Apr24 M1,2-Introduction to Basic Medical Bacteriology Flashcards
taxonomy of bacteria
genus with capital letter + species in lower case, all in italic. Mendelian structure
keys ways to identify bacteria
- morphology (microscopy)
- organization (microscopy)
- gram stain (microscopy)
- colony appearance
key test to identify bacteria (molecular profiles and genetics)
MS-MALDI-TOF (Mass Spectrometry -Matrix Assisted Laser Desorption Ionisation - Time of Flight)
what an MS-MALDI-TOF does
- cristallize colony
- zap it with laser
- vaporize specimen into electrically charged particles with a mass to charge ratio
- plot particles obtained
- determine corresponds to which bacteria
what is the scheme of identification of bacteria that is the most ACCURATE
Amplification and sequencing of 16S rRNA genes
what is the scheme of identification of bacteria that is the MOST COMMONLY USED
culture and biochemical analysis
To guide the appropriate EMPIRIC Abx) treatment, what is the scheme of identification of bacteria that is SUFFICIENT IN MOST CASES?
gram stain
gram + external structure
in to out
- single lipid bilayer
- thick murein or peptidoglycan cell wall for rigidity
gram - external structure
in to out
- lipid bilayer
- periplasmic space with thin peptidoglycan (murein) layer
resistance mechanisms present in periplasmic space in gram - bacteria
- enzymatic degradation of Abx (so enzymes that degrade Abx are there)
- porins
- pumps
- manipulation
2 most important bacteria categories
- gram positive cocci (staph spp, strep spp, enterococcus spp)
- gram negative bacilli (enterobacteriaceae, haemophilus spp., e.coli)
some gram + bacilli
- cornybacteria spp
- bacillus spp.
- listeria monocytogenes (important in neonatal sepsis)
some gram - cocci
- neisseria
- moraxella
- acinetobacter spp
some gram + anaerobes
- peptostreptococcus (coccus)
- clostridium spp (bacillus)
- nocardia (branching)
- actinomyces (branching)
- mycobacteria (branching)
some gram negative anaerobes
bacilli = bacteroides, prevotella, fusobacterium spiral = helicobacte, treponema, leptospira, borrelia curved = vibrio, campylobacter
(imp?) most common bacterium in the gut
bacteroides spp (gram negative anaerobic bacilli)
exceptions to the gram + and gram - separation
atypical bacteria
- the IC organisms
- ones with few or no cell wall
- ones with bizarre morphology
- ones difficult to culture
- ones difficult to stain (chalmydia, chlamydophila, coxiella, rickettsiae, mycoplasma, ureaplasma)
chlamydia vs chlamydophila
chlamydia = infection below the belt chlamydophila = infection above the belt
coxiella causes what
Q fever
mycoplasma bacteria cause what
- respiratory or immune diseases
- are agents of STDs
most dangerous gram + bacterium
staph aureus
how to differentiate staph aureus from other staff
coagulase test in rabbit serum
- put colony in rabbit serum
- if contains coagulase (staph aureus does), serum will coagulate
other test to check for staph aureus
agglutination test with a bench top test
- look for clamping
- involves an enzyme other than coagulase
alpha vs beta vs gamma hemolysis
some gram+ can hemolyze RBCs in sheep blood agar
- alpha = partial hemolysis (greeny hue)
- beta = complete hemolysis (see through): like staph that has clumps of round cells + coagulase positive
- gamma = 0
Strep pyogenes is what type of bacteria specifically
gram positive, beta hemolytic group A strep
subdivisions of gram positive COCCI
- tetrads and clusters (catalase +) VS pairs and chains (catalase -)
- in tetrads and clusters, are coagulase + or -
- in pairs and chains, are beta or alpha or gamma hemolytic
- in beta hemolytic, have a specific Lancefield grouping (A, B, G, G)
alpha hemolytic cocci examples
- Strep pneumoniae
- Viridans strep family (CAUSES CARIES)
gamma AND alpha hemolytic cocci examples
enterococci
staph aureus vs strep skin infection
- staph is pyogenic (purulent infection)
- strep = red dry skin
how staph aureus colonizes
- surface proteins that bind fibronectin
- surface targetting molecules like MSCRAMMs
pyogenic (pus forming, infection and inflammation) effects of staph aureus (types of infection you get)
- cellulitis
- abscesses
- osteomyelitis
- endocarditis
