Microbiology Flashcards
What are coliforms?
E.coli and similar organisms that inhabit the large bowel such as Klebsiella sp., Proteus sp., Enterobacter sp., Serratia sp. etc.
In what type of environment (aerobic, anaerobic, etc) does Pseudomonas sp. survive?
It is strictly aerobic
What does the normal mouth flora include?
Strep. viridans, Neisseria sp., anaerobes
Candida
Staphylococci
What is the normal flora of the stomach and duodenum?
It is usually sterile
A few candida sp. and staphylococci may survive
What is the normal flora of the jejunum?
Small numbers of coliforms and anaerobes
Describe the normal colon flora?
Large numbers of coliforms
Anaerobes
Enterococcus faecalis
Describe the normal flora of the bile ducts
Normally sterile
How are abdominal abscesses managed?
Small abscesses can be treated with antibiotics
Large collections need incision and drainage
What antibiotic is used to treat coliforms?
Gentamicin
What antibiotic is used to treat anaerobes?
Metronidazole
What antibiotic is used to treat enterococcus sp.?
Amoxicillin
What antibiotics are used to treat intra-abdominal sepsis?
AMet-a-Gent
Amoxicillin
Metronidazole
Gentamicin
What antibiotics are used for prophylaxis against intraabdominal sepsis (GI/hepatobiliary surgery)?
Metronidazole
Gentamicin
What aspects of the immune system are defective in neonates?
T lymphocytes
Natural killer cells
Which aspects of the immune system are defective in the elderly?
Complement
Macrophages
NK cells
What aspects of the immune system are defective in alcohols?
Cytokines
What pathogens does the complement target?
Bacteria
What pathogens does phagocytes target?
Bacteria
Fungi
What pathogens do T lymphocytes target?
Viruses
Fungi
Protozoa
What pathogens do B lymphocytes and antibodies target?
Viruses
Bacteria
What pathogens do eosinophils target?
Worms
Protozoa
Fungi
What pathogens do mast cells target?
Worms
What are the SIRS criteria?
A non-specific clinical response involving at least two of:
- Temperature >38 or 90 beats/min
- Respiratory rate >20/min
- White blood cell count >12,000/mm3 or 10% immature neutrophils
Apart from infection, what else can cause SIRS?
Trauma
Burns
Pancreatitis
What is sepsis?
SIRS with a presumed or confirmed infective process.
What is the definition of severe sepsis?
Sepsis with signs of at least one acute organ dysfunction: Renal Respiratory Hepatic Haematological (e.g. DIC) CNS Unexplained metabolic acidosis Cardiovascular (hypotension)
What is the definition of septic shock?
Severe sepsis with hypotension refractory to adequate volume resuscitation.
What are the main causes of community acquired bacteraemia?
E.coli (urine/abdomen)
S.pneumoniae (respiratory)
S.aureus (usually MSSA - skin)
What are the main causes of hospital acquried bacteraemia?
E.coli (catheter related or abdomen) S.aureus (usually MRSA - line or wound) Enterococci (urine, wound, line) Klebsiella (urine, wound) Pseudomonas spp.
Which drug is associated with concerns over nephrotoxicity, and must have its levels checked?
Gentamicin
What is the sepsis 6 bundle?
Give high flow oxygen
-Target sats 94-98 unless COPD (88-92) or severe sepsis
Start IV fluid resuscitation
-500mls saline STAT
Take blood cultures
- and other cultures e.g. urine, wound swabs
Give IV antibiotics
- In severe sepsis, mortality increase by 7.6% for each hour delay in giving antibiotics
Measure lactate and FBC
- Higher lactate may require higher level of care
Monitor accurate hourly urine output
-
Describe the normal vagina flora
Lactobacillus spp. predominate (produce lactic acid +/- hydrogen peroxide which suppresses growth of other bacteria) Other organisms which may be present: - strep viridans - Group B beta-haemolytic strep - candida spp. (small numbers)
What are the three non-sexually transmitted genital tract infections?
Candida infection
Bacterial vaginosis
Prostatitis
What proportion of females are colonised with small numbers of candida in their vagina and have no symptoms?
30%
List predisposing factors for development of candida infection
Recent antibiotic therapy
High oestrogen levels (pregnancy, certain types of contraceptives)
Poorly controlled diabetes
Immunocompromised patients
How is vaginal thrush diagnosed?
Clinical diagnosis (intensely itchy with white vaginal discharge) Can do high vaginal swab for culture - the majority of cases are candida albicans.
How is vaginal thrush treated?
Topical Clotrimazole (pessary or cream) Oral fluconazole
What is the appearance of candida balanitis?
Spotty
What microorgansims are involved in bacterial vaginosis?
Gardnerella vaginalis
Mobiluncus sp.
others, including anaerobes
What are the symptoms of bacterial vaginosis?
Thin, watery, fishy smelling discharge
How is bacterial vaginosis diagnosed?
Clinical diagnosis
Raised vaginal pH (pH >4.5)
Lab testing: high vaginal swab - examined for presence of CLUE cells
How is bacterial vaginosis treated?
Oral metronidazole
How is prostatitis classified?
Acute bacterial prostatitis
Chronic bacterial prostatitis
Chronic prostatitis/chronic pelvic pain syndrome
How does acute prostatitis present?
Symptoms ofUTI
May have lower abdo pain, back, perineal, penile pain and tender prostate on examination
What are the causative organisms of acute bacterial prostatitis?
Same as UTI (E.coli and other coliforms, enterococcus sp.)
Check for STI (chlamydia, gonorrhoea) in men
How is acute prostatitis diagnosed?
