Clinical Microbiology

name 3 gram + cocci

staph aureus, s. pneumoniae, s. pyogenes

gram + shape of b h. influenzae

gram - bacilli

name 2 curved/spiral gram - bacteria

vibrio cholerae, borrelia burgdorferi

while viruses are not living, what do viruses have in common with living

• has RNA/DNA

• reproduces (in host)

• has organization

basic virus structure

DNA/RNA + capsid protein = nucleocapsid = naked capsid virus

envoloped virus = naked capsid virus + glycoproteins + lipid membrane

2 states of virus

standalone

provirus (integrated in host cell’s genome)

fungal structure

• hyphae - non/septate

• mycelia

• yeast cells with buds

• pseudomycelium (yeast chains)

opportunistic pathogen

microorganism causing infection only during immunosuppression

functions oif human microbiome

• immunity

• defense from pathogens

• host for production of short chain fatty acids (for metabolism, vitamin creation)

• human behaviour

infection vs infectious disease

multiplication of a pathogen in the body

infectious disease : disease from pathogenic microbes, w/ lesions

innaparent infection

presence of infection in host without symptoms/signs, but normal functioning of body isn’t affected

incubation

time bw exposure to pathogen and from when symptoms start

prodromal phase

infectious agents increasing + immune system responds

early symptoms

steps of the infectious process

1. entry

2. adherence

3. multiplication

4. dissemination

5. elimination

minimum needed data on specimen collection

name, age, gender, personal ID number, type of pathological product, needed analyses from PP

purpose of cultivation

identification and evaluation of atb/antifungal susceptibility

what are EUCAST and CLSI

AST standards from pure bacterial cultures

what are VITEK 2C and MALDI TOF-MS

automated systems of microbial identification

__________ is the working principle of all imunne assays (ex: quick tests, ELISA, fluorescence, western blot)

ag-ab immune complex

In AB detection assays, what do IgM vs IgG detect

IgM - acute infections

IgG - chronic/past infections, post vax

where is IgA (Ab detection assays)

resp tract + digestive system lining, saliva, breast milk

when do neutralizing Ab appear

by disease or after vax

which Ag-Ab test is qualitative

Quick immune-chromatographic tests

Agglutination assays

what are agglutination tests from serum (Ab) or cultures (Ag) used for

RPR syphilis

typing of strep, salmonella, e coli

what is the main disadvantage of quick tests

not good specificity - cross rxns (false + results)

what pathogens do agglutination assays detect

meningitis, syphylsis, ALSO, CRP, rheumatoid factor

types of pcr tests

• endpoint pcr - qualitative, for research

• quantitative realtime pcr ‘qPCR’ - detects dna micorbes

• quantitative reverse transcription relatime pcr ‘qRT-PCR’ - detects RNA viruses, research of gene expression assays

what test is the most reliable (best sensitivity and specificity)

PCR tests

what bacteria cause respiratory tract infections

s pneumoniae

klebsiella pneumoniae

h influenzae

what viruses cause respiratory tract infections

influenza

rhinovirus

covid

adenovirus

what parasites cause respiratory tract infections

entamboeba, ascaris, pneumocystis

what fungi cause respiratory tract infections

aspergillus

histoplasma

coccidiodes

exams for pharyngitis depending on pathogen

viral - nothing

bacterial - swab, rapid test

fungal - swab

pharyngeal swab isolation method + incubation

streak plate technique

• blood agar for strep spp, diphtheria

• OCST, Loffler, Tinsdale for diphtheria

incubation 18-24h 37 dg in CO2 atmosphere

in pharyngitis, bacteriological examination is recommended for a Modified Centor Score of

2-3

what bacteria can cause pharyngitis + rush + sinusitis + cellulitis + sepsis

arcanobacterium hemolyticus

what pathogens are causes of pharyngitis in transplant patients

pseudomonas aeruginosa, enteric rods, candida

what pathogens to detect for pharyngitis in patients with cystic fibrosis

s aureus

p aeruginosa

what kind of pharyngitis is caused by borrellia vincentii

vincent angina

when to screen for s aureus pharyngeal swab

pre surgery

dg of diphtheria

pseudomembranes on pharynx

elek test (immunodiffusion assay)

when do you not collect pharyngeal swab

epiglottitis (h influenzae, s pneumoniae)

chronic tonsilitis

rapid test for pharyngitis tests what pathogen

group A strep

what to do if rapid test for pharyngitis is negative

follow-up culture if strong clinical suspicion

examsn for otitis media depending on type of microorganism

bacterial - tympanocentesis, ear swab if chronic + otorrhea

viral - nasopharyngeal swab

bacterial causes of otititis media

s pneumoniae

s aureus

h influenzae

m catarrhalis

s pyogenes

p aeruginosa

exams for sinusitis based on microorganism

viral + bacterial - nothing

fungal - if discharge, serology

what viruses cause the common cold

rhinoviruses, covid

pathogens causing community acquired pneumonia

s pneumoniae

mycoplasma pneumonia (young)

h influenzae, m catarrhalis (HIV)

s aureus (recent viral infection, COPD)

pathogens causing hospital acquired pneumonia

p aeruginosa

acinetobacter baumannii

enterobacterales

MRSA

when should you test urine for LRTs (lower resp tract infections)

legionella pneumophilia and s pneumoniae Ag

what will nasopharyngeal swab show if whooping cough

bordetella para/pertussis

indications for sputum examination

LRT infection, TB

type and incubation of sputum

gram stained smear

37 dg in CO2 atmosphere 24-48 h

Bartlett score (Q score)

