Taxonomy and Overview of Human Pathogenic Bacteria

■ Taxonomy includes the two disciplines of classification and nomenclature. The bacteria are classified in a hierarchic system based on phenotypic characteristics (morphological, physiological, and chemical characteristics). The basic unit is the species. Similar and related species are classified in a single genus and related genera are placed in a single family. Classification in yet higher taxa often takes practical considerations into account, e.g., division into "descriptive sections." A species is designated by two Latin names, the first of which denotes the genus, both together characterizing the species. Family names end in -aceae. Table 3.9 provides an overview of human pathogenic bacteria. ■


Bacteria are grouped in the domain bacteria to separate them from the domains archaea and eucarya (see p. 5). Within their domain, bacteria are further broken down into taxonomic groups (taxa) based on relationships best elucidated by knowledge of the evolutionary facts. However, little is known about the phylogenetic relationships of bacteria, so their classification is often based on similarities among phenotypic characteristics (phenetic relationships). These characteristics are morphological, physiological (metabolic), or chemical (see Table 3.8, p. 215) in nature. The role of chemical characteristics in classification is growing in importance, for instance, murein composition or the presence of certain fatty acids in the cell wall. DNA and RNA structure is highly important in classification. DNA composition can be roughly estimated by determining the proportions of the bases: mol/l of guanine + cytosine (GC). The GC content (in mol%) of human pathogenic bacteria ranges from 25% to 70%. Measurement of how much heterologous duplex DNA is formed, or of RNA-DNA hybrids, provides information on the similarity of different bacteria and thus about their degree of relationship. Another highly useful factor in determining phylogenetic relationship is the sequence analysis of the (16S/23S) rRNA or (16S/23S) rDNA. This genetic material contains highly conserved sequences found in all bacteria alongside sequences characteristic of the different taxa.

In formal terms, the prokaryotes are classified in phyla, classes, orders, families, genera, and species, plus subtaxa if any: Family (familia) Enterobacteriaceae Genus Escherichia

Species E. coli

Var(iety) or type Serovar O157:H7 Strain xyz

Taxonomic classification is based on the concept of the species. Especially in an epidemiological setting, we often need to subclassify a species in vars or (syn.) types, in which cultures of a species that share certain characteristics are grouped together. Examples: biovar, phagovar, pathovar, morphovar, serovar (also biotype, phagotype, etc.). Use of the term strain varies somewhat: in clinical bacteriology it often designates the first culture of a species isolated from an infected patient. In an epidemiological context, isolates of the same species obtained from different patients are considered to belong to the same epidemic strain.

There is no official, internationally recognized classification of bacteria.

The higher taxa therefore often reflect practical considerations.

Table 3.9 Overview of the Medically Most Important Bacteria1


Genus, species


Clinical manifestations

Section 1. Gram-positive



Cluster-forming cocci, nonmotile; catalase-positive

Staphylococcus aureus

Coagulase-positive, yellow-pigmented colonies

Pyogenic infections, toxicoses

S. epidermidis

Coagulase-negative, whitish colonies, normal flora

Foreign body infections

S. saprophyticus


Urinary tract infections in young women


Chain-forming cocci and diplococci, nonmotile, catalase-negative

Streptococcus pyogenes

Chain-forming cocci, Lance-field group A, b-hemolysis

Tonsillitis, scarlet fever, skin infections

S. pneumoniae

Diplococci, no group antigen present, a-hemolysis

Pneumonia, otitis media, sinusitis

S. agalactiae

Chain-forming cocci, group antigen B, b-hemolysis

Meningitis/sepsis in neonates

" Enterococcaceae"

Chain-forming cocci and diplococci, a, b, or y-hemo-lysis, group antigen D, catalase-negative

Part of the flora of intestines of humans and animals

Enterococcus faecalis Enterococcus faecium

Aesculin-positive, growth in 6.5% NaCl, pH 9.6

Opportunistic infections

Section 2. Endospore-forming Gram-positive rods


Aerobic soil bacteria

Bacillus anthracis

Nonmotile, ubiquitous



Anaerobic soil bacteria

Clostridium tetani

Motile, anaerobic, tetanus toxin (tetanospasmin)


1 (Nomenclature according to Bergey's Manual of Systematic Bacteriology, 2001, Vol. 1, pp. 155-166. Names in quotation marks not yet validated).


