Microbiology Notes

Microbiology Notes

Classification of Organisms

Bacteria

Subtypes / Examples / Investigation
Gram +ve / Cocci
- Clusters
- Chain / - Staphylococcus
- Streptococcus / Coagulase positive
- Staph. Aureus
Coagulase negative
- S. epidermidis
- S. saprophyticus
Bacilli / Bacillus, Listeria, Corynebacteria
Branching / Nocardia
Gram -ve / Cocci / Neisseria
Bacilli / Coliforms
Comma-Shaped / Vibrio, campylobacter, H. pyloria
Spirals / Borrelia / Borrelia burgdorferi, Borrelia vincentii
Treponema / Pallidum
Leptospira / L. interrogans
Acid fast / Mycobacterium / M. Tuberculosis complex
M. Leprae / Ziehl-Neelsen stain
Culture on Lowenstein-Jensen medium (lipid rich)
Cell wall deficient / Mycoplasma penumoniae
Ureoplasma urealyticum

Viruses

Subtypes / Examples / Features
DNA Viruses / Adenovirus / A – Asymptomatic Enteric Infection
B/C – Respiratory disease
D - Keratoconjunctivitis
E - Conjunctivitis
F – Infantile Diarrhoea
Herpes Family / α- Herpesviruses
- HSV
- VZV / Fast growing + Latent in neurones
β - Herpesviruses
- HHV 6/7
- Cytomegalovirus / Slow growing + latent in secretory glands
γ – Herpesviruses
- HHV 8
- Ebstein-Barr Virus / Latent in lymphoid tissue
RNA Viruses / Orthomyxoviruses / Influenza
Paramyxoviruses / Measles, Mumps, Pneumovirus (RSV)
Togaviruses / Rubella
Picornaviridae / Enterovirus, Rhinovirus
Retroviruses / HIV

Anti-Microbial Therapy

Anti-virals

Target / Examples
Viral binding / Fusion inhibitors
Uncoating / (Important for future)
Replication / Most current drugs e.g. acyclovir, ganciclovir
Assembly / e.g protease inhibitors
Release / e.g. interferons
Organism / Rationale / 1st line / 2nd line
HSV/VZV / Aciclovir / Famciclovir
Valaciclovir
CMV / Ganciclovir / Valaciclovir
Foscarnet
HIV / “HAART”
2 NRTI + NNRTI/PI
Chronic HBV / 40% success rate / Interferon-α + Lamivudine / Famciclovir
Chronic HCV / 60% success rate
Genotypes 2,3 - better
prognosis. Rx for 6/12
Genotypes 1,4 - worse
prognosis. Rx for 12/12 / Peginterferon-α
Ribavirin
Influenza / Only use in at-risk adults
Must be started within
48h of symptoms / Influenza A - Amantadine
Influenza A + B -
Neurainidase inhibitor
(Zanamivir/Olseltamivir)

Antibiotics

Action / Sub-types / Drugs
Inhibit Cell Wall Synthesis / β- Lactams / Penicillin, Cephalosporins
Glycopeptides / Vancomycin, Teicoplanin
Carbapenems / Imipenem
Monobactams / Aztreonam
Inhibit Protein Synthesis / Aminoglycosides / Gentamicin
Tetracycline / Tetracycline, Doxycycline
Macrolides / Erythromycin, Clarithromycin
Others / Chormapheicol, Fusidic acid
Inhibit Nucleic Acid Synthesis / Quinolones / Ciprofloxacin, Ofloxacin
Others / Metronidazole, Trimethoprim, Rifampicin, Sulphonamides
Inhibit Folate Synthesis / Sulphonamides / Trimethoprim, Septrin
Di-aminopyrimidines
Type / Drugs / Sides effects / Interactions/ Containdications
Penicillins
Basic / Benzylpenicillin, penicillin G,
Phenoxymethypenicillin, penicillin / Rash
Anaphylaxis
Nausea/vomiting / Reduced efficacy of COC
Hypersensitivity
Broad-spectrum / Amoxicillin
β-lactamase resistant / Flucloxacillin, Co-amoxiclav
Anti-pseudomonal / Tazocin
Cephalosporins
1st Generation / Cefelexin / C. Difficile
Bleeding
Thrombophlebitis / Hypersensitivity (10% who are allergic to penicillin will also be allergic)
2nd Generation / Cefuroxime
3rd Generation / Cefotaxime, Ceftazidime,
Ceftriaxone
Glycopeptides
Vancomycin, Teicopanin / Ototoxicity
Nephrotoxicity
Thrombophlebitis / Loop diuretics ↑ ototoxicity, Cyclosporin or
Aminoglycosides ↑
nephrotoxicity
Carbapenems
Imipenem, Meropenem / Nausea/vomiting
Seizures
Aminoglycosides
Gentamicin, Streptomycin / Nephrotoxicity Ototoxicity
Thrombophlebitis / Pregancy, MG
Loop diuretics or cyclosporine ↑ nephrotoxicity
Antagonise anitcholinesterases
Tetracyclines
Tetracycline, Doxycycline / Teeth/bone deposits / Renal impairement Absorption affected by
Ca2+, Iron tablets, Mg2+
Macrolides
Eryhtromycin, Clarithromycin / Nausea/vomiting Cholestatic jaundice / CP450 inhibitor, Stop statins
Quinolones
Ciprofloxacin, Ofloxacin / GI disurbance
Tendon damage / CP450 inhibitor Epilepsy (lower seizure threshold)
Hx of tendon damage
Nitromidazoles
Metronidazole / GI disturbance Antabuse reaction with
alcohol / Hepatic impairement, Hx of tendon damage, ↑phenytoin levels, ↑warfarin levels

