Microbiology Flashcards
Presentation of TB
weight loss
cough
haemoptysis
fever with night sweats
where is post primary TB found
in the upper lobes
who is affected by post primary TB
young adults
how does post primary TB heal
fibrosis and calcifications
what is the classic lesion in post primary TB
caseating granuloma
What is the Ghon focus?
multiplication of TB at pleural surface
what sort of cells are in a TB granuloma
Langhan’s giant cells
buzzword for miliary TB
rich foci
haemotological spread
First line treatment for TB
Rifampicin
Isoniazid
Pyrazinumide
Ethambutol
Give all for 2 months then R and I for another 4 months
Rifampicin side effects
orange secretions
CYP450 induction
hepatotoxic
raised transaminases
second line treatments for TB
Injectables- capreomycin, anamycin and kanamycin quinolones- moxifloxacin ethionamide/ protionamide Linelozid PAS chlofazamine
treatment of TB meningitis
RIPE for 4 months then R and I for 8-10 months
Treatment of post primary TB
RIPE for 2 months then R &I for 4 months
treatment of latent TB
8 months of isoniazid
what is mono drug resistent TB resistant to
one drug (duh)
what is MDR TB resistant to
Rifampicin and isoniazid
what is XDR TB resistent to
rifampicin
isoniazid
injectables (kanamycin and amakacin)
quinolones
imaging for TB
CXR
cultures for TB
3x cultures
broncho-alveolar lavage
EMU
lowenstein-jensen sputum sample
gold standard for TB diagnosis
pus in lowenstein jensen medium
what do you see on microscopy of TB
acid fast aerobic bacilli
waxy cell wall
investigations in TB
mantoux/ heaf test
interferon gamma assays e.g. ellispot
NAAT- PCR probes
liquid culture mediums
TB meningitis symptoms
personality change, focal neurological deficit and declining GCS
neck stiffness, headache
weight loss, malaise, fever night sweats
diagnosis of TB meningitis
tuburculotoma on head CT
lymphocytes in lumbar puncture
treatment of TB meningitis
12 months of RIPE plus steroids
extra pulmonary TB symptoms
lymphadenitis CVS: pericarditis GIT: ileitis, peritonitis GUM: renal, testes skin and liver also can be affected
risk factors for reactivating latent TB
immunosupression
aging
chronic alcohol intake
malnutrition
pathology of spinal TB
haematogenous spread of TB leading to discitis
this then leads to vertebral destruction and collapse
this can then lead to anterior extention and ileo-psoas abscess
BCG efficacy
0-80%
bad for pulmonary TB but good against leprosy, TB meningitis and disseminated TB
why is the BCG contraindicated inPLWH
-HIV –ve latent TB –> active TB 5-10% lifetime risk
-HIV +ve latent TB –> active TB 5-10% yearly risk
-
mycobacteria in leprosy
M leprae and M lepromatosis
treatment for leprosy
rifampicin
dapsone
clofazimine if multibacteria
leprosy symptoms
skin: depigmentation, plaques, macules, nodules
nerves: sensory neuropathy, thickened nerves
eyes: iridocyclitis, keratitis
bones: periositis, aseptic necrosis
tuberculoid leprosy is mediated by
Th1
lepromatous leprosy is mediated by
Th2
M Avium symptoms
in children: pharyngitis, cervical lympth adenitis
lung sx if underlying pulmonary disease
if cytoxic/ lymphoma disease then disseminated
If AIDS then disseminated multibacilliary infection with bacteraemia
M marinarum
swimming pool/ aquarium owner getsa single/ cluster of papules
Baruli ulcer (m bulurans)
a painless ulcer which progresses to a huge deformity with scarring, ulceration and contractures
how to decude if IV or oral treatment for pneumonia
CURB65 score
pathology of pneumonia
inflammation of alveoli
pathology in bronchitis
cough for most days of three months with phlegm for 2 or more consecutive years
strep pneumoniae pneumonia
sx
microscopy
gram positive diplococci
rusty brown sputum
haemophilis influenzae
microscopy and vulnerable group
associated with smoking/ COPD
gram negative coccobacillae
M catarrharis
microscopy and vulnerable group
associated with smoking
gram negative coccus
staph aureus as a cause of pneumonia
what is it associated with and what is seen on microscopy
associated with a recurrent viral infection (post flu in emq land)
gram +ve cocci (grape bunch clusters)
klebsiella pneumona
susceptible person
sx
micro
alcoholic/ elderley pt
sx: haemotysis
micro: gram negative rod, enterobacter
Atypical pneumonia microbes
legionella pneumophilia bordatella pertuccusis chlamydia psittici chlamydia pneumonia mycoplasma pneumonia TB
legionella pneumophilia
risk factors and findings
low sodium
