Microbiology Flashcards

(145 cards)

1
Q

Meningitis

A

Acute - key = Neisseria meningitidis, Strep pneumonia Hemophilia influenzae. Others - listeria, group B strep, ecoli

chronic - CT here will show changes (thickening of dura)

aseptic - enterovirus - cocksackie group B, echovirus

Mortality - 10%
Morbidity - 5, deafness most common

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2
Q

Encephalitis

A

Rabies virus, arbovirus eg West Nile
Amoeba - Naegleria fowleri
Bacteria - listeria
Trypansoma species
Prions
Toxoplasmosis

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3
Q

Brain abscess

A

Otitis media, mastoiditis etc
Staph etc

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4
Q

Spinal

A

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5
Q

CSF studies, how to Interpret results

A

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6
Q

Listeria meningitis management?

A

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7
Q

Viral hepatitis A B C D E

A

Jaundice dark urine , pale stools, pruritus

Check what antibodies/ surface markers mean

HbsAg = surface antigen most important. Positive means current infection
HbcIgM = recent infection
AntiHbc = exposure to HbV, could be past or present
AntiHbs = surface antibody = immunity due to vaccination or cleared infection

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8
Q

Which immunoglobulin class shows recent infection?

A

IgM

IgG = past/ chronic

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9
Q

Insert table interpreting hep B findings

A

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10
Q

Hep B medications

A

Nucleoside/tide analogues
Entecavir, tenofovir

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11
Q

If treatment history is unknown , what assay will help establish previous patients HBV status

A

HBV DNA viral load

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12
Q

Why are genotypes 1 and 2 of hep B important?

A

30% mortality in pregnant women

Chronic infection of hep e only happens in immunocompromised

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13
Q

Hep D requires infection with hep what to enter?

A

Hep B

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14
Q

Diagnosing pyrexia of unknown origin (PUO)]

History taking?




examination





investigation

A

definition = Fever >38.3 lasting for at least 3 weeks

1. B symptoms, localising symptoms
2. Medications - doses and initiation date
3. Contact history, pets/animal exposures
4. injecting drug use, sexual history
5. foreign travel


physical including fundoscopy (e.g roth spot endocarditis), look at spine

PET scan, Echo, brucella serology e.g patient from lebanon, HIV test for all patients, must test malaria if travel in last 2 days

if BP is 75/50 -> start Antibiotics immediately!!!!, this is sepsis and not PUO.

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15
Q

Infective causes of PUO

A

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16
Q

Inflammatory causes of PUO

A

SLE
rheumatoid arthritis
sjogrens syndromes
vasculitis syndromes

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17
Q

Malignant causes of PUO

A

lymphoma - especially non-hodgkins
leukaemia
renal cell carcinoma

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18
Q

Miscellaneous causes of PUO

A

endocrine - thyroiditis, addisons disease

TFTs screening

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19
Q

4 urgent causes of PUO

A

1. infective endocarditis
2. disseminated TB
3. central nervous system TB
4. Giant cell/ temporal arteritis

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20
Q

specific zoonoses

A

- farm/wild animals - UK or tropical
- companion animals - UK or tropical

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21
Q

managing patients with zoonoses

A

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22
Q

classic zoonoses

A

- campylobacter - chicken - diarrhoea - stool pcr for diagnosis - self resolving

- salmonella - chicken

- bartonella henslae - cats- bacilliary angiomatosis if immunosuppressed

- cats - toxoplasmosis

- brucellosis - unpasteurised milk from cattle/goat - fever, back pain, night sweats/weight loss - can present like TB. psoas abscess. psoas pus culture important


- coxiella burnetii - goat and sheep feces/milk, is aerosolised. learn presentation

- rabies - dogs, bats, cats

- rat bite fever -athralgia, fever

- hantavirus - rodents/rates - pulmonary-renal syndrome

- viral hemorrhagic fever - ebola, marburg, lassa, CCHF

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23
Q

opportunistic viral infections

A

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24
Q

51 year old with recent HSCT is unwell with ALT=800, what is the important test to do?

A

serology tests e.g EBV, hepB are not useful in immunosuppressed.

HEV PCR is useful

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25
which type of immunosuppression carries the greatest relative risk of developing a viral infection?
allogenic stem cell transplant
26
EBV
in tansplant patients, you worry about lymphoma (post-transplant lymphoproliferative disease) Rituximab treatment
27
CMV
HIV/AIDS - retinitis - polyradiculopathy - pneumonitis - GI tract inclusion bodies seen Ganciclovir
28
JC virus
polyomavirus progressive multifocal leukoencephalopathy - personality change, motor deficit, cognitive dysfunction - demyleination of white matter -> MRI
29
BK virus
polyomavirus cystits post SCT Nephropathy post renal transplant
30
Hepatitis B
tenofovir
31
Herpes simples 1,2
immunoglobulins given to bone marrow transplant patients
32
varicella zoster
chicken pox -purpura fulminans, hepatitis, encephalitis, pneumonitis shingles - reactivation
33
SOT vs HSCT CMV
SOT CMV concern = positive donor and negative recipient. give prophylaxis ganciclovir (can cause bone marrow suppression) HSCT CMV concern = positive recipient and negative donor
34
Influenza A and B treatment in immunosuppresed
oseltamivir
35
the natural reservoir of influenza A virus is?
Ducks
36
influenza
hemaglutinn neuraminidase PB2E627K virus antigenic shift - alone is not sufficient to cause a pandemic. you need antigenic shift + hemaglutinn adaptation (to allow transmission) influenza entry to human is also pH dependent influenza drugs are used separately and not together - neuraminidase inhibitors
37
The influenza vaccine given to those at greater risk of complications from flu in the UK is
inactivated virus the live attenuated is given instead to children, not adults *children are the key flu spreaders hemaglutinnin has been the molecule used for vaccines
38
most likely origin of SARS COV2?
bats
39
Treatment for Covid
dexamethasone monoclonal antibodies - Sotrovimab, remdesivir etcmRNA vaccines encoding stabilized spike - omicron variant less well controlled by this
40
antibiotics that inhibit cell wall syntheisis
beta lactam antibiotics eg penicillins, cephalosporins, carbapenems(carbapenems stable to ESBL enymes) - ineffective against bacteria that lack peptidoglycan cell walls eg mycoplasma, chlamydia. only kill bacteria actively dividing - may be ineffective against abscess, biofilm glycopeptides - vancomycin, teicoplanin - used for MRSA infections
41
antibiotics that inhibit protein synthesis
Aminoglycosides (e.g. gentamicin, amikacin,tobramycin) Tetracyclines Macrolides (e.g. erythromycin) / Lincosamides (clindamycin) / Streptogramins (Synercid) – The MSL group Chloramphenicol Oxazolidinones (e.g. Linezolid)
42
finish antimicrobials notes
-------
43
bacteria that cause TB
m tuberculosis m bovis m africanum m microti m caneti (m avium complex does not cause TB) not all AFB is TB!
44
what percentage of world population has latent TB? post latent infection, what is lifetime risk for active TB?
1/4 to 1/3 10%
45
HSV in pregnancy and neonates
neonates - SEM -> SEM + CNS -> disseminated
46
Maternal varicella and congenital VZV
treat maternal infection with oral acyclovir
47
entervoviruses in pregnancy and neonates most commonly cocksackie
rash, hand foot and mouth disease, encephalitis, myocarditis neonates are at higher risk of myocarditis, encephalitis, meningitis
48
Rubella in pregnancy, congenital, neonates
rash that spreads from head down to trunk congenital rubella: cataracts, hearing loss, hepatospleenomegaly
49
Measles in pregnancy
conjuctivitis, rash from head to trunk, koplik spots SSPE risk in neonates
50
Parvovirus B19
slapped cheek, polyarthropathy, aplastic crisis fetal hydrops
51
CMV
maculopapular rash, infectious mono congenital - microcephaly, retinitis, IUGR,
52
zika virus
send a serum and save and alert obstetric team if 4 week pregnant with recent travel to antigua and worried about zika if NO symptoms. -> if symptoms do serum and urine sample
53
Hep B, HIV in pregnancy
54
pregnant woman presents with a rash, what do you do?
gestation date of onset, clinical features past history of infection/antibody testing past immunisation testing tests: antibody blood samples pcr
