microbiology Flashcards
cough + haemoptysis + fever + night sweats + weight loss + malaise for several weeks
TB
what may induce reactivation a latent TB infection in patients?
immunosuppression chronic alcohol excess malnutrition ageing reinfection
TB treatment 1st line
Rifampicin, Isoniazid (with B6 pyridoxine to prevent peripheral neuropathy), Pyrazinamide and Ethambutol for 2 months then Rifampicin and Isoniazid for the next 4 months
Rifampicin Side effects
orange-red secretions (tears/ urine etc) induces cytochrome p450 - many drug interactions
Isoniazid Side effects
peripheral neuropathy (give B6 pyridoxine) hepatotoxicity
Pyrazinamide side effects
hyperuricaemia, neurotoxicity
Ethambutol side effects
optic neuritis, visual disturbances
TB meningitis tx?
all four drugs (RIPE) for 2 months then R+I for next 10 months
Latent TB treatment?
Isoniazid alone for 6 months or Isoniazid + rifampicin for 3 months
Ghon focus
TB - Ghon focus refers to a calcified tuberculous caseating granuloma - subpleural
caveating granulomas in the lung, upper lobes usually affected. may progress rapidly to cavitation.
TB
how to diagnose/ investigate a TB infection?
Imaging: CXR/ CT For diagnosis- Culture: sputum (x3) for microscopy (ZN/ aura mine staining showing gram +ve rods, acid fast, aerobic, intracellular)
screening for TB infection?
Mantoux test (a type IV hypersensitivity) - but also positive in those with BCG vaccination/ latent TB IGRA (IFN gamma release assay) - cannot distinguish active and latent TB but no cross reaction w BCG vaccination
Auramine- rhodamine stain
+ve for mycobactacterium helps visualise acid fast bacilli
ziehl Neelson stain/ lowenstein-jensen medium
+ve for mycobacterium
BCG vaccine contains an attenuated strain of?
mycobacterium bovis
BCG vaccine used in?
at risk babies. e.g. from areas of high prevalence/ TB contacts contraindicated in HIV pts
spinal TB disease
Potts disease fever, sweats, weight loss, back pain verterbral destruction + collapse + anterior extension (causing iliopsoas abscess)
pneumonia, low Na, hepatitis, assoc w travel, air conditioning units and water towers
legionella pneumophlia
most common cause of lobar pneumonia, rusty coloured sputum. what organism?
strep pneumoniae
pneumonia associated with recent viral infection (e.g. post influenza) + cavitation on CXR what organism?
staph aureus
pneumonia associated with heavy smoking and COPD what organism
haemophilus influenzae a gram -ve rod
pneumonia associated with alcoholism, elderly people and usually presents w haemoptysis. what organism
klebsiella pneumonia gram -ve rod
community acquired pneumonia associated with smoking. microscopy and staining shows a gram -ve coccus.
Moraxella catarrhalis
pneumonia associated with younger children to young adults, may trigger erythema multiforme (SJS), cold agglutinin test (AIHA).
mycoplasma pneumonia
most common cause of atypical pneumonia in adults
mycoplasma pneumonia
atypical pneumonia associated w birds, splenomegaly, rash and haemolytic anaemia
chlamydia psittaci
pneumonia with poor response to Abx, where CXR shows upper lobe cavitation. Dx on Auramine/ Zn stain
TB
pneumonia associated with farm animals and hepaitis
coxiella burneti (Q fever)
pneumonia/ whooping cough in those unvaccinated.
bordatella pertussis
what organisms cause Pneumonia assoc w HIV
Pneumocystis Jiroveci (PCP) esp if CD4<200 TB Cryptococcus neoformans
most common causes of pneumonia in a 0-1 month old
e coli GBS listeria
most common causes of pneumonia in a 1-6 month old
chlamydia trachomatis staph aureus RSV
most common causes of pneumonia in a 6 month to 5 yr old
mycoplasma pneumonia, influenza
most common causes of pneumonia in a 16-30 yr old
mycoplasma pneumonia, strep pneumoniae
most common resp tract infection if one has neutropenia
fungal infection- aspergillus spp
silver GMS (Gomori methenamine silver) stain +ve, boat shaped organisms, bilateral ground glass shadowing on CXR
pneumocystis jiroveci PCP
post splenectomy- more at risk of which organisms?