hepatitis
risk in water towers/ air con
mycoplasma pneumonia
symptoms
test
systemic symptoms erythema multiforme, joint pain
cold agglutinin test
risk of SJS
bordella pertussis
often travelling community in EMQ
whooping cough in unvaccinated people
pathogen causing RTI in cystic fibrosis
psuedomonas aeringosa
burkholderia cepacia
pathogen causing RTI in BMT
aspergillus
CMV
pathogen causing RTI in neutropaenic patients
aspergillus spp
pathogen causing RTI in HIV patients
pneumocystitis jirovii
TB
cryptococcus neoformans
pathogen causing RTI in splenectomy patient
haemophilus influenzae
strep pneumoniae
neisseria meningitidis
which organisms do you identify with paired serum tests for pneumonia
legionella
chlamydia
if at 10 weeks
how to identify PCP on lab testing
silver staining in the cytology lab- boat shaped organisms
which pneumonias can you identify by urine antigen
legionella
strep pneumoniae
define hospital acquired pneumonia
pneumonia after >48 hours into hospital stay with no previous infection
treatment of classical community acquired pneumonia
if mild a macrolide/ amoxicillin for 5-7 days
if moderate to severe then use clarithromycin +coamxiclav/ cefuroxamine for 2-3 weeks
how to treat atypical community acquired pneumonia
use a macrolide/ tetracycline
what does clarithromycin interact with
WARFARIN
treatment of hospital acquired pneumonia
1st line: ciprofloxacin +/- vancomycin
2. piptazobactam + vancomycin
treatment of aspiraton pneumonia
metronidazole + cefuxamine
treatment of legionella pneumonia
rifampicin + macrolide
treatment of staph aureus pneumonia
flucloxacillin
treatment of pseudomonas HAP
ciprofloxacin plus gentamycin
ortazocin + piperacillin
treatment of MRSA HAP
vancomycin
Isoniazid side effects
hepatotoxicity
peripheral neuropathy
(give pyroxidine or B6)
Pyrazinamide
hyperuricaemia
hepatotoxicity
Ethambutol
visual disturbances (red-green colour blindness) optic neuritic
second line treatment of TB
1) injectables (amakacin, capreomycin, kanamycin)
Painful genital ulcers are most likely to be
Herpes
Chancroid (less likely)
Painless genital ulcers could be
Syphilis
Lymphogranuloma venereum
granuloma inguinale
What is seen on microscopy of gonorrhea
Gram negative diplococcus
What complication occurs when a baby contracts gonorrhea from mums birth canal
Ophthalmia neonatorum
The baby develops a conjunctivitis is left untreated
What happens to a patient with a complement deficiency if they contract gonorrhea
They get disseminated gonorrhea, septicaemia, arthritis and/ or rash
Gold standard diagnosis of gonorrhea
Culture from urethral swab (95% sensitive) rectal swab is 20% sensitive
Treatment of gonorrhea
200mcg of cefrtriaxone IM
or 400 mcg of oral ceftriaxone
What antibiotic is used if gonorrhea is resistant to ceftriaxone
Spectinomycin 2g im
Consequences of gonorrhea
Prostatitis or salpingitis
What is seen on microscopy of chlamydia
Intracellulaire pathogen
Ovoid and gram negative ( non spore forming)
What are the two stages of chlamydia’s life cycle
Intracellular reticular bodies that are metabolically active
Extracellular stable elementary bodies
Complications of chlamydia
PIX, ectopic risk, endometriosis
Reiters syndrome
Gold standard for chlamydia diagnosis
NAAT
Treatment of chlamydia
1g azithromycin P.O.
Alternatively 7 days100mcg BD doxycycline P.O.
Contraindicated in pregnancy ( give erythromycin 7/7 500mcg QDS )
What is lymphogranuloma venereum
Lymphatic infection with chlamydia trachomatis Serovars L1-3
syphilis on microscopy
what shape
gram positive or negative
obligate gram negative sphirochaete (helically coiled- squiggly)
use dark ground microscopy
how do you detect treponemes
PCR is gold standard
dark ground microscopy
what reagents cause a false positive on syphilis testing
cariolipin
lecathin
cholesterol
non treponomal tests for syphilis
useful in primary infection and to check the treatment response
detect non-specific antigens
VDRL slide test
treponomal tests for syphilis
these test specific antigens for t. pallidum
Enzyme immuno-assay (EIA)
flourescant treponemal antibody (FTA)
T. pallidum haemagglutinin test (TPHT)
pros and cons of treponemal tests for syphilis
it is more sensitive than non-treponemal tests
the results stay positive for years despite effective treatment
appearance of primary syphilis infection
macule –> papule
–>painless lump that appears 1-12 weeks after infection and persists for 4-6 weeks.