55
HIV in children describe certain presentations how to prevent
molluscum contagiosum tb of spine rashes HIV encephalopathy - basal ganglia calcification, cortex atrophy CMV - retinitis - blindness First born twin is more at risk than second twin -> sits in birth canal and dilates it 16% excess risk of HIV with breastfeeding in Nairobi study - balance against increased rissk from formula feeding only in certain places in world triple therapy for pregnant women, infant should get prophylaxis for 6 weeks, uninfected infants should be exclusively BF for 6 months
56
what is prion disease? what gene is prion protein found on? what polymophism predisposes to disease? presentation?
an infectious protein chromosme 20 - condon 129 MM polymorphism predisposes to disease (3 polymoprhisms MM, MV, VV) Rapid neurodegeneration (cjd maximum survival 6 months), spongiform enceophalopathies paresethesia unseteadiness jerky tremor
57
state the different types of prion disease
1. Sporadic - CJD - 80% 2. Acquired <5% - Kuru - papua new guinea, cannibalisms. ataxia & myocolonus. dementia late or absent - Variant CJD - mad cow disease - Iatrogenic CJD - GH, blood, surgery 3. Genetic 15% - PRNP mutations eg Gerstmann-Straussler-Sheinker Syndrome, Familial fatal insomnia
58
what is the most common form of prion disease? symptoms? median survival and mean age of onset cause? diagnosis? neuropathology?
Sporadic CJD rapid dementia with: - myoclonus!! - cortical blindness - problem with occipital cortex, optic nerve normal - akinetic mutism - LMN signs <6 months, 65 years cause is unclear - may be environmental exposure, PRNP mutation etc EEG: periodic triphasic complexes - non specific, not always present MRI: - increased signal in basal ganglia, cortex CSF: - elevated markers of rapid neurodegeneration; 14-3-3 protein, S100 neurogenetics to rule out mutation tonsillar biopsy NOT useful - only useful in variant CJD spongiform vacuolation, Prp amyloid plaques - Alzheimers - vascular dementia - CNS neoplasm - Cerebral vasculitis - Paraneoplastic syndrome
59
Variant CJD symptoms? median survival and mean age of onset cause? diagnosis? neuropathology?
psychiatric onset: - dysphoria, anxiety, paranoia, hallucinations then neurological: - peripheral abnormal sensations -ataxia - myoclonus - dementia 14 months, 26 years median onset linked to mad cow disease, few cases linked to blood transfusion MRI: - positive pulvinar sign = high signal in posterior thalamus/putamen EEG: - non specifc slow waves CSF markers not raised Neurogenetics: - almost everyone is MM at codon 129 Tonsil biopsy = 100% sensitive and specific florid plaques in brain
60
Iatrogenic CJD causes? symptoms?
1. human cadaveric growth hormone 2. corneal transplants 3. neurosurgical procedures 4. blood and blood products transfusions progressive ataxia initially dementia and myoclonus later stages speed of progression depends on route of inocculation
61
Genetic prion disease questions to ask? symptoms diagnosis
GSS, FFI, CJD FH is important: - dementia, MS, ataxia, psychiatric GSS: - slow progressive ataxia and dementia - survival 2-10 years FFI: - untreatable insomnia, ataxia, dysautonmia (BP surges) neurogenetics
62
CJD treatment?
1. myoclonus = clonazepam research into antiprion antibodies, depleting prion protein
63
secretory diarrhea presentation? organisms?
- no or low fever - no wbc in stool - cholera, ETEC, EPEC, EHEC, EAggEC
64
inflammatory diarrhea presentation? organisms?
- fever - wbc in stool - neutrophils - campylobacter, shigella, non typhoidal salmonella, EIEC
65
Enteric fever diarrhea presentation? organisms?
- fever - wbc in stool - mononuclear cells - typhoidal salmonella, enteropathogenic yersinia, brucella
66
s. aureus food poisoning
prominent vomiting and watery non-bloody diarrhea self limiting skin cells shedding into food
67
b cereus food poisoning
gram positive-rod spores reheating rice water non blooding diarrhea can cause bacteremia
68
clostridium botulinum/ botulism cause? symptoms treatment
canned or vaccumed packed foods/honey blockage of ACh receptors -> paralysis antitoxin
