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Overview of Bacteria

By Hans P. Schlecht, MD, MSc, Assistant Professor of Medicine, Department of Medicine, Division of Infectious Diseases & HIV Medicine, Drexel University College of Medicine
Christopher Bruno, MD, Assistant Professor of Medicine, Division of infectious Diseases & HIV Medicine, Drexel University College of Medicine

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Bacteria are microorganisms that have circular double-stranded DNA and (except for mycoplasmas) cell walls. Most bacteria live extracellularly. Some bacteria (eg, Salmonella typhi; Neisseria gonorrhoeae; Legionella, Mycobacterium, Rickettsia, Chlamydia, and Chlamydophila spp) preferentially reside and replicate intracellularly. Some bacteria such as chlamydiae, Chlamydophila sp, and rickettsiae are obligate intracellular pathogens (ie, able to grow, reproduce, and cause disease only within the cells of the host). Others (eg, Salmonella typhi, Brucellasp, Francisella tularensis, N. gonorrhoeae, N. meningitidis, Legionella and Listeria spp, Mycobacterium tuberculosis) are facultative intracellular pathogens.

Many bacteria are present in humans as normal flora, often in large numbers and in many areas (eg, in the GI tract). Only a few bacterial species are human pathogens.

Bacteria are classified by the following criteria (see Table: Classification of Common Pathogenic Bacteria).


Bacteria may be

  • Cylindric (bacilli)

  • Spherical (cocci)

  • Spiral (spirochetes)

A few coccal, many bacillary, and most spirochetal species are motile.


The most common stain for general bacterial identification is Gram stain. Gram-positive bacteria retain crystal violet dye (appearing dark blue) after iodine fixation, alcohol decolorization, and counterstaining with safranin; gram-negative bacteria, which do not retain crystal violet, appear red. Gram-negative bacteria have an additional outer membrane containing lipopolysaccharide (endotoxin), increasing the virulence of these bacteria. (For other factors that enhance bacterial pathogenicity, see Factors Facilitating Microbial Invasion.)

Ziehl-Neelsen and Kinyoun stains are acid-fast stains used to identify mainly mycobacteria, particularly M. tuberculosis. They also can identify Nocardia and Cryptosporidia spp. Carbolfuchsin is applied, followed by decolorization with hydrochloric acid and ethanol and then counterstaining with methylene blue. Fluorochrome stains (eg, auramine-rhodamine) also identify acid-fast organisms, but a special fluorescent microscope is required.


Some bacteria are enclosed in capsules; for some encapsulated bacteria (eg, Streptococcus pneumoniae, Haemophilus influenzae), the capsule helps protect them from ingestion by phagocytes. Encapsulation increases bacterial virulence.

Oxygen requirements

Aerobic bacteria (obligate aerobes) require O2 to produce energy and to grow in culture. They produce energy using aerobic cellular respiration.

Anaerobic bacteria (obligate anaerobes—see also Overview of Anaerobic Bacteria) do not require O2 and do not grow in culture if air is present. They produce energy using fermentation or anaerobic respiration. Anaerobic bacteria are common in the GI tract, vagina, dental crevices, and wounds when blood supply is impaired.

Facultative bacteria can grow with or without O2. They produce energy by fermentation or anaerobic respiration when O2 is absent and by aerobic cellular respiration when O2 is present. Microaerophilic bacteria prefer a reduced O2 tension (eg, 2 to 10%).

Chlamydiae are obligate intracellular parasites that acquire energy from the host cell and do not produce it themselves.

Classification of Common Pathogenic Bacteria



Obligate aerobic

Gram-negative cocci

Moraxella catarrhalis, Neisseria gonorrhoeae, N. meningitidis

Gram-positive bacilli

Corynebacterium jeikeium

Acid-fast bacilli

Mycobacterium avium complex, M. kansasii, M. leprae, M. tuberculosis, Nocardia sp

Nonfermentative, non-Enterobacteriaceae

Acinetobacter calcoaceticus, Elizabethkingia meningoseptica (previously Flavobacterium meningosepticum), Pseudomonas aeruginosa, P. alcaligenes, other Pseudomonas sp, Stenotrophomonas maltophilia

Fastidious gram-negative coccobacilli and bacilli

Brucella, Bordetella, Francisella, and Legionella spp

Treponemataceae (spiral bacteria)

Leptospira sp

Obligate anaerobic

Gram-negative bacilli

Bacteroides fragilis, other Bacteroides sp, Fusobacterium sp, Prevotella sp

Gram-negative cocci

Veillonella sp

Gram-positive cocci

Peptococcus niger, Peptostreptococcussp

Non–spore-forming gram-positive bacilli

Actinomyces, Bifidobacterium, Eubacterium, and Propionibacteriumspp

Endospore-forming gram-positive bacilli

Clostridium botulinum, C. perfringens, C. tetani, other Clostridium sp

Facultative anaerobic

Gram-positive cocci, catalase-positive

Staphylococcus aureus(coagulase-positive),S. epidermidis (coagulase-negative), other coagulase-negative staphylococci

Gram-positive cocci, catalase-negative

Enterococcus faecalis, E. faecium, Streptococcus agalactiae (group B streptococcus), S. bovis, S. pneumoniae, S. pyogenes (group A streptococcus), viridans group streptococci (S. mutans, S. mitis, S. salivarius, S. sanguis), S. anginosus group (S. anginosus, S. milleri, S. constellatus), Gemella morbillorum

Gram-positive bacilli

Bacillus anthracis, Erysipelothrix rhusiopathiae, Gardnerella vaginalis(gram-variable)

Gram-negative bacilli

Enterobacteriaceae (Citrobacter sp, Enterobacter aerogenes, Escherichia coli, Klebsiella sp, Morganella morganii, Proteus sp, Plesiomonas shigelloides, Providencia rettgeri, Salmonella typhi, other Salmonella sp, Serratia marcescens, Shigella sp, Yersinia enterocolitica, Y. pestis)

Fermentative, non-Enterobacteriaceae

Aeromonas hydrophila, Chromobacterium violaceum, Pasteurella multocida

Fastidious gram-negative coccobacilli and bacilli

Actinobacillus actinomycetemcomitans, Bartonella bacilliformis, B. henselae, B. quintana, Eikenella corrodens, Haemophilus influenzae, other Haemophilus sp


Mycoplasma pneumoniae

Treponemataceae (spiral bacteria)

Borrelia burgdorferi, Treponema pallidum


Curved bacilli

Campylobacter jejuni, Helicobacter pylori,

Vibrio cholerae, V. vulnificus

Obligate intracellular parasitic


Chlamydia trachomatis, Chlamydophila pneumoniae, C. psittaci


Coxiella burnetii


Rickettsia prowazekii, R. rickettsii, R. typhi, R. tsutsugamushi, Ehrlichia chaffeensis, Anaplasma phagocytophilum

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