POM ID Overview - Claire's

Claire's version

pathogen

biological agent that can produce a disease

virulence

a measure of an organism's capacity to cause disease

Microbiota

the collection of microbes residing in and on mammalian organisms

Virus

a microscopic, non-living particle that can infect living cells and replicate within them

Virion

a fully formed virus that is able to establish an infection in a host cell; DNA or RNA with a protein coat

bacteria

prokaryotes, occupy every environment in the world

-infection, normal flora, biological weapons, abx resistance

Fungus

spores in air or soil, infections start in the lungs or skin

-rarely contagious

-kept in check by bacteria

Parasite

organism that lives in/on a host at the detriment to that host

protozoa

-one-cell, replicate in humans

-fecal-oral

-transmission via arthropod vector

Helminths

-multicellular, cannot replicate in humans

-visible to naked eye

-worms

Ectoparasites

-depend on blood meal from human host

-often vectors for other pathogens

-fleas, mites, lice

HepA, polio, rhinovirus

what are examples of non-enveloped viruses?

Enveloped Virus

-phospholipid bilayer from host cell membrane; virus specific

-acquired as virus exits host cell

-often LESS stable

Enveloped Viruses

influenza, measles, rubella, HIV, HSV2, Hep B, Hep C

DNA Virus

-mostly double-stranded with replication in the nucleus, more stable

-EBV and HPV

RNA Virus

-mostly single-stranded with replication in the cytoplasm

-more UNSTABLE, can be more virulent

-high mutation rate

-Ex: HIV, HCV

Viral Replication

Process by which viruses reproduce within host cells

Attachment --> penetration --> uncoating --> early transcription --> early translation --> DNA synthesis and late transcription --> late translation --> assembly --> release of virus and lysis of infected cell

what are the 9 steps, in order, of viral replication cycles?

Virus Transmission

-person-to-person

-fecal-oral

-mother-fetus

Virus replication and cell damage

symptoms of the virus begin due to cell damage/death

Gram Stain

a differential staining technique used in microbio to classify bacteria into two major groups (Gram + and Gram -) based on differences in their cell wall structure

Gram Positive Bacteria

-thick cell wall of peptidoglycan

-no outer lipid membrane

-produce exotoxins

-staph and strep

Gram Negative (red/pink)

-thin peptidoglycan layer

-outer lipid membrane present

-produce exotoxins and endotoxins

-N. meningitidis, H. influenzae

Non-staining bacteria

-mycobacteria

-treponema pallidum

-mycoplasma pneumoniae

-legionella pneumophila

-chlamydiae

-rickettsiae

Microbial entry and adherence

-must have entry point to host and adhere to tissue surface cells, normally mucosal surfacae

pili and fimbriae

what are examples of adhesins?

Microbial Growth Factors

presence of O2, temperature, pH, presence of light, etc

Capsules

protective coating made of sugars

Spores

inactive forms of bacteria that can survive for years

Toxins

proteins that can harm the host and help bacteria invade tissues

Siderophores

-iron-binding factors to allow bacteria to compete with host for iron

Biofilms

-S. epidermidis, S. aureus, P. aeruginosa

-Dental plaques

-can make infxn persistent, difficult to treat

antiphagocytic factors

normal host surface components, polysaccharaide capsule

IgA1 proteases

pathogens can inactivate mucosal surface antibodies (IgA)

-N. gonorrhae, H. influenzae

Direct transmission

contact or droplets

Indirect transmission

airborne, vector, vehicle

Blood Pathogenic microbiota

-pseudomonas

-serratia

-staph

-acinetobacter

Skin Pathogenic Microbiota

-staphylococcus epidermidis

-staphylococcus aureus

-Streptococcus pyogenes

-often differ by area

Mouth Gram (+) pathogenic Microbiota

-streptococcus

-corynebacterium

-lactobacillus

Mouth Gram (-) pathogenic microbiota

-neisseria

-prevotella

Nasopharynx Pathogenic Microbiota

-Nasal predominant: corynebacterium, staphylococcus

-Nasopharynx: moraxella, haemophilus, streptococcus, fusobacterium

Stomach pathogenic microbiota

-veillonella, prevotella

-increased firmicutes in gastric cancer and H. pylori infxns

-decreased gastric acid secretion, gastric atrophy leads to increased microbes normally killed by acid