Clinical signs + MSSU for C&S
+/- first pass urine for chlamydia/gonorrhoea tests
What is the treatment for acute prosatitis?
Ciprofloxacin for 28 days
altered depending on culture result
Trimethoprim for 28 days if high C diff risk
What are the bacterial STIs?
Chlamydia trachomatis
Neisseria gonorrhoea
Treponema pallidum (syphilis)
What are the viral STIs?
HPV
Herpes simplex
Hepatitis and HIV
What are the parasitic STIs?
Trichomonas vaginalis
Pthirus pubis (pubic lice)
Scabies
What is the commonest bacterial STI in the UK?
Chlamydia
What areas does chlamydia infect?
urethra, rectum, throat, eyes, endocervix
Describe chlamydia trachomatis
An obligate intracellular bacteria with a biphasic life cycle
Does not reproduce outside a host cell
Does not stain with gram stain (no peptidoglycan in the cell wall)
What are the serological groups of chlamydia trachomatis and what infections do they cause?
Serovars A-C: trachoma (eye infection) - not an STI
Serovars D-K: Genital infection
Serovars L1-L3: Lymphogranuloma venerum
What is the treatment for uncomplicated chlamydia?
Azithromycin (1g oral dose stat) and doxycycline 100mg BD x 1 week
What areas does gonorrhoea infect?
Urethra, rectum, throat, eyes and endocervix
Describe neisseria gonorrhoea
Gram negative diplococcus
looks like 2 kidney beans facing each other
easily phagocytosed by polymorphs so often appear intracellularly on gram film
Does not survive well outside the body
How are chlamydia and gonorrhoea diagnosed?
Combined nucleic acid amplication tests (NAATs) or PCR - tests for both organisms in one test
Male patients: first pass urine sample
female patients: HVS or VVS or endocervical swab (if patient having speculum examination)
Rectal and throat swabs
Eye swabs (babies and adults)
Other tests for gonorrhoea:
microscopy of urethral/endocervical swabs - done in SRH clinic. 90+% specificity in males, less in females.
Culture on selective agar plates:
- done on endocervical, rectal and throat swabs but not high vaginal swabs (only done in SRH clinic)
What are the advantages of PCR/NAATs over culture?
Much less invasive specimens required
Much more sensitive than culture
Will be positive even if organisms died in transit
Test takes hours, not days
What are the disadvantages of PCR/NAATs?
Cannot test antibiotic sensitivities
Will detect dead organisms, so have to wait 5 weeks to do test of cure.
What is the treatment for gonorrhoea?
IM ceftriaxone plus oral azithromycin
What organism causes syphilis?
Treponema pallidum
How is syphilis diagnosed?
Dark ground microscopy of exudate from primary/secondary lesions to look for spirochaeates can be done (not done in Tayside).
Swab of primary or secondary lesions sent for PCR
Serology - tests for specific antibodies (confirms diagnosis, not representative of disease activity) and for non-specific antibodies (monitor disease activity and response to treatment).
What are the non-specific serological tests for syphilis?
VDRL
RPR
What are the specific serological tests for syphilis?
TPPA (T. pallidum particle agglutination assay)
TPHA (T. haemagglutination assay)
IgG and IgM ELISA - used as screening for syphilis
How is syphilis treated?
Injectable long-acting penicillin
What HPV types cause genital warts most commonly?
6 and 11
What HPV types are associated with an increased risk of cervical cancer?
16 and 18
How are genital warts treated?
cryotherapy
podophyllin toxin cream/lotion
Does HSV 1 and 2 contain RNA or DNA?
Double stranded DNA
How is HSV diagnosed?
Blister deroofed, swabbed and swab sent for PCR
How is genital herpes treated?
Aciclovir may be helpful if taken early enough
Pain relief
What is trichomonas vaginalis?
A single celled protozoal parasite transmitted by sexual contact
What are the symptoms of trichomonas vaginalis?
Vaginal discharge and irritation in females and urethritis in males
How is trichomonas vaginalis diagnosed?
High vaginal swab for microscopy
How is trichomonas vaginalis treated?
Oral metronidazole
How is pubic lice treated?
Malathion lotion
What percentage of women with chlamydia develop PID?
9%
What are the symptoms of chlamydia in females?
PCB/IMB
Lower abdominal pain
Dyspareunia
Muculopurulent cervicitis
What are the symptoms of chlamydia in males?
Urethral discharge
Dysuria
Urethritis
Epididymo-orchitis
How long after exposure do you test for chlamydia?
14 days
What is the incubation period of urethral infection of men with gonorrhoea
2-5 days
What are the symptoms of gonorrhoea?
Males: may be asymptomatic, urethral discharge >80%, dysuria
Pharyngeal/rectal infections mostly asymptomatic
Females: 50% asymptomatic, increased/altered vaginal discharge, dysuria, pelvic pain
What is second line treatment for gonorrhoea?
Cefixime 400mg oral (only if IM injection contraindicated or refused by patient)
How is syphilis transmitted?
Sexual contact
Transplacental/during birth
Blood transfusions
Non-sexual contact - healthcare workers
What are the stages of acquired syphilis?
Early infectious: Primary Secondary Early latent Late non-infectious: Late latent Tertiary
What is the incubation period of syphilis?
9-90 days (mean 21 days)
What is the lesion known as in primary syphilis?
Chancre
Appear at site of innoculation
Painless
What other signs (apart from a chancre) may be present in primary syphilis?
non-tender local lymphadenopathy
What is the incubation period of secondary syphilis?
6 weeks to 6 months
What are the features of secondary syphilis?
Skin (macular, follicular or pustular rash on palms and soles)
Lesions of mucous membranes