toxin mediated effects of staph aureus
released locally but can have systemic effects
- food poisoning
- toxic shock syndrome (overwhelming sepsis)
how staph interacts with the immune systems and the WBCs
- uses coagulase to form clots to escape immune system
- causes hemolysis
- targets leukocytes with leukocidin
- using its protein A, it binds Igs in inverse sense to disrupt opsonization
late visible sign of toxic shock syndrome
palmar erythema with desquamation
cause of toxin shock syndrome
a toxin that is a superantigen
- cross-links MHC2 (of APCs) and TCRs (of T cells) non specifically and outside of binding cleft
- get uncontrolled immune response (fever, cytokine prod, shock)
MRSA, VRSA and VISA are what
MRSA = methicillin resistant staph aureus (very common) (use vanco) VISA = vancomycin intermediate staph aureus (vanco works) VRSA = vanco resistant staph aureus (has the vanA gene). rare and very bad scenario
MSSA means what
methicillin sensitive staph aureus (it expresses a penicilinase so we point out that it is therefore sensitive to methicillin)
characteristics of resistance in hospital acquired bugs
- more virulent
- multi-drug resistant
- *resistant to everything except vancomycin and daptomycin**
charact of resistance in community acquired bugs
-more sensitie (less resistance)
-MORE aggressive
bc have PVL (Penton Valentin Leukocidin) = cutaneous and deep abscesses, tissue destruction
3 coagulase negative staphylococci and characteristics
- staph epidermidis (common in skin flora and is opportunistic)
- staph saprophyticus (common in UTIs)
- staph lugdunensis and staph schleiferi (aggressive disease, endocarditis)
beta hemolytic group A strep causes what types of infections
- tonsilitis, skin infections, soft tissue infections
- toxic shock syndrome
- scarlet fever
- necrotizing fasciitis (flesh eating disease), myositis, meningitis
- acute post-strep GN
- acute rheumative fever (carditis, polyarthritis)
(imp?) primary reason to treat group A strep PHARYNGITIS
prevention of rheumatic heart disease
acute post strep GN will happen no matter what if right host + right strain
(IMP) important protein for adhesion and other things in group A strep
M protein
- adhesion
- anti-complement
- responsible for molecular mimicry (our Ags attack heart valves instead of M protein)
most common group B strep organism
streptococcus agalactiae
what streptococcus agalactiae gives (what problems) (group B strep)
- neonatal sepsis* (prenatal screening programs. if infected start Abx at delivery)
- neonatal meningitis
- diabetic wound infections
streptococcus pneumoniae on CXR (alpha hemolytic) + symptoms of that + pther diseases it can cause
LOBAR pneumonia
symptoms = chest pain, cough, rusty sputum
(strep pneumo also causes meningitis, bacteremia, acute otitis media)
strep pneumo cell shape
edges and internal aspects caved on itself, bc created an autolysin so self destructed with time forming doughnut shape
PRSP stands for what
penicillin resistant strep pneumo
19A is what
a strain of strep pneumo found to be resistant (now covered in Prevnar vaccine)
what organisms cause dental caries
the Viridans Streptococcus species
viridans species charact and cause what
- alpha hemolytic, less virulent member of the normal flora
- dental caries, bacteremia, endocarditis, abscesses
two viridans strep species and what they do
- Strep mutans, Strep sanguis = dental plaque and carries
- S anginosus (deep tissue abscesses)
enterocccus species charact
- gram + cocci
- non hemolytic (gamma), but group with Lancefield group D
- in normal biliary tract and GIT flora (are bile resistant and like high Na content)
2 enterococcus species
E faecalis = less resistant to penicillin and ampicillin
E faecium = penicillin and ampicillin resistant
diseases enterococci cause
- abdomen abscesses
- is a bystander in infections (treat the rest = entero goes away)
- bacteremia, endocarditis
- UTIs
tx of enterococcus infection
- limited options (less and less things are working) + use combinations
- vancomycin if not VRE
VRE is what
vancomycin resistant enterococcus
- has vanA gene on plasmid that mediates that
- VRE tends to colonize rather than infect (but nocosomial careful in central lines, wounds, etc.)
