investigation of specific infections Flashcards
what is the main function of testing?
to identify the cause, treatment and risk of the patient
what is the issue with testing?
no test is infallible - there will be a positive and negative error rate for all
when should you not do a test?
if it does not add to the management or prognosis
what types of sampling are there?
local and general
what is local sampling?
it is sampling from the source of infection - assist with the diagnosis and identify appropriate treatment
what is general sampling?
it is part of sepsis investigation and includes blood cultures such as FBCs, U&Es, LFTs, clotting and CRP
what is meningitis?
it is inflammation of the meninges that is caused by bacteria, viruses, mycobacteria, fungi and parasites
how would you identify meningitis?
through a lumbar puncture to sample CSF, blood cultures - CRP, glucose, LFTs, U&Es and FBCs, blood culture for bacterial PCR for N meningitidis or S pneumoniae, and CSF cryptococcal antigen or TB culture PCR in immunosupressed
what is encephalitis?
it is inflammation of the brain that is usually viral - herpes
how would you test for encephalitis?
CSF requesting viral PCR specifically
`what is the cause of brain abscesses?
there is a wide aetiology including bacteria, mycobacterial, fungal and parasitic
what can help to identify brain abscess?
the history - ear, sinuses, blood and post op
what should be discouraged in identifying brain abscess?
lumbar puncture as it is rarely positive and high risk
what should be done to identify brain abscess?
local sampling
pus - biopsy or drainage - gram, culture, sensitivity and PCR
blood cultures
what are the characteristics of healthy CSF?
the opening pressure should be 5-20 cmH20
the appearance should be clear
the WBC count should be <3x10^6/L
there should not be any cell differentiation
the protein should be from 0.2-0.5g/L
the glucose in CSF:blood should be 0.6
what are the characteristics of CSF in viral infection?
the opening pressure should be normal or slightly raised
the appearance should be clear
the WBC count should be <1000x10^6/L
the cell differentiation should be mainly lymphocytes
the protein should be <1g/L
the glucose in CSF: blood should be >0.6
what are the characteristics of CSF in bacterial infection?
the opening pressure >30cmH20 the appearance of CSF turbid the WBC count >500x10^6/L the cell differentiation is mainly polymorphs the protein >1g/L the glucose in CSF:blood <0.4
what are the characteristics of CSF in fungal and TB infection?
the opening pressure if variable - however if it is a crypto fungal infection it is greatly increased
the appearance of CSF is variable
the WBC is variable
the cell differentiation is mainly lymphocytes
the protein is <0.5g/L
the glucose in CSF:blood is less than 0.4
what are the two most common infections of the ear?
acute otitis media and externa
how will you manage media?
clinical diagnosis - viral or bacterial
if the ear drum is perforated then send a pus sample off
how will you manage externa?
ear swab to identify the cause and sensitivity
what is the most common nose infection?
sinusitis/rhino-sinusitis
majority are viral or secondary bacterial
caused by upper respiratory tract flora
what is the management if suspected sinusitis?
swab in all cases - except severe as this is unhelpful
severe cases - pus from operative sinus lavage and FBC and blood cultures
what are the most common throat infections?
pharyngitis - viral and bacterial sore throat
diphtheria
what is the management if suspect pharyngitis?
majority are viral
only swab if evidence of bacterial - looking for B-haem streps
the additional tests would be diphtheria swab, EBV serology, pus swab if quinsy abscess
what are the four most common respiratory infections?
influenza, pneumonia, pulmonary Tb and atypical infection in the immunocompromised
what is the epidemiology of influenza?
it can be seasonal and sporadic or epidemic and highly transmissible
it is not necessary to test everyone for influenza, who is tested?
those who may require treatment and those at risk of transmitting it
how do you test for influenza?
nose and throat swabs for immunofluoresence / PCR
what is beneficial about PCR?
the sensitivity is over 90% and the specificity is over 99% - fast, scalable and cost friendly
what is pneumonia?
it is a clinical diagnosis based on respiratory symptoms, signs and chest XR changes
how is pneumonia severity assessed?
using CURB65 - score out of 5
what is low CURB65?
it is a low risk of 0-1 out of 5 where there is no investigations required
what is a moderate to severe risk of pneumonia?
a CURB of 2-5 where there is sputum, blood cultures, atypical screen and might include serum
what is an atypical screen?
