Clinical Microbiology Intro

Strain

Same at the molecular/genetic level

Isolate

Microbes recovered from the same source

Prokaryotes

70S ribosomes, no organelles, usually has cell wall, no nucleus

Eukaryotes

80S ribosomes, no cell wall (usually), cell membrane, nucleus

Virus

Simple RNA or DNA core with protein coat

Virus envelope

Host derived membrane, many with spikes

Spikes

Aka peplomers, glycoprotein attachment to envelope surface

Fungi

Eukaryotes, cell wall w/ chitin, can be multicellular (mold) or unicellular (yeast)

Dimorphic

Fungi that has both yeast (unicellular) and mold (multicellular) phases

Parasites

Eukaryotes, includes helminths (multicellular) and protozoa (unicellular)

Bacteria

Prokaryotes, reproduce w/ binary fission, major needs of carbon, nitrogen, and energy (often same as carbon), prefer near neutral pH

Halophilic bacteria

Need salt/salt loving

Pili and fimbriae

Adhere bacteria to a surface, might mediate DNA exchange

Capsule

Protective polysaccharide coating in some bacteria

Endospore

Durable spore that protects DNA until favorable conditions arise (ex anthrax)

Gram test

Stains thick peptidoglycan cell walls dark purple (Gram positive), thin peptidoglycan cell walls pink (Gram negative), doesn’t stain membranes (no reaction if no cell wall)

Bacilli

Rod

Cocci

Spherical

Spirochetes

Spiral/corkscrew

Gram positive characteristics

Thick peptidoglycan cell wall, no lipopolysaccharide, has teichoic acid and endospores, stains purple

Gram negative characteristics

Thin peptidoglycan cell wall, outer lipopolysaccharide (LPS, has lipid A—endotoxin), no teichoic acid, stains pink

Acid fast bacteria

Waxy layer over gram positive bacteria preventing stain - GP but no reaction

Cocci groupings

Pairs (diplo), chains (strepto), clusters (staphylo)

Diplococci gram test

GP are lancet shape, streptococcus pneumoniae; GN are bean shape, Neisseria spp.

Obligate aerobes

Need O2

Facultative anaerobes

Aerobe that can go without O2

Capnophilic and microaerophilic

Like extra CO2

Obligate anaerobes

Hate O2, oxygen is toxic

Tube coagulase test

Detects enzyme that binds fibrinogen, forms clot if positive (aureus)

Staphylococcus

Gram positive cocci, looks grape like, facultative anaerobe, form clusters, catalase positive; sort by coagulase test

Streptococcus

Twisted, facultative anaerobe, G+, in chains, catalase negative, group by presence of Lancefield antigen and hemolysis on blood agar

Catalase test

3% H2O2, forms bubbles if positive

Alpha hemolysis

Partial lysis, green/brown color

Beta hemolysis

Complete lysis, clear

Gamma hemolysis

No hemolysis, red/normal blood agar

Beta-hemolytic strep

Group A strep (pyogenes), group B strep (agalactiae), group C and G

Alpha-hemolytic strep

Viridians group (many species), strep pneumoniae, group D strep

Enterococcus

Historically group D strep, entero-faecalis and faecium

Anaerobic Gram positive cocci

Finegoldia magna and Peptostreptococcus spp.

Gram positive bacilli

Classify by oxygen tolerance and spore production

Spore forming aerobic GPB

Bacillus ceres and anthracis

Spore forming anaerobic GPB

Clostridium perfringens, botulinum, tetani; Clostridiodes difficile (C diff)

Non spore forming aerobic GPB

Listeria monocytogenes, Corynebacterium diphtheriae, Gardnerella vaginalis, Nocardia species

Non-spore forming anaerobic GPB

Cultibacterium acnes, Actinomyces spp., Lactobacillus

Gram negative cocci

Neisseria and Moraxella catarrhalis

GNC characteristics

Anaerobic, prefer increased CO2, diplococci (bean shaped)

Significant Gram negative diplococci

Neisseria gonorrheae, miningitidis, and catarrhilis

Enterobacterales (Enterics)

Non-sporulating, facultative anaerobes, Gram negative rod, ferment glucose, reduce nitrates to nitrites, no cytochrome oxidase production

Oxidase test

Cytochrome c oxidase becomes deep purple if bacteria uses oxidative phosphorylation

80-95% of enteric bacterales in hospital setting are:

Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis

Opportunistic pathogens

Usually found in intestinal microbiota, ex Escherichia spp., Klebsiella spp., Citrobacter spp., Serratia spp., Proteus spp.