Anti-Mycobacterium Drugs

Drug / Indications / Adverse effects
Rifampicin / Tuberculosis, Leprosy
Contact prophylaxis in meningitis / Deranged LFTs
Orange secretions
CP450 inducer
Isoniazed / Tuberculosis / Peripheral neuropathy (Rx - pyridoxine), Hepatotoxicity
Pyrazinamide / Tuberculosis / Hepatocellular toxicity
Ethambutol / Tuberculosis (if isoniazid resistance is likley) / Retrobulbar neuritis (< 8 weeks therapy)

Infections by Organ system

Cerbral Infections

Disease / Organisms / Features/Ix / Treatment
Cerebral Abscess / Local infection: Bacterial (strep milleri, bacteroides, staph) or fungal
Metastatic infection: pneumonia, infective endocarditis / An acute focal suppuration in the brain substance
Cerebrum or cerebellum
25% mortality
General: usually none
Specific: mass effects
Signs pyrexia (50%), focal signs, papilloedema / Aerobes - cephalosporin
Anaerobes – metronidazole + dexamethasone +/- anti-fungal
? Surgery to reduce pressure
Encephalitis / Bacterial: secondary to meningitis
Viral: Herpes simplex, rabies
Fungal: histoplasma, cryptococcus
Protozoal: toxoplasma, plasmodium / Inflammation of the brain substance
Ill (fever, headache, malaise)
Alt consciousness/seizures, Photophobia
Confirmed with viral picture in CSF sample +/- focal inflammation on CT and slow
EEG activity. / Mostly due to herpes simplex so use acyclovir I.V.
Meningitis / Viral: Enteroviruses
Bacterial: N. meningitidis, Group B strep, Gram -ve bacilli, Listeria Fungal: Cryptoccous, candida / Inflammation of the meninges
Stiff neck, headache, fever, photophobia, non-blanching rash, vomiting, confusion, joint pain, seizures
Ix: LP / Emergency:
1.2 g benzypenicillin IM
Cefotaxime 2g 6-hourly IV
+/- ampicillin for Listeria
Contacts – rifampicin or ciprofloxacin
Vaccination

Lung Infctions

Disease / Organisms / Features/Ix / Treatment
CAP / Typicals (85%)
S. pneumoniae, H. influenza, staph. aureus (elderly), M. catarrhalis (smoking), Klebsiella (alcoholic)
Atypicals (15%)
Mycoplasma, Legionella
Zoonoes: Chlamydia, Coxiella, bordetella
Viruses:
Influenza A & B, Varicella and Herpes pneumonitis / General symptoms, Cough +/- sputum, SoB, Pleuritic chest pain
Reduced air entry, Dullness to percussion, Tactile vocal fremitus, Bronchial breathing, Crackles coarse
Chest X-ray: Consolidation / Typicals - β lactams, Amoxicillin, Cefuroxime
Atypicals – Macrolides, Clarithromycin/Erythromycin
Anti-virals - amantadine +/- neuraminidase inhibitors
HAP / Gram -ve, few Gram +ve
Klebsiella, Serratia, Enterobacter, Pseudomonas / Gram +ve - Vancomycin,
Gram –ve – Ceftazidime, Gentamicin
AP / Nearly always Gram -ve organisms from the gut / Cefuroxime and metronidazole
TB / Mycobacterium tuberculosis / AFB on Ziehl-Neelson staining
Culture up to 7 weeks! Mantoux - Does not distinguish vaccinated and infected/Not reliable in HIV / Rifampicin, Isoniazed, Pyrazinamide, Ethambutol

