Bacteria overview

Last updated: July 28, 2023

Summary

The nomenclature of bacteria is complex. Human pathogenic bacteria can be classified according to their characteristics: morphology (cocci, bacilli, coccobacilli, spiral, or presence of branching filaments), Gram staining properties (gram positive, gram negative, and atypical), metabolic activity (aerobic, anaerobic, microaerophile, or facultative), or virulence factors (e.g., presence of capsule, pili, proteins, formation of coagulase, catalase or enterotoxins) among other traits. This article provides an overview of the most important human pathogenic bacteria. For an overview of the basics of bacteriology, including diagnosis and genetics, see “General bacteriology.”

Overview

The following table provides an overview of the nomenclature of important human pathogenic bacteria, according to their form and Gram staining properties.

Overview of bacteria

Pathogens with typical Gram staining properties

Cocci (sphere-shaped)
- Gram-positive cocci
  - Grape‑like arrangements (Staphylococcus)
  - Chain‑like arrangements (Streptococcus, Enterococcus)
- Gram-negative cocci: diplococcus (e.g., Neisseria, Moraxella)
Bacilli (rod-shaped)
- Gram-positive bacilli (e.g., Clostridium, Listeria)
- Gram-negative bacilli
  - E.g., Legionella pneumophila, Helicobacter pylori, Pseudomonas, Bartonella henselae
  - Enterobacteriaceae (e.g., Yersinia, Shigella, Salmonella, Klebsiella, Proteus, Escherichia coli)
Coccobacilli (very short rods almost resembling cocci): e.g., Haemophilus, Brucella, Bordetella
Branching filamentous (fungus-like)
- Actinomyces
- Nocardia

Classification of gram-positive bacteria Classification of gram-negative bacteria Cell walls of gram-positive and gram-negative bacteria

Pathogens with atypical Gram staining properties

Mycobacterium and Mycoplasma
Spirochetes (e.g., Borrelia, Leptospira, Treponema)
Obligate intracellular pathogens (e.g., Rickettsia, Chlamydia, Coxiella)

Gram-positive cocci

Staphylococcus ^[1]

All staphylococci are catalase positive.

Overview of staphylococci
Pathogen		Reservoir	Bacterial culture	Virulence factors and resistances	Associated conditions	Antibiotic of choice
Coagulase positive Staphylococcus (CoPS)
Staphylococcus aureus	Methicillin-susceptible Staphylococcus aureus (MSSA)	Skin Colonizes nares (most commonly ), ears, pharynx, axilla, hands, groin, and perineum ^[2]	Grape‑like cluster arrangement Characteristic gold‑yellow colonies Beta-hemolysis Mannitol fermenter on mannitol salt agar	Enzymes Catalase: protection against ROS Coagulase: protection against phagocytosis Hemolysins Hyaluronidase Lipase Penicillinase: a β-lactamase Toxins Superantigens ^[3] Toxic shock syndrome toxin-1 (TSST-1) Enterotoxin B (heat stable) Exfoliative toxin Leukocidin: creates pores in the membranes of infected cells → necrotic skin and mucosal lesions Alpha toxin: creates pores → apoptosis Proteins Clumping factor A: binds to fibrinogen → platelet activation, aggregation, and blood clumping Protein A (binds to the Fc region of IgG) Modified penicillin-binding protein (PBP) in MRSA Capsular polysaccharides Found on the cell surface Promote colonization and persistence in host tissues See “Resistance and virulence of staphylococci.”	Infections Skin and soft tissue (e.g., cellulitis, impetigo) Abscess Acute bacterial endocarditis Pneumonia (classically after influenza virus infection) Septic arthritis Osteomyelitis MRSA: nosocomial and community-acquired infections Toxin-mediated diseases TSS SSSS Food poisoning See “Staphylococcal infections.”	Isoxazolyl penicillin (e.g., oxacillin) or clindamycin See “Staphylococcal diseases” for details.
Staphylococcus aureus	Methicillin-resistant Staphylococcus aureus (MRSA)					Vancomycin or linezolid See “Staphylococcal diseases” for details.
Coagulase-negative staphylococci (CoNS)
Staphylococcus epidermidis		Natural skin flora	Grape‑like cluster arrangement Novobiocin-sensitive Mannitol nonfermenter	Urease producer Adherent biofilm production Protects S. epidermidis from host defense mechanisms and antibiotics Facilitates colonization of surfaces of prosthetic material and IV catheters → device-associated infections	Foreign body infections Prosthetic devices (e.g., heart valves, orthopedic implants) IV catheters (frequent contaminant of blood cultures)	Isoxazolyl penicillin (e.g., oxacillin) or clindamycin In case of methicillin resistance: vancomycin or daptomycin See treatment of “Staphylococcal diseases.”
Staphylococcus saprophyticus		Natural flora of the female genital tract and perineum	Grape‑like cluster arrangement Novobiocin-resistant	Urease producer	Urinary tract infection	1st generation cephalosporin (e.g., cephalexin) Amoxicillin-clavulanate Fluoroquinolone (e.g., ciprofloxacin) Nitrofurantoin TMP-SMX

NO StRESs: NOvobiocin sensitivity patterns, Saprophyticus (Resistant), Epidermidis (Sensitive) Staphylococcus aureus (S. aureus)

Streptococcus ^[1]

All streptococci are catalase negative.
They are classified based on the type of hemolysis on blood agar medium (alpha-hemolysis, beta-hemolysis, gamma-hemolysis).
Most are sensitive to penicillin