Primary pathogens

Never considered normal fecal flora, not normal, ex Escherichia coli O157:H7, Salmonella spp. (includes typhi and non-typhi serotypes), Shigella, Yersinia pestis and enterocolitica

Shigella

Dirty Fingers Bring Shigella - dysenteriae (Group A) flexneri (Group B) boydii (Group C) soneii (Group D)

Genus Vibrio

Facultative anaerobes, curved Gram negative rods/bacilli, oxidase positive, tolerate or require salt

Genus Vibrio species

Vibrio cholerae, vulnificus, parahaemolyticus

Other curved GNR species

Campylobacter jejuni (microaerophilic, gull wing shape, oxidase positive), Helicobacter pylori (different shapes from jejuni but same characteristics)

Non-fermenters

GNR or GNC, obligate aerobes, high intrinsic resistance to antibiotics, common nosocomial (healthcare related) infections,

Non fermenting GNR/GNC spp.

Carbapenum-Resistant Acinetobacter (CRAB, very serious), most common NFGNR - Pseudomonas aeruginosa (oxidase positive), Acinitobacter spp. (GNC, can stain irregularly, oxidase negative), Strenotrophomonas multophilia and Burkholderia spp.

Fastidious

Hard to grow, require additional growtth factors (picky eaters)

Fastidious GNB

Bacilli or coccobacilli, often pleomorphic, don’t grow on MacConkey agar, some >24 hrs to grow

Haemophilius

Pleomorphic coccobacilli or bacilli, only grow on chocolate agar

Haemophillius spp.

Haemophilius influenzae, parainfluenzae, ducreyi

Fastidious spp.

Bordetella pertussis and parapertussis, Legionella pneumophilia, Brucella spp., Francisella tularensis, Pasturella multocida

Anaerobic GNB/GNR

Obligate anaerobe, often endogenous

Endogenous

Self infection, bacteria came from same person as who as infected

Aerobic GNB/GNR spp.

Bacteriodes fragilis group, Prevotella spp., Pophyromonas spp., Fusobacterium spp. (fusiform - tapered cells)

Bacteria not seen on Gram stain

Intracellular bacteria, no cell wall, spirochetes, acid fast bacilli

Genus Chlamydia

Obligate intracellular parasites, can’t make ATP, includes Chlamydia trachomatis, psittachi, and pneumoniae

Other intracellular species

Those spread by arthropods - Richettsia rickettsii, typhi, and prowazekii; Ehrlichia spp., Anaplasma spp., Coxiella bumetii (facultative intracellular, not obligate)

No cell wall

Mycoplasma and Ureaplasma, slow growing, highly fastidious aerobes or facultative anaerobes, reistant to cell wall antibiotics (like Beta lactam)

No cell wall spp.

Mycoplasma pneumoniae, genitalium, and hominis; Ureaplasma urealyticum (tiny)

Spirochetes characteristics

Spiral shaped, periplasmic flagella (axial filaments), classified by coil tightness, includes Genus Borrelia, Leptospira, and Treponema

Genus Borrelia

Spread by arthropods, can see with light microscopy but not Gram stain, includes Borrelia burgdorferi and recurrentis

Genus Leptospira

Spread by arthropods, tightly coiled, cannot see with light microscopy, most common zoonosis, Leptospira interrogans

Genus Treponema

Very thin, can see with dark field microscopy, Treponema pallidium

Acid fast bacilli/mycobacteria

Obligate aerobes, slow growing, cell wall has waxy outer layers of mycolic acid (long, branched fatty acid), blocks Gram stain

Tuberculosis

Acid fast bacteria, Mycobacterium tuberculosis and bouis

Nontuberculosis Mycobacterium (NTM)

Mycobacterium avium-intracellular complex, kansasii, marinum, and scrofulacem; also includes leprosy - Mycobacterium leprae

Host

Infected or fed upon by a parasite or pathogen

Intermediate host

Required host for larval development, temporary host

Definitive host

Host in which adult/sexually reproductive form of parasite occurs

Parasitism

Association where parasite depends on host and causes adverse effects

3 groups of parasites

Helminths, protozoa, and arthropods

Helminths groups

Cestodes (tapeworms), nematodes (roundworms), trematodes (flukes)