Small Intestine Pathogenic Microbiota

-lactobacillus, streptococcus, veillonella, clostridium

-facultative anaerobes thrive here

Colon Pathogenic Microbiota

-highest density of all GI tract, prioritize dietary starch

-lachnospiraceae, Akkermansia

Vagina Pathogenic Microbiota

-lactobacillus

-varies based on life stage, estrogen levels, pH, glycogen

-disturbance can lead to candidiasis or BV

Osteomyelitis Pathogens

-Chronic: S. epidermidis, S. aureus

-Hemoglobinopathies: S. aureus

-IV drug use: S. aureus

S. aureus

what is the most common pathogen for joint septic arthritis?

S. aureus, S. epidermidis

what are the two common pathogens for prosthetic joints?

Viral Bronchitis

-85-95% of cases

-rhinovirus, adenovirus, flu A and B, parainfluenza virus, RSV

Bacterial Bronchitis

-often in patients with underlying health conditions (COPD)

-H. influenzae

Cervicitis Pathogens

-chlamydia is most common

-BV and group A streptococci

Diverticulitis pathogens

-E. coli, B. fragilis, anaerobes

-bacteria get trapped in diverticulum

Acute Mastoiditis Pathogens

S. pneumoniae, H. influenzae, M. catarrhalis, S. aureus, S. pyogenes, P. aeruginosa

Chronic Mastoiditis pathogens

-usually from recurrent otitis media and prior abx use

-P. aeruginosa, S. aureus, enterobacteriaceae, anaerobes, mycobacterium tuberculosis

Acute Otitis Externa Pathogens

-primarily bacterial

-P. aeruginosa, S. aureus

Chronic otitis Externa Pathogens

-consider allergies or underlying inflammatory derm conditions

-more likely to be fungal

Otitis Media Pathogens

-S. pneumoniae

-H. influenzae

-M. catarrhalis

S. aureus

what is the most common pathogen that causes native valve endocarditis?

S. aureus

what is the most common pathogen that causes endocarditis in IV drug users?

Staph (early), staph and strep (late)

what are the common pathogens for prosthetic valve endocarditis?

H. influenzae

what is the most common cause of viral epiglottitis?

Bacterial epiglottitis pathogens

-S. pyogenes

-S. pneumoniae

-S. aureus

Immunocompromised Epiglottitis Pathogens

-P. aeruginosa

-Candida

Cholecystitis Pathogens

-E. coli, Klebsiella, E. faecalis

-anaerobes more common in patients with DM, Age >70, or previous surgery

-20% of cases

Cholangitis Pathogens

-E. coli (25-50% of cases), Klebsiella, E. faecalis

Viral Gastroenteritis Pathogens

-Norovirus, rotavirus, adenovirus

-watery diarrhea, vomiting more common

Bacterial gastroenteritis Pathogens

-Salmonella, campylobacter, shigella

-diarrhea may be bloody

-more likely to cause fever

Viral Meningitis Pathogens

-less severe, enteroviruses

Bacterial Meningitis Pathogens

-N. meningitides, S. pneumoniae all ages

-Infants/elderly: e. coli, listeria monocytogenes

-Infants: group B strep

PID pathogens

-Chlamydia trachomatis, Neisseria gonorrhoeae

-Post-menopausal: e. coli and colonic anaerobes

-polymicrobial infxn

Peritonitis Pathogens

-Secondary infxn: E. coli, S. aureus, Klebsiella

-Dialysis: staph

Viral Pharyngitis pathogens

-rhinovirus, influenza, adenovirus, coronavirus, and parainfluenza

Bacterial Pharyngitis Pathogens

-S. pyogenes (GABS) 5-36% of all cases

-more severe, often arises after initial viral infection

Pneumonia Pathogens

-S. pneumoniae (declining d/t vaxx)