assesses quality of sputum

identification characteristics of S pneumoniae on sputum sample medium

crateriform a-hemolytic colonies on blood agar

AST

susceptible to optochin and bile

identification characteristics of m catarrhalis on sputum sample medium

oxidase + colonies on blood agar, sliding around on the surface

DN-ase +

B lactamase production tested

identification characteristics of H influenaze on sputum sample medium

dewdrop colonies on choco agar

AST and b-lactamase production tested

identification characteristics of P aeruginosa on sputum sample medium

lactose - glossy colonies on MacConkey medium

oxidase +

growth w/ cetrmidie, @ 44 dg

identification characteristics of S aureus on sputum sample medium

big creamy colonies with b hemolysis, manito +

what medium to grow enterobacterale and acinetobacter spp sputum

macconkey

how to dg fungal LRT infection from sputum

predomination of candida colonies (if a few, no dg)

filamentous fungi in any quantity

direct exam of myco TB on Ziehl-Neelsen stain

long, thin bacilli, curved, stained red

direct exam of myco TB on Kinyoun stain

acid fast (cold) stain

types of stains for myco TB

Ziehl-Neelsen

Kinyoun acid-fast

Auramine

Acid-fast stain positive for what pathogens

mycobacterium spp, nocardia spp, legionella, rhodococcus spp

what is VerstaTREK, MGIT 960

AST for Myco TB

indirect dg for myco tb

skin test (mantoux, tuberculin test)

what is a + rxn to skin test for myco TB

erythema, swelling and induration >10mm = recent/past infection

disadvantages to indirect dg of Myco TB by serology (IGRAs)

• not for <17yr old or ID

• can’t distinguish active and latent infections

exams for atypical pneumonia

m pneumoniae + chlamydophilia pneumonia = NAATs

legionella pneumophilia = urine Ag test, culture, PCR

exams for fungal respiratory tract infections

histoplasma capsulatum, coccidiodes immitis = serology, culture, pcr

pneumocystic jirovecii = microscopy, pcr

what makes a uti complicated

• in men

• pregnant

• anatomical abnormalities

• catheter

• kidney disease

• comorbidities

what dictates recurrent UTI

3/yr or 2/6 months

colonization of urinary tract

asymptomatic bacteriuria in urinary tract

risk factors uti

neuro disorders, obstacles in urine elimination, sex for women

ways that a uti can spread

ascending

blood - rare, risk renal abscess

causes of macro hematuria

• bacterial or adenovirus (hemorrhagic cystitis)

• complication post chemo, radio, immunosuppression

• stones

signs and symptoms pyelonephritis

• aeg, vomiting, fever

• lumbar/hypogastric pain, low UTI symptomes

• leukocytosis

• urine - leukocyte cylidners

dg uti

clinical

exams to do if establising etiology for uti in symptomatic patients

• urinalysis (visual, dipstick, micro)

• urine culture

• blood culture if urosepsis

indications dipstick screening urine

• uncomplicated cystitis (women)

• asymptomatic patients (pregnant women)

what pathogens are possible for a + nitrite test on dipstick screening?

gram - rods

• e coli

• klebsiella

• proteus

what pathogens are possible for a negative nitrite test on dipstick screening?

• staph saprophyticus

• pseudomonas

• candida

• enterococcus

• acinetobacter

• enterococcus

when should urine culture be collected

first urine or 3 hours after last urination

how to collect an indwelling catheter urine culture

only in symptomatic patients, after changing catheter - puncture catheter @ 10cm insertion after disinfection of tube

transport of urine culture

examination done within max 2h after collection OR fridge 4 dg

indications urine culture

• complicated cystitis

• recurrent utis

• ttt failure

renal trauma, uti, calculi, carcinomas and clotting disorders can cause ________ in the microscopic exam of urine

hematuria

what amount of wbc in urine is abnormal for microscopic exam

>10/ml

sterile pyuria may reflect

atb therapy, neoplasm, urinary calculi, infection with organisms not detected by routine methods

verdict of micro urine culture results + AST yes/no : symptoms + leukocytes + >10³ e coli/s. saprophyticus / 10^5 other / 50k gram + enterococci

acute cystitis, yes ast

verdict of micro urine culture results + AST yes/no : symptoms + leukocytes + <10³ CFU/ml

inflammation but no infection or slow-growing bacteria associated with genital infections

no AST

verdict of micro urine culture results + AST yes/no : symptoms + >10^5 CFU/ml + <2 species

immuno competent = repeat culture + strip test

immunosuppressed = do ast

verdict of micro urine culture results + AST yes/no : asymptomatic, 10³-4 CFU/ml >/ 1 species

contamination, no ast

verdict of micro urine culture results + AST yes/no : variable symptoms + <10³ CFU/ml

no uti, no ast

how many CFU/ml do we need for a catheterized sample to diagnose UTI + do AST

>10^5

for urine exam of a newly inserted catheter, what # colony types and of colonies do we need to diagnose and do AST

1 colony type + >10 cfu/ml

2 colony types + 1/bothb >10cfu/ml

3 colony types + 1 >10cfu/ml

for urine exam of a newly inserted catheter, what # colony types and of colonies do we need to only have to mention the suspected germs?

2 colony types + 1 <10cfu/ml

3 colony types + <10cfu/ml

for urine exam of a newly inserted catheter, what # colony types and of colonies can we ignore the results

>4 colony types and all >10cfu/ml

<10cfu/ml