Microbiology Flashcards
Name 3 examples of an URTI?
pharyngitis, sinusitis, and tonsillitis.
Which pulmonary structure is affected in pneumonia?
lung alveoli
Which scoring criteria is used to risk stratify pneumonia?
CURB-65
Examples of LRTI (5)
- Pneumonia
- Bronchitis
- Empyema
- Abscess
- Bronchiectasis
Which is the most common cause of CAP?
Streptococcus pneumoniae
Which gram positive ‘grape-like clusters” bacteria is a common cause of CAP?
o Staphylococcus aureus
List the common causative organisms for CAP (5)?
o Streptococcus pneumoniae (most common) – Gram-positive cocci, chains.
o Haemophilus influenzae
o Moraxella catarrhalis (Gram-negative cocci)
o Staphylococcus aureus (Gram +ve grape-like clusters)
o Klebsiella pneumoniae
Which is the number one most common causative organism for HAP?
o Enterobacteriaceae (most common) – E. coli and Klebsiella – 31%
Name the 2 most common Enterobacteriaceae?
E coli
Klebsiella
Name the common causative organisms of HAP?
o Enterobacteriaceae (most common) – E. coli and Klebsiella – 31%
o S. aureus – 19%
o Pseudomonas spp – 17%
o Acinetobacter baumanii – 4%
o Haemophilus – 5%
o Fungi (Candida spp) – 7%
Which are the most common organisms for pneumonia in neonates (0-1 month)?
E. coli
Group B streptococcus
Listeria monocytogenes
Which pathogen is the K1 antigen associated with?
E coli
Which organism is associated with the following description?
‘Beta-haemolysis on agar, Lancefield Group B, catalase-negative”
Group B streptococcus
Strep Agalactiae
Sputum colour for Streptococcus pneumoniae
Rusty coloured
Type of pneumonia associated with Streptococcus pneumoniae
Lobar
Microscopy findings for Streptococcus pneumoniae
+ve diplococci
Optochin sensitive, Alpha haemolysis on agar
* Draughtsmen colonies
* Urinary antigen positive.
Draughtsmen colonies are associated with which pathogen in pneumonia?
Streptococcus pneumoniae
Which pathogen is the most common cause of bronchpneumonia?
Haemophilus influenzae
Glossy colonies are associated with which organism in pnuemonia?
Haemophilus influenzae
Which type of bacteria is Moraxella catarrhalis?
Gram-negative diplococci
+ve cocci “grape-bunch clusters”
Pneumonia?
Staphylococcus aureus
Which organism is associated with a post-influenza pneumonia?
Staphylococcus aureus
Which pneumonia is associated with alcoholics?
Klebsiella pneumoniae
Define typical pneumonia?
Typical – Classic signs and symptoms, classic CXR changes (Consolidation) and penicillin-responsive.
Define atypical pneumonia?
- Atypical: No/atypical signs and symptoms, not in keeping with CXR and does not respond to penicillin antibiotics (absent cell wall).
- Exhibit extra-pulmonary features e.g., hepatitis, hyponatraemia, arthralgia – managed with macrolides.
Which class of antibiotics are used to manage atypical pneumonia?
Macrolides
Name 4 common atypical pneumonia organisms?
- Legionella
- Mycoplasma pneumoniae
- Coxiella Burnetti (Q fever) from exposure to farm animals.
- Chlamydia Psitacci from exposure to birds
Which pneumonia type is associated with desaturation upon walking around the room?
Pneumocystis Jirovecci (PCP)
Which CXR appearance is associated with Pneumocystis Jirovecci (PCP)?
Bat’s wing appearance on CXR
(Ground-glass shadowing)
What is the management of Pneumocystis Jirovecci (PCP)?
Co-trimoxazole
What is the presentation associated with Pneumocystis Jirovecci (PCP)?
Presentation:
* Dry cough
* Weight loss, malaise
* dyspnoea
- Desaturation upon exertion
Which stain is associated with Pneumocystis Jirovecci (PCP)?
