Microbiology Revision – Lecture 1

Dr Anna Goyder and Dr Helen McKenna

19/03/13 - 21/03/13

Outline

2 lectures x 90mins each:

• Bacteria and Abx• Viruses and Antivirals• Vaccinations• Infections by system:

- CNS- Cardio- Resp- GI/hepatitis- GU/gynae- Musculoskeletal

• Mycobacterial• Zoonoses• Malaria

Bacteria

Bacteria simplified• Gram positive- Cocci

staphylococcus streptococcus enterococcus- Rods/bacilli

ABCDL (see next slide)

• Gram negative- Cocci

the diplococci - neisseria (gonorrhoea, meningitidis ‘meningococcus’), moraxella

- Rods/bacilli ENTERICS - E Coli, salmonella, shigella, klebsiella, proteus,

campylobacter, helicobacter, vibrio… ie most other things!- Coccobacilli haemophilus, legionella, brucellosis, bordetella,

chlamydia* rickettsia* *obligate intracellular- Spiral spirochetes – treponema (syphilis), leptospira (Weil’s), borrelia (lyme)

Gram + rods:ABCD L

ActinomycesBacillus (anthracis, cereus)Clostridium (difficile, botulinum, perfringens)Diphtheria (corynebacterium diphtheriae)Listeria

Diplococcus

Neisseria

Moraxella

Anaerobes

• WHAT ARE THEY?

Anaerobes

• Do NOT require O2 for growth• Therefore suspect them in unhealthy/dying

tissues/reduced blood supply, necrotic tissue• From GI tract including mouth E.g. suspect in bites,

• Foul smell! Free gas under skin! Nasty

• Treat with metronidazole, cephamycins (cefoxitin, cefotetan, cefmetazole, flomoxef)

• Aminoglycosides do NOT cover anaerobes – O2 needed for them to enter the cell.

Anaerobes

• OBLIGATECANNOT use O2/grow

where there is oxygen

Bacteroides

Clostridium

Actinomyces

• FACULATIVECan grow where there is OR

isn’t oxygen

Staphylococcus, E. Coli, Listeria

Antimicrobials

• Antibiotics

• Antivirals

• Antifungals

Antibiotics (antibacterials)

• A) Cell wall synthesis inhibitors• B) Protein synthesis inhibitors• C) DNA synthesis inhibitors• D) RNA synthesis inhibitors• E) Anti-folate drugs

Antibiotics (antibacterials)

• A) Cell wall synthesis inhibitors• B) Protein synthesis inhibitors• C) DNA synthesis inhibitors• D) RNA synthesis inhibitors• E) Anti-folate drugs

A. Cell wall synthesis inhibitors β-lactams

1. Penicillins

2. Cephalosporins Crossreactivity – caution if hx

anaphylaxis1st generation – gram + > -2nd generation – gram + and -3rd generation – gram - > +

- have T in them – T for ‘third’ cefotaxime, ceftazidime, ceftriaxone

3. Carbapenems B R O A D spectrum

GlycopeptidesRequire therapeutic drug monitoring

(TDM)

1. VancomycinUsually IV – covers MOST GRAM +

incl MRSA - but NOT VRE!Exception - oral vancomycin – for

C. Difficile diarrhoea (where metronidazole has failed)

2. Teicoplanin

Antibiotics (antibacterials)

• A) Cell wall synthesis inhibitors• B) Protein synthesis inhibitors• C) DNA synthesis inhibitors• D) RNA synthesis inhibitors• E) Anti-folate drugs

B. Inhibitors of protein synthesis

5 to remember:1. Macrolides2. Tetracyclines 3. Aminoglycosides 4. Chloramphenicol5. Oxazolidinones

erythromycin, clarithromycin, azithromycin

doxycycline, lymecycline

gentamicin, amikacin – TDM needed

(for your EYES only)

Linezolid – don’t need to know any more

Antibiotics (antibacterials)

• A) Cell wall synthesis inhibitors• B) Protein synthesis inhibitors• C) DNA synthesis inhibitors• D) RNA synthesis inhibitors• E) Anti-folate drugs