Serous exudate with clean base
regional adenopathy
symptoms of secondary syphilis
general: malaise, low grade fever
derm: symmetrical non-pruritic maculopapular rash on back, trunk, palms, soles, trunk, face, arms, legs
genital: genital ulcers
mouth: snail track ulcers, mucosal lesions
eyes: uveitis, choroidoretinitis
alopecia
neuro: aseptic meningitis, cranial nerve palsies, acute nerve deafness, optic neuritis
when do symptoms of secondary syphilis occur
1-6 months after infection
tertiary syphilis
cardio: aortitis
granuloma
meningitis: “pariesis of the insane”,
tabes dorsalis: degeneration of the dorsal columns resulting in hyporeflexia, loss of proprioception and sensation and therefore causes ataxia
treatment of syphilis
single dose IM penecillin (doxycyclin if allergic)
what is the jarisch-heimer reaction
(fever, headache, myalgia, sometimes exacerbation of
syphilitic symptoms) – common, develops within hours of syphilis abx administration and clears within 24hrs.
congenital syphilis
occurs during birth/ pregnancy hepatosplenomegaly rash neurosyphilis fever pneumonitis
what pathogen causes chancroid
haemophilus ducreyi
what are the symptoms of chancroid
multiple painful ulcers
often in african tropical countries
what will be seen on microscopy of chancroid
gram negative cocco-bacillus
how do you diagnose chancroid
PCR
culture on chocolate agar
what pathogens are contracted from oral-anal contact
shigella, salmonella, giardia
trichomonias infection symptoms
urethritis in men
discharge in women
strawberry cervix
what pathogen causes trichomoniasis
T. vaginalis
how is trichomoniasis diagnosed
wet prep microscopy
how is trichomoniasis treated
metronidazole
what is the abnormality in bacterial vaginosis
reduced lactobacilli
polymicrobial
abnormal vaginal flora
how to diagnose BV
gram stain the discharge
positive whiff test
candidiasis symptoms
cottage cheese discharge: thick white discharge with itching, soreness and skin breaking
balanitis in men
vulvo-vaginitis in women
mollascum contagiosum
spread by touch/ sexual contact
dsDNA pox virus
huge lesions if immunocompromised, assume HIV until proved otherwise
genital warts pathogen
HPV virus usually strains 6 and 11 which ARE NOT associated with cervical cancer
dsDNA
(16, 18 is increased risk of cervical dysplasia, though the quad vaccine does protect against all 4 strains)
incubation time and appearance of genital warts
3 weeks to 8 months
can be keratinised, pedunculated, planar, carpeted, pigmented or papular
viral STIs
HAV, HBV,HCV (usually HIV+ MSM)
HIV
HSV
Examples of disease from tinea infection
ringworm
athletes foot
diseases from pyteriasis
t versicolour
sebhorreic dermatitis
how to test for candida
culture: mannan
antibodies
how to test for aspergillus
PCR
ELISA
beta glucan test
grows on czapek dox agar
how to test for cryptococcus
cryptococcal antibodies in serum/ CSF
india ink staining
example of a polyene
what do they target
give e.g. of organism affected
amphotericin
cell wall integrity
yeast
example of an azole
what do they target
give e.g. of organism affected
fluconazole
cell membrane synthesis
yeast
Terbinafine
what do they target
give e.g. of organism affected
targets cell membrane
against dermaphytes/ mould
what does flucytosine do
targets DNA synthesis in fungal infection
echinocandin
against yeast
targets cell membrane
e.g. capsofungin
what is used to treat cryptococcal meningitis/ invasive fungal disease
amphotericin B
what are the types of PUO
classical
healthcare associated
neutropenic
HIV assocaited
causes of classical PUO
infection returning traveller neoplasm malignancy genetic
causes of healthcare acquired PUO
c diff
immobilisation
surgical lines
drugs: vancomycin, penecillin, serotonergics
causes of neutropaenic PUO
GVHD chemo haematological malignancy mycobacteria drug fever
causes of HIV associated PUO
seroconversion TB kaposis sarcoma PCP cryptococcus lymphoma histoplasmosis
what to screen for in PUO
vasculitis: cANCA, pCANCA
genetics: fabry’s, FMF, cyclic neutropenia
Bence jone proteins
casts i nurine
differentials for fever in a returning traveller
malaria dengue typhoid rickettsia brucella viral haemmorhagic fever e.g. lassa/ ebola
typhoid bacteria type
gram negative bacillus
typhoid pathogen
salmonella typhi
salmonella paratyphi
what is the infection in typhid