Silver stain
Which type of organisms are more prone to infection following a splenectomy?
encapsulated organisms including Influenzas and S. pneumoniae.
Which organisms are associated with cystic fibrosis patients?
Pseudomonas aeruginosa (worse prognosis) – ceftazidine.
- Burkholderia cepacia.
Halo sign on CT is associated with what respiratory tract infection.
Aspergillus Fumigatus
What is the management for Invasive aspergillosis?
Amphotericin B
What is the diagnostic test for Legionella pneumophilia ?
Urinary antigen testing
What electrolyte abnormality is associated with Legionella pneumophilia ?
Hyponatraemia
What culture is used for Legionella pneumophilia ?
Charcoal Yeast
Which rash is associated with Mycoplasma pneumoniae ?
Erythema multiforme
Which ABx is used to manage Mycoplasma pneumoniae ?
Tetracycline or macrolide
Which investigation is used to diagnose Mycoplasma pneumoniae ?
cold agglutinin test
Which atypical pneumonia is associated with birds?
Chlamydia psittaci
What are the parameters of the CURB-65 score?
CURB-65 Score:
* Confusion
* Urea >7 mmol/L
* RR >30 breaths per minute
* BP <90 systolic or <60 diastolic
* Age 65+
Urea range for CURB-65?
> 7 mmol/L
RR range for CURB-65?
> 30 breaths per minute
BP (systolic and diastolic ranges) for CURB-65?
BP <90 systolic or <60 diastolic
CURB-65 cut off for admission
2
Management for CURB-65 score of 0-1?
Outpatient Abx
Amoxicillin PO 5 days
Management for CURB-65 score of 2? (which 2 ABx)
Amoxicillin PO + Clarithromycin PO
Note: Consider admission
Which ABx are prescribed for CURB-65 score of 3-5?
Co-amoxiclav IV + Clarithromycin IV
Admission and consider ITU
What is the first line ABx treatment for HAP?
Ciprofloxacin + vancomycin
What ABx are indicated for the management of aspiration pneumonia?
Tazocin + metronidazole
Classic presentation of empyema?
Spiking fevers despite ABx management (Due to wall encapsulation and inactivation of ABx due to acidotic pus).
What are the CHESS organisms?
Campylobacter jejuni, Enterohaemorrhagic E. coli, Entamoeba, non-typhoidal salmonella, shigella.
Which proteins are associated with clostridium botulinium?
SNARE proteins
What do SNARE proteins do in Botulinum?
Prevent ACh release
What is the characteristic presentation of C. Botulinum?
Descending paralysis
Which type of clostridium is associated with gas-gangrene?
Perfringens
Which 3 ABx are associated with precipitating C. difficile?
Cephalosporins, Ciprofloxacin (fluoroquinolones), Clindamycin
Which type of colitis is associated with C Difficile?
Pseudomembranous colitis
Which IL is released in response to staph aureus enterotoxins?
IL-1/2
Traveller’s diarrhoea affects which part of the GI tract?
Jejunum and Ileum
Which pathogen is associated with EHEC?
0157:H7 STEC
Which toxin is produced by O157:H7 E coli?
Shiga-like toxin
What are the manifestations associated with EHEC?
Microangiopathic anaemia
Thrombocytopenia
Acute renal failure
HUS
Dysentery
Which type of E.coli is associated with paedaitrics?
EPEC - Infantile (Paeds)
Rose spots are associated with what type of bacteria?
Salmonella Typhi (+paratyphi)
What is the clinical presentation of Salmonella Typhi?
Enteric fever: constipation, fever, rose spots, splenomegaly.
Where does Salmonella Typhi replicate?
Peyer’s Patches
What is the management for C. Botulinum?
Antitoxin
Which is the first line ABx for c. difficle?
vancomycin
Which ABx is prescribed for the management of Salmonella Typhi?
IV ceftriaxone then PO azithromycin
What are the three types of Shigella?
Flexneri (MSM)
Sonnei
Dysenteriae
Rice water stools are associated with what type of diarrhoea?
Vibrio Cholera
Which enterotoxins are associated with Vibrio Cholera?