C. DNA synthesis

1. Quinolones – Ciprofloxacin, Moxifloxacin, Levofloxacin (think

Ciprofloxaquin, Moxifloxaquin etc)

Act on DNA Gyrase

Active mostly against Gram negatives –

use for UTIs, bacterial gastroenteritis

2. Nitroimidazoles –

MetronidazoleUseful against anaerobes and protozoa

3. Nitrofurantoin - UTIs

Antibiotics (antibacterials)

• A) Cell wall synthesis inhibitors• B) Protein synthesis inhibitors• C) DNA synthesis inhibitors• D) RNA synthesis inhibitors• E) Anti-folate drugs

D. RNA synthesis

• Rifampicin, Rifabutin

Treatment - as part of combination therapy because resistance develops quickly – mycobacteria – TB

Prophylaxis – single agent - Meningococcal

Antibiotics (antibacterials)

• A) Cell wall synthesis inhibitors• B) Protein synthesis inhibitors• C) DNA synthesis inhibitors• D) RNA synthesis inhibitors• E) Anti-folate drugs

E. Anti-folate drugs

TrimethoprimUTIs

Sulphonamides

Co-trimoxazole ‘Septrin’

= Trimethoprim + Sulphamethoxazole P. Jiroveci prophylaxis in AIDs

TB treatment

• RIPE – Rifampicin, Isoniazid, Pyrazinamide, Ethambutol

• Normally 2m of 4 drugs, then 4m of 2 drugs

Exceptions – spinal (12 months), MDR TB (minimum 18 months)

• Side Effects – - Ethambutol - E for Eye – optic neuritis- R/I/P – hepatotoxicity- Isoniazid – peripheral neuropathy – co-prescribe pyridoxine

Viruses

ClassificationDNA viruses

Double-stranded:Adenovirus Herpes virus Pox viruses

Double-stranded plus reverse transcriptase:Hepadnavirus

Single stranded:Parvovirus

RNA viruses

Double-stranded:Reovirus

(+)Single-stranded:PicornavirusTogavirusFlavivirus

(+) Single-stranded plus reverse transcriptase:Retrovirus

(-)Single-stranded:OrthomyxovirusParamyxovirusRhabdovirus

ClassificationDNA viruses

Double-stranded:

Adenovirus

Herpes virus (LATENT)

Pox viruses

Double-stranded plus reverse transcriptase:

Hepadnavirus Hepatitis B

Single stranded:

Parvovirus B19 – slapped cheek, 5th disease

Clinical Site of latent infection

Pregnancy Test Treatment

HSV1+2

Painful vesicular rashOrofacial/GenitalCutaneous disseminationVisceral involvement:Oesophagitis, ColitisHepatitis

Sensory nerve ganglia

Primary maternal infection in 3rd trimester:Neonate:Lesions of Skin, Eyes, Mouth (SEM)Disseminated disease (especially to BRAIN)

PCR

Test for Ab

Aciclovir/Valaciclovir (pro-drug)Ophthalmic: topical idoxuridine

CS (Avoid PROM)

VZV Varicella zoster (chicken pox)Flu-like prodromeCentripetal crops of vesicles

Sensory nerve ganglia (Herpes zoster – shingles)

Early pregnancy:Congenital Varicella syndrome:ScarringEye defectsLimb hypoplasiaMicrocephaly and LD

7 day pre/post-partum:Mother: increased risk pneumonia/encephalitis

Neonatal VaricellaPurpura fulminans

Vesicle fluid:PCR/EM/Ab

If exposed: check for AbIf not immune: VZIgIf confimed/rash: aciclovir

CMV Usually asymptomatic (40% infected by 16)Rarely – maculopapular rashImmunosuppressed:Encephalitis, retinitis, pneumonitis, hepatitis, BM suppression, enterocolitis

B cells Commonest congenital viral infectionAsymptomaticHearing defectsCognitive impairment10% Cytomegalic inclusion disease:IUGR, hepatosplenomegaly, chorioretinitis, encephalitis, thrombocytopenia