69
clostridium perfringens food poisoning
reheated food -> meat superantigen watery diarhea, cramps, vomiting anaerobic infection!!!
70
c difficile
diarrhea hospitalisation and antibiotics = risk anaerobic infection!!!
71
listeria monocytogenes symptoms? sources? treatment?
febrile gastroenteritis b hemolytic bacteria with tumbling motility unpasteurised dairy, refrigerated food ampicillin
72
ecoli diarrhea source
etec = travellers EHEC = hemorrhagic food/water contaminated with faeces
73
salmonella enteritidis presentation?
non bloody diarrhea, self limiting poultry, eggs, meat bacteremia and fever infrequent
74
salmonella typhi presentation?
typhoid fever bacteremia slow onset FEVER and CONSTIPATION spleenomgaly, rose spots anemia, leucopenia positive blood cultures ceftriaxone treatment
75
Shigella presentation?
dysentery avoid antibiotics
76
vibrio cholera presentation and treatment vibrio parahemolytics cause and treament vibrio vulnificus presentation?
rice water stool treat loss, electolyte and fluid replacement raw or undercooked seafood, self limiting cellulitis in shellfish handlers, risk of septicemia
77
campylobacter source? presentations?
poultry, meat, unpasteurised milk diarrhea -> GBS syndrome
78
Yersinia enterocolitica presentation?
enterocolitis, mesenteric adenitis food contaminated with waste from domestic animals
79
abdominal symptoms +/- diarrhea -> always think could this be mycobacterium eg TB
80
entamoeba presentation?
dysentery, tenesmus, flatulence, liver abscess metronidazole + paramomycin for luminal disease
81
Giardia presentation?
2 nuclei and flagella malabsorption of protein and flat stool microscopy - ova cysts and parasites metronidazole
82
cryptospordium parvum
severe diarrhoea in immunocompromised oocytes in stool no treatment
83
Viruses that cause diarrhea?
norovirus - CAN CAUSE OUTBREAKS!! - big concern rotavirus - Exposure can cause immunity adenovirus (polio, enteroviruses, hep A )
84
all forms of gasteroenteritis are notifiable
85
congenital toxoplamosis presentation
classic triad: 1. intracranial calcifications 2. hydrocephalus 3. chorioretinitis +/- blueberry muffin rash 60% asymtomatic at birth but can develop -> deafness, low iq, microcephaly *contrast to CMV which causes hearing loss and chorioretinitis but PERIVENTRICULAR calcifications and no hydrocephalus
86
congenital rubella presentation
Eyes: cataracts!!!; microphthalmia; glaucoma; retinopathy Ears: deafness Heart : PDA!!!; ASD/VSD ("Ruby red heart") +/- blueberry muffin rash
87
name common organisms that cause neonatal infection
1. group b strep - meningitis, bacteremia, joint infection 2. E coli - bacteremia, meningitis, UTI 3. listeria monocytogenes
88
maternal sepsis risk factors
PROM/prem. Labour Fever Foetal distress Meconium staining Previous history
89
neonatal sepsis rfs
Birth asphyxia Resp. distress Low BP Acidosis Hypoglycaemia Neutropenia Rash Hepatosplenomegaly Jaundice
90
neonatal sepsis investigations?
Full blood count C-reactive protein (CRP) Blood culture Deep ear swab Lumbar puncture (CSF) Surface swabs Chest X-ray (full body)
91
neonatal sepsis treatment
Ventilation Circulation Nutrition Antibiotics: e.g. benzylpenicillin & gentamicin
92
what is late onset sepsis? features? investigations? treatment
after 48 -72 hours Bradycardia Apnoea Poor feeding/bilious aspirates/ abdominal distension Irritability Convulsions Jaundice Respiratory distress Increased CRP; sudden changes in WCC/platelets Focal inflammation – e.g. Umbilicus; drip sites etc. FBC CRP Blood culture(s) Urine ET secretions if ventilated Swabs from any infected sites 1st line: cefotaxime & vancomycin 2nd line: meropenem
93
Learn CSF to diagnose type of meningitis - viral fungal bacterial
94
list the organisms that cause meningitis in children by age group
<3/12: N. meningitidis; S. pneumoniae; (H. influenzae (Hib) if unvaccinated); GBS; E. coli; Listeria sp. 3/12 - 5 years:N. meningitidis; S. pneumoniae; (Hib if unvaccinated) >6 years: N. meningitidis; S. pneumoniae
95
common causes of respiratory infections in children
