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Microbiology Flashcards

1
Q

Which patients are you more concerned about with UTIs

A

Children and pregnant women

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2
Q

Why is a midstream sample used for UTIs

A

The urethra isn’t sterile so midstream washes out any colonising bacteria

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3
Q

What is a complicated urinary tract infection

A

UTI + functional or structural abnormalities in urinary tract - eg catheter and cauculi.
Men, pregnant women, children, patients in a healthcare setting

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4
Q

What is the most common causative agent of UTIs

A

Single bacteria species. E.coli as its got many virulence factors.

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5
Q

What are the 5 other causative agents of UTI and their associations
(Hint its not pseudomonas)

A

Proteus mirabilis - associated with patients who have kidney stones

Klebsiella aerogenes - resistance - often associated with catheter

Enterococcus faecalis - uncommon HAP and resistant

Staph saprophyticus - common in young women 2nd most common

Staph epidermis - Iatrogenic- catheter and surgery

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6
Q

What are the host defence against UTIs

A

Urine - pH, osmolality, urinary flow, urinary tract mucosa is bactericidal

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7
Q

What is the route of infection in UTI

A

Urethra colonise often the vagina first ( from the GI tract due to proximity), sex increases this risk due to introduction.
Introduction can be done by a catheter.
Hematogenous - staph aureus abscess in the kidney (from bacteremia or endocarditis) - not a true UTI

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8
Q

Causes of urinary outflow obstruction

A 
mechanical
Extrarenal
 - valves, stenosis, bands, calculi, extrinsic urethral compression (BPH)
Internal 
-nephrocalcinosis, uric acid, analgesic, PCKD, hypokalemia, renal lesions of SCD
neurogenic - 
poliomuselitis
(Neurosyphilis) tabes dorsalis
diabetic neuropathy
spinal cord injuries
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9
Q

What is vesicoureteric reflux?

A

Pooling of urine in the bladder after voiding. Can cause scarring of the kidneys`

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10
Q

What are the S&S of upper UTI?

A

fevers, rigours, flank pain, + all lower symptoms, frequency, pain- burning, small volume, turbid/ bloody tinge.

In elderly patients may be more atypical - abdo pain and change in mental state

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11
Q

What are the investigations for UTIs - low, upper, complicated.

A

Urine dip - leukcocytes (inflam) and nitrites (made by E.coli)
( not for diagnosis in >65s due to asymptomatic bacteria)
MSU - MC&S
Bloods - FBC, U&Es, CRP

Complicated

  • Renal USS
  • Intravenous urography
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12
Q

Dx for UTI

A

Paeds - any other infection

Young men and women - Upper UTI, STI, prostatitis

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13
Q

What are the signs of a contaminated MSU sample

A

Mixed growth, squamous epithelial cells (more likely from the urethra).
Sterile pyuria - consider STI eg chlamydia, previous treatment, bladder neoplasm or nonculturable organisms eg TB

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14
Q

General treatment of UTI

A

Short course 3 dose standard does for lower UTI in women.
Everyone else needs longer, 7 days.
Remove the catheter +/- replace

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15
Q

When would you image in pyelonephritis

A

Women after the second incidence

Men after the first more likely a structural cause

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16
Q

How do influenza pandemics arise?

A

An endemic avian influenza virus crosses over from an animal reservoir, most commonly ducks or birds

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17
Q

What are the issues associated with H5 and H7 flu?

A

H5 and H7 infect poultry and cause huge economic strain.
H5N1 multi basic cleavage allowing for cleavage anywhere in the body (no longer isolated to infect respiratory tract-> high fatality

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18
Q

What are the factors required of a virus for it to have pandemic capability?

A

Novel antigenicity
Ability to infect human airways
Efficient transmission

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19
Q

What causes antigenic changes?

A

When there is coinfection in a single cell by a human and avian virus.
RNA swapping, most commonly the capsid making the animal viruses able to infect humans

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20
Q

What 3 factors affect influenza transmission (cellular)

A

Neuraminidase stalk length - longer =^virulence to go through the mucous barrier
Virion stability- stability in air droplets conveyed by HA
Receptor binding- bind to salic acid on cells via alpha-2,3 in avian, humans is 2,6

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21
Q

Why did swine flu affect some people much worse than others?

A

Older people had experienced a similar type of flu before (1980 Spanish flu-> seasonal)
High respiratory dose
Mutant virus
Superimposed bacterial infection
Genetic predisposition - IFITM3
Co-morbid: Asthma, pregnancy, obesity, DM

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22
Q

What are the 3 classes of antiretrovirals for Influenza?