Hepatitis: GanciclovirHIV: CidofavirSevere: Foscarnet

If primary infection/reactivation in pregnancy – refer to Fetal medicine(but no treatment)

EBV Infectious mononucleosis (sore throat, lymphadenopathy, maculopapular rash with ampicillin)Post-Tx lymphoproliferative disease, lymphomaHIV: oral hairy leukoplakia

B cells No adverse outcome in pregnancy Monospot

Serology

HHV 8

Kaposi’s sarcomaCastleman’s disease (body cavity-associated lymphoma)

B cellsEpithelial cells

HHV 6 + 7 Immunocompromised:Graft failure, hepatitis

T cellsEpithelial cells

Questions

Which herpes virus?

A HHV 1/HSV 1

B HHV 2/HSV 2

C HHV 3/ VZV

D HHV 4/ EBV

E HHV 5/CMV

F HHV 6/ Roseola

G HHV 7

H HHV 8

1. A 50 year old man presents to HIV clinic with a widespread purple rash

2. A 6 year old child presents with 1 week of fever and malaise and develops crops of vesicles on scalp and mouth

3. 18 year old student presents with excessive fatigue and repeated bouts of pharyngitis. He is found to have cervical lymphadenopathy and enlarged spleen.

4. 1 week old baby, not feeding, vesicular lesions on face and mouth. Mother had painful genital rash in last week.

Clinical features Complications In Pregnancy Treatment

Measles(RNA - single-strandedparamyxovirus)

CongestionConjunctivitisKoplik’s spotsRash starts behind ears and forehead

Secondary bacterial infection:Otitis mediaPneumoniaPneumonitisEncephalitisSSPE

Rare

Fetal lossPre-term deliveryNot associated with fetal anomalies

Ig to attenuate

LIVE vaccine

Mumps(RNA- single-strandedparamyxovirus)

ParotitisOrchitisOophoritisPancreatitisMeningitis and deafness

LIVE vaccine

Influenza(RNA-single strandedorthomyxovirus)

A: pAndemicB: outBreakC

BronchitisSecondary bacterial pneumonia

In pregnancy:Still birthPre-term delivery

A: amantadineA+B: neuraminidase inhibitorsZanamavir (inhaled)Oselatamavir (oral)

Rubella(RNA+ single-strandedtogavirus)

50% subclinicalPinpoint macular rashlymphadenopathy

1st trimester (90% if <10 weeks)Fetal lossCongenital Rubella SyndromeCataracts, glaucomaHeart defectsDeafnessMental retardation>20 weeks: no risk

LIVE vaccine

Enterovirus(Polio, coxsackie, echovirus)RNA+ single-stranded

Hand, foot and mouth diseaseEncephalitisMyocarditis

Congenital myocarditisNeonatal hepatitis and IDDM

Parvovirus B19(DNASingle-stranded)

AsymptomaticErythema infectiosumPolyarthropathyTransient aplastic crisis

< 20 weeks:3% hydrops fetalisOther anomalies rare

>20 weeks: no risk

Intrauterine transfusion

Antivirals

HSV: Encephalitis, Disseminated (Genital, Oal)VZV: immunocompromise, pregnancy, pneumonitisAciclovirGuanosine analogue-Blocks viral DNA extensionRequires activation by viral TK

CMV (lacks TK)GanciclovirResistant: Foscarnet

Antivirals

HAART• Triple therapy – usually 2xNRTI + NNRTI/PI• Start when CD4 count <250

• NRTIs end in –ine (exceptions: tenofovir and abacavir)

• NNRTIs – nevirapine, efavirenz• PIs end in -vir (exceptions: tenofovir and abacavir = NRTIs)

Vaccinations

UK ScheduleDTaP/IPV/Hib 2, 3, 4 monthsPCV 2, 4 monthsMen C 3, 4 months

Hib + MenC 12 months boosterMMR + PCV 12-13 months

DTaP/IPV/MMR 3-5 yearsBCG high risk babies, 10-14y

HPV (16 and 18 - oncogenic) girls 12-13yDT + IPV 13-18 years

Rubella seronegative women

Which of the following is a LIVE vaccine?