n meningitidis s pneumonia h influenza
what organisms are associated with chronic infection in cystic fibrosis patients?
pseudomonas aeruginosa burkholderia cepacia (v high mortality)
post bone marrow transplant lung infection - what organisms
Aspergillus + CMV
what organisms can you test for with urine antigen test? (pneumonia)
strep pneumoniae legionella
in pneumonia, antibody tests - paired serum samples comparing values at presentation and 2 wks after- are useful with?
organisms that are difficult to culture. can show the rise of Ab over time. e.g. chlamydia, legionella
Community acquired pneumonia 1st line tx if mild-moderate severity?
Amoxicillin or Clarithromycin if penicillin allergic for 5-7 days
community acquired pneumonia 1st line if moderate-severe severity?
co-amoxiclav + clarithromycin for 2-3 wks if pen allergic: cefuroxime + clari
atypical pneumonia 1st line?
protein synthesis inhibitors clarithromycin + doxycycline
what Ix is useful in pneumonia?
FBC, WCC, CRP, U&Es Blood cultures, Sputum MCS ABG (Cap blood gas in children) CXR
CURB-65
if 2-5 admit to hospital. manage as severe
Pseudomonas pneumonia tx?
Piperacillin + tazobactam (Tazocin) or Ciprofloxacin +/- Gentamicin
MRSA pneumonia tx?
Vancomycin
Staph aureus pneumonia Tx?
flucloxacillin
Legionella Hosp acquired pneumonia Tx?
clarithromycin + rifampicin
Hospital acquired pneumonia 1st line tx?
Ciprofloxacin + Vancomycin
Hospital acquire pneumonia 2nd line/ in ITU?
Piptazobactam + Vancomycin
Aspiration pneumonia tx?
need gram +/ - and anaerobic cover cefuroxime + metronidazole
what causes genital ulcers?
painful- herpes simplex, chancroid painless- syphilis, donovanosis, LGV
what may cause rashes/ lumps/ growths in the genital area?
genital warts- HPV pubic lice scabies molluscum contagiosum
what is the most common cause of septic arthritis in a young adult?
neisseria gonorrhoea
complications of gonorrhoea
bartholins abscess salpingitis with irreversible tube damage, infected males - dysuria, frequency, mucopurulent discharge, prostatitis
disseminated gonococcal infection symptoms? who gets it?
pts with complement deficiencies present with fever, vasculitic rash, arthritis, septicaemia
Diagnosis of gonorrhoea
urethral / rectal smears MCS - gold standard gram -ve diplococcus
treatment for gonorrhoea
IM ceftriaxone if resistant- spectinomycin IM
what chlamydia serovars are associated with genital tract infection?
chlamydia trachomatis serovars D-K
how to diagnose chlamydia STI?
NAAT (nucleic acid amplification tests) are gold standard as chlamydia is an obligate intracellular pathogen and cannot be cultured on agar
complications of chlamydia STI
chronic pelvic pain ascending salpingitis-> PID increased risk ectopic and infertility increased risk endometriosis epididymitis reiters syndrome adult conjunctivitis opthlalmia neonatorum
tx of chlamydia
doxycycline BD for 7 days or Azithromycin stat
tx of chlamydia in pregnancy
azithromycin
SEs of Doxycycline
photosensitivity, contraindicated in pregnancy due to disturbance of bone growth and discolouration of immature bones
Lymphogranuloma venereum - what organism?
chlamydia trachomatis serovars L1,2,3 causing a lymphatic infection
Lymphogranuloma venereum presentation
generally painless ulcer + balanitis, proctitis, cervicitis -> painful inguinal buboes + inguinal lymphadenopathy (2/3 unilateral) -> abscess formation rectal presentations - more common in MSM in developed world. pain, tenesmus, rectal bleeding, mucous discharge.
chlamydia: exists in two forms. which forms are stable and extracellular, and which are intracellular and metabolic active?
elementary bodies- stable and extracellular reticulate particles- intracellular and metabolically active
Lymphogranuloma venereum tx?
same as chlamydia but for longer doxycycline for 21 days or azithromycin once a wk for 3 wks/ erythromycin for 21 days
syphilis organism?
treponema pallidum an obligate gram -ve spirochaete
diagnosis of syphilis?
to diagnose: detect antibodies against T pallidum antigens e.g. TPHA (t palladium haemagluttinin test) TPPA (t pallidum particle agglutination test) tests
what test is useful to monitor response to treatment of syphilis?
RPR as titre falls in response to treatment
syphilis tx?
IM single dose benzathine penicillin if pen allergic doxycycline -monitor RPR, need a four fold reduction for tx to be considered successful
common side effect of syphilis tx that causes fever, headache, myalgia and usually clears within 24 hours?
JH (jarisch-heimer) reaction
primary syphilis presentation
painless genital ulcer often solitary. may persist for 4-6 wks. + bilateral lymph node enlargement
secondary syphilis presentation usually few months after infection
maculopapular rash on back, trunk, face, palms, soles mucosal lesions e.g. oral ulcers, genital warts low grade fever, malaise neuro involvement - cranial n palsies, optic neuritis, acute nerve deafness
latent syphilis?
no obvious signs but serology positive
neurosyphilis presentation
argyll-robertson pupil - accommodates but does not react to light. small, irregular pupils. CSF shows spirochaete. psychosis with muscular reflex abnormality, dementia and seizures.
pupils accommodate but do not react to light.
argyll-robertson pupil in neurosyphilis
congenital syphilis presentation?
hepatosplenomegaly, rash, fever, neurosyphilis and pneumonitis. often develops over the first 2 years of life.
neurosyphilis tx?
procaine penicillin
chancroid what organism responsible?
haemophilus ducreyi a gram -ve cocobacillus
tropical ulcer disease, frequently painful multiple ulcers. diagnosis via chocolate agar medium culture + PCR
chancroid.
protein synthesis inhibitors - abx
30s subunit (AT) Aminoglycosides e.g. Gentamicin Tetracyclines e.g. Doxycycline 50s subunit (MOC) Macrolides- e.g. clarithromycin, erythromycin Oxazolidinone e.g. Linezolid Chloramphenicol
molluscum contagiosum, what organism?
pox virus
donovonasis = granuloma inguinale, what organism?
klebsiella granulomatis. gram -ve bacillus
large expanding ulcers starting as papule or nodule that breaks down. + beefy red appearance. diagnosis via Giemsa stain of biopsy + Donovan bodies
donovanosis
donovanosis tx
azithromycin
greenish gray offensive discharge in women. + vulval soreness. O/E strawberry cervix diagnosis shows flagellated protozoan
trichomonas vaginalis trichomoniasis
Trichomoniasis tx
metronidazole
clue cells, high pH, whiff test +ve
bacterial vaginosis tx with metronidazole. assoc w preterm delivery
white thick discharge, itching, soreness, redness. usually assoc w pregancy, diabetes mellitus, HIV, use of ABx, other immunosuppressive drugs
candidiasis candida albicans
candidiasis tx?
oral fluclonazole, topical clotrimoazole
facial molluscum contagiosum in adults?
HIV until proven otherwise
if tx required for molluscum contagiosum?
cryotherapy
genital warts tx?
1st line home tx: podophyllotoxin cream 2nd line: imiquimod or clinic tx- cryotherapy
seborrhoea dermatitis what organism?
malassezia furfur aka pityrosporum orbiculare
tinea/ pityriasis versicolor (depigmentation in those with dark skin) what organism?
malassezia furfur aka Pityrosporum orbiculare
athletes foot aka tinea pedis what organism?
most commonly - trichophyton rubrum caused by dermatophytes - fungi which inhabit dead layers of the skin and digests keratin
invasive candidiasis tx?
amphotericin B
often presents as pneumonia in immunocompromised, assoc with building work, cavitating lesion. also produces aflatoxin B1 which is carcinogenic and increases risk of Hepatocellular carcinom
aspergillus
tx for aspergillus
voriconazole
fungus that grows on czapek dox agar
aspergillus
insidious onset meningitis in HIV/ immunocompromised patients + associated with birds/ pigeons!
cryptococcus
tx of cryptococcal infection
amphotericin B
roseola infantum aka?
exanthem subitum
Roseola infantum - what causative organism?
HHV6
most common cause of febrile convulsions
Roseola infantum HHV6 infection
CMV complications in immunocompromised
pneumonitis (in post BMT patients) retinitis (AIDs) hepatitis
1st line tx of CMV infection
ganciclovir
Infant with IUGR, jaundice, hepatosplenomegaly, microcephaly, chorioretinitis, late progressive sensorineural deafeness, with periventricular calcification.
CMV congenital infection
Owls eyes inclusions highly specific for?
CMV infection !! different from owls eyes appearance of entire nucleus (pathognomonic of reed Sternberg cells of Hodgkins lymphoma)
diagnosis of CMV?
serology- IgM and IgG CMV (if primary infection, IgM will be dominant) Blood PCR
reactivation of CMV in post-transplant patients may cause?
encephalitis, bone marrow suppression, pneumonitis, hepatitis
what is a worrying complication of genital HSV infection
urinary retention
if pregnant woman gets primary HSV infection during third trimester, tx?
before treating, do check if this is primary infection - type specific HIV Ab test oral acyclovir 6 weeks before estimated delivery date. if primary infection and less than 6 wks til estimated delivery, c-section
neonatal HSV presentation
greatest risk of transmission from mother to fetus is if mother gets primary infection in third trimester (greatest at delivery) assoc w foetal loss, skin, eye, mouth lesions -> long term ocular and neuro sequelae encephalitis disseminated disease + vesicles (high mortality rate due to fulminant hepatitis and multi organ failure)
neonatal HSV tx?
IV aciclovir
complications of HSV?
erythema multiforme eczema herpeticum herpetic whitlow - painful red finger herpes gladiators - painful blisters + inguinal LNapothy, rugby players/ wrestlers
what do you expect to see in a fetus with congenital varicella syndrome?
limb hypoplasia eye defects - cataracts, choreoretinitis skin scarring neuro defects - microcephaly, cortical atrophy disseminated haemorrhagic varicella infection if within 7 days of delivery - purpura fulminans (30% mortality)
chicken pox post exposure prophylaxis
VZIG, within 10 days of exposure.
in pregnant women, increased risk of which complications with chicken pox infection?
pneumonitis encephalitis hepatitis
complications of shingles (VZV reactivation)
painful rash in specific dermatome
post herpetic neuralgia
ramsay-hunt syndrome (reactivation in facial n near ear- vesicles in ear, hearing loss, facial n palsy)
Guillain-barre syndrome
infectious mononucleosis most common cause
EBV
fever, tonsillar enlargement + exudates, pharyngitis, lymphadenopathy + splenomegaly + maculopapular rash + atypical lymphocytosis
glandular fever, infectious mono
diagnosis of infectious mono?
blood film (atypical lymphocytes)
EBV antibodies (IgM EBV)
Paul Bunnell test/ monospot test
important risk/ complication of infectious mono?
risk of splenic rupture -> may need abdo USS and splenectomy ask patients to avoid contact sports for next few wks
HHV8 assoc with?
Kaposis Sarcoma Castlemans disease (non cancerous growth in the Lymph nodes) Primary effusion lymphoma (HIV associated malignant effusions without tumour mass)
PUO? definition?
>38.3 fever on several occasions persisting >3/52 without diagnosis despite >1/52 of intensive Ix
which malaria species causes a quartan fever?
a quartan fever is one every 72 h plasmodium malariae
which malaria species causes a tertian fever?
a tertian fever is one every 48h plasmodium falciparum p vivax p ovale
fever in returning traveller- always consider?
malaria, dengue, typhoid fever, bacterial diarrhoea etc
what organisms cause typhoid/ enteric fever?
salmonella typhi and paratyphi
infecting Peyer’s patches. Rose spots, fever, headache, abdo pain, constipation, relative bradycardia, hepatosplenomegaly.
Typhoid fever -salmonella typhi/ paratyphi. - gram -ve rods
typhoid fever tx?
Iv fluids, IV/oral abx (Ceftriaxone)
diagnosis of typhoid fever?
blood cultures (usually bactaraemia present) stool culture shows gram - rod
which organism causes the most severe form of malaria
p falciparum
which organism causes a benign Malaria which may manifest more than 1 year after infection?
plasmodium malariae
which organisms cause the more indolent malaria, with hypnozoites in the chronic liver stage?
p vivax and p ovale
what is primaquine used for?
eradicates hypnozoites which are dormant forms in the life cycles of the plasmodium species. - useful in p vivax and p ovale
blood film shows young trophozoites (rings) in the absence of mature trophozoites and schizonts. crescent-shaped gametocytes. + Bloods show >2% parasitaemia
p. falciparum malaria infection
blood film shows schuffners dots
p vivax and p ovale
blood film shows schuffners dots and >20 merozites/ schizont
p vivax
p falciparum tx?
exchange transfusion if >10% parasitaemia
if uncomplicated: Quinine + doxycycline or Clindamycin if pregnant or
Malarone (Atovoquone/ Proguanil) or
Riamet (artemether/lumefantrine)
if complicated: IV artesunate
medical emergency
Always admit!!!
p vivax and p ovale tx?
choroquine then primaquine
what is the thick and thin blood film used for?
thick blood film used to diagnose malarial infection
thin blood film to allow species identification
Primaquine - contraindications?
contraindicated in pregnancy and breastfeeding
and increases risk of haemolysis in G6PD deficiency
fever, splenomegaly, rigors, headache, flu-like illness, myalgia, n+v
+
thick blood film +ve
malaria
malaria ix?
70% patients have low Platelets,
50% deranged LFTs,
30% anaemia
if severe:
acidosis, renal impairment, hypoglycaemia, anaemia, DIC, shock, haemoglobinuria, jaundice
first line tx of UTI?
trimethoprim
nitrofurantoin in pregnancy
quinine side effects
nausea, deafness, tinnitus, monitor blood glucose
IV:
arrhythmogenic and causes hypoglycaemia
-> cardiac and Blood gluc monitoring
fever, headache, myalgia, eschar (dark scab/ falling away of dead skin)
- > vasculitis
- > spread by vector: tick, mite, lice
Rickettsia
rickettsia tx?
doxycycline
what abx inhibit cell wall synthesis?
Beta lactams
- Penicillins e.g. Benzylpenicillin
- Cephalosporins e.g. Ceftriaxone
- Carbapenems e.g. meropenem
and
Glycopeptides
e.g. vancomycin, teicoplanin
e.g. of glycopeptide?
vancomycin for MRSA, 2nd line C.diff
teicoplanin
most common cause of UTI
e coli
chloramphenicol side effects?
given as eye drops for bacterial conjunctivitis e.g.
risk of aplastic anaemia, grey baby syndrome in neonates
what abx inhibit DNA synthesis?
Fluoroquinolones
e.g. Ciprofloxacin
for gram -ve
Nitroimidazoles
e.g. Metronidazole
for anaerobes
what UTI-causing organism is assoc with function/ anatomical abnormalities of the renal tract
klebsiella
what antibiotics inhibit RNA synthesis?
Rifamycin e.g. Rifampicin
indicated for mycobacteria e.g. TB
what antibiotics inhibit folate metabolism
sulfonamides
e.g. sulphamethoxazole
(indicated for PCP, forms co-trimoxazole with trimethoprim)
diaminopyrimidines
e.g. trimethoprim
what antibiotics target cell membranes?
polymxin
e.g. colistin
cyclic lipopeptide
e.g. daptomycin
what is the 2nd most common cause of uncomplicated UTI?
staph saprophyticus
GI infection + ate canned/ vacuum packed foods e.g. honey in kids, beans in students. -> ingestion of preformed toxin.