Genus, species


Clinical manifestations

Continued: Section 2. Clostridium botulinum

Clostridium perfringens and further clostridiae

Clostridium difficile

Motile, neurotoxins A, B, and G

Nonmotile, exotoxins, and exoenzymes

Motile, enterotoxin (toxin A), cytotoxin (toxin B)

Botulism, usually ingestion of toxin with food

1. Anaerobic cellulitis

2. Gas gangrene (myonecrosis)

Pseudomembranous colitis (often antibotic associated)

Section 3. Regular, nonsporing, Gram-positive rods

Listeria monocytogenes

Gardnerella vaginalis

Slender rods, weak b-hemo-lysis on blood agar, motile at 20°C, ubiquitous (soil)

Flora of the normal genital mucosa

Meningitis, sepsis (neonates, immuno-compromised persons), epidemic gastroenteritis

Erysipeloid (today rare) Contributes to vaginosis

Erysipelothrix rhusiopathiae Transmitted from diseased pigs

Section 4. Irregular, nonsporing, Gram-positive rods


Corynebacterium diphtheriae


Actinomyces israelii and further Actinomyces spp.


Mostly normal bacterial Only few species cause flora of the skin and mucosa, disease aerobic

Club shape, pleomorphic, diphtheria exotoxin (A + B)

Normal bacterial flora of the mucosa, anaerobic or micro-aerophilic

Filaments (also branched)

Nonmotile, obligately aerobic, filaments, partially acid-fast

Diphtheria (throat, nose, wounds)

Actinomycosis (cervicofacial, thoracic, abdominal, pelvic)

Habitat: soil and aquatic biotopes

Table 3.9 Continued: Overview of the Medically Most Important Bacteria


Genus, species


Clinical manifestations

Continued: Section 4.

Nocardia asteroides Nocardia brasiliensis and further species

Infections in patients with impaired cell-mediated immunity

Pulmonary, systemic, and dermal nocardioses

Section 5. Mycobacteria (acid-fast rods)


Mycobacterium tuberculosis

Mycobacterium leprae

Nontuberculous mycobacteria (NTM) (e.g., Mycobacterium avium/intracellulare complex, and numerous other species)

Slender rods, Ziehl-Neelsen staining (Gram-positive cell wall), aerobic, nonmotile

Slow proliferation (culturing 3-6-8 weeks)

In-vitro culture not possible

Ubiquitous. Low level of pathogenicity, opportunists

Tuberculosis (pulmonary and extrapulmonary)

Leprosy (lepromatous, tuberculoid)

Pulmonary disease, lymphadenitis, infections of skin, soft tissue, bones, joints, tendons. Disseminated disease in immunosuppressed patients (AIDS)

Section 6. Gram-negative aerobic cocci and coccobacilli


Neisseria gonorrheae

Neisseria meningitidis Eikenella corrodens Kingella kingae

Coffee bean-shaped diplococci, nonmotile, oxidase (+), catalase (+)

Cocci often in phagocytes, acid from fermentation of glucose

Acid from fermentation of glucose and maltose

HACEK-group. Low pathogenicity

HACEK-group. Low pathogenicity



Nosocomial infections

Nosocomial infections

Table 3.9 Continued: Overview of the Medically Most Important Bacteria


Genus, species


Clinical manifestations

Continued: Section 6. Moraxellaceae

Moraxella catarrhalis

Cocci and short rods

Normal respiratory tract flora Sinusitis, otitis media in children

Acinetobacter baumannii Ubiquitous, coccobacillary Acinetobacter calcoaceticus rods