Overview of streptococci
Pathogen	Reservoir	Bacterial culture	Virulence factors and resistances	Associated conditions	Antibiotic of choice
Alpha-hemolysis (partial hemolysis)
Streptococcus pneumoniae (pneumococcus)	Nasopharynx	Encapsulated, lancet-shaped diplococci May form chains Facultative anaerobe Optochin-sensitive Bile-soluble	Capsular polysaccharides IgA1 protease	Otitis media (especially in children) Sinusitis, pharyngitis Pneumonia (rusty-colored sputum) Meningitis OPSI (in individuals with asplenia or sickle cell disease)	Penicillin 3^rd generation cephalosporin (e.g., ceftriaxone) Macrolide (patients with penicillin allergy)
Viridans streptococci (e.g., S. mutans, S. mitis, and S. sanguinis)	Oropharynx	Chain‑like arrangement Facultative anaerobe Optochin-resistant Bile-insoluble	Dextran: facilitates binding to fibrin-platelet aggregates on damaged heart valves Biofilm formation (dental plaque) by S. mutans and S. mitis	Dental caries (S. mutans and S. mitis) Subacute bacterial endocarditis (S. sanguinis)
Beta-hemolysis (complete hemolysis)
Streptococcus pyogenes (Group A Streptococcus) ^[4]^[5]	Nasopharynx Humans are the sole host	Chain‑like arrangement Lancefield group A Facultative anaerobe Bacitracin-sensitive Pyrrolidonyl arylamidase (PYR) positive	Toxins Erythrogenic exotoxin A Streptolysin O Streptococcal pyrogenic exotoxins Bridges MHC class II molecules on antigen-presenting cells and T-cell receptors on T cells outside of the normal binding sites Results in a large release of IL-1, IL-2, IFN-γ, and TNF-α Enzymes DNase: destroys neutrophils → potentiates infection and transmission ^[6] Streptokinase Hyaluronidase Proteins Protein F: fibronectin‑binding protein that mediates adherence to epithelial cells M protein (virulence factor): prevents opsonization by C3b Hyaluronic acid capsule: inhibits phagocytosis	Head and neck Pharyngitis Tonsillitis Peritonsillar abscess Otitis media Skin and soft tissues (pyogenic) Erysipelas Cellulitis Impetigo (“honey-crusted” lesions) Necrotizing fasciitis Perianal streptococcal dermatitis Toxin-mediated disease Scarlet fever Streptococcal toxic shock-like syndrome Immunologic complications (after primary infection) Acute rheumatic fever Poststreptococcal glomerulonephritis	Penicillin OR 1^st generation cephalosporins OR 2^nd generation cephalosporins Macrolide (patients with penicillin allergy)
Streptococcus agalactiae (Group B Streptococcus, GBS)	Genital tract Gastrointestinal tract	Chain‑like arrangement Lancefield group B Facultative anaerobe CAMP factor : enlarges the hemolysis area in a culture formed by S. aureus Bacitracin-resistant Hippurate positive Pyrrolidonyl arylamidase (PYR) negative	Capsule	Infection is typically asymptomatic in adults. Symptomatic conditions in adults include: ^[7] Urinary tract infection Meningitis Pneumonia Soft tissue infection Newborns Neonatal meningitis and pneumonia Neonatal sepsis ^[8] Early-onset group B streptococcal infection Late-onset group B streptococcal infection	Penicillin OR 1^st generation cephalosporins OR 2^nd generation cephalosporins Patients with penicillin allergy: 1^st generation cephalosporins (e.g., cefazolin) OR Clindamycin
Streptococcus gallolyticus ^[9]	Gastrointestinal tract	Chain‑like arrangement Lancefield group D Facultative anaerobe Beta-hemolysis or gamma-hemolysis Growth in bile, not 6.5% NaCl	Capsule ^[10] Pil 1: binds to collagen, allows attachment and colonization of host cells	Bacteremia Endocarditis Colorectal carcinoma	Penicillin (e.g., IV penicillin G) 3^rd generation cephalosporins (e.g., IV ceftriaxone) PLUS gentamicin
Streptococcus anginosus ^[2]^[11]	Oropharynx, gastrointestinal, and genitourinary tract	Small colonies Lancefield group E, F, G, and L Facultative anaerobe Nonmotile	Group F antigen	Soft tissue infections (e.g., cellulitis, necrotizing fasciitis) Abscesses (e.g., brain abscess, abdominal abscess) Septicemia	Penicillin Ampicillin 3^rd generation cephalosporins

B is for Babies: group B streptococci primarily affect neonates.

PaSsVORd: Pnemunoniae is Sensitive and Viridans is Optochin-Resistant.

BBRAS: Bacitracin sensitivity pattern of group B streptococci (Resistant) and for group A streptococci (Sensitive).

Sanguinis vessels lead to your heart: S. sanguinis can cause endocarditis.

Streptococcus pneumoniae (pneumococci) Streptococcus pneumoniae with capsule Beta-hemolytic Streptococcus pyogenes

Other gram-positive cocci ^[1]

Peptostreptococci and enterococci are catalase negative.

Overview of other gram-positive cocci
Pathogen	Reservoir	Bacterial culture	Diseases	Antibiotic of choice
Peptostreptococcus (e.g., P. anaerobius, P. magnus)	Mucocutaneous surfaces	Chain‑like arrangement Gamma-hemolysis Anaerobe	Lung abscess Wound infection (soft tissue, bone) Brain abscess Dental infection Pelvic infection in women	Penicillin OR 1^st generation cephalosporins OR 2^nd generation cephalosporins Macrolides (patients with penicillin allergy)
Enterococcus (e.g., E. faecium and E. faecalis) ^[12]	Gastrointestinal tract	Diplococci, chain‑like arrangement Lancefield group D Alpha-hemolysis and gamma-hemolysis Facultative anaerobe Pyrrolidonyl arylamidase (PYR) positive Growth in bile and 6.5% NaCl (higher resilience than streptococci)	May be triggered by GI/GU procedures Include the following: UTI Cholecystitis Subacute endocarditis Vancomycin-resistant enterococcus (VRE): nosocomial infection	Intrinsic resistance to cephalosporins and penicillin G Ampicillin Vancomycin (patients with penicillin allergy) Vancomycin-resistant enterococcus (VRE): linezolid OR daptomycin

Bovis in the blood, cancer in the gut: S. bovis is associated with colon cancer.

Entero (intestine), faecalis (feces), strepto (twisted), and coccus (berry): the etymology of Enterococci describes its characteristics.

Enterococcus faecalis Types of hemolysis

Gram-positive bacilli

Clostridia ^[1]

All Clostridia are gram positive, obligate anaerobic, spore-forming rods.