1. s pneumonia = most important bacterial cause 2. mycoplasma = >4 years old, treat with macrolide. cold aggluttinins (IgM Antibodies). neurological signs in 1% eg encephalitis 3. also consider whooping cough, tb
96
causes of UTI in children managment?
E. coli = MOST COMMON Other coliforms e.g. Proteus species, Klebsiella Enterococcus sp. Coagulase negative Staphylococcus Staph saprophyticus treatment renal tract imaging antibiotics as prophylaxis recurrent may be sign of immunodeficiency either congenital or acquired - HIV, SCID
97
Risk factors for fungal disease? diagnostic tests? 3 targets of antifungals and types of drugs for each?
1. immunocompromised 2. inhaled steroids 3. malignancy, burns, complicated post ops, long lines -> invasive candida 4. diabetes -> mucormycosis 5. moisture, gentetics, CMI -> dermatophytes MC&S, Bx- Histology, serology, PCR, imaging cell membrane - polyene (eg ambisome, amphoceritin B ), Azoles DNA/RNA synthesis - pyrimidine analogues (flucytosine) cell wall - echinocandins
98
what are yeasts? give examples
single cell fungi, reproduce by budding 1. candida 2. cryptococcus 3. Histoplasma - dimorphic
99
what are moulds? give examples
multicellular hyphae fungi. grow by branching and extension 1. dermatophytes 2. aspergillus 3. agents of mucormycoses
100
what is the most common cause of fungal infections in humans? what infections does it cause? treatments for each?
candida 1. oral thrush = topical nystatin 2. candida oesophagitis = oral fluconazole 3. vulvovaginitis = topical clotrimazole or oral fluconazole 4. cutaneous -> localised or generalised = topical clotrimazole 5. invasive candida infections
101
list types of invasive candida infections
candidemia cns endocarditis bone and joint urinary tract eg vulvovaginitis intraabdominal
102
which animal is cryptococcus associated with? rfs? presentation? diagnosis? management
pigeons immunodeficiency c gatti -> meningitis in immunocopetent, space occupying lesions in brain and lung (sob, cough) imaging eg brain india ink staining of CSF serum/CSF Ag amphotericin b and flucytosin then consolidation and maintenance with fluconazole
103
Aspergillosis diagnosis? management?
- can colonize preformed cavities and debilitated tissues eg tb cavity imaging, sputum looking for antibodies = precipitins OR serology for galactomannan (polysaccharide) voriconazole ambisome
104
why might antifungals targeting cell wall not work in PCP? pcp symptoms
it lacks ergosterol in cell wall pneumnia -> fever cough sob
105
name some dermatophytes
tinea corporis tinea cruris tinea pedis tinea capitis pityriasis versicolor -> Malassezia furfur
106
amphotericin B key side effect?
nephrotoxicity
107
azoles key side effect?
abnormal LFTs
108
polyenes key side effect?
nephrotoxicity
109
pyrimidine analogues key side effect?
blood disorders
110
what is the most likely organism causing intracranial abscesses?
MRSA
111
Diagnosis of septic arthritis requirement?
> 50,000 White cells on synovial fluid analysis negative culture does not exclude
112
most likely organism causing a prosthetic joint infection?
coagulase negative staphylococcus
113
adult onset stills disease
114
most common cause of lobar pneumonia?
strep penumoniae
115
CRB-65 score
116
50 year old man LLL pneumonia Hemoptysis cavitation of CXR patient not particularly unwell what organism would you suspect?
Hemophilus influenzae - gram negative coccobacillus
117
coxiella burnetti pneumonia typically caused by contact with?
domestic/farm animals
118
74 year old woman, penumonia, on antibiotics but not getting better. most likely diagnosis?
empyema
119
64 year old treated for lymph node TB increasing SOB and cough ground glass diffuse shadowing on CXR Most likely organism?
pneumocysitis jirovecii
120
22 year old man. chemo for leukemia prolonged neutropenia ongoing fevers and raised inflammatory markers what is the likely organism?
aspergillus fumigatus (patient immunosuppressed)
121
which antibiotics inhibit cell wall synthesis? give examples from each class
B-lactams = Penicillins, cephalosPorins, carbaPenems (carbapenems stable to ESBLs) Glycopeptides = vancomycin and Teicoplanin
122
