Microbiology Notes
Classification of Organisms
Bacteria
Gram +ve
Gram -ve
Subtypes
Cocci
- Clusters
- Chain
Examples
Bacilli
Bacillus, Listeria, Corynebacteria
Branching
Nocardia
Cocci
Bacilli
Neisseria
Coliforms
Comma-Shaped
Vibrio, campylobacter, H.
pyloria
Borrelia burgdorferi, Borrelia
vincentii
Pallidum
L. interrogans
M. Tuberculosis complex
M. Leprae
Spirals
Borrelia
Acid fast
Treponema
Leptospira
Mycobacterium
Cell wall deficient
Investigation
Coagulase positive
- Staph. Aureus
Coagulase negative
- S. epidermidis
- S. saprophyticus
- Staphylococcus
- Streptococcus
Ziehl-Neelsen stain
Culture on Lowenstein-Jensen
medium (lipid rich)
Mycoplasma penumoniae
Ureoplasma urealyticum
Viruses
DNA Viruses
Subtypes
Adenovirus
Herpes Family
RNA Viruses
Retroviruses
Examples
α- Herpesviruses
- HSV
- VZV
β - Herpesviruses
- HHV 6/7
- Cytomegalovirus
γ – Herpesviruses
- HHV 8
- Ebstein-Barr Virus
Orthomyxoviruses Influenza
Paramyxoviruses Measles, Mumps,
Pneumovirus (RSV)
Togaviruses
Rubella
Picornaviridae
Enterovirus, Rhinovirus
HIV
Features
A – Asymptomatic Enteric Infection
B/C – Respiratory disease
D - Keratoconjunctivitis
E - Conjunctivitis
F – Infantile Diarrhoea
Fast growing + Latent in neurones
Slow growing + latent in secretory
glands
Latent in lymphoid tissue
Anti-Microbial Therapy
Anti-virals
Target
Viral binding
Uncoating
Replication
Examples
Fusion inhibitors
(Important for future)
Most current drugs e.g.
acyclovir, ganciclovir
e.g protease inhibitors
e.g. interferons
Assembly
Release
Organism
HSV/VZV
Rationale
1st line
Aciclovir
CMV
HIV
Chronic HBV
Chronic HCV
Influenza
2nd line
Famciclovir
Valaciclovir
Valaciclovir
Foscarnet
Ganciclovir
“HAART”
2 NRTI + NNRTI/PI
40% success rate
60% success rate
Genotypes 2,3 - better
prognosis. Rx for 6/12
Genotypes 1,4 - worse
prognosis. Rx for 12/12
Only use in at-risk adults
Must be started within
48h of symptoms
Interferon-α + Lamivudine
Peginterferon-α
Ribavirin
Famciclovir
Influenza A - Amantadine
Influenza A + B Neurainidase inhibitor
(Zanamivir/Olseltamivir)
Antibiotics
Action
Inhibit Cell Wall Synthesis
Inhibit Protein Synthesis
Inhibit Nucleic Acid Synthesis
Inhibit Folate Synthesis
Sub-types
β- Lactams
Glycopeptides
Carbapenems
Monobactams
Aminoglycosides
Tetracycline
Macrolides
Others
Quinolones
Others
Sulphonamides
Di-aminopyrimidines
Drugs
Penicillin, Cephalosporins
Vancomycin, Teicoplanin
Imipenem
Aztreonam
Gentamicin
Tetracycline, Doxycycline
Erythromycin, Clarithromycin
Chormapheicol, Fusidic acid
Ciprofloxacin, Ofloxacin
Metronidazole, Trimethoprim,
Rifampicin, Sulphonamides
Trimethoprim, Septrin
Type
Basic
Broad-spectrum
β-lactamase
resistant
Anti-pