guide for clinical microbiologists, health care professionals, and students seeking a reliable and accessible resource to enhance their knowledge and practice.
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Christopher D. Doern, PhD, D(ABMM) is a professor of pathology at Virginia Commonwealth School of Medicine and director of clinical microbiology at Virginia Commonwealth University Health System, Richmond, VA.
Alexandra L. Bryson, PhD, D(ABMM) is an assistant professor of pathology at Virginia Commonwealth School of Medicine and associate director of clinical microbiology at Virginia Commonwealth University Health System, Richmond, VA.
Content
Preface xi
About the Authors xv
Section 1 Taxonomic Classification of Medically Important Microorganisms 1
General Comments 2
Taxonomic Classification of Bacteria 2
Table 1.1 Reclassification of the Former Family Enterobacteriaceae 10
Table 1.2 Newly Assigned Genera for Former Mycobacterium 11
Table 1.3 Enterobacter cloacae Complex Organisms 12
Table 1.4 Klebsiella oxytoca Complex Organisms 12
Table 1.5 Taxonomy of Citrobacter freundii Complex 12
Table 1.6 Taxonomy of Pseudomonas fluorescens Group Organisms 12
Table 1.7 Taxonomy of Pseudomonas putida Group Organisms 13
Table 1.8 Taxonomy of Pseudomonas aeruginosa Group Organisms 13
Table 1.9 Taxonomy of Acinetobacter calcoaceticus-baumannii Complex 13
Table 1.10 Taxonomy of Burkholderia cepacia Complex 13
Table 1.11 Taxonomy of Mycobacteria 14
Table 1.12 Taxonomy of the Staphylococcus aureus Complex 16
Table 1.13 Taxonomy of the Staphylococcus intermedius Group 16
Table 1.14 Taxonomy of the Viridans Group Streptococci 16
Taxonomic Classification of Human Viruses 17
Taxonomic Classification of Fungi 21
Table 1.15 Revised Species Names of Selected Clinically Relevant Fungi 22
Taxonomic Classification of Parasites 25
Section 2 Indigenous and Pathogenic Microbes of Humans 31
General Comments 32
Table 2.1 Human Indigenous Flora 32
Table 2.2 Summary of Notifiable Infectious Diseases: United States, 2016 and 2020 43
Table 2.3 Arthropod Vectors of Medically Important Diseases 48
Table 2.4 Fungal Pathogens and Geographic Distribution 51
Table 2.5 Parasitic Pathogens and Geographic Distribution 62
Microbes Responsible for Human Disease 70
Section 3 Specimen Collection and Transport 93
General Comments 94
Table 3.1 Bacteriology: Collection and Transport Guidelines 96
Table 3.2 Specimen Collection and Transport Guidelines for Infrequently Encountered Bacteria 114
Table 3.3 Guidelines for Collection of Specimens for Anaerobic Culture 115
Table 3.4 Possible Rejection Criteria for Specimens Submitted for Bacterial Culture 116
Virology: General Specimen Guidelines 117
Virology: Specific Specimen Guidelines 118
Table 3.5 Recommended Blood Volumes to Collect for Blood Cultures 121
Table 3.6 Mycology: Collection and Transport Guidelines 122
Table 3.7 Parasitology: Specimen Guidelines 127
Table 3.8 Guidelines for Processing Stool Specimens for Parasites 132
Section 4 Bacterial Diagnosis 135
General Comments 136
Table 4.1 Detection Methods from Clinical Specimens for Clinically Relevant Bacteria 136
Table 4.2 Recommendations for Gram Stain from Primary Specimen and Plating Media 139
Table 4.3 Screening Specimens for Routine Bacterial Culture 143
Table 4.4 Processing Specimens for Mycobacterial Identification 144
Microscopy 144
Primary Plating Media: Bacteria 146
Primary Plating Media: Mycobacteria 159
Specific Diagnostic Tests for Pathogen Detection 161
Aerobic Gram-Positive Cocci 161
Aerobic Gram-Positive Rods 162
Acid-Fast and Partially Acid-Fast Gram-Positive Rods 164
Aerobic Gram-Negative Cocci 164
Aerobic Gram-Negative Rods 165
Anaerobic Bacteria 172
Curved and Spiral-Shaped Bacteria 173
Mycoplasma spp. and Obligate Intracellular Bacteria 176
Identification Tables 178
Section 5 Viral Diagnosis 217
General Comments 218
Table 5.1 Detection Methods for Viruses 218
Table 5.2 Cells Used for Viral Isolation 220
RNA Viruses 221
DNA Viruses 229
Table 5.3 EBV Serologic Profiles Under Different Conditions 231
Table 5.4 Clinical Diseases of Parvovirus B19 and Method of Diagnosis 232
Table 5.5 Hepatitis B Virus Markers in Different Stages of Infection and Convalescence 233
Transmissible Spongiform Encephalopathies 235
Section 6 Fungal Diagnosis 237
Mycology: Specimen Collection and Transport Guidelines 238
Table 6.1 Methods for the Identification of Fungi 240
Microscopy 240
Table 6.2 Characteristic Fungal Elements Seen by Direct Examination of Clinical Specimens 243
Primary Plating Media 246
Table 6.3 Mycology Plating Guide 249
Specific Diagnostic Tests 251
Aspergillus Species 251
Blastomyces dermatitidis 251
Candida Species 252
Coccidioides Species (Coccidioidomycosis) 252
Cryptococcus neoformans and gattii (Cryptococcosis) 253
Histoplasma Species 253
Malassezia Species 254
Paracoccidioides brasiliensis 254
Talaromyces (Penicillium) marneffei 255
Pneumocystis jirovecii 255
Sporothrix schenckii 255
Mucormycetes (Zygomycetes) 255
Identification Tables 257
Section 7 Parasitic Diagnosis 271
General Comments 272
Microscopy 272
Table 7.1 Detection Methods for Parasites 273
Specific Diagnostic Tests 277
Free-Living Amebae 277
Intestinal and Urogenital Protozoa 277
Blood and Tissue Protozoa 280
Microsporidia 282
Helminths: Nematodes 283
Helminths: Trematodes 285
Helminths: Cestodes 286
Identification Tables and Figures 287
Table 7.2 Trophozoites of Common Intestinal Amebae 287
Table 7.3 Cysts of Common Intestinal Amebae 290
Figure 7.1 Intestinal Amebae of Humans 293
Table 7.4 Trophozoites of Flagellates 294
Table 7.5 Cysts of Flagellates 296
Figure 7.2 Intestinal and Urogenital Flagellates of Humans 297
Table 7.6 Morphological Characteristics of Ciliates, Coccidia, Microsporidia, and Tissue Protozoa 298
Table 7.7 Morphological Characteristics of Protozoa Found in Blood 300
Table 7.8 Morphological Characteristics of Blood and Tissue Nematodes 302
Table 7.9 Morphological Characteristics of Helminths 303
Figure 7.3 Relative Sizes of Helminth Eggs 305
Section 8 Susceptibility Testing and Methods of Organism Identification 307
General Comments 308
Susceptibility Testing Methods 308
Table 8.1 Clinical and Laboratory Standards Institute (CLSI) Documents Related to Antimicrobial Susceptibility Testing from Humans 308
Table 8.2 Summary of CLSI Antimicrobial Susceptibility Test Methods for Select Bacteria, Mycobacteria, and Fungi 311
Antimicrobial Treatment Information 315
Table 8.3 Organisms Included in CLSI and EUCAST Breakpoint Tables 315
Table 8.4 Guide to Interpretive Criteria for Select Organisms for Commonly Tested Antimicrobials 317
Table 8.5 Surrogate Antibiotic Susceptibility Prediction 330
Table 8.6 Routes of Administration and Drug Class for Select Antimicrobial Agents 334
Table 8.7 Routes of Administration and Drug Class for Select Antifungal Agents 337
Table 8.8 Routes of Administration and Drug Class for Select Antiparasitic Agents 338
Table 8.9 Antibacterial Agents for Specific Bacteria 339
Antimicrobial Resistance Mechanisms 345
Table 8.10 Intrinsic Resistance of Selected Gram-Negative Bacteria 345
Table 8.11 Intrinsic Resistance of Selected Gram-Positive Bacteria 346
Table 8.12 Important Mechanisms of Multidrug Resistance in Bacteria 346
Table 8.13 Activity Profiles of Select Beta-Lactam Antibiotics Against Commonly Encountered Gram-Negative Beta-Lactamases 350
MALDI-TOF MS and Sequencing 351
Table 8.14 Summary of MALDI-TOF MS Identification of Bacteria, Mycobacteria, and Fungi 351
Table 8.15 Gene Sequencing Targets for Organism Identification 356
Index 359
SECTION 1
Taxonomic Classification of Medically Important Microorganisms
General Comments
Taxonomic Classification of Bacteria
Table 1.1 Reclassification of the Former Family Enterobacteriaceae
Table 1.2 Newly Assigned Genera for Former Mycobacterium
Table 1.3 Enterobacter cloacae Complex Organisms
Table 1.4 Klebsiella oxytoca Complex Organisms
Table 1.5 Taxonomy of Citrobacter freundii Complex
Table 1.6 Taxonomy of Pseudomonas fluorescens Group Organisms
Table 1.7 Taxonomy of Pseudomonas putida Group Organisms
Table 1.8 Taxonomy of Pseudomonas aeruginosa Group Organisms
Table 1.9 Taxonomy of Acinetobacter calcoaceticus-baumannii Complex
Table 1.10 Taxonomy of Burkholderia cepacia Complex
Table 1.11 Taxonomy of Mycobacteria
Table 1.12 Taxonomy of the Staphylococcus aureus Complex
Table 1.13 Taxonomy of the Staphylococcus intermedius Group
Table 1.14 Taxonomy of the Viridans Group Streptococci
Taxonomic Classification of Human Viruses
Taxonomic Classification of Fungi
Table 1.15 Revised Species Names of Selected Clinically Relevant Fungi
Taxonomic Classification of Parasites
In order to remain true to the tradition set forth by the first four editions of this pocket guide, the first section will be devoted to describing the taxonomy of common (and some uncommon) organisms which are associated with humans and may be isolated by the clinical microbiology laboratory. The rate of taxonomic change continues to increase such that publishing a taxonomic list of organisms would quickly be out of date, rendering it obsolete. This is a product of ongoing 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 groupings and provide the resources and references one would need to identify the most up-to-date taxonomic classifications.
The International Code of Nomenclature of Bacteria governs bacterial taxonomy, and all bacteria named after 1980 must be validly published in the International Journal of Systematic and Evolutionary Microbiology. A current listing of bacteria can be found at https://lpsn.dsmz.de. The International Committee on Taxonomy of Viruses (ICTV) governs viral taxonomy, and all currently recognized viruses can be found at https://ictv.global. The International Code of Nomenclature for algae, fungi, and plants governs fungal classification, and additional information can be found at https://www.iapt-taxon.org/nomen/main.php.
Taxonomic Classification of Bacteria
Classification and taxonomy of prokaryotes (bacteria) is complicated and is governed by the International Code of Nomenclature of Bacteria (ICNB)(last revised in 1990). By definition, each prokaryotic species must include a genus level name that is included within a hierarchy or ranks, which includes (from highest to lowest rank) domain (or empire), kingdom, phylum, class, order, family, genus, and species.
Most importantly, there is no such thing as an official classification of prokaryotes. This is because in contrast to eukaryotes, the prokaryotic designations are a matter of scientific judgment. Therefore, the closest things that we have to "official" taxonomic designations are those names that are generally accepted by the microbiology community. Despite this fact, microbiologists have achieved some amount of consensus by relying on resources such as the International Journal of Systematic and Evolutionary Microbiology and Bergey's Manual of Systematics of Archaea and Bacteria, which was last updated in 2012. In 2015 publication of this resource moved to continuous publication in an online format.
Initially bacteria were classified according to their phenotypic properties back in the 1920's. The product of these classification methods was published in Bergey's Manual of Determinative Bacteriology. Scientific methods for classification have evolved and now include genetic analyses which provide a more objective and reproducible mechanism for differentiating organisms. A number of DNA-based methods can now be used for bacterial classification including small subunit ribosomal RNA (typically 16S), DNA-DNA hybridization, DNA G+C content, pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), and lastly, whole genome-based analyses. Not only have these methods been instrumental in revolutionizing bacterial classification, but they have highlighted the enormous amount of microbial diversity that was being missed by culture-based methods.
The following is a consolidated taxonomic outline, which will focus on the taxonomic organization of those organisms that are most likely to be encountered in the clinical microbiology laboratory. This is not meant to be an exhaustive list of all bacteria. 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 following way.
- Domain
- Phylum
- Class
- Order
- Family
- Genera
- Species
- Order
- Class
- Phylum
- Domain: Bacteria
- Family. Acetobacteraceae
- Genus. Roseomonas
- Family. Actinomycetaceae
- Genus. Actinobaculum
- Genus. Actinomyces
- Genus. Actinotignum
- Genus. Arcanobacterium
- Genus. Mobiluncus
- Genus. Trueperella
- Family. Aerococcaceae
- Genus. Abiotrophia
- Genus. Aerococcus
- Genus. Dolosicoccus
- Genus. Facklamia
- Genus. Globicatella
- Family. Aeromonadaceae
- Genus. Aeromonas
- Family. Alcaligenaceae
- Genus. Achromobacter
- Genus. Alcaligenes
- Genus. Bordetella
- Genus. Kerstersia
- Genus. Oligella
- Family. Atopobiaceae
- Genus. Atopobium
- Family. Azospirillaceae
- Genus. Inquilinus
- Family. Bacillaceae
- Genus. Bacillus
- Family. Bacteroidaceae
- Genus. Bacteroides
- Family. Bartonellaceae
- Genus. Bartonella
- Family. Bifidobacteriaceae
- Genus. Alloscardovia
- Genus. Bifidobacterium
- Genus. Gardnerella
- Family. Borreliaceae
- Genus. Borrelia
- Family. Brachyspiraceae
- Genus. Brachyspira
- Family. Brevibacteriaceae
- Genus. Brevibacterium
- Family. Brucellaceae
- Genus. Brucella
- Genus. Ochrobactrum
- Family. Acetobacteraceae
NOTE: The taxonomy of these organisms is controversial. In 2020 taxonomists proposed that the genus Ochrobactrum be included within the genus Brucella. For the purposes of this text and the practice of clinical microbiology, we reject this proposal and will retain Ochrobactrum nomenclature. It is our contention that Ochrobactrum is a distinct genus which is not a cause of brucellosis, a severe form of human disease. Referring to Ochrobactrum as Brucella will present serious issues in interpreting the clinical significance of culture results. Readers are referred to Moreno E et al. 2023. J Clin Microbiol 61(8):e0043823 for a detailed discussion of the issue.
- Family. Burkholderiaceae
- Genus. Burkholderia
- Genus. Cupriavidus
- Genus. Pandoraea
- Genus. Ralstonia
- Family. Campylobacteraceae
- Genus. Campylobacter
- Family. Cardiobacteriaceae
- Genus. Cardiobacterium
- Genus. Suttonella
- Family. Carnobacteriaceae
- Genus. Alloiococcus
- Genus. Dolosigranulum
- Genus. Granulicatella
- Family. Caulobacteraceae
- Genus. Brevundimonas
- Family. Cellulomonadaceae
- Genus. Cellulomonas
- Family. Chlamydiaceae
- Genus. Chlamydia
- Family. Clostridiaceae
- Genus. Clostridium
- Genus. Sarcina
- Family. Comamonadaceae
- Genus. Acidovorax
- Genus. Comamonas
- Genus. Delftia
- Family....
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