clinical microbio lab med

most important starting step to microbio when seeing pts

get a good culture

clinical approach to microbio

see pts and pick which organs/tissues affected → get good samples and order most likely applicable tests (before starting abx)→ begin empiric tx → lab identifies whats wrong → adjust tx to get more specific

microorganisms that live on and in the body, that can be both beneficial and potentially harmful

microbiome aka normal flora

a usually low pathogenicity agent that causes an infection when the immune system is comp and the agent grows like nuts

opportunistic pathogens aka facultative

what sites in the body are normally sterile (NO normal flora)

brain/CSF, blood, bone/bone marrow, organs

is the respiratory tract sterile in the absence of disease

no

factors that influence normal flora

amounts/types of nutrients, diet, prior exposure to abx, age, pH, oxidation-reduction (aerobes vs anaerobes), resistance to bactericidal substances and microbials, affinity for specific site (specity types of epithelial cells to which they attack)

how is normal flora helpful for the host

stimulate the immune system, prevent colonization by potential pathogens, affect pH and nutrients avaliable, contributes to vitamin production, occupies the space the pathogens want

try to destroy bad bugs w/o killing good ones when treating pts

common blood pathogens (normally sterile)

staph aureus, strep pneumo

common CSF pathogens (normally sterile)

strep pneumo, neisseria meningitidis, H flu, M catarrhalis, strep pyogenes

common urine pathogens (normally sterile)

e. coli, klebsiella spp, psuedomonas spp, enterococcus spp

common sputum pathogens (normally sterile)

strep pneumo, h. flu, moraxella catarrhalis

atypicals: mycoplasma pneumonia, chlamydophilia pneumonia, legionella pneumophilia

common stomach pathogens (normally sterile)

h. pylori

common skin pathogens

staph aureus, strep pyrogens

common intestines pathogens

salmonella spp, shigella spp

common throat/mouth pathogens

group A strep pyrogens

common GU pathogens

neisseria gonorrhoeae, chlamydia

normal flora found in GU tract

in women only is lactobacillus spp, streptococcus spp, staphylococcus spp, sterile in men

normal floral in throat/mouth

actinomyces spp, viridans strep, anaerobic strep, veillonella spp

normal flora in intestines

e.coli, bacteroides spp, enterococcus spp, anaerobic strep)

normal flora in skin

staph or strep

dude comes in w cough and has coarse rales on expiration L lower on posterior chest auscultation what labs would we do

chest xray first

sputum culture (if comorbid conditions or less common pathogen or youre gonna admit him)

CBC/blood culture

CMP (see if their kidneys work well enough to eliminate abx or not)

preg test (some abx C/I in preg)

most important factor in proper dx of infection, must follow instructions for proper collection and transport before abx initiated

specimen collection

optimal specimens for collection

body fluids, tissues, aspirates (swabs are low yield and prone to contamination)

first morning sputum is optimal cause itll be real concentrated

common biologic specimens for wounds

abscess, lesion, pustule = swab or aspirate it

common biologic specimens for blood

phlebotomy

common biologic specimens for body fluids

amniotic fluid, abdominal fluid, bile, pericardial, peritoneal, pleural fluid, synovial fluid, aspirate

common biologic specimens for bone/tissue

biopsy

common biologic specimens for CSF

lumbar puncture or sample from shunt

common biologic specimens for cutaneous

hair or nail clippings, skin scrapings, aspirations, biopsy

common biologic specimens for ear/eye/nose

swab, scraping, fluid, biopsy

common biologic specimens for GI

rectal swba, aspirate, biopsy, stool specimine

common biologic specimens for genitals

swab, aspirate, biopsy

common biologic specimens for respiratory tract

sputum, tracheal aspirate, bronchial wash, naso/pharyngeal swab, aspirate

common biologic specimens for urine

1st morning void, clean catch midstream, straight catherterization, suprapubic aspirate

common biologic specimens for foreign body

submit specimine

lab tests for infectious agents in general

direct stains and microscopic exam, culture (biochemical and enzymatic testing, organism ID, susceptibility testing), antigen detection, nucleic acid detection, serology

how long does it take for the lab to ID an organism generally

3 days ish

test tp differentiate bacteria by chemical and physical properties. this test is gotten first (within 24hrs) , and is most commonly used. done on direct microscopic examination and is reported ASAP (get results in 2hrs)

direct gram stain

gram pos (purple) = thick cell wall

gram neg (pink) = thin cell wall

common gram pos bacteria (purple)

staph (cocci in clusters)

strep (cocci in chains)

common gram neg bacteria (pink)

e. coli, klebsiella, pseudomonas (rods), neisseria (cocci in pairs)

treatment based on knowledge and experience and innitatted on teh bases of a clinical “educated guess” wothout complete information or verification of cause (specimin has been collected and sent to lab but results havent gotten back yet)

empiric therapy

things to consider when picking empiric therapy

pt characteristics: immune status, age, organ fxn, comorbidities, severity of illness, med allergies, disabilities

med characteristics: spectrum of activity, pharmacokinetics, efficacy, route of admin, cost, duration of therapy, side effects, med interactions

infectin characterisitcs: site, type, potential pathogen

hospital formulary/insurnace

appropriate dx is key

interpretation of culture is based on ____

context of the body site, normal flora present, pathogens identified, and the concept of predominance

what do biochemical or enzematic tests do

allow the observation of visible biochemical rxns (oxidation, fermentation, gas production, urea hydrolysis, indole production)

uses isolated bacterial colonies and can have a rapid response or may require timed incubation

methods used to identify bacteria

traditional: gram stain and microscopic exam, growth rate and colony appearance on various types of agar mediaa, reactivity w various chemicals/reagents

modern: DNA/RNA content of microorganisms, protein profile (MALDI-TOF MS) of microorganisms

first line pneumonia tx

amoxicillin (good for kids) or doxycycline

augmentin if DM or other immunocomp/comorbid

minimal inhibitory concentration (lowest conc of drug that inhibits bacterial growth)

MIC

antimicrobial susceptibility tests and how are results reported

disk diffusion (kirby bauer) and broth microdilution MIC

susceptible (S) = drug will work

resistant (R) = drug wont work

intermediate (I) = drug might work depending on site of infxn and pt status

meds that staph aureus is susceptible to

vancomycin, trimethoprim/sulfonamide, tetracyclines (doxycycline, minocycline, etc), rifampin

reflects how effective antibiotics are against specific organisms, compiles from local clinical specimen data that serves to inform empiric therapy before culture results are reast, monitor resistance trends in a hospital/region, support antimicrobial stewardship and appropriate use, and refine hospital guidelines

hospital susceptibility report (antibiogram)

key concepts and considerations of an antibiogram

organisms: common bacterial pathogens isolated

antimicrobial: antibiotics tested against the organisms

susceptibility rates % of isolates susceptible to each drug

local data is key (tailored to the facilities pt pop), clinical context matters (consider infection site, severity and pt status), not a standalone tool (use w pt hx, guidelines, and potential med interactions, dont overuse abx, encourage targeted abx use to reduce abx resistance