Pathogen	Reservoir	Bacterial culture	Virulence factors and resistances	Associated conditions	Antibiotic of choice
Clostridioides difficile	Gastrointestinal tract	Facultative pathogen	Toxin A (enterotoxin) Toxin B (cytotoxin)	Pseudomembranous colitis See “Clostridioides difficile infection.”	One of the following: Metronidazole Oral vancomycin Fidaxomicin
Clostridium perfringens ^[13]	Soil Skin Gastrointestinal tract	Club‑shaped bacilli Hemolysis “double zone” in blood agar	Exotoxins Clostridium perfringens alpha toxin Enterotoxin (heat-labile)	Gas gangrene (clostridial myonecrosis) Food poisoning ^[14]	Piperacillin-tazobactam PLUS clindamycin
Clostridium tetani ^[15]	Soil worldwide	Drumstick-shaped bacilli Obligate pathogen	Exotoxins Tetanospasmin Tetanolysin	Tetanus	Penicillin G or metronidazole
Clostridium botulinum	Soil Intestinal tracts of birds and fish Agricultural products (e.g., vegetables)	Club‑shaped bacilli with flagella Obligate pathogen	Botulinum toxin	Foodborne botulism Infant botulism Wound botulism See “Botulism”	Only in case of secondary bacterial infection
Clostridium septicum ^[16]	Soil Gastrointestinal tract	Drumstick-shaped bacilli	Four toxins (alpha, beta, gamma, and delta) with hemolytic, DNAse, and hyaluronidase activity	Colon cancer Gas gangrene (clostridial myonecrosis)	Penicillin AND clindamycin for gas gangrene ^[17]

Clostridium perfringens Clostridium tetani Mechanism of action: botulinum toxin Clostridium botulinum

Listeria, Corynebacteria, and Bacillus ^[1]

Overview of Listeria, Corynebacteria, and Bacilli
Pathogen	Reservoir	Bacterial culture	Virulence factors and resistances	Associated conditions	Antibiotic of choice
Listeria monocytogenes	Unpasteurized milk products Cold deli meats Transplacental transmission/vaginal transmission during birth	Facultative anaerobe Facultative intracellular Flagella: characteristic tumbling motility in liquid culture	Actin rocket tail Cold resistance: replication at temperatures of 4–10°C Listeriolysin O	Listeriosis Congenital listeriosis Amnionitis, septicemia, spontaneous abortion during pregnancy Gastroenteritis	Ampicillin or penicillin G
Corynebacterium diphtheriae	Respiratory tract Humans are the only hosts	Club-shaped rods in angular arrangements Facultative anaerobe Stainable using Neisser stain: detection of characteristic metachromatic granules (red and blue) Positive Elek test for toxin Black colonies on cystine-tellurite agar Löffler medium: metachromatic granules	Diphtheria toxin (exotoxin): inhibits protein synthesis by inactivating ef2	Diphtheria	Macrolide (e.g., erythromycin) OR Penicillin G Diphtheria antitoxin can be added as well
Bacillus anthracis	Soil Mammals	Aerobe Bamboo stick-shaped Colonies show a halo of projections (Medusa head)	Polypeptide capsule (contains d-glutamate) Spore formation Anthrax toxin, an exotoxin that consists of the following: Edema toxin Lethal factor Protective antigen	Anthrax	Ciprofloxacin (OR penicillin G) PLUS clindamycin (OR linezolid) PLUS meropenem in case of meningitis
Bacillus cereus	Contaminated food (particularly rice that is kept warm and/or reheated)	Aerobe or facultative anaerobe	Cereulide: enterotoxin → emesis Spore formation	Food poisoning See “Bacillus cereus infection.”	Not indicated, only supportive care

Cell-to-cell spread of Listeria monocytogenes Bacillus anthracis (Gram stain) Bacillus anthracis spores

Gram-negative cocci

Neisseria and Moraxella ^[1]^[18]

Overview of Neisseriae and Moraxella
Pathogen	Reservoir	Bacterial culture	Virulence factors and resistances	Diseases	Antibiotic of choice
Neisseria meningitidis (meningococcus)	Nasopharynx Humans are the only hosts (most commonly affects individuals living in close vicinity to one another, e.g., college students or soldiers).	Diplococcus Facultative intracellular Aerobe Bacterial growth on culture medium is usually challenging Selective medium: Thayer-Martin agar Maltose and glucose fermenter	IgA1 protease Capsular polysaccharides Lipooligosaccharide (LOS): serum LOS levels correlate with severity of symptoms Adhesins: pili and opacity proteins (allow cell adherence and impair lymphocyte activation) facilitate nasal colonization → systemic infection	Meningitis Waterhouse-Friderichsen syndrome Meningococcemia with petechial bleeding	3^rd generation cephalosporins (e.g., ceftriaxone) Penicillin G (if penicillin-susceptible) Prophylaxis: only close contacts (ciprofloxacin, rifampin, OR ceftriaxone)
Neisseria gonorrhoeae (gonococcus)	Genital tract Humans are the only hosts	Diplococcus Often intracellular (within neutrophils) Aerobe Bacterial growth on culture medium is usually challenging Selective medium: Thayer-Martin agar Glucose fermentor Maltose nonfermenter	IgA1 protease Lipooligosaccharide (LOS) Adhesins: attach to the host's epithelial cells (antigenic variation of pili allows avoidance of neutralizing antibodies that would prevent reinfection)	Gonorrhea Septic arthritis Pelvic inflammatory disease Fitz-Hugh-Curtis syndrome Neonatal conjunctivitis	3^rd generation cephalosporins (e.g., ceftriaxone) PLUS azithromycin OR doxycycline
Moraxella catarrhalis ^[19]	Nasopharynx Humans are the only hosts	Diplococcus Aerobe Maltose nonfermenter	Outer membrane vesicles: complement evasion and colonization Biofilm formation ^[20]	Sinusitis Otitis media Bronchitis Bronchopneumonia in COPD	Amoxicillin-clavulanate OR 2^nd generation cephalosporins OR 3^rd generation cephalosporins OR TMP/SMX

MeninGococci: Maltose + Glucose production and Gonococci: Glucose production. Neisseria gonorrhoeae Neisseria meningitidis