Enterotoxin A and B
Which type of diarrhoea is associated with Shigella?
Bloody
Which type of diarrhoea is associated with Campylobacter Jejuni?
Bloody
What associated conditions are associated with Campylobacter Jejuni?
GBS
Reactive arthritis
Which ABX is prescribed for Campylobacter Jejuni?
Erythromycin or cipro for the first 5 days.
What are the common sources of Listeria Monocytogenes ?
Refrigerated food, unpasteurised dairy (monocyto-cheese!) – cold enhancement.
What is the common source for Yersinia Entero-colitica?
Undercooked pork
What are the symptoms of Yersinia Entero-colitica?
Fever, abdominal pain, diarrhoea (terminal ileitis)
What are the complications associated with Yersinia Entero-colitica?
Erythema nodosum and reactive arthritis
Flask-shaped ulcers on histology is associated with what protozoan infection?
Entamoeba Histolytica
On histology, what is the characteristic finding associated with Entamoeba Histolytica infection?
Flash-shaped ulcers
How many trophozoite nuclei is associated with Entamoeba Histolytica?
4
What is the presentation of Entamoeba Histolytica?
Dysentery
Flatulens
Tenesmus
Which ABx is indicated for the management of Entamoeba Histolytica?
Metronidazole
What is the hepatic complication associated with Entamoeba Histolytica?
Liver abscess
Pear-shaped trophozoites are associated with what protozoan infection?
Giardia Lamblia
Giardia Lamblia is associated with what characteristic finding ?
Pear-shaped trophozoites with 2 nuclei
What is the ABx of choice for Giardia Lamblia?
Metronidazole
What is the presentation of Giardia Lamblia?
Causes malabsorption of fat - foul-smelling non-bloody diarrhoea
Which stain is used to detect Cryptosporidium Parvum?
Kinyoun Acid Fast stain
What is present in the stool for a Cryptosporidium Parvum infection?
Oocytes
Which ABx of choice is used to manage Cryptosporidium Parvum?
Paromycin
Name 3 causes of viral diarrhoea?
Norovirus
Adenovirus
Rotavirus
What are the causes of complicated UTI?
- Complicated – Functionally/structurally abnormal tract, men, catheters, pregnant.
UTI of the bladder is termed what?
Cystitis
Why are women predisposed to developing UTIs?
Shorter urethra
Which is the most common causative organism for UTIs?
E coli
Which is the second most common cause of UTI?
Klebisella
Name a nitrite negative staphylococcus that is a a common cause of UTI in young women?
Staphylococcus saprophyticus
Which bacteria is urease-positive and is associated with struvite stones?
Proteus
What type of renal stones are produced as a result of urease activity?
Struvite stones
Which causative organisms is implicated in indwelling catheter-associated UTI?
Candida
Which 4 factors promote a UTI?
- pH< 5
- High urea levels
- Hyperosmolality
- Urinary proteins – Tamm–Horsfall glycoproteins, nitrites, and urea
Presentation of UTI?
- Dysuria
- Frequency
- Hesitancy, urgency
- Suprapubic pain or discomfort
- Bladder spasms
- Haematuria
- Foul-smelling cloudy urine
What are the features of a UTI in older/frail patients?
Mental status changes – unexplained lethargy, disorganised speech or altered perception, delirium + falls.
Features of UTI in <2 years old?
Fever, vomiting, not eating.
Features of Pyelonephritis
Systemically unwell, fever, rigours + loin pain
What 2 positive findings on a urine dipstick is consistent with a diagnosis of uti?
Nitrite
Leukocyte
Which urinanalysis parameter is specific for UTI?
Nitrites
What urine MC&S culture finding is diagnostic of UTI?
> 104 colony forming units
What are the ABx of choice for a lower UTI?
nitrofurantoin / trimethoprim / cephalexin
What is the Mx for · Pyelonephritis?
Admit, IV co-amox + gent
Which organisms are associated with SSIs?
S. aureus (MRSA + MSSA), E. coli, Pseudomonas
Clue cells are associated with which STI?