A Diphtheria

B Yellow fever

C Rabies

D Tetanus

E Pertussis

Breaktime

• 5 mins

• Only go to the toilet if you’re desperate

• Don’t talk about medicine

• Talk about something else

• Might be a good time to start filling in your feedback form

SYSTEMS

CNS (including prion disease)

Heart

Respiratory Tract

Gastrointestinal Tract

Urinary Tract

Sexually transmitted diseases

Musculoskeletal and skin

CNS and Prion disease

Meningitis Encephalitis Abscess Myelitis Neurotoxin

FeverHeadacheVomitingPhotophobia

Nuchal rigidityKernig’s signFocal neurologyLong tract signs (6th and 3rd CN)Rash

(VIRAL: no focal neurology or alteration of consciousness)

Fever HeadacheDisturbance of brain function(reduced level of consciousness,disorientation,seizures)

VIRAL

HSVEBVMumpsInfluenzaAdenoArboJapanese BRabies

ACICLOVIR

Mass effect: focal neurology, seizures(Fever in <50%)

StrepStaphGram –TBFungiParasitesActinomycesNocardia

Reduced nerve transmission

VIRAL

PolioEBV

Paralysis

Clostridia

-Flaccid (Clostridium botulinum)

-Rigid (Clostridium tetani)

MeningitisACUTE Subacute/

Chronic

Neonates Children Elderly

E. ColiGram negative bacilliGroup B strep

Neisseria meningitidis (meningococcus)Strep pneumoniae (pneumococcus)VIRAL

Gram negative bacilliPneumococcusLISTERIATBSyphilis (treponema)

LeptospiraTBSyphilisBorreliaCryptococcus

Interpreting CSFClarity

Cells (x10^6) Gram stain

Protein Glucose Organism

Normal Clear WCC 0-5 No organisms

0.15 – 0.4 2.2 – 3.3(60% of blood glucose)

Purulent Meningitis

Turbid WCC 100-2000

neutrophils

Organisms

Increased0.5 – 3.0

Decreased0 – 2.2

Bacterial:MeningococcusPneumococcusListeria

Aseptic Meningitis

Clear/Slightly turbid

WCC 15-500

Lymphocytes

No organisms

Increased0.5 - 1

Normal VIRALPartially treated bacterialEncephalitisAbscessTB/fungal

TB Clear/Slightly turbid

WCC 30-500

LymphocytesAND Polymorphs

Scanty AFB (or nothing)

INCREASE1 - 6

Decreased0 – 2.2

TB(Cryptoccoccus,Abscess)

Questions50 year old manHeadache and neck stiffnessCT brain normalLP – opening pressure 15 cmH20

CSF:CloudyWCC 100 (70% lymphocytes)Protein 0.7Glucose 3.3 (serum glucose 4.7)

Diagnosis?A Bacterial meningitisB Viral meningitisC TBD Normal CSFE Cryptococcal

Clarity

Cells (x10^6) Gram stain

Protein Glucose Organism

Normal

Clear WCC 0-5 No organisms

0.15 – 0.4 2.2 – 3.3(60% of blood glucose)

Purulent Meningitis

Turbid

WCC 100-2000

Organisms

Increased0.5 – 3.0

Decreased0 – 2.2

Bacterial:MeningococcusPneumococcusListeria

Aseptic Meningitis

Clear/Slightly turbid

WCC 15-500

Lymphocytes

No organisms

Increased0.5 - 1

Normal VIRALPartially treated bacterialEncephalitisAbscessTB/fungal

TB Clear/Slightly turbid

WCC 30-500

LymphocytesAND Polymorphs

Scanty AFB (or nothing)

INCREASE1 - 6

Decreased0 – 2.2

TB(Cryptoccoccus,Abscess)

20 year old manHeadache and sore throatFeverPhotophobia

CSF:ClearLymphocytes 2; Polymorphs 0Protein 0.3Glucose 4.1 (serum glucose 5.9)

Diagnosis?A Guillian-Barre SyndromeB Viral meningitisC Bacterial meningitisD Cerebral MalariaE Normal CSF

Clarity

Cells (x10^6) Gram stain

Protein Glucose Organism

Normal

Clear WCC 0-5 No organisms

0.15 – 0.4 2.2 – 3.3(60% of blood glucose)

Purulent Meningitis

Turbid

WCC 100-2000

Organisms

Increased0.5 – 3.0

Decreased0 – 2.2

Bacterial:MeningococcusPneumococcusListeria

Aseptic Meningitis

Clear/Slightly turbid

WCC 15-500

Lymphocytes

No organisms

Increased0.5 - 1

Normal VIRALPartially treated bacterialEncephalitisAbscessTB/fungal

TB Clear/Slightly turbid

WCC 30-500

LymphocytesAND Polymorphs

Scanty AFB (or nothing)

INCREASE1 - 6

Decreased0 – 2.2

TB(Cryptoccoccus,Abscess)

Which of the following types of viral meningitis may be associated with a characteristically LOW CSF glucose level?

A Mumps

B CMV

C Measles

D HIV

E Echovirus

Prion disease: Infectious proteinCauses rapid

neurodegeneration (Dementia, ataxia)No

inflammatory/immune reaction

Genetic 15% Sporadic 80% Acquired < 5%

Familial CJD;Gerstmann-Straussler-Sheinker SyndromeFamilial Fatal Insomnia

Sporadic CJD KuruVariant CJDIatrogenic

Germline mutation in human prion protein gene (PRP)All autosomal dominant

? Somatic mutation or spontaneous conversion(1 in a million)

Eating infected human (Kuru) or animal CNS matter (VARIANT CJD)

Iatrogenic (GH, surgery, blood)

GSS: Onset: 30-70Slowly progressive ataxia - Death in 2-10yFamily history (dementia, ataxia, psychiatric)

Onset: 65Rapid dementia – death in 6m

Onset: 26Psychiatric symptoms before neurological symptomsDeath in 14 months

EEG: non-specific

MRI: may be increased signal in basal ganglia

Neurogenetics: reveals mutationGSS PRNP P102LFFI PRNP D178N

EEG: pseudoperiodic triphasic complexes (2/3)

MRI: increased signal in basal ganglia

CSF: raised markers of neuronal damage ( 14-3-3; S100)

Neurogenetics: No genetic cause

Brain biopsy: PRP immunohistochemistry

EEG: Non-specific SLOW waves

MRI: positive pulvinar sign (increased signal in bilateral posterior thalamus)

CSF: markers not useful

Neurogenetics: all methionine homozygous at codon 129 (MM)

TONSILLAR BIOPSY :PRPsc type 4t (100% sensitive and specific – no need for brain biopsy)

Questions

Which of the following statements about variant CJD is true?

A Mainly affects the elderlyB More rapidly progressive than sporadic CJDC Initial symptoms are always neurologicalD Tonsillar biopsy is often diagnosticE EEG is usually abnormal

Which of the following statements is true?

A Familial CJD is more rapidly progressive than sporadic CJD

B Familial CJD is inherited in a recessive fashion

C Familial prion disease does not cause ataxia

D All cases of variant CJD are methionine homozygous at codon 129

E Tonsillar biopsy is used to diagnose sporadic CJD

Cardio

EndocarditisSubacute versus acute

General points –

•Blind therapy – fluclox/benpen/vancomycin + gent

•If penicillin allergic/MRSA - use vancomycin

•Mortality – 30% with staph, 5% with strep

Who Treatment Complications

Streptococcus viridans

Native valves Benpen +/- gent

Staph epidermidis Prosthetic valve if <2 months post surgery

Fluclox +/- gent(+ rifampicin if prosthetic valve)

Staph aureus IVDUs Fluclox +/- gent Abscesses

Strep bovis Colorectal ca Benpen +/- gent

Culture-negative Endocarditis

• Caused byA) taking blood cultures AFTER starting antibiotics

B) Organisms difficult to culture:

brucella, coxiella, chlamydia, mycoplasma,

HACEK organisms:

Haemophilus, Actinobacillus, Cardiobacterium, Eikenella

Kingella

-> do serology

That’s all for now

• Please fill in a feedback form if you have not done so already