screening urine for legionella antigen and nose or throat for mycoplasma PCR
what does pulmonary TB require as a disease?
exposure and then reactivation at a later stage in life with pulmonary symptoms
what is the exposure testing in TB?
there is mantoux and IGRA - interferon gamma releasing assay which rely on an intact immune system
how would you investigate the pulmonary symptoms of TB?
microscopy and culture for 8 weeks, PCR - rapid, costly, lower sensitivity
what needs to be considered in the immunosupressed?
haemato-oncology - in chemo and solid organ transplants
steroids, diabetes, CKD and underlying disease
travel
what can cause infection in immunosupressed?
viral - RSV - viral PCR
fungal - aspergillus - aspergillus antigen and culture
pneumocystis - PCP PCR
what is needed to guide immunosupressed investigations?
history as they are not routinely done - best investigated by deep respiratory samples using BAL
what are some localised skin infections?
impetigo, erysipelas and cellulitis
what is an extensive severe infection of skin?
necrotising fasciitis
what are some methods of investigation for localised skin infections?
wound swabs, send blister or abscess fluid, needle aspirates in cellulitis, blood cultures
what are the issues with these investigation of localised skin infections?
wounds swabs are not helpful if the skin is intact
needle aspirates are poor as they only determine the pathogen in 10-30% of cases
blood cultures are only positive in the most sever 5% of infections - if sepsis then send off
what is necrotising fasciitis?
it is a rapidly spreading synergistic infections that is surgical emergency with high mortality
what comprises the management of NF?
debrided tissue and pus
what is debridement of tissue and pus?
it is the removal of dead or infected tissue and pus
what is MCS for pus?
microscopy culture and sensitivities
what blood cultures are done for BF?
2 sets
FBCs, U&Es, LFTs and CRP
what types of diabetic foot infection are there?
non-infected wounds or ulcers
mild infection
moderate or severe deep infection
what is the presentation of non infected diabetic foot ulcer?
exudate, smelly and weeping - not evidence of infection therefore no swabs
what is the management for mild foot infections?
wound swabs
these only have a 49% sensitivity and 62% specificity
what is the management for a deep foot infection?
debride wound then collect and clean
bone or tissue sample by a specialist
what types of UTIs are there?
lower or upper UTIs - cystitis or pyelonephritis
prostatitis
epididymo-orchitis
in lower or upper UTIs what does microbiology do?
supports the clinical diagnosis, identified the organism and the treatment
what makes a UTI probable?
if there is dysuria and frequency then >90%
what is identified in urine samples?
WBC, RBC, epithelial cells, bacterial growth and sensitivity
how would you interpret a urine sample for lower or upper UTIs?
Krass criteria - threshold for significant bacteriuria
what is automated analysis with respect to UTIs?
it is microscopy to predict a culture positivity
how is urine collected for UTIs?
MSU - midstream urine
CSU - catheter
Bag
SPA - suprapubic aspiration - usually in neonates if suspected UTI
what is the prevalence of prostatitis?
50% of patients with recurrent UTIs and 90% with febrile UTIs have prostatitis
what are the methods of investigation for prostatitis?
imaging, post prostatic massage, blood and urine tests
what is epididymo orchitis?
it is inflammation of the epididymis and/or testes due to infection such as UTI or STI or enteric bacteria
what is urine tests used for for EO?
cultures, chlamydia and gonorrhoea NAAT/PCR
what is NAAT?
nucleic acid amplification test
what is the management if EO is severe?
there is bloods, cultures and USS with potential drainage
what are the main GI infections?
diverticulitis, cholangitis or cholecystitis, liver abscesses, H pylori or infectious diarrhoea
what can cause infectious diarrhoea and give examples?
viral gastroenteritis - rota or norovirus
bacteria - salmonella - campylobacter, shigella, E coli and Vibrio
parasitic - giradia, goreign travel parasites and cryptosporidium
C difficile
how does the lab work with infectious diarrhoea?
uses clinical details and risk factors to help
what is the characteristic of most viral or bacterial infection?
it is self limiting diarrhoea
what is the management of infectious diarrhoea?
stool sample - public health, transmission and treatment purposes
what other investigations are there in infectious diarrhoea?
parasites will have 3 samples
bloods for FBC, clotting, U&Es, LFTs and CRP
cultures and abdominal imaging used plane film or CT
in H pylori infection what what tests are used, and what are their relative specificities and sensitivities to guide AB treatment?
antibody test - sens 92% and spec 83%
stool antigen sens 95% and spec 94%
urea breath test sens 88-95% and spec 95-100%
biopsy urease treatment sens 90-95% and spec of 95-100%
what is the issue with antibody test?
it is insensitive - it does not tell us if the infection is past or active
why use the stool antigen test?
non invasive, cheap and simple
why use the breath test?
gold standard for test of cure
however is patient experience dependent and expensive
what is the issue with the biopsy urease test?
it is invasive with cross reactions
what must be ensured before H pylori testing?