Gram-negative coccobacilli

Overview of gram-negative coccobacilli ^[1]
Pathogen		Reservoir	Bacterial culture	Virulence factors and resistances	Diseases	Antibiotic of choice
Haemophilus	Haemophilus influenzae (e.g., Haemophilus influenzae serotype b)	Nasopharynx (particularly in young children) Aerosol transmission	Hemophilic bacteria: isolation on chocolate agar Satellitism in culture: S. aureus produces factor V via hemolysis → H. influenzae can grow in the hemolytic zone	IgA protease Capsular polysaccharides (polyribosylribitol phosphate) Contained in Hib vaccine, conjugated to a protein (e.g., diphtheria toxoid) Infections are usually caused by unencapsulated strains (vaccine protects against encapsulated H. influenzae type B)	Mucosal infection Otitis media Conjunctivitis Epiglottitis Sinusitis Pneumonia (CAP) Invasive infections: meningitis	Mucosal infection: amoxicillin PLUS/OR clavulanate OR 2^ndgeneration cephalosporins OR 3^rd generation cephalosporins (e.g., cefotaxime) Meningitis: ceftriaxone Prophylaxis for close contacts: rifampin
Haemophilus	Haemophilus ducreyi	Humans are the only hosts	Hemophilic bacteria Facultative anaerobic	Hemolysin Cytolethal-distending toxin: ulcer formation ^[21]	Chancroid	Macrolides (e.g., azithromycin) OR 3^rd generation cephalosporins (e.g., ceftriaxone)
Brucella	Brucella melitensis	Goats and sheep serve as hosts	Facultative intracellular (within macrophages) Aerobic Charcoal yeast extract agar	Lipopolysaccharide Type IV secretion system (T4SS) Superoxide dismutase Catalase positive Urease Cytochrome oxidase ^[22]	Brucellosis	First-line therapy: doxycycline PLUS rifampin Second-line therapy: doxycycline PLUS streptomycin ^[23]^[24]
Brucella	Brucella abortus	Unpasteurized dairy Cattle are the only hosts			Brucellosis
Bordetella (e.g., Bordetella pertussis)		Humans are the only hosts (particularly adults and adolescents)	Strictly aerobic Cultured in Bordet-Gengou agar or Regan-Lowe medium	Capsule Pertussis toxin Tracheal cytotoxin	Pertussis (whooping cough)	Macrolides (e.g., azithromycin, erythromycin)
Pasteurella multocida		Oropharynx of animals (especially dogs and cats)	Facultative anaerobe Can be cultured on charcoal yeast extract agar with cysteine and iron Bipolar staining	Capsule Catalase positive Lipopolysaccharide (LPS)^[25] Fimbria and adhesins	Cellulitis (secondary to dog and cat bites) Respiratory tract infections	Amoxicillin OR fluoroquinolones (e.g., ciprofloxacin, levofloxacin) TMP/SMX
Acinetobacter baumannii ^[26]		Human skin, oropharynx, and respiratory tract	Strictly aerobic Oxidase negative Catalase positive	Outer membrane protein A (OmpA): biofilm formation and immunomodulation ^[27]	Hospital-acquired, multidrug-resistant infections (especially in immunocompromised patients) Ventilator-associated pneumonia Bloodstream infections Meningitis	3^rd generation cephalosporins (e.g., cefotaxime) OR carbapenems OR polymyxins (for resistant strains)

Influenza virus causes the flu whereas H. influenzae causes epiglottitis and meningitis.;
Bordetella pertussis grows on Bordet-Gengou agar.

Brucella melitensis

Gram-negative bacilli

Enterobacteriaceae ^[1]

Escherichia coli ^[28]

Sorbitol and lactose fermenters (except for EHEC, which does not ferment sorbitol)
Form pink colonies on MacConkey agar
Form green colonies with a metallic sheen on eosin-methylene blue agar
Present the enterobacterial common antigen (ECA) on their surface
Produce beta-galactosidase (cleaves lactose into galactose and glucose)
Common virulence factors
- LPS endotoxin → septic shock
- Resistance against bile salts → proliferates in GI tract

Overview of E. coli
Pathogen	Reservoir	Characteristics	Important virulence factors	Diseases	Antibiotic of choice
EPEC (enteropathogenic E. coli)	Natural gut flora	Usually in children	Adherence to intestinal epithelium → destruction of microvilli (inhibits absorption) No toxin is produced	Gastroenteritis (see “Diarrheagenic E. coli”) Independent of subtype: nosocomial infections, cholecystitis, peritonitis	Ciprofloxacin OR TMP/SMX EHEC: antibiotic treatment is not recommended See “General guidelines for treating E. coli infections.”
ETEC (enterotoxin E. coli)	Fecal contaminated food and water	Common cause of traveler's diarrhea	Heat-labile toxin Heat-stable toxin
EIEC (enteroinvasive E. coli)	Natural gut flora	Sporadic cause of diarrhea	Direct invasion of the intestinal epithelium and formation of enterotoxins → bloody diarrhea (similar to Shigella)
EAEC (enteroaggregative E. coli)	Fecal contaminated food and water	Usually causes persistent diarrhea	Aggregation ("stacked-brick" pattern) with one another and adherence to intestinal mucosa → inflammation → watery (possibly bloody) diarrhea ^[29]
EHEC (enterohemorrhagic E. coli)	Undercooked meat, raw leafy vegetables	Most common serotype: O157:H7	Shiga-like toxin: bloody diarrhea Enhanced cytokine release (mainly renal epithelial cells) → HUS (no invasion of host cells) ^[30]
UPEC (uropathogenic E. coli)	Natural gut flora	Most common cause of UTIs ^[31]	P fimbria (pyelonephritis‑associated pili): specifically bind to the urogenital epithelium → cystitis, pyelonephritis	Cystitis Pyelonephritis
NMEC (neonatal meningitis-causing E. coli) ^[32]	Natural gut flora	Common cause of neonatal bacterial meningitis in industrialized countries	K1 capsular polysaccharide: protects against phagocytosis	Neonatal meningitis Pneumonia	Ampicillin OR 3^rd generation cephalosporins (e.g., cefotaxime) PLUS gentamicin

Light as Air: (heat-Labile toxin upregulates ↑ cAMP and Adenylate cyclase), Stable as Granite: (heat-Stable toxin: upregulates ↑ cGMP and Guanylate cyclase).