A 
Polymerase inhibitors
  -Favipiravir, baloxavir
Neuraminidase inhibitors - - - 
  -Tamiflu (oseltamavir oral), Relenza (zanamivir (inhaled or IV), permavir (IV)-not used UK)
Amantadine
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23
Q

What is the MOA and resistance pattern of Amantadine?

A drug for dyskinaesia in parkinsonism and influenza A

A

targets M2 ion channel

One AA change in M2 = resistance (not effective against Influenza B or H3N2)

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24
Q

What types are the flu vaccines?

A

Children - live attenuated nasal

Adult - Purified NA and HA proteins from inactive viruses + adjuvant

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25
What is the potential target for a universal influenza vaccine?
Neuraminidase stalk as its invariant (whereas the head is highly variable)
26
What are the different types of anti-virals?
``` Direct acting Viral protein targets - antiretrovirals -nucleotide/side Immune modulation -Interferons ```
27
What factors effect efficacy of anti-virals?
``` Host-immune response -difficult in immunocompromised pts Adherence Antiviral drug resistance Drug toxicity Drug interactions ```
28
What are the different herpes viruses
``` Alpha: HSV1 & 2 (Cold sores and genital) VZV (Chickenpox and Shingles) Beta: CMV (mononucleosis-like) HHV6 (6th disease exanthemsubitum) HHV7 Gamma- oncogenic EBV- infective mononucleosis and Burkitt's HHV8 - Kaposi's ```
29
What are the first line agents for HSV1,2 and VZV? | 2nd line, why second line?
``` (Val)Aciclovir Famciclovir 2nd line- Foscarnet or Cidofovir if resistant Ganciclovir used for co- infection with CMV as toxic ```
30
What is the MOA of aciclovir?
Guanosine analogue pro drug | Selectivity for HSV DNA pol 1>2>VZV
31
What is the treatment of HSV encephalitis | fever, confusion and new-onset seizures
Treat empirically (DO NOT WAIT) IV aciclovir 10mg/kg tds confirm and treat for 14-21 days
32
What are the indications for treatment of VZV?
``` Pregnancy neonates Treat if risk of pneumonitis Zoster in adults Immunocompromised ```
33
What are some complications of CMV (and typical histopathological appearance?)
``` Latency is in monocytes and dendritic cells so can cause : Pneumonittis Encephalitis Heptatitis Colitis Retinitis BM suppression (OWL's eye inclusions can be sign and highly specific for CMV in the infected tissue) ```
34
What are the antivirals for CMV?
``` 1st line Ganciclovir IV (Val is PO) +IVIG for pneumonitis 2nd Foscarnet (IV) 3rd Cidofovir (IV) Letermovir new and high risk BMT ```
35
What is the MOA of ganciclovir
Guanosine analogue strong selectivity for CMV DNA pol (+ HSV, VZV, EBV and HHV6 but not used)
36
Why is val/ganciclovir not used in bone marrow transplant?
Bone marrow toxicity -> BM suppression | also renal and hepatic toxicity
37
Foscarnet and Cidofovir have the same major SE what is it and how can it be mitigated?
Nephrotoxictiy Hydration (and U&Es monitoring) (+ probenicid for CIdofovir improves mobilisation)
38
What is the management of CMV in transplant patients?
Treat - Ganciclovir/(Val), reduce immunosuppression prophylaxis- GCV/vGCV (or ACV/vACV) - mainly for organ transplant pre-emptive- monitor weekly CMV PCR. start Tx when +ve (HSCT)
39
What is the MOA and use of letermovir?
CMV DNA terminase inhibitor specific to CMV | Nb - nil activity against other HSVs
40
What is the high-risk period after BMT?
<100 days
41
What is the use of palivizumab?
IM Monoclonal antibody against RSV - used for prophylaxis in high-risk infants (eg prem, severe heart or lung disease)
42
What are the classes of drugs used in the treatment of SAR Cov2?
Antivirals Remdesevir (broad-spectrum adenosine analogue IV), Molnupiravir (broadspectrum viral RNA mutagen), Palovid +ritonavir(PI) Neutralising monoclonal antibodies - sotrovimab Immunomodulators - Dexamethasone Tocilizumab and Sarilumab (IL-6 anta) ANAKINRA (il1 ANTAG)
43
What is the treatment of BK haemorrhagic cystitis? and BK nephropathy?
Bladder washout v Immuno suppressants Cidofovir (+probenicid) nephropathy v immunosuppression +IVIG