Bacterial vaginosis
Chancre is associated with which STI?
Syphillis
Gumma is associated with what?
Tertiary Syphillis (ulcerative deep subcutaneous nodule)
What is the pathogenic sign associated with TV?
Strawberry cervix
Klebsiella granulomatis is associated with what?
Donovan bodies
What type of bacteria of gonorrhoea?
Obligate intracellular gram-negative diplococcus
Which protein facilitates adhesion of gonococci to epithelial cells?
CR3
What are the uncomplicated manifestations of gonorrhoea in men?
Gonococcal urethritis
Post-gonococcal urethritis
Rectal proctitis - mainly in MSM
What is the uncomplicated manifestation of Gonococcal disease in women?
Mucopurulent cervicitis
What are the complicated manifestations of Gonococcal disease in men?
Epididymytiis
Prostatitis
What is the complicated manifestation of Gonococcal disease in women?
Pelvic inflammatory disease
What is Ophthalmia neonatorum?
Ophthalmia neonatorum (neonatal conjunctivitis) develops if left untreated when transmission to the child in the birth canal.
What is the complication of disseminated gonococcal infection?
Septic arthritis
Endocarditis
Sepsis
How is gonococcal disease confirmed?
1st line -Smears for NAAT
Which 1st ABx is indicated for the management of gonococcal disease?
Ciprofloxacin 500 mg oral – single dose (STAT)
If antimicrobial susceptibility is not known, what is the ABx of choice for gonococcal diseases?
Ceftriaxone 1 g IM
When should a test of cure be arranged for gonococcal disease following ABx management?
7 days
What type of pathogen is Chlamydia trachomatis ?
Obligate intracellular gram-negative pathogen
What is ascending chlamydia?
Pelvic inflammatory disease.
Which chlamydia serovars result in trachoma?
Serovars A-C
What are the clinical features of trachoma?
rachoma is a serious ocular illness that is endemic in Africa and Asia – Characterised by chronic conjunctivitis and can cause blindness.
What are the consequences of chlamydia serovars D-K?
Genital chlamydia, ophthalmalgia neonatorum
Lymphogranuloma venereum is caused by which pathogen?
Chlamydia trachomatis
Which chlamydia serovars are associated with Lymphogranuloma venereum ?
L1-L3
What is the first line of investigation for chlamydia?
Vulvovaginal/endocervical/Genital swab
Which cell type is observed on direct microscopy for chlamydia?
Neutrophils
What is the first line drug for the management of Chlamydia (dose and duration)?
Doxycycline 100 mg BD for 7 days
Which drug is indicated for the management of chlamydia for pregnancy and breastfeeding women (dose included)
Azithromycin 1 g single dose
What are the complications associated with Chlamydia infection?
- Pelvic inflammatory disease – leading to tubal factor infertility, ectopic pregnancy, and chronic pelvic pain.
- Epididymitis
- Reiter’s syndrome
- Adult conjunctivitis, ophthalmalgia neonatorum.
LGV is caused by which organism?
Chlamydia Trachomatis
What is the characteristic primary stage for Lympho-Granuloma Venereum ?
Painless genital ulcers or papules
What is the second stage of Lympho-Granuloma Venereum ?
Unilateral or bilateral tender inguinal/femoral lymphadenopathy (buboes) (2 weeks to 6 weeks).
- Lymphoproliferative reaction – binding occurs via heparin sulphate receptors.
- Anorectal Syndrome: Proctitis, proctocolitis-like symptoms – pain during urination, rectal bleeding, pain during passing stools, abdominal pain, anal pain, tenesmus.
- Rare complications: Hepatitis, Meningocepahlitis, pneumonitis.
What are the clinical manifestations of LGV?
Necrosis and rupture of the lymph nodes.
- Anogenital fibrosis and strictures.
- Anal fistulae – rectal symptoms (pain, tenesmus, bleeding).
- Genital elephantiasis.
Genital elephantiasis is associated with what STI?
Lympho-Granuloma Venereum
What is the management for LGV?