- VRE more frequent than VRSA
how gram positive BACILLI are classified
- spore forming (large rods) or not
- in spore forming = large rods, either aerobic catalase + (bacillus) or not (clostridium)
- in non spore forming, either small irregular rods, regular rods or branching rods
listeria spp (gram+ small irregular rods) charact
- major foodborne illness
- virulence factors = listerolysin, ActA (for IC parasitism immune evasion)
2 types of diseases with listeria spp
- invasive (meningitis, chorioamnionitis, granulomatous infantiseptica, bacteremia, endocarditis)
- non invasive (febrile diarrhea syndrome, where cultures are negative)
listeria often confused with what bacteria
corynebacteria (are gram + rods, also smaller irregular rods) in palisades or chains
cornybacteria (smaller irregular rods) give some species
- C.diphtheriae (toxin mediated URTI, multiorgan involvement)
- C. urealyticum (renal disease calculus)
- C jeikeium (multiresistant, bacteremia)
bacillus (large rods) main diseases (say the species)
- bacillus cereus = toxin mediated food poisoning and immunocompromised infections
- Bacillus anthracis = acquired from animals (zoonoses), bio weapon, non motile white colonies that stick to plates and form medusa heads (projections)
enterobacteriaceae (gram NEGATIVE rods) main charact
- *ferment glucose**
- in the gut
- usually commensals
diseases with enterobacteriaceae
(some opportunistic and some virulent)
- enteric pathogens
- urinary pathogens
- bacteremia
5 most important enterobacteriaceae and 2 very common in them
- escherichia coli
- klebsiella pneumoniae
- salmonella enterica
- shigella
- yersinia
lactose fermenting enterobacteriaceae some examples
-klebsiella spp
-e.coli
-enterobacter
-serratia
(kees)
lactose non-fermenters in enterobacteriaceae family some examples
- salmonella spp
- shigella spp
- yersinia enterocolitica
prototype gram negative rod and definition of a coliform
- e.coli = prototype
- coliform = gram negative rod that ferments lactose
- e.coli is a coliform
- a coliform will appear like e.coli
goal of Macconkey plate and charact
check if organisms are lactose fermenting (coliforms) + select for gram negative rods
- pH indicator, bile salts, chemicals selecting for gram negative
- grow on plate
- if ferment lactose, pH change. colour = pink (otherwise stays translucent)
which is more dangerous lactose fermenting or lactose non fermenting enterobacteriaceae
lactose non-fermenting (salmonella, shigella, yersinia)
what’s common to all coliforms (enterobacteriaceae)
ferment glucose
how macconkey plate can help identify salmonella and shigella
you have to workup the translucent colonies more
main UTI causing organism
e.coli
what e.coli causes
- UTIs
- intra-abdominal infection
- bacteremia
- seeds
two types of e.coli
ETEC (enterotoxic) and EHEC (enterohemorrhagic)
e.coli outbreak associated with vegetables was what
a shigatoxin producing e.coli
E coli O157:H7 charact
- zoonosis
- an EHEC strain
- hamburger disease
E coli O157:H7 pathophysiology
shigatoxin like toxin is produced
- damage to endothelium, glomerulus, CNS endothelium
- TTP in adults
- HUS in children
how bacteriophages influence E coli O157:H7
a specific lytic phage (virus for bacteria) can convert a non hemorrhagic strain to a hemorrhagic strain