GI Infections

Disease / Organisms / Features/Ix / Treatment
Throat Infections / Herpes
Tonsillitis
Glandular fever
Candidiasis
Upset Tummy / Bacteria - staph. aureus, bacillus cereus, lostridium, listeria
Viruses - Rota virus, Noraviruses, Adenovirus, Hepatitis A
Protozoa - Entamoeba histolytica, Giardia lamblia
Cryptosporidium / Diarrhoea - Frequent passage of loose stools
Dysentry - Frequent passage of blood and mucus in the stools”
Staph. aureus - rapid onset of vomiting and diarrhoea
Bacillus cereus in reheated rice
Clostridium botulinum in canned food
C. difficile -pseudomembranous colitis (usually cephalosporin related)
Travellers’ Diarrhoea - due to exposure of new E.coli strains
Rotavirus - kids, explosive and distinctive smell
Salmonella - eggs and poultry
Camplylobacter complications – GB syndrome or Reiter’s / Support with fluids, loperamide
Antibiotics for neonates, elderly and immunocompromised (Ciprofloxacin)
Treat protozoals with metronidazole
Hepatitis A / Faeco-oral spread
Incubation: few weeks
Acute never chronic
Systemic symptoms + jaundice
Elevated AST/ALT
Hepatitis B / Spread through sex, blood products, vertical
Incubation - up to 6 months
Acute or chronic
Increased risk of cirrhosis and HCC / Interferon alpha, lamuvudine (NRTI) or adefovir
Only a 40% success rate
Vaccination for certain groups
Transplantation
Hepatitis C / As for Hep. B - but blood spread most common
Acute or chronic
Complications of chronicity - 30% cirrhosis, 5% hepatocellular carcinoma / Peginterferon alpha

Sexually Transmitted Infections

Disease / Organisms / Features/Ix / Treatment
Chlamydia / Chlamydia trachomatis / Incubation a few weeks
Clear mucoid discharge
Mucopurulent cervicitis
Asymptomatic (80% female, 50% male)
Dx requires: Urine, Endocervical swab / Single dose of azithromycin
Gonorrhoea / Gram -ve intracellular cocci / Site of infection: cervix, urethra, rectum and pharynx
Short incubation period
95% symptomatic in men, 50% in women
Diagnosis - Microscopy for gram -ve intracellular diploccoci / Ciprofloxacin/ofloxacin
3rd gen cephalosporin - ceftriaxone
NSU / Men only
Inflammation of the urethra leading to discharge and dysuria
Dx of exclusion (absence of gram neg. cocci on microscopy) e.g. chlamydia, mycoplasma, uroplasma, trichomonas / Single dose azithromycin
Complication - epidydimo-orchitis, reactive arthritis
Syphilis / Treponema pallidum / Primary (painless ulcer/chancre + lymphadenopthy)
Secondary (serocoversion illness and condylomata late)
Latent syphilis
Tertiary syphilis (granulomata, meningovascular disease, tabes, bone and skin gumma)
Diagnosis
Cannot be cultured
Visualised with dark ground microscopy or using serology (VDRL) / 2.4 MU penicillin
LGV / Lymphogranuloma venereum caused by L1/L2/L3 variant of Chlamydia / Painless ulcerative papule
Heals to give painful lymphadenopathy/buboes / Doxycycline
HSV / Type I - cold sores, gingivostomatitis
Type II - genital sores / Topical or systemic acyclovir
HPV / Low Grade (types 6/11) - painless warts
High Grade (types 16/18/31/32) - CIN/AIN / Podophyllin extract
Cryotherapy

HIV

A retrovirus with an RNA genoma
Relies on reverse transcriptase to integrate into genome
Infects the immune system
CD4+ T helper cells (reduced number and function)
CD4+ dendritic cells (failure of antigen presentation and immune memory)

Primary Infection (first 12 weeks)

Large increase in viral load
Dramatic decline in CD4 and gradual increase in CD8 that control viral load