Doxycycline 100 mg BD for 21 days.
What is the causative organism for syphillis?
Treponema pallidum
What is the causative organism of Chandcroid?
Haemophilus ducreyi
Haemophilus ducreyi causes which disease?
Chancroid
Which STI is characterised by a ‘school of fish’ or ‘Railroad track’ apperance?
Chancroid
What is the clinical presentation of Chandcroid?
Painful ulcers (multiple)
erythematous papules at the site of inoculation
What type of agar is implicated for the diagnosis of chancroid?
Chocolate agar culture
Which ABx is used for the maangement of chancroid?
Azithromycin STAT dose 1 gm.
Which bacteria is implicated in pathogenesis of Dnovanosis/Granuloma inguinale?
Klebsiella granulomatis
On a Giemsa-stained smear which histological feature is characteristic of Donovanosis/Granuloma Inguinale?
Donovan bodies
What is the classic appearance of the painless papule or subcutaneous nodule in Donovanosis/Granuloma Inguinale?
Beefy red appearance
What are Donovan bodies are associated with Donovanosis?
Large mononuclear (pund) cells - gram-negative intracytoplasmic cysts
What is the management for Donovanosis?
Azithromycin 1 g followed by 500 mg daily
What causes Brucellosis?
Brucella species (Mediterranean fever)
How is brucellosis transmitted?
Unpasteurised milk, and dairy products, undercooked meat, skin penetration of those in contact with livestock (Animal to human transmission e.g., sheep, pigs, cattle and dogs).
How is Brucella transported throughout he body?
Brucella organisms are phagocytosed by circulating macrophages and PMNs – transported into the lymphatic system and replicated locally.
Spinal tenderness and cyclical fever following the consumption of unpastuerised milk is associated with which disease?
Brucellosis
What is the presentation of Brucellosis?
Presentation:
* Headache
* Cyclical fever (peaks in the evening)
* Migratory arthralgia
* Myalgia
* Asthenia
* Anorexia, fatigue, malaise, weakness
* Spinal tenderness – sacroiliitis, spondylodiscitis
* Septic arthritis
* Miscarriage
* Epidiymo-orchitis
FBC findings of Brucellosis
Neutropenia + Anaemia
What serologic testing is used for Brucellosis?
Standard agglutination testing, ELISA, and Rose Bengal testing.
What medium is used to grow Brucellosis?
Castaneda medium.
On radiography, what characteristic sign is observed in Brucellosis associated lumbar vertbrae?
Pedro pons signs
Which antibody is associated with brucellosis?
- Anti-O polysaccharide antibody
What ABx is indicated for the management of Brucellosis?
Doxycycline + streptomycin/rifampin/gentamicin for 4-6 weeks.
What are the complications associated with Brucellosis?
Endocarditis, meningoencephalitis, osteomyelitis.
How is Rabies transmitted?
Transmission – Through saliva via a bite by an infected mammal (e.g., bats, dogs).
What is the first stage of Rabies?
First few days – tingling sensation at the bite site.
What is stage 2 of rabies?
Stage 2:
Non-specific viral prodrome (flu-like illness): Fever, malaise, headache, sore throat – progress to anxiety, agitation, and frank delirium.
What is stage 3 of rabies?
- Encephalitic form (85%): Hydrophobia or aerophobia – spasms develop as a result of stimuli; autonomic dysfunction, increased deep tendon reflexes, nuchal rigidity and positive Babinski sign.
- Progresses to hyperactivity stage.
- Paralytic form (less common) – Weakness, altered mentation, ongoing fevers, and bladder dysfunction.
What is stage 4 of Rabies?
Stage 4:
Coma stage (within 10 days of stage 3) – hydrophobia, prolonged apnoea periods and flaccid paralysis.
* Cardiopulmonary failure.
What is the first line investigation for suspected Rabies?
IgM antibodies
On autopsy what characteristic feature is seen in patients with Rabies?
Negri bodies
(dense, ovoid, intracytoplasmic inclusions – observed within neurones of the CNS).