how most E coli O157:H7 are found in stools
stool culture using a special sorbitol MacConkey plate. E coli O157:H7 doesn’t ferment sorbitol (sorbitol non-fermenting): you then investigate further the translucent colonies
diseases salmonella causes
- gastroenteritis
- typhoid fever (name it like that for shigella)
- infection of vascular endothelium
- infection of organ systems (osteomyelitis)
disease shigella causes
- mucosal endothelium damage
- shigatoxin causes direct invasion (apoptosis of cells) leading to Na and water accum in the lumen
vibrio cholerae type of bacteria and problems causes
- curved gram negative rod
- toxin mediated disease
- profuse diarrhea
tx of cholera (vibrio cholerae infection)
most important thing is rehydration
2nd most important is Abx
cholera dx
gram stain of stool smear
other diseases of fibrio species
vibrio vulnificus = bullae on skin + liver disease association (hemochromatosis and cirrhosis)
typical scenario = large yosters meal then 3 days of purpura then 3 days of bullae
pseudomonas spp type of bacteria and charact
- gram negative bacilli (rods)
- forms a biofilm** (harder for Abx to get to it)
- NOT an enterobacteriaceae
most common non glucose fermenter gram negative bacteria
pseudomonas
pseudomonas species to be concerned about + its charact
Pseudomonas aeruginosa
- green apperance
- bc of 2 pigments: pyocyanin, pyoverdin
pseudomonas implications and disease
- important nocosomial pathogen
- problematic in immunosuppressed (FEBNEUT**, burns, CF pts)
- complicated UTIs**
- ventilator associated PNEUMONIAS**
- line associated infections
- bacteremia, endocarditis, septic arthritis
pseudomonas: what’s quorum sensing
- express molecules between individual cells to make cells act in a community fashion and use autoinducers to upregulate each other’s specific genes
- some gram negative NON fermenters do that
key issue with pseudomonas
- multi drug resistant (MDR) pseudomonas aeruginosa
- alteration of outer membrane permeability. limited therapy options
virulence factors of pseudomonas spp
- pili
- flagella
- LPS
- exotoxin A
- proteases
- phospholipases
- etc
3 main gram negative non fermenter rods
-pseudomonas aeruginosa
-stenotrophomonas maltophilia
-acinetobacter baumanii
(2 other than pseudomonas = ventilator, ICU issues)
Neisseria charact
- gram negative diploCOCCUS (pairs)
- higher susceptibility in C5-C8 deficient and Ab deficient people
main concern with Neisseria spp infections (species we worry about)
- Neisseria meningitidis
- agent of meningitis
- sepsis, shock, DIC, necrosis, purpura fulminans
- most worrysome form is encapsulated
Neisseria gonorrhoeae diseases it causes
causes gonorrhea, PID (pelvic inflammatory disease), epididymitis
Neisseria gonorrhoeae 2 ways it evades the immune system
- phase variation (ctly switching virulence factors on-off)
- antigenic variation (program diff pili by genetic recombination so are not recognized)
dx of Neisseria gonorrhoeae done how
cervix swab, gram negative diplococci with WBCs
Haemophilus spp charact
- coccoid-rods gram negative
- opportunistic
- serotypes a to f are encapsulated
diseases caused by haemophilus
- haemophilus influenza type B associated with epiglotitis
- all types cause pneumonias, otitis media, etc.