Descending paralysis
clostridia botulinum
clostridia botulinum tx
antitoxin
pseudomembranous colitis caused by abx use (usually cephalosporins/ ciprofloxacin/ clindamycin). releases 2 exotoxins A and B.
c difficile
c difficile pseudomembranous colitis tx
metronidazole
2nd line- vancomycin
reheated rice and sudden vomiting.
heat stable emetic toxin and heat labile diarrhoeal toxin. watery non bloody diarrhoea.
bacillus cereus
what organism causes gas gangrene?
clostridia perfringens
gas gangrene is a bacterial infection that produces gas in gangrenous tissues - medical emergency caused by exotoxin - alpha toxin.
reheated meats, superantigen enterotoxin, watery diarrhoea + cramps, lasts 24 hours
+ may cause gas gangrene
clostridia perfringens
gram + cocci in clusters, beta haemolytic. Catalase, coagulase +ve
produces entertoxin that acts as superantigen -> causing prominent vomiting and watery, non bloody diarrhoea.
Main virulence factor: protein A.
staph aureus
most common cause of travellers diarrhoea
e coli
Anaemia, thrombocytopenia, renal failure following diarrhoea + recent visit to farm
Haemolytic Uraemic Syndrome (E. coli strain 0157)
rice water stool
enterotoxin with A/B subunit -> efflux of Cl- to lumen and loss of H2O and electrolytes
massive diarrhoea
vibrio cholera
tx: supportive, fluids and electrolytes
ingestion of raw undercooked seafood, shellfish. comma shaped organism.
vibrio parahaemolyticus
cellulitis in shellfish handlers,
fatal septicaemia with diarrhoea and vomiting in HIV patients.
comma shaped organism
vibrio vulnificus
Tx of vibrio parahaemolytics and vibrio vulnificus
doxycycline
unpasteurised milk/ food e.g. poultry
headache, fever + abdo cramps + bloody foul smelling diarrhoea.
curved, s shaped, motile bacteria
assoc w guillain barre syndrome, reactive arthritis
campylobacter jejuni
Beta haemolytic, aesculin +ve, tumbling motility
GI: watery diarrhoea, cramps, headache, fever
assoc with immunocompromised patients, perinatal infection
unpasteruised dairy, veggies
listeria monocytogenes
motile trophozoite in diarrhoea. histology shows flask shaped ulcer.
dysentery, wind, tenesmus
chronic weight loss + RUQ pain due to *liver abscess + swinging fevers
assoc w MSM
entamoeba histolytica
what organism is associated with recurrent aseptic lymphocytic meningitis?
HSV type 2
Pear shaped trophozoite
trophozoites/ cysts in stool
assoc w travellers/ hikers/ MSM
malabsorption of protein and fat + foul smelling non bloody diarrhoea. may be of very long duration
giardia lamblia
tx for giardia lamblia
metronidazole
causes severe diarrhoea in the immunocompromised. e.g. HIV
profuse, water diarrhoea
oocytes seen in stool
Kinyoun acid fast stain +ve
cryptosporidium parvum
most common cause of gastroenteritis in <6 yrs. assoc w outbreaks
rotavirus
what is a prion disease?
protein-only infectious disease
rare transmissable spongiform encephalopathies resulting in rapid neuro degeneration and death in months
untreatable
due to variant PrP protein (PrPsc) abnormally folding to form insoluble configurations
hospital actuired surgical site infection: consider which organisms?
MRSA
Coagulase negative staphylococcus
CSF: 14-3-3 protein +ve
sporadic CJD
what biopsy is 100% specific and sensitive in diagnosing variant CJD?
tonsillar biopsy
rapid, progressive dementia with myoclonus, cortical blindness, akinetic mutism and LMN signs
mean onset 45-75 yrs
mean survival time 6 months
EEG shows periodic triphasic changes.
Genetics: most have 129 codon MM polymorphism
Post mortem shows spongiform vacuolation on brain biopsy, and PrP amyloid plaques
Sporadic CJD