44
What are the criteria for CURB-65? | And score management
``` Confusion Urea >7mmol/L Respiratory rate>30 BP <90mmHg or <60mmHg >65 2> admit 2-5- sever consider ITU ```
45
What are the most common causative organisms of CAP?
Strep pneumonia, Haemophylis Influenza | (Staph A, Morazella catarrhalis
46
What is the microscopic appearance of Strep pneumonia?
Gram +ve (Purple) Cocci (alpha haemolytic and optochin sensitive) Looks green on plate
47
What does Hib look like on microscope
``` Gram negative (red), coci-bacilli. On agar - look like mucus so on chocolate plate ```
48
What are the most common causative organisms of CAP?
Strep pneumonia, Haemophylis Influenza | Staph A, Morazella catarrhalis, s aureus, Klebsiella Pneumoniae
49
``` What organisms are prevalent 0-1mnth 1-6mnth 6mnth-5y/o 16-30y/o ```
0-1mnth GBS, E.coli, listeria monocytogenes 1-6mnth Chlymydia Trochomatis , S.aureus RSV 6mnth-5y/o - Mycoplasma pneumoniae, influenza 16-30y/o - Strep p and mycoplasma pneumonae
50
Which organisms can cause respiratory cavitation? (3)
Staph. aureus Klebsiella pneumoniae TB
51
What are the RFs for hepatitis A?
Poor sanitation, endemic areas,
52
What are the causative agents for HAP? (7)
``` Enterobacteria: E.coli, Klebsiella pneumonia Staph a Pseudomonas Haemophilus influenza Acintobacter baumanni Fungal ```
53
What are the reason why someone may fail antibiotics (6)?
``` Poor adherence Empyema/ abscess Resistance organisms Poor absorption of ABX Immunosuppression Comorbidity : lung cancer, cryptogeni organism pneumonia ```
54
What are the investigations for m TB?
CXR- cavitating lesion (upper) | Stain with auramine or Ziehl-Neelson shows red Acid fast bacilli
55
What are the s&s of legionella?
Confusion, abdo pain, diarrhoea, lymphopenia, Hyponatraemia
56
What are the stages of Hep B infection?
``` Immune tolerant Immune reactive Inactive HBV carrier state HBe(envelope) negative = Chronic hep B HBsAg negative ```
57
``` What is the incubation period for hepatitis A B C D E? ```
``` A 2-6 weeks B 2-6 mnths C 2-8 weeks D 3-6 weeks E 2-8 weeks ```
58
Which viruses belong to the Flavivirdae family?
Hep C, yellow fever, dengue , western nile, zika
59
How does Hep C serology differ to Hep A and B?
In Hep C anti HCIgG is raised after ALT
60
Is confection or superinfection with Hep D worse?
Superinfection is significantly worse and those with chronic HBV should be monitored for HDV
61
What is the management of chronic Hep B
Anti-virals Inf A Tenofovir, Entecavir, Emtricitabine and Lamivudine Liver failure: Liver transplant+ immunosuppression (do not use interferons)
62
What are the different types of drugs used in the management of Hep C
Protease inhibitors NS5A inhibitors NS5B inhibitors
63
Is confection or superinfection with Hep D worse?
Confection can cause a nasty acute hepatitis Superinfection has a significantly worse associated risk of cirrhosis and those with chronic HBV should be monitored for HDV (as antivirals for HBV are not effective against HDV)
64
What is the PC of HAV?
Fever, Malaise, anorexia, nausea, abdominal discomfort, diarrhoea, jaundice, 99% resolution
65
What is the pre and post exposure prophylaxis for HAV?
Pre- Vaccination of at risk people | Post- exposure - HAV vaccine +/- HNIG for at risk
66
What is the pre and post-exposure prophylaxis for HAV?
Pre- Vaccination of at-risk people | Post-exposure - HAV vaccine +/- HNIG for at risk
67
What type of Virus is Hepatitis | ABCDE?
A- quasi enveloped SS positive sense RNA B- dsDNA with reverse transcriptase, enveloped virion C- SS positive sense RNA E - SS positive sense RNA
68
What are the pre and post-exposure prophylaxis for HBV?
Pre- routine vaccination in children 2017, at risk population Post- Neonates (HBV+ mother) Sexual partner - HBV vaccine +/- HBIG (<7 days from contact) Needlestick
69
Why doesn't penicillin work against atypical pneumonias? | What would you use instead?
Penicillin affects the cell wall and atypical agents do not have cell walls Use agents that interfere with protein synthesis Macrolide or Tetracyclines
70
What are the exam buzz word RF for coxiella burnetti and Chlamydia psittaci?
Coxiella burnetti - domesticated farms (aerosol / milk) - give macrolides Chlamydia psittaci - birds - inhalations (macrolides)
71
What is the investigation finding and management for pneumocystis jirovecii?
Investigate with BAL, vSat on exertion, CXR - BAT wing shadow Co-trimoxazole (same for prophylaxis)
72
What diseases are associated with aspergillus
Aspergilloma (often preexisting cavity eg TB) Allergic bronchopulmonary aspergillosis Invasive aspergillosis (immuno comp and needs amphotericin B)
73
``` What LRTI infection are associated with HIV Neutropenia BMT splenectomy? ```
HIV - PCP, TB, atypicals Neutropenia - aspergillus BMT - CMV Splenectomy - encapsulated viruses eg S. pneumoniae, H. Influenzae, malaria
74
What are the investigations of LRTI?
Sputum culture (can be induced) BAL Pleural fluid CXR FBC, U&Es Antigens - urine Legionalla and S. pneumoniae (severe CAP) Antibody tests - needs paired acutely unwell and getting better - Chlamydia and legionella as difficult to culture Immunoflurescence - PCP (+silver stain in cytology) PCR
75
What is the empirical treatment for CAP? And allergy
Mild - Amoxicillin or Erythromycin/ Clarithromycin Moderate/ severe - Co-amox and clarithomycin Allergy cefuroxime + Clari
76
What is the empirical treatment for HAP?
1st - Cipro +/- Vancomycin 2nd (/ITU)- Piptazobactam + Vancomycin If MRSA - Vancomycin Pseudomonas - piptazobactam or ciprofloxacin +/- gentamicin
77
What is the MOA of Foscarnet
Non competitive inhibitor of vDNA pol - no phosphorylation
78
What is the MOA of cidofovir
Nucleoside (cytidine) analogue (not a prodrug)
79
How do you diagnose PTLD and treat?
Post-transplant lymphoproliferative disease >10^5 c/ml viral load reduce immunosuppression Rituximab (anti CD20)
80
What antiviral drugs are used for COVID
Resmdesevir (broad spectrum adenosine nucleotide analogue pro drug) Molnupiravir - vRNA mutagen Paxlovid PI (so + ritonavir)
81
What immune moduation is used for COVID
Dexamethasone Tocilizumab (anti IL-6) Sarilumab (anti IL-6 Anakarin (anti IL-1)
82
What neutralising monoclonal antibodies are used for COVID
Ronapreve Sotrovimab (targets S protein to prevent entering cell via ACE2)
83
What and when would you treat adenovirus?
paeds, transplant or sever multi-organ involvement cidofovir + IVIG
84
How does most ACV resistance occur in HSV?
Viral thymidine kinase mutations (>95%) | DNA pol is rare
85
How does most CMV drug resistance occur?
Protein kinase gene (DNA pol is rare)
86
What are the mechanisms of antiobitic resistance?
Altered target Decreased concentration - ^efflux or v uptake Abx destruction/ neutralisation
87
What is the order of narrow to broad spectrum of penicillins?
``` penicillin amoxicillin co-amoxicillin pipperacillin tozoacin ```
88
Why is co-amox not helpful in MRSA?
MRSA is not due to beta-lactamases, it is a change in the penicillin binding protein so Clauvonic acid as an beta-lactamase inhibitor doesn't help
89
What is the difference between the different generation cephalosporins? (name examples)
Increasing G- coverage 1st gen- cephalexin 2nd gen- Cefruoxime 3rd gen- cefutaxime, ceftriaxone, ceftazidime
90
What is the use of glycopetides - give examples?
Vancomycin Teicoplanin Oral for c.diff IV for MRSA
91
Which antibiotics are affective against pseudomonas (5 groups)
``` Aminoglycosides - gentomycin, amikacin, atreptomycin Colistin Fluroquinolones (not moxifloxacin) - Pipperacillin 3rd gen cephlosporins - ceftazidime ```
92
Which antibiotic is helpful in necrotising fascitis and why?
Clindamycin as it is bacteriostatic and prevents toxin production which is the main pathological factor
93
Why is Linozolid only used if recommended by micro or ID? | What is an alternative abx
thrombocytopenia and optic neuritis and very expensive - is effective against MRSA and VRE Daptomycin
94
What antibiotic has the side effect of orange urine?
Rifampicin - must check LFTs and watch out for DDIs
95
Why is nitrofurantoin used in UTIs
Urinary excretion means it builds up in the bladder
96
What is co-trimoxazole and why is it useful?
Sulphonylurea + dihydropyridine (Sulfamethoxazole + trimethoprim) Both are anti-folate but act of sequential parts of the metabolism so have a synergistic effect
97
What is the management of c.diff
stop abx most likely Ceftriaxone (cephalosporines) | Start PO vancomycin or metronidazole
98
What are the different patterns of antibiotic dosing action - give examples
T1 - peak (max dose dependent - aminoglycosides, daptomycin, fluroquinolones - T2- time dependent - penicillins, carbepenems, cephalosporins , erythomycin, linezolid T3- AUC (combo of both) Glycopeptides - vancomycin, tetracycline, clindamycin, oxazolidones, azithromycin
99
What are the common reasons for misuse of antibiotics
``` No infection Wrong drug Wrong treatment length Not needed - would self resolve Wrong pharmacokinetics for the infection ```
100
What should you take into account before starting antibiotics?
Take cultures before empiracle treatment. Start broad> culture and sensitivity > narrow spectrum (bacteriocidal) CHAOS Host - pregnancy, neonates, immunosuppression, Antimicrobialy susceptibility Organism Site of infection Pharmacokinetics - if septic pure GI perfusion, ^GI transit, cannot tolerate oral intake - think IV. Necrotic tissue - topical will not work without debrinement
101
What antibiotic treatment should be given for a. simple UTI b. HAP uti c. strep A d. CAP e. Meningitis - adults and children
a. 3 days trimethoprim or nitrofurintoin b. cefatriaxone +/- gentamicin if catheter c. 10 days to prevent Rheumatic fever and glomerulonephritis d. mild - amoxicillin or clindamycin moderate to severe co-amox + clindamycin e. cefrtiaxone or high dose benpen, neonates <3months cefuroxime
102
What are the side effects of antibiotics
Gi upset Rash Anaphylaxsis
103
Give examples of DNA viruses
``` HSV EBV VZV CMV HBV HHV8 Pox virus (eg Molluscum contangiosum, HPV) ``` Uneveloped JCV and BK, adeno, parvovirus B19
104
Give examples of RNA viruses | Positive and negative sense
Positive sense Rubella, Zika, HAV (une), HCV (enveloped), HEV Negative sense Influenza, HDV, morbillivirus (measles)
105
What are the prophylaxis and treatment of PCP
Co-trimoxazole
106
What is the causative agent of meningenitis specific to HIV
Cryptocoides
107
What is the causative agent of a. cat scratch fever b. hookworm c. tape worm d. Chagas disease e. sleeping sickness f. Schistomiasis - bladder and liver
a. Typhi gondii b. nematodes c. Tapes solnium d. amoeba bordella e. amoeba 2 f. Schitoma
108
What is the treatment for schistomiasis?
Steroids and anti protazonas
109
Define pyrexia of unknown origin
Pyrexia >3 weeks without diagnosis despite intensive investigation Hospital >3 days in hospital Neutropenic - PUO + v neutrophils
110
What should be considered in PUO
``` Normal infections HAP - lines, surgery, c.diff, VRE, MRSA STIs HIV seroconversion Vasculitides - cANCA, pANCA MAlignancy Rheumatoid ```
111
What causes neutropenic PUO
Chemo therapy | Clozapine, Clopramide
112
Describe the PC of a. Typhoid b. Dengue c. falciparum d. non-falciparum malaria
a. enteric fever - rose spots, constipation 1-2 weeks, incubation, hepatosplenomegaly (G-ve bacili) b. mild pyrexia, myalgia onset days self limiting (reinfection = dengue hemorrhagic fever) c. 48hr recurrent fever, myalgia, anaemia hepatosplenomegaly. d. Same but milder (except malariae which is 72hrs)
113
What is the treatment for a. Typhoid b. Dengue c. falciparum d. non-falciparum malaria
a. Typhoid - IV ceftriaxone > PO azithromycin b. Dengue - supportive c. falciparum - Mild artemesin (artemether +lumefantrine) Severe - IV artesunate d. non-falciparum malaria Chloquine + primaquine
114
What are the causative agents fro a. tinea (ringworm and athlete's foot) b. Pitariasis (sebhorreic dermatitis and vesiculor) c. systemic fungal infections (3)
a. Tricophyton rubrum b. Malassezia globosa/ FurFur c. Candida, Cryptocoides, Aspergillus
115
What is the treatment for | a. cryptococcosis encephalitis
IV amphotericin B +/- flucytosine

Pathology (6 decks)

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