Escherichia coli Flagellated E. coli

Other Enterobacteriaceae

Surface antigen: enterobacterial common antigen (ECA)
Common virulence factors: resistance against bile salts → proliferates in gastrointestinal tract

Overview of other Enterobacteriaceae
Pathogen			Reservoir	Characteristics		Virulence factors and resistances	Diseases	Antibiotic of choice
Yersinia	Yersinia pestis ^[33]		Primarily rodents Obligate pathogen Transmission: flea bites	Facultative intracellular Bipolar staining (“closed safety pin” appearance)		Cold enrichment possible	Plague See “Zoonotic diseases.”	Aminoglycosides (e.g., streptomycin or gentamicin) OR tetracyclines
Yersinia	Yersinia enterocolitica, Yersinia pseudotuberculosis ^[34]		Contaminated pork and milk products Pet feces Obligate pathogen	Pleomorphic: Yersinia can be classified as a coccobacillus or a rod. ^[35] Bipolar staining		Cold enrichment possible	Yersiniosis Reactive arthritis Acute diarrhea See “Bacterial gastroenteritis.”	Only in severe cases Fluoroquinolones (e.g., ciprofloxacin) OR 3^rd generation cephalosporins (e.g., ceftriaxone)
Shigella: S. dysenteriae, S. flexneri, S. boydii, S. sonnei (in order of decreasing severity) ^[36]			Humans are the only host Obligate pathogen	Spread from cell to cell → invasion of M cells (MALT) Resistant to gastric acid → low infectious dose required ^[37] Fastidious: stool samples require prompt testing Slow/absent lactose fermentation Immune response primarily via PMN infiltration		Shiga toxin	Shigellosis (bloody diarrhea) Reactive arthritis HUS See “Bacterial gastroenteritis.”	Shortens the period in which Shigella is shed in stool ^[36] Fluoroquinolones (e.g., ciprofloxacin) OR 3^rd generation cephalosporins (e.g., ceftriaxone)
Salmonella (e.g., Salmonella enterica)		Salmonella enterica serotype Enteritidis,Salmonella enterica serotype Typhimurium	Humans, animals, animal products (e.g., reptiles, poultry, pets, eggs) serve as hosts Obligate pathogen	High infectious dose required → not resistant against gastric acid Hematogenous dissemination is possible Produces H₂S Facultative intracellular	Immune response primarily via PMN infiltration No lactose fermentation	Flagellar motility Endotoxin	Salmonellosis (diarrhea, possibly bloody) Reactive arthritis See “Bacterial gastroenteritis.”	Prolongs the period in which Salmonella is shed in stool Only in severe cases Fluoroquinolones (e.g., ciprofloxacin) OR 3^rd generation cephalosporins (e.g., ceftriaxone)
Salmonella (e.g., Salmonella enterica)		Salmonella enterica serotype Typhi,Salmonella enterica serotype Paratyphi	Humans are the only hosts Obligate pathogen		Immune response primarily via monocytes	Flagellar motility Vi capsule: evasion of neutrophil chemotaxis ^[38] Endotoxin	Typhoid fever and paratyphoid fever (constipation, then diarrhea) Osteomyelitis (in patients with sickle cell disease)	Prolongs the period in which Salmonella is shed in stool Fluoroquinolones (e.g., ciprofloxacin) OR 3^rd generation cephalosporins (e.g., ceftriaxone)
Klebsiella	Klebsiella pneumoniae		Natural flora of the gastrointestinal tract	Very mucoid colonies Lactose fermenter: eosin-methylene blue agar changes to purple		Capsular polysaccharides → large mucoid capsule Urease Multidrug resistance	Nosocomial UTI Aspiration pneumonia and lung abscess Especially in individuals with alcohol use disorder and/or diabetes Currant jelly sputum: thick, mucoid, blood-tinged sputum Hepatic abscess ^[39] Kidney stones (struvite stones)	Fluoroquinolones OR 3^rd generation cephalosporins
Klebsiella	Klebsiella granulomatis ^[40]		Genital tract (endemic in tropical and subtropical developing countries)	Challenging to grow on culture medium Lactose fermenter Facultative anaerobe		Capsular polysaccharides → large mucoid capsule Urease	Granuloma inguinale	Azithromycin Doxycycline
Proteus (Proteus vulgaris; Proteus mirabilis)			Natural flora of the gastrointestinal tract	Swarming motility on agar Produces H₂S		Urease	Nosocomial infections (particularly UTI) Kidney stones (struvite stones)	Fluoroquinolones (e.g., ciprofloxacin OR 3^rd generation cephalosporins (e.g., ceftriaxone) OR TMP/SMX
Serratia (Serratia marcescens) ^[41]			Animals, insects, plants, soil, water, starchy food (e.g., bread)	Catalase-positive Weakly lactose fermenting Produces prodigiosin (a red pigment) Facultative anaerobe		Serralysin (a protease enzyme) Exotoxin Biofilm Multidrug resistance	Nosocomial infections (pneumonia and UTI) Wound infections Ocular infections (e.g., keratitis) Meningitis Bacteremia Endocarditis	Aminoglycoside (e.g., amikacin) and antipseudomonal beta-lactam OR fluoroquinolones Meningitis: 3^rd or 4^th generation cephalosporins Multidrug-resistant: carbapenems

Mac and Cheese: MacConkey agar is used for lactose fermentors (Cheese).
PADDOCK: Aspiration Pneumonia, lung/liver Abscess, Diabetics, Drug resistance, alcOhOlics, Currant jelly, Klebsiella are most common features of Klebsiella infection.

Yersinia pestis Acral gangrene due to bubonic plague Shigella dysenteriae Salmonella Klebsiella pneumoniae Klebsiella pneumoniae colonies Serratia marcescens colonies Struvite crystals

Other gram-negative bacilli ^[1]