What post-exposure prophylaxis is available for Rabies?
Rabies IgG post-exposure (before symptoms) + full rabies vaccination course.
What is the causative organism of the plague?
Yersinia pestis
What is the primary vector for the plague?
Rattus rattus, and rattus novegicus
Which is the efficient vector for the plgue?
Xenopsylla cheopis
What are the two types of plague?
Bubonic
Pneumonic
What is the first line ABx for the plague?
Aminoglycosides
Which ABx is prescribed for plague meningitis?
Chloramphenicol
What type of bacteria causes leptospirosis?
Gram-negative spirochete bacterium Leptospira
How is leptospirosis transmitted?
Transmitted through exposure to the urine of infected animals (e.g., cattle, pigs, and horses).
contaminated soil and water – organism shed in the infected animal’s urine; swimming.
What is the Anicteris syndrome of Leptospirosis?
Anicteric syndrome – Self-limiting and non-specific flu-like illness – headache, cough, non-pruritic rash, fever, rigours, myalgia, anorexia, and diarrhoea
- Aseptic meningitis (immune stage, recurrence).
- Associated with uveitis.
- Conjunctival hyperaemia (Conjunctival erythema without purulent discharge).
Which zoonotic infection is associated with conjunctival hyperaemia and aseptic meningitis?
Leptospirosis
What causes Weils disease?
Leptospira
What zoonotic infection is characterised by the following presentation (hint: Rat urine)?
- Severe infection – fever, renal failure, jaundice (scleral icterus, and conjugated hyperbilirubinemia), haemorrhage, and respiratory distress’?
Weils disease
What is the Ix of choice for leptospirosis?
- Positive PCR of blood or urine
- Nuclei acid detection
- Positive serologic testing
- IgM and IgG antibodies against Leptospira organisms.
What antibiotic therapy is indicated for leptospirosis?
Amoxicillin, doxycycline, ampicillin or erythromycin.
What is the complication associated with leptospirosis during pregnancy?
Can cross the placenta Miscarriage in the first two trimesters (<24 weeks) or stillbirth/IUD.
What is the causative organism implicated in Anthrax?
gram-positive spore-forming rod (Bacillus anthracis);
How is Anthrax transmitted?
Under-cooked meat contaminated with spores - exposure to livestock
What are the three types of anthrax?
Inhalation
GI
Cutaneous
What dermatological presentation is characterised by Anthrax?
Non painful eschar
A non-painful Eschar is associated with which zoonotic infection?
Anthrax
What CXR findings are found on imaging for Anthrax?
Widened mediastinum, and hilar adenopathy
What is the ABx of choice for anthrax?
- Doxycycline or ciprofloxacin
What is the causative organism for Lyme disease?
Borrelia burgdorferi
What type of bacteria is Borrelia burgdorferi?
Spirochete
How is Lyme disease transmitted?
By tick-bite of the Ixodes genus
What is the first presenting sign of Lyme disease?
Erythema migrans rash - appears as a targetoid appearance
What are the neurological manifestations of Lyme disease?
Facial nerve palsy
Lymphocytic meningitis
Radiculopathy
What are the cardiovascular manifestations of Lyme disease?
Myopericarditis + heart block
What is the appearance of the rash in stage 1 of Lyme disese?
Bullseye rash
What is stage 2 of Lyme disease?
Stage 2 (3-12 weeks): General malaise, fever, neurological features (dizziness, headache), muscle pain and cardiac symptoms (chest pain, palpitations, and dyspnoea).
- Cranial neuropathy – diplopia, eye pain.
- Arthritis
- Bell Palsy (5%)
FACE pneumonic for Lyme disease presentation
FACE: facial nerve palsy, arthritis, carditis, erythema migrans.
What is the diagnostic investigation for confirming Lyme Disease?
Serum antibodies for B burgdorferi
What is the antibiotic of choice regarding the management of lyme disease?
Doxycycline for 10 days
What additional investigation is implicated to monitor complications of Lyme Disease?
ECG for heart block
What causes Q fever?
Coxiella Burnetti