Nosocomial infections, often multiple resistance against anti-infective agents

Section 7. Gram-negative facultatively anaerobic rods


Escherichia coli

Salmonella enterica

Shigella dysenteriae, S. flexneri, S. boydii, S. sonnei

Klebsiella, Enterobacter, Citrobacter, Proteus, Serratia, Morganella, Providencia, and other genera

Yersinia pestis

Yersinia enterocolitica

Calymmatobacterium granulomatis

Inhabitat intestine of man and animals. Genera (41) and species (hundreds) identified biochemically

Lactose-positive, most frequent human pathogen, various pathovars.

Lactose-negative, motile, over 2000 serovars


(in most cases), nonmotile,


Opportunists, frequently resistant to antibiotics

Bipolar staining, motile, no acid from lactose. Rodent pathogen

Reservoir: wild animals, domestic animals, pets

Encapsulated, nonmotile

Nosocomial infections, Gut disease caused by pathovars EPEC, ETEC, EIEC, EHEC, and EAggEC

Typhoid/paratypoid fever, gastroenteritis

Bacterial dysentery

Nosocomial infections

Bubonic plague, pulmonary plague

Enteritis, lymphadenitis

Granuloma inguinale (venereal disease)

Table 3.9 Continued: Overview of the Medically Most Important Bacteria


Genus, species


Clinical manifestations

Comma-shaped, polar flagella, oxidase-positive

Alkaline tolerance, exotoxin, no invasion of the small intestine's mucosa

Cholera, massive watery diarrhea

Aquatic biotopes, fish infections

Small straight rods, nonmotile

Pathogen of various animals (sepsis)

Occasionally the cause of enteritis in man

Infections via dermal injuries (rare)

X and V factors for culturing, Meningitis, respiratory capsule serovar "b" (Hib) tract infections

Continued: Section 7. Vibrionaceae

Vibrio cholerae


Aeromonas spp.


Pasteurella multocida Haemophilus influenzae


Cardiobacterium hominis

HACEK group. Normal mucosal flora of humans, nonmotile

Endocarditis (rare). Opportunistic infections

Section 8. Gram-negative aerobic rods

Pseudomonadaceae Straight or curved rods, Nosocomial infections motile, oxidase-positive. Ubiquitous bacteria

Pseudomonas aeruginosa and many further species


Burkholderia cepacia

B. mallei B. pseudomallei

Fluorescent pigments produced. Other properties as above

Nosocomial infections, frequent multiple antibiotic resistance

Nosocomial infections. Often resistance to multiple antibiotics

Skin abscesses. Very rare Melioidosis (Asia)


Malleus of horses Habitat: soil




Genus, species


Continued: Section 8.



Low pathogenicity

Nosocomial infections.


Often resistance to multi-

ple antibiotics


Motile, difficult to stain,

requires special culturing


Legionella pneumophila

Most frequent species,

Legionnaire's pneumonia,

aquatic biotopes

Pontiac fever


Short rods, nonmotile,


facultative intracellular

parasite, fastidious growth

Brucella abortus

Transmission via direct

Brucellosis (Bang disease,

Brucella melitensis

contact or foods (milk and

Malta fever)

Brucella suis

milk products)

Brucella canis


Bordetella pertussis

Short rods, nonmotile,

Pertussis (whooping

only in humans



Francisella tularensis

Minute pleomorphic rods.

Tularemia, zoonosis

Requires enriched media


for culturing

Section 9. Gram-negative rods, straight, curved, and helical, strictly anaerobic

Bacteroidaceae Pleomorphic rods, major Subacute necrotic




Bacteroides spp. Porphyromonas spp. Prevotella spp. Fusobacterium spp.

component of normal mucosal flora infections, mostly together with other bacteria

Necrotic abscesses in CNS, head region, lungs, abdomen, female genital tract

Table 3.9 Continued: Overview of the Medically Most Important Bacteria


Genus, species


Clinical manifestations

Continued: Section 9.