Asymptomatic phase (CD4 & CD8 stable)

AIDS

Virus seeps out of cell and alters CD4 function and number.
CD4+ < 200 or AIDs-defining illness

Diagnosis

Anti-HIV antibodies (ELISA)
Screening test
Viral load (PCR)
Very sensitive and definitive test
Initial baseline plasma viral load predict time for active disease to appear

Monitoring

Viral load
CD4+ T cell counts
HIV-resistance tests
Expensive tests that look at resistance to anti-retroviral medication

Therapies

“HAART”

Reverse transcriptase inhibitors
Protease inhibitors

Type / Drug / Side Effects
NNRTs - nucleoside analogues / Zidovudine (AZT) / Myelotoxicity -anaemia and neutropenia
Muscle wasting
Didanosine (DDI) / Pancreatitis
Peripheral neuropathy
Zalcitabine (DDC) / Peripheral neuropathy
Lamivudine (3TC) / Well tolerated so used first line
Abacavir / May cause SJS so required screening before using
NNRTI - non-nucleoside analogue / Nevirapine / May cause SJS
Enzyme inducer
Efavirenz / Popular at present - O.D. dosing
25% develop minor skin rash
Protease Inhibitors / Saquinavir / Deranged LFTs
Efavirenz / Perioral hyperaesthesia
Indinavir / Kidney stones

Urinary Tract Infections

Disease / Organisms / Features/Ix / Treatment
Simple Cystitis / E.coli, proteus, staphylococcus saprophyticus, Klebsiella, Enterococcus / Dysuria, Frequency, Suprapubic pain, urgency / Trimethoprim, amoxicillin, nitrofurantoin, cephalosporin
Pyelonephritis / Systemic sx, Loin pain and tenderness / Requires IV antibiotics - Cefuroxime + Gentamicin
Men and children require urography post-infection

Skin Infections

Disease / Organisms / Features/Ix / Treatment
Cellulitis / Staph. and strep. / Infection and inflammation of
connective tissue underlying skin
Often following minor skin trauma / Flucloxacillin + co-amoxiclav
Infected eczema / Impetigo -Usually caused by Strep. pyogenes / Superficial bacterial skin infection common in kids / Topical fusidic acid, mupirocin
oral if severe
Eczema herpeticum - Caused by HSV 1 & II / Serious
Widespread vesicular rash / Topical and oral aciclovir
Dermatophytosis / Trichophyton and microsporum are most common / A group of skin infections caused by dermatophytes
- Tinea corporis
- Tinea crucris
- Tinea pedis
- Onychomycosis / Cotrimazole (Imidazole)
Miconazole (Imidazole)
Terbinafide (Allylamines)

Tropical Infections

Disease / Organisms / Features/Ix / Treatment
Malaria / P. falciparum
P. vivax
P. ovale
P. malariae / Anyone returning from endemic area
Fever/rigors, Headache/myalgia, Nausea and vomiting, Diarrhoea, Dark urine, Jaundice
Thick film (it is present?)
Thin film (what species?) / Prophylaxis
Avoid getting bitten - nets, repellants etc.
Treatment
P. Falciparium - quinine + tetracycline
Non-falciparium - chloroquine + primaquine
Leptospirosis / a.k.a Weil’s disease
Contact with animal resorvoirs e.g. rat urine
Systemic upset + conjunctival suffusion + hepatosplenomegaly
Haemolysis and renal failure if
severe
IgM antibodies / Erythromycin
Lyme Disease / Spirochaete - Borreli burgorferi / Ticks on infected deer/mice
Localised early disease: erythema chronic migrans + minor systemic
Disseminated disease: systemic disease (arthritis, carditis, neurol symptoms) / Erythromycin
Schistosomiasis / Schistosomal cerceriae / Common but people are rarely unwell
Penetrate skin after fresh water exposure and spread to Swimmer’s itch - transient rash 1-2 days after exposure
Bladder - haematuria, urinary symptoms and eosinophilia
Gut (intestinal schistosomiasis) - vague abdo. symptoms / Priziquantel
Trypanosomiasis / Trypanosomal protozoans / 2 types:
• African (Sleeping sickness) - Gambiense/rhodesiense
• American (Chagas disease) - Cruzi
Leishmaniasis / Baghdad boil, kala azar, dum-dum fever
Spread by sandflies
Cutaneous (skin sores) or Visceral
(hepatosplenomegaly, anaemia) / Amphotericin or Miltefosine