enteric fever infecting peyers patches
how is typhoid fever transmitted
water and food
symptom of typhoid
ROSE SPOTS RELATIVE BRADYCARDIA hepatosplenomegaly abdo pain and diarrhoea/ constipation fever headache
consequences of chronically carrying typhoid
gallstones
immunospression
diagnosis of typhoid
stool culture
blood test
is typhoid a notifiable disease
yes
what the the subtypes of malaria
p falciparum
p vivax
p ovale
p malariae
which is the severe type of malaria
p falciparum
what is the common type of malaria
p vivax
what is the benign type of malaria
p malariae
what is seen on blood film of p falciparum
immature ring trophozoites/ mature trophozoites and schizont
crescent shaped gametocytes
how is p falciparum treated
quinine + doxycyclin/ clindamycin/
riamet (artemether/ lumefantrine)/
malarone
what is seen on blood film of p vivax
schuffner dots
>20 merozoites. schizont
what is seen on blood film of p ovale
schuffner dots
how is p ovale treated
chloroqiune then primaquine
how is p vivax treated
chloroquine then primaquine
what is a thick film used for in malaria
to discover parasitaemia
what is the thin film used for in malaria
to determine species
blood findings in p falciparum malaria
wcc normal
reduced platelets
deranged LFTs
anaemia
symptoms of malaria
fever/ rigors
flu like disease- myalgia, headache
N&V
splenomegaly
may have focal neurology- reduced gcs or shock
rarely dark urine- diarrhoea, abdo cramps
when is parenteral therapy indicated i p falciparum
parasitaemia>2%, pregnancy, comiting
what GI infections are caused by anaerobes
clostridium (difficicle, perfringens and botulinium)
what are the symptoms of c. botulinum
descending paralysis
pathology of c bolutlinum
preformed toxin blocks ach release from peripheral nerves
treatment of c botulinum
antitoxin
clostriium perfringens pathology
superantigen enterotoxin binds to MHC/ TCR
massive cytokine production and supression of immune response
where does clostridium perfringens act
small bowel
incubation period of clostridium perfringens
8-16 hours
symptoms of clostridium perfringens
watery diarrhoea and cramps
risk of gas gangrene
symptoms of c difficile infection
pseudomembranous colitis
what abx cause c diff infection
flouroquinolones or cephalosorins
treatment of c diff
metronidazole
PO vancomycin
gram negative lactose fermenting gi infection
e coli
subtypes of e coli
ETC
EIEC
HIS
EPEC
ETEC
travellors diarrhoea
EIEC
invasive dysentary
EPEC
infantile diarrhoea
treatment of ecoli
ciprofloxacin
no lactose fermenting git infections
salmonella
shigella
yersina enterocoli
enteritides
enteritides symptoms
self limited non blood diarrhoea
treatment of enteritides
ceftriaxone or ciprofloxacin
shigella symptoms
fever
pain
bloody diarhorrea
pathology of shigella
affects distal ileum and colon
shiga enterotoxin
yersinia enterocolitis pathology
mesenteric adenitis with necrotising granulomas
association sof yersinia
erythema nodosum
reactive arthritis
what are the characteristics of vibriosis
late lactose femeneters
oxidase positive
gram negative
campylobacter jejuni microscopy
gram negative
s shaped
oxidase positive
campylobacter symptoms
prodrome of headache and fever
abdo cramps
foul smelling diarrhoea
treatment of campylobacter
erythromycin
causes of campylobacter
drinking unpasturised milk
listeria monocytogenes
V/L shaped
tumbling motility
beta haemolytic
aesulin positive
symptoms of listeria
watery diarrhoea cramps headache fever little vomiting febrile gastroenteritis
entamoeboeba histolytica
MSM
non motile cyst in diarrhoeal illness
flask shaped ulcer on histology
symptoms of entamoeba histolytica
dysentery, wind, tenesmus, wt loss
RUQ pain and liver abscess
giardia lamblia buzzwords
hikers/ trvellers/ MSM/ mental hospitals
pathology of giardia lamblia
pear shaped trophozoites- 2 nuclei
trophozoites in stool
symptoms of giardia lamblia
malabsorptio nof protein and far- foul smelling non bloody diarrhoea
treatment of giardia lamblia
metronidazole
cyptosporidium parvum
severe diarrhoea in immunocompromised
oocytes in stool
treatment of cryptosporidium parvum
paromycin
viruses causing secretory diarrhoea
rotavirus adenovirus norovirus poliovirus enterovirus hep A
Examples of HAI
C diff
E. coli (UTI)
MRSA causing bacteraemia
Predisposing factors to C diff infection
The three c’s
Cephalosporins, clindomycin and ciprofloxacin