Streptobacillus moniliformis (belongs new to Fusobacteriaceae)

Normal flora in rats, mice, and cats

Rat-bite fever

(also caused by Spirillum minus (= Sodoku)

Section 10. Aerobic/microaerophilic, motile, helical/vibrioid Gram-negative rod bacteria


Campylobacter jejuni Campylobacter fetus


Helicobacter pylori

Thin, helical, and vibrioid, culturable

Animal pathogen

Helical, culturing difficult, produces large amounts of urease


Opportunistic infections: sepsis, endocarditis

Type B gastritis, peptic ulcers of stomach and duodenum

Section 11. The Spirochetes. Gram-negative, helical bacteria


Treponema pallidum

Borrelia burgdorferi B. afzelii B. garinii

Borrelia duttonii Borrelia hermsii and further species

Borrelia recurrentis


Leptospira interrogans

Helical, motile, thin

Only in humans, not culturable

Tickborne, culturable

Tickborne, antigen variability

Transmitted by body lice

Helical, motile, culturable

Serogroups and serovars (e.g., icterohemorrhagiae, pomona, grippotyphosa, etc.)

Syphilis, three stages Lyme disease, three stages

Endemic relapsing fever

Epidemic relapsing fever Leptospirosis, morbus Weil

Table 3.9 Continued: Overview of the Medically Most Important Bacteria


Genus, species


Clinical manifestations

Section 12. Rickettsiae, Coxiellae, Ehrlichiae, Bartonellae, and Chlamydiae


Rickettsia prowazekii Rickettsia rickettsii


Coxiella burnetii


Ehrlichia chaffeensis

Ehrlichia ewingii and Anaplasma (formerly Ehrlichia) phagocytophilum


Bartonella bacilliformis

Small short rods, usually intracellular bacteria transmitted by arthropods

Transmitted by body lice

Transmitted by ticks

Reservoir: sheep, cattle, rodents; infection by inhalation

Coccobacillary. Culture possible

Transmission by ticks

Bartonella henselae and Bartonella claridgeia

Bartonella quintana Chlamydiaceae

Chlamydia trachomatis

Transmission by ticks

Short pleomorphic rods

Tropism for erythrocytes/ endothelia. Transmitted by sand flea

Animal reservoir: cats

Transmission by body lice

Obligate intracellular pathogen, reproductive cycle

Biovar trachoma

Biovar lymphogranuloma venerum



Rocky Mountains Spotted Fever (RMSF)

Q fever (pneumonia)


Human monocytrophic ehrlichiosis (HME)

Human granulocytotrophic ehrlichiosis (HEG)

Oroya fever and verruga peruana

Sepsis, bacillary angio-matosis in immuno-suppressed patients (AIDS). Cat scratch disease in immunocompetent persons

Five-day fever

Trachoma, inclusion conjunctivitis, urethritis (nonspecific)

Lymphogranuloma venereum

Table 3.9 Continued: Overview of the Medically Most Important Bacteria


Genus, species


Clinical manifestations

Continued: Section 12.

Chlamydia psittaci Reservoir: infected birds.

Ornithosis (pneumonia)

Infection by inhalation of pathogen-containing dust

Chlamydia pneumoniae Only in humans, aerogenic transmission

Infections of the respiratory tract, often subacute. Role in atherosclerosis of coronary arteries still unclear

Section 13. Mycoplasmas (bacteria without cell walls)

Mycoplasmataceae Pleomorphic; no murein, therefore resistant to antibiotics that attack the cell wall

Mycoplasma pneumoniae Reservoir human, aerogenic Pneumonia (frequently

Ureaplasma urealyticum Component of the normal Urethritis (nonspecific) flora of the urogenital tract

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