- encapsulated cause septicemia, meningitis
examples of encapsulated organisms + how this helps
- neisseria meningitidis (gram-)
- haemophilus influenzae (gram-)
- streptococcus pneumoniae (gram+)
- capsule helps evade immune system and Abs*
fastidious gram negative bacilli 5 classical ones and cause what
HACEK agents of endocarditis
- haemophilus (aggrigatibacter) aphrophilus
- aggrigatibacter actino…
- cardiobacterium hominis
- eikenella corodens
- kingella kingae
dog, cat and human bite organisms and problems
cat bite = pasteurella multocida (cellulitis) dog bite (have cleanest mouth) = capnocytophyga canimorsus and cynodegnmi (if immunocompromised: shock, DIC) human bite = eikenella corrodens (HACEK list + suppurative infection, septic arthritis**** bc bites near joints)
bordetella pertussis disease caused and virulence factors
- whooping cough that has 3 sages (catarrhal, paroxysmal, recovery) or chronic cough
- virulence factors = pertussis toxin (cAMP modulator), tracheal cytotoxin, LPS, pili, etc.
example of organisms that mediate disease by toxins and that are NOT invasive
- B pertussis
- C diphtheriae
- V cholarae
- C diff
anaerobes (don’t like cold and oxygen) typical diseases
polymicrobial infections (pulmonary abscess, abd abscess, pelvic infection, UTI)
anaerobe that is very important and charact
C.difficile
-spore forming gram+ bacillus
risk factors for c diff
- Abx use
- immunocompromised pt
- PPI use
- NG tube use
C diff toxin, strains and tx
- 2 toxins - TcdA and TcdB
- NAP1 strain is important (hypervirulent and fluoroquinolone resistant)
- Tx = vancomycin, metronidazole, etc.
- note: pathophgy = pseudomembranous colitis
diarrhea after Abx exposure approach to that
consider c diff until proven otherwise
c diff usual course of illness
- 50% = mild version
- 50% serious
- recurs if proper tx BUT have risk factors
most prevalent organisms in the colonic flora
- bacteroides (gram neg anaerobic bacilli)
- opportunistic
bacteroides how resistance spreads and tx now
- transmission of resistance elements by conjugative transposons
- metronidazole = tx (clindamycin less good now)
anaerobes in places other than colon
- oral spirochetes like fusobacterium necrophorum
- aspiration can lead to lung abscesses and empyema
atypical pneumonia on CXR
diffuse interstitial pattern
note: walk in pneumonia
how atypical pneumonias are diagnosed
serology (serovar Ag detection)
standard set of organism called atypical pneumonias some examples (are called WALKING pneumonias)
- chlamydophila pneumoniae and psitacci
- coxiella burnetti
- mycoplasma pneumoniae
- legionella pneumophilia
- mycobacterium TB
charact of chalmydia
- pelvic infections, peri-hepatic inflammation
- STIs
- ocular disease
- asymptomatic carriage
2 variants of chlamydia that cause genital disease
- LGV (lymphogranuloma venerum): much worse
- cervicitis
tx of chalmydia
azythromycin
legionella charact
- gram negative atypical rod
- survives after phagocytosed and evades immune system
- replicates
legionella main symptom
pontiac fever (name specific for legionella spp. non fatal resp prob + fever)
legionella main virulence factor causing the signs and symptoms
flagellin
some mycoplasma organisms (are atypical organisms) and critical one
**M pneumoniae** (resp tract) M genitalium (UTI) M hominis (UTI) U urealyticum (UTI)
how to stain mycoplasma organisms
use acridine orange (bc otherwise stain badly)
mycoplasma pneumoniae diseases
- adhere to resp epithelium. resp problems
- extra pulm infections that are immune mediated (hemolytic anemia, inflam disorders, rashes, arthritis, pericarditis, endocarditis)
rickettsiae charact
- small gram - rod atypical (rarely stain)
- IC pathogen
- independent metabolism and very adapted to their environment
- transmitted through insect bites
2 main groups of rickettsiae
- spotted fever group
- typhus group
prototypical rickettsiae organism
rickettsiae rickettsii
-rocky mountain spotted fever dog tic
spirochettes (spirally bacteria) some examples
- H pylori
- Leptospira interrogans
- Treponema spp
- Borrelia spp
agent of syphilis
treponema pallidum
agent of lime disease, fever, borreliosis
borrelia (curved)
leptospira causes what
liver, lungs, CNS problems
borrelia recurrentis causes what
relapsing fever