B lactams mechanism of action? what are they inefective against?
inactivate transpeptidases/penicillin binding proteins which are involved in cell wall synthesis only effective against rapidly dividing bacteria ineffective for organisms without peptidoglycan cell wall - mycoplasma, chlamydia
123
function of clavulanic acid and tazobactam?
B-lactamase inhibitors. protect penicillins from enzymatic breakdown
124
name examples of cephalosporins from each generation. how do they change with generation
1st generation = cephalexin 2nd generation = cefuroxime 3rd = cefotaxime, ceftriaxone, ceftazidime as generation increases, more gram negative cover and less gram positive
125
What bacteria are glycopeptides active against? mechanism of glycopeptides action
gram+ve only - too large to penetrate gram negative cell walls binds to peptide chain -> prevents formation of glycosidic bonds and peptide cross linkes
126
name antibiotic classes that inhibit protein synthesis state their mechanisms of action.
aminoglycosides - gentamicin, amikacin, tobramycin - bind to 30s ribosomal subunit, prevent elongation of polypeptide chain tetracylines - bind 30s subunit and prevent trna binding to ribosomal site. active against intracellular pathogens eg chlamydia, rickettsia, mycoplasma. may cause light-sensitive rash macrolides(bind 50s subunit, interfere with translocation, stimulate dissociation of trna), lincosamides eg clindamycin, streptogramins eg synercid ( the MSL group) Chloramphenicol - binds peptidyl transferase of 50s subunit. rarely used due to risk of aplastic anaemia and grey baby syndrome Oxazolidinones eg linezolid - highly active against gram positives mostly, including MRSA and VRE. optic neuritis and thrombocytopenia risk!
127
name an antibiotic class that is ototoxic
aminoglycoside
128
name antibiotic clases that inhibit DNA synthesis
Quinolones - ciprofloxacin, levofloxacin, movifloxacin. act on DNA Gyrase nitroimidazoles - metronidazole, tinidazole - active against anaerobes and protozoa
129
what antibiotic class inhits RNA synthesis?
Rifamycins - rifamipicin (inhibits dna dependent rna polymerase), rifabutin
130
State 2 cell membrane toxins used
Daptomycins - complex gram +ve eg MRSA Colistin - gram -ves
131
state 2 antibiotics that inhibit folate synthesis
sulfonamides diaminopyrimidines eg trimethoprim
132
describe mechanisms of resistance to antibiotics
1. modification/ inactivation of antibiotic = penicillin resistance, ESBL ecoli resistance to ceftriaxone 2. modification/replacement of target - MRSA Have a MecA gene making them resistant to flucloxacillin!! -> new PBPs with low affinity for B-lactams, strep pneumonia acquires multiple mutations in PBPs genes. fluclox was developed to not be broken down by beta lactamases 3.reduce antibiotic accumulation - impared uptake - increased efflux 4. bypass antibiotic sensitive step - eg in trimethprim and sulfonamides
133
avibactam mechanism of action?
inhibits ox-48 and most kpc enzymes
134
meropenem verobactam mechanism?
inhibit kpc enzymes
135
cefiderecol mechanism of action?
enters through ion channels
136
make notes for antimicrobial 2 lecture
137
Covid 19 treatment
Kaletra = lopinavir + ritonavir hydroxychloroquine Remdesivir dexamethasone
138
host proteins in influenza infection
butrophilin a3 = inhibits influenza polymerase ANP32 = host proteins - copted by influenza virus
139
Oral thrush treatment?
Topical nystatin
140
Oseophagitis treatment?
Oral fluconazole
141
Which organism is cryptococcus associated with ?
Pigeons ! = infects lungs and can disseminate into blood C gattii = particular strain that can cause meningitis in immunocompetent patients
142
PCP cxr findings?
Diffuse ground glass changes Microscopy Pcr Beta d glucan Co trimoxazole to treat
143
Tinea cruris affects where?
Groin
144
Most common side effects with 1. Azoles 2. Polyenes 3. Echinocandins 4. Pyrimidine analogues Learn what each antifungal targets!
Azoles = abnormal lfts Polyenes = nephrotoxicity Echinocandins = relatively safe Pyrimidine analogues = blood disorders
145
fever in a returning traveller dengue - transmitted by aedes mosquito typhoid malaria