PPIs must be stopped
what is the aetiology of liver abscess?
pyogenic bacteria, hydatid or amoebic - history will guide this
what should happen with pus? - liver abscess related
drain - if safe to do so
what is OCP and how is it managed? - liver abscess related
it is ova, cysts and parasites and stool samples
what is used for bloods for liver abscess?
FBCs, U&Es, LFTs and CRP
what other investigations are done in liver abscess?
imaging including USS and CT and if appropriate hydatid serology
what are the bloods done for cholangitis or cholecystitis?
FBCs, LFTs, amylase, clotting, U&Es
what imaging is done for cholecystitis or cholangitis?
USS or CT
what can also be done in cholecystitis or cholangitis?
bile fluid or pus if aspirated or drained
what is diverticulitis?
inflammation of abnormal pouches of the LI
complicated or uncomplicated
what is complicated diverticulitis?
abscess, perforation, obstruction or fistula
what can be sampled in diverticulitis?
pus from the abscess, blood
what bloods are done in diverticulitis?
LFTs, FBCs, U&Es, clotting and amylase
what imaging can be done in diverticulitis?
CT
what types of vascular infections are there and what are some examples?
heart valves - endocarditis that it prosthetic or native
vessels - mycotic aneurysms, prosthetic vascular graft infections
what directs management of endocarditis?
blood cultures as there is 96% positivity
how are blood cultures done in suspected endocarditis?
three sets of cultures over first 24 hours with FBC, CRP, LFTs and U&Es
what other investigations are there for endocarditis?
echocardiography - transthoracic echo - sensitivity of less than 60% but spec of 98%
transoesophageal - sens and spec of over 94%
what is always done for suspected PVE?
transoesphageal echocardiography
what is done for specific organisms in endocarditis?
serology - coxiella, chlamydia, brucella and bartonella
valve tissue MCS and PCR if replaced
what blood cultures are done for suspected PVGI or mycotic aneurysm?
three sets over first 24 hours
lower culture positivity rate than endocarditis
what further investigations are there for PVGFi and mycotic aneurysm?
imaging such as WBC, PET and CT
looks at fluid around the graft and fistulae
what else can be done with fluid around a graft?
cultured and PCR
what is hepatitis A, B and C?
they are viruses
what is the identification of hep based on?
serology (and PCR)
what does serology comprise?
detection of antibody from the bodys immune response and antigen which is a component of the organism
what is the bodys immune repsonse?
acute IgM and chronic IgG
what does PCR detect?
the presence of DNA or RNA from an active or dead organism but generally indicates is active
what rises suddenly at the start of Hep A infection?
fecal HAV
what gradually increases over the infection of hep A?
IgG Anti-HAV
what increases and then drops over the course of hep a infection?
IgM anti-HAV
what are characteristics of the course of Hep A infection?
incubation period of 15-35 days
acute disease of 2-12 weeks
jaundice symptoms
convalescence and recovery of over 3 months
what is the course of a Hep B infection?
you are infected
the incubation period until are infectious is 2weeks-3months
this is when symptoms start as the antigen rises
IgM starts to be made - anti HBc which then drops back to nothing at 6-12 months
from around 3-6 months the IgG anti Hbc start to rise and stay high so you are immune for life / 20 years
what rises and then drops suddenly, with continuing fluctuations through a Hep C infections?
alanine transaminase
what rises and then plateaus in hep C infections?
total anti-HCV antibody
what types of syphilis are there?
early, latent and late and congenital
what is early and late?
early could be primary or secondary and late is tertiary - cardiovascular, gummatous and neuro
how is syphilis detected?
PCR superseded by microscopy and serology
what is involved in serology?
treponemal specific and non treponemal specific antibodies, screening test including IgM for primary infections, expressed as a dilution (ratio)