-influenza, COVID

-1/3 of cases are due to respiratory viruses

Acute Sinusitis Pathogens

-S. pneumoniae

-H. influenzae

-M. Catarrhalis

-S. pyogenes

Chronic Sinusitis Pathogens

-Staphylococcus

-Anaerobes

Immunocompromised/Nosocomial Sinusitis Pathogens

-P. aeruginosa

-other anaerobes

-gram (-) rods

Skin Bacterial pathogens

-S. aureus

-Streptococcus species

-Coryneform

Viral Skin pathogens

-HSV

-Molluscum contagiosum

-Herpes Zoster

-Varicella Zoster

Fungal Skin Pathogens

-trichophyton rubrum m/c

Nosocomial infection

-infection acquired during the course of receiving healthcare treatment for other conditions

-not present or incubating at time of admission and developing >48 hr after admission

Common nosocomial infections

urinary, bloodstream, surgical wounds, pneumonia, MRSA, C. diff

Bloodstream Infection

-RF: indwelling vascular lines, critical illness, repeated tx with broad-spectrum abx

-S. aureus

-Diagnostic: blood cultures, CXR

-Tx: remove indwelling catheters or devices, consider abx lock therapy, abx (vanco), refer to ID if needed

Pneumonia

-RF: ICU patients, mechanical vent

-S. aureus, MRSA, pseudomonas, gram (-) rods

-Diagnostic: at least 2 of: fever, leukocytes, purulent sputum; new or progressive opacities on CXR, cultures of sputum, blood, pleural fluid

-TX: empiric Abx

Urinary tract infection

-RF: indwelling urinary catheters or urologic procedures, long-stay male elderly patients, debilitated patients

-Endogenous organisms (2/3), E. coli

-Diagnostic: urinalysis and urine culture

-Tx: empiric abx, remove catheter

Surgical Wound

-present usually 5-10 days after surgery

-deep more common than superficial

-RF: poor skin preparation, wound contamination/drainage, age/general health of patient, duration of surgery, skill of surgeon

Surgical Wound Pathogens

-S. aureus, K. pneumoniae, P. aeruginosa, E. coli

Superficial Surgical Wound

-Wound appearance consistent with infxn, within 30 days of operation, and one of the following:

--purulent discharge, organism growth from culture, surgical wound exploration with no culture, OR surgeon diagnosis

Deep Surgical Wound

-Within 30 days of operation or 1 year if implant is in place, infxn appears to be related to procedure and one of the following:

--purulent drainage from deep incision, spontaneous dehiscence, +/- culture with fever, pain, or tenderness; an abscess OR dx made by physician

Surgical Wound Tx

-abx (>1 week PO or IV), wound debridement, drainage, and dressing changes, removal of implanted materials if necessary

GI Infection

-RF: abx use, age >60, exposure to other patients with infxn, underlying disease, recent surgery, immunosuppression

-C. diff, Salmonella, rotavirus, norovirus

-Diagnostic: stool cultures

-Tx: prevention, discontinue causative abx, IV abx, hydration, occasionally surgery to remove diseased colon, FMT, probiotics

FUO Etiology

-TB, endocarditis

-Adults: infxn (25-40%) and cancer (25-40%)

-Children: infxn (30-50%) and cancer (5-10%)

-Autoimmune disorders

FUO diagnosis

fever present with no diagnosis after 3 outpatient visits or 3 days of hospitalization

FUO manifestations

-chills, tachycardia, piloerection

FUO workup

-thorough hx to determine clues

-any abn findings should be investigated

-lab work --> blood and other cultures

-tests for specific pathogens

-imaging --> CXR for all

FUO Tx

-find underlying cause and treat

-empiric antimicrobials NOT recommended

FUO management

-treat symptoms and discover cause

-consider ID consult

-monitor closely, admit if necessary