Overview of other gram-negative bacilli
Pathogen		Reservoir	Characteristics	Virulence factors and resistances	Diseases	Antibiotic of choice
Helicobacter pylori ^[42]		Humans are the predominant hosts	S‑shaped or spiral‑shaped Flagellated (motile) Microaerophile Silver stain Oxidase, catalase, and urease positive (triple positive)	Urease: ammonia formation increases the pH and enables survival in the acidic environment of the gut.	Type B gastritis (see “Atrophic gastritis”) Duodenal peptic ulcers Increases risk for gastric adenocarcinoma and MALT lymphoma	Clarithromycin PLUS amoxicillin PLUS PPI See “Helicobacter pylori eradication therapy.”
Legionella pneumophila		Natural aquatic habitats Transmitted by water aerosols (e.g., air conditioning systems)	Facultative intracellular Aerobic Flagellated Buffered (with cysteine and iron) charcoal yeast extract agar Silver stain Waterborne bacteria	Lipopolysaccharide (LPS) Flagella and pili ^[43]	Legionellosis (Legionnaire disease, Pontiac fever) Atypical pneumonia	Fluoroquinolones (e.g., levofloxacin) Macrolides
Campylobacter (e.g., Campylobacter jejuni)		Poultry, unpasteurized milk (natural gut flora in birds) Contact with infected persons or infected animals (e.g., pigs, dogs, cats)	Curved or spiral‑shaped with polar flagellum Microaerophile Grows best at 37°C–42°C Oxidase positive	Type IV secretion system (T4SS) Cytolethal-distending toxin ^[44]	Enterocolitis (bloody diarrhea, especially in children) Commonly precedes reactive arthritis and Guillain‑Barré syndrome See “Bacterial gastroenteritis.”	Macrolides (e.g., erythromycin)
Pseudomonas (e.g., Pseudomonas aeruginosa) ^[45]^[46]		Water and humid conditions (e.g., hot tubs, contaminated contact lens solution)	Lophotrichous flagella (motile) Aerobic Catalase positive Oxidase positive Produces pyocyanin (blue-green pigment) → formation of blue‑green pus in infection Sweet odor when grown in culture Nonlactose fermenting	Mucoid polysaccharide capsule → biofilm formation Endotoxin → fever, shock Exotoxin A: inactivates EF-2 → inhibition of protein synthesis → death of host cells Phospholipase C: degrades cell membranes Pyoverdin and pyocyanin: siderophores that help Pseudomonas grow and proliferate in iron-deficient conditions → generate reactive oxygen species Intrinsic and acquired resistance are common, some strains are multidrug-resistant	Upper respiratory infections Nosocomial pneumonia (e.g., ventilator associated pneumonia) Chronic pneumonia in individuals with cystic fibrosis Skin infections Nosocomial burn wound infections Hot tub folliculitis Ecthyma gangrenosum in immunocompromised individuals Corneal ulcers and/or keratitis in contact lens wearers or after eye injuries Malignant otitis externa in elderly individuals with diabetes ^[47] Endocarditis or osteomyelitis in individuals who use IV drugs Nosocomial UTI Sepsis	Extended-spectrum penicillins with β-lactamase inhibitors (e.g., ticarcillin-clavulanate, piperacillin-tazobactam) OR ceftazidime (a 3^rd generation cephalosporin) OR 4^th generation cephalosporins (e.g., cefepime) OR fluoroquinolones (e.g., ciprofloxacin, levofloxacin) in severe infections OR carbapenems OR aminoglycosides OR monobactams OR polymyxins (e.g., colistin, polymyxin B)
Burkholderia (e.g., Burkholderia cepacia)		Aquatic environments	Aerobic Catalase positive	Lipopolysaccharide (LPS) Flagella and pili Type III secretion system (T3SS): invades host cells ^[48] Resistance to many antibiotics (antibiogram should always be performed)	Pneumonia in association with cystic fibrosis Chronic granulomatous disease	Cotrimoxazole OR meropenem OR ceftazidime OR fluoroquinolones
Vibrio cholerae ^[49]		Contaminated water Uncooked seafood (e.g., raw shellfish)	Straight or curved (comma-shaped) Polar flagella Grows in alkaline media → acid-labile →requires large infectious dose Facultative anaerobe Oxidase positive	Cholera toxin (enterotoxin): “rice-water” diarrhea	Cholera See “Bacterial gastroenteritis.”	Doxycycline ^[50] Azithromycin OR tetracycline OR ciprofloxacin OR TMP/SMX
Vibrio vulnificus ^[51]		Contaminated water Raw or undercooked seafood (e.g., raw shellfish, fish intestines) Wounds infected by contaminated water or seafood	Curved (comma-shaped) Polar flagella Motile Lactose fermenter	Lipopolysaccharide (LPS) Capsular polysaccharide Exotoxins (hemolysin and metalloproteases)	Inflammatory diarrhea Cellulitis, bullous skin lesions Septic shock and necrotizing fasciitis See “Bacterial gastroenteritis.”	Doxycycline Fluoroquinolone (e.g., ciprofloxacin)
Vibrio parahaemolyticus ^[52]		Contaminated water Raw or undercooked seafood (e.g., mussels)	Curved (comma-shaped Facultative anaerobe Nonlactose fermenting	Thermostable direct hemolysin Type III secretion system (T3SS)	Inflammatory diarrhea Septic shock See “Bacterial gastroenteritis.”	Doxycycline
Fusobacteriaceae ^[53]		Oral cavity	Anaerobic → produce CO₂ and H₂in tissue Bile-resistant Foul smelling	Possibly capsule formation Primary resistance against aminoglycosides	Pneumonia in patients with chronic alcohol use → lung abscess Nosocomial infections (e.g., decubitus ulcers, surgical wound/drain infection) Possibly peritonitis and sepsis	Metronidazole OR clindamycin OR extended-spectrum penicillin with penicillinase inhibitor
Bacteroides (e.g., Bacteroides fragilis)		Up to 40% of fecal flora ^[54]
Bartonella (e.g.,	Bartonella henselae ^[55]	Cats are asymptomatic carriers	Facultative intracellular Microaerophile	Lipopolysaccharide (LPS)	Cat scratch disease (see “Collection of dermatological disorders”) In HIV patients: bacillary angiomatosis Bacterial endocarditis	Macrolides (e.g., azithromycin, clarithromycin)
	Bartonella quintana ^[56]	Ectoparasites (Pediculus humanus/Phthirus pubis) are vectors	Facultative intracellular Microaerophile	Lipopolysaccharide (LPS) Type IV secretion system (T4SS) Adhesins Hemin-binding proteins ^[57]	Trench fever	Doxycycline PLUS gentamicin
	Bartonella bacilliformis				Carrión disease Oroya fever Verruga peruana
Eikenella corrodens ^[58]^[59]		Normal flora of oral cavity and mucosal surfaces	Small, straight rod Nonmotile Facultative anaerobic Grows slowly in blood or chocolate agar Causes pitting (corrosion) of the agar ^[60] Oxidase positive Reduces nitrites	Outer membrane proteins (OMP) Lipopolysaccharide (LPS) Resistant to macrolide, clindamycin, and metronidazole.	Oral cavity infections: periodontitis Skin and soft tissue infections due to: Human bites Chronic nail-biting Intravenous drug use Head and neck infections: sinusitis Respiratory tract infections Pneumonia Empyema Septic emboli Cardiovascular infections Native valve endocarditis Purulent pericarditis Abdominal infections: appendicitis, periappendiceal abscess Gynecologic infections: chorioamnionitis Other Osteomyelitis Septic arthritis Necrotizing fasciitis Internal jugular vein thrombosis (postanginal sepsis)	Penicillin OR 3^rd generation cephalosporins Fluoroquinolones TMP/SMX Tetracyclines

Pseudomonas produces PEEPP: Phospholipase C, Exotoxin A, Endotoxin, Pyoverdin, and Pyocyanin are P. aeruginosa virulence factors.

CAMPFIRE: Carbapenems, Aminoglycosides, Monobactams, Polymyxins, Fluoroquinolones, thIRd and fourth-generation cephalosporins, Extended-spectrum penicillins are the drugs used to treat P. aeruginosa infections.

Helicobacter pylori gastritis Gastric tissue with Helicobacter pylori Amoeba catching Legionella pneumophila Campylobacter jejuni Pseudomonas aeruginosa bacteria Pseudomonas aeruginosa on cetrimide agar Ecthyma gangrenosum Vibrio cholerae

Branching filamentous bacteria

Gram positive bacteria that develop fungi-like long, branching filaments

Overview of Actinomyces and Nocardiae ^[1]
Pathogen	Reservoir	Characteristics	Virulence factors and resistances	Diseases	Antibiotic of choice
Actinomyces israelii ^[61]	Oral cavity Intestinal tract Reproductive tract	Gram positive with branching filaments Anaerobic Not acid-fast Filaments form yellow sulfur granules	No known virulence factors	Actinomycosis Caries and periodontitis → oral/facial abscess Possibly PID in women that use an IUD	Penicillin G: high-dose Alternatively: tetracyclines OR erythromycin
Nocardia asteroides and Nocardia brasiliensis ^[62]	Soil worldwide	Gram positive with branching filaments Aerobe Weakly acid-fast staining (Ziehl-Neelsen stain) Catalase positive	Urease	Nocardiosis Posttraumatic cutaneous infection in immunocompetent individuals Pneumonia in immunocompromised Possible spread to CNS	Sulfonamides (TMP/SMX) In severe disease and CNS involvement: add meropenem OR linezolid

They are NOw ACTually gone with the SNAP of a finger: To treat NOcardia and ACTinomyces use Sulfonamides, Nocardia, Actinomyces, and Penicillin.

Conglomerates of Actinomyces in actinomycosis Nocardia in blood culture

Atypical Gram-staining bacteria

Mycobacterium, Mycoplasmataceae (Mycoplasma), and Gardnerella ^[1]

Overview of Mycobacteria, Mycoplasma, and Gardnerella
Pathogen		Reservoir	Characteristics	Virulence factors and resistances	Diseases		Antibiotic of choice
Mycobacterium tuberculosis		Humans	Acid-fast bacilli Ziehl-Neelsen stain Auramine-rhodamine stain Gram neutral (do not stain well) Facultative intracellular Aerobic Löwenstein-Jensen agar Middlebrook medium Generation time: ∼12 hours ^[63]	Cord factor: arranges M. tuberculosis in a serpentine cord → ↑ TNF-α release and activation of macrophages → granuloma formation Surface glycolipids: (sulfatides) inhibit phagolysosomal fusion Infiltration of nonactivated macrophages → escape of humoral immune response Multi-drug resistance: mutation in KatG (catalase-peroxidase) → INH conversion to its active metabolite → INH resistance	Tuberculosis		Isoniazid PLUS rifampicin PLUS ethambutol PLUS pyrazinamide See “Tuberculosis treatment.”
Mycobacterium leprae ^[64]		Humans and armadillos	Acid-fast bacilli: Ziehl-Neelsen stain Obligate intracellular Generation time: up to 13 days ^[65]	Phenolic glycolipid I (PGL-1) Lipoarabinomannan	Leprosy		Dapsone PLUS rifampicin (tuberculoid leprosy) Clofazimine (add in lepromatous leprosy)
Nontuberculous mycobacteria M. kansasii, M. ulcerans	M. avium-intracellulare	Ubiquitous	Acid-fast bacilli: Ziehl-Neelsen stain PCR Generation time: varies among the subtypes (faster than other mycobacteria)	M. avium-intracellulare are frequently multi-drug resistant	Mycobacterium avium complex infection: disseminated nontuberculous disease mainly in immunocompromised patients (e.g., HIV/AIDS) See “HIV-associated conditions.”	Soft tissue infections with draining sinuses (newly formed channels that lead from the focus of infection to the skin surface via a draining orifice)	Are more drug-resistant than M. tuberculosis Clarithromycin OR azithromycin PLUS rifabutin (OR rifampin) PLUS ethambutol
	M. marinum				Fish tank granuloma: skin infection usually of the hand that occur in individuals handling fish (e.g., aquarium handlers)
	M. scrofulaceum				Cervical lymphadenitis in children
Mycoplasma pneumoniae		Humans are the only host	Microaerophile Incomplete/absent cell wall (not visible on gram stain) Bacterial membrane stabilized by cholesterol Pleomorphic Generation time: (1–3 weeks) ^[66] M. pneumoniae: grows on Eaton agar → “fried egg” appearance	Unresponsive to beta-lactam antibiotics due to lacking cell wall	Mycoplasma pneumonia (atypical pneumonia) Cold antibody hemolytic anemia (IgM) Erythema multiforme Acute interstitial nephritis Stevens-Johnson syndrome (affects mostly children and adolescents)		Macrolides (e.g., erythromycin) OR doxycycline OR fluoroquinolones
Ureaplasma urealyticum		Normal urogenital flora			Urocystitis		Doxycycline OR macrolides (e.g., erythromycin)
Gardnerella vaginalis ^[67]^[68]^[69]^[70]		Normal vaginal flora (considered a dysbiosis, occurs when vaginal Lactobacilli decrease)	Pleomorphic Gram variable rod Facultative anaerobic	Pili Capsule Phospholipase C Protease Vaginolysin, cytolysin Biofilm formation	Bacterial vaginosis See “Vulvovaginitis.”		Metronidazole OR clindamycin

Mycobacterium tuberculosis Mycobacteria Mycobacterium leprae Mycoplasma pneumoniae

Spirochetes

Overview of Spirochetes
Pathogen	Reservoir	Characteristics	Diseases	Antibiotic of choice
Treponema pallidum	Humans	Dark-field microscopy Direct fluorescent antibody (DFA) microscopy Thin wall	Syphilis	Penicillin G
Treponema vincentii	Humans		Acute necrotizing ulcerative gingivitis (Vincent angina)	Penicillin G, tetracyclines OR clindamycin
Borrelia burgdorferi	Ticks (e.g., Ixodes deer tick) or mammals (e.g., mouse)	Largest spirochete Visible in light microscopy using: Wright or Giemsa stain (aniline dyes)	Lyme disease	Doxycycline OR 3^rd generation cephalosporins (e.g., ceftriaxone) Amoxicillin OR cefuroxime in pregnant women and children
Borrelia recurrentis	Louse		Relapsing fever (recurs because of surface antigen variation)
Leptospira interrogans, Leptospira kirschneri	Animal urine in water (e.g., rats, cattle, sheep, and goats)	Very thin wall Hook-shaped ends	Leptospirosis Weil disease	Penicillin G OR tetracyclines

SPecial for SPirochetes and SPecial BLT sandwich: Spirochetes are Borrelia, Leptospira, and Treponema .

Borrelia is the Biggest of all the Spirochetes.

Spirochetes on dark-field microscopy Borrelia burgdorferi Borrelia spirochetes

Obligate intracellular bacteria

Obligate intracellular bacteria cannot produce ATP outside of their host cell. ^[1]

Overview of obligate intracellular bacteria
Pathogen	Reservoir	Characteristics	Virulence factors and resistances	Diseases	Antibiotic of choice
Chlamydia trachomatis	Humans are the only host	Lacks muramic acid in cell wall Cytoplasmic inclusion bodies (reticulate bodies) visible on Giemsa stain Culture: requires tissue medium	Various pathogenic serotypes with different organ associations (see table in “Chlamydia infections”) Major outer membrane protein (MOMP) → protective surface antigens Polymorphic outer membrane protein (pmp) → elicit proinflammatory cytokine responses Cytotoxin → causes actin reorganization (similar to clostridial toxin B) Lipopolysaccharide (LPS) ^[71]	Chlamydial genitourinary infections (e.g., nongonococcal urethritis, cervicitis, PID) Follicular conjunctivitis (blindness) Lymphogranuloma venereum Reactive arthritis See “Chlamydia infections.”	Doxycycline OR macrolides Conjunctivitis prophylaxis in infants: erythromycin eye drops
Chlamydophila psittaci	Parrots and other birds Aerosol transmission			Ornithosis (atypical pneumonia) See “Chlamydia infections.”
Chlamydophila pneumoniae	Humans are the only host Aerosol transmission			Atypical pneumonia See “Chlamydia infections.”
Rickettsia rickettsii	Arthropods (dog ticks)	Weakly gram-negative bacteria Visible on Giemsa stain	Type IV secretion system (T4SS) Surface adhesion proteins: OmpA, OmpB	Rocky Mountain spotted fever See “Zoonotic diseases.”	Doxycycline Chloramphenicol (pregnant patients)
Rickettsia prowazekii	Human to human (body louse)			Spotted fever Epidemic typhus See “Lice infestation.”
Rickettsia typhi	Arthropods (fleas)			Endemic typhus See “Zoonotic diseases.”
Coxiella burnetii	Cattle, sheep, and goats Aerosol transmission	Gram-negative bacteria Ability to survive in very harsh environments	Lipopolysaccharide (LPS) Surface adhesion protein: OmpA	Q fever (pneumonia) Bacterial endocarditis See “Zoonotic diseases.”	Doxycycline OR erythromycin
Ehrlichia chaffeensis, Ehrlichia ewingii ^[72]^[73]	Whitetail deer Transmission: bite of the lone star tick	Gram-negative bacteria Wright-Giemsa stain: detection of morulae inside infected monocytes	Envelope proteins Obtains cholesterol derived from host cells Type IV secretion system (T4SS)	Ehrlichiosis See “Zoonotic diseases.”	Doxycycline OR tetracyclines
Anaplasma phagocytophilum ^[73]^[74]^[75]^[76]	White-footed mouse, White-tailed deer, and other wild animals Transmission Ticks (Ixodes scapularis, Ixodes pacificus) Blood transfusion (rare cause)	Gram-negative bacteria Wright-Giemsa stain: detection of morulae inside infected granulocytes	Replication within cytoplasmic vacuoles of PMNs → evasion of neutrophils Obtains cholesterol derived from host cells Type IV secretion system (T4SS)	Anaplasmosis (human granulocytic anaplasmosis) See “Differential diagnoses of tick bite.”	Doxycycline

When it's Rainy and Chilly outside, Cozy up and Eat Apple pie: Rickettsia, Chlamydia, Coxiella, Ehrlichia, Anaplasma are obligate intracellular bacteria. Chlamydia trachomatis in McCoy cell culture

Common associations of bacteria

	Diagnostic associations of bacteria
Bacteria	Diagnostic hint	Clinical scenario
Actinomyces israelii	Branching filamentous bacteria Forms yellow sulfur granules	Patient with odontogenic infection develops an oral/facial abscess.
Borrelia burgdorferi	Visible on light microscopy using Wright or Giemsa stain	Patient develops bilateral facial nerve palsy after a trip to Northeast.
Clostridium perfringens	Club‑shaped bacilli	Patient with a traumatic open wound develops gas gangrene.
Clostridium tetani	Drumstick shaped	Patient punctures their sole with a dirty nail and develops trismus.
Klebsiella pneumoniae	Mucoid colonies	A patient with alcohol use disorder presents with pneumonia and currant jelly sputum.
Pasteurella multocida	Facultative anaerobic gram-negative coccobacillus	A patient that owns 3 cats present with signs of cellulitis.
Legionella pneumophila	Cultured on charcoal yeast extract agar with cysteine and iron Silver stain	Patient presents with productive cough, nausea, and confusion after a cruise trip.
Haemophilus influenzae	Isolated on chocolate agar Requires factor X and factor V for culture	An unvaccinated child presents with high fever, drooling, and muffled voice.
Haemophilus influenzae		Patient with a history of severe abdominal trauma develops fulminant sepsis.
Encapsulated bacteria	S. pneumoniae: gram-positive diplococci N. meningitidis: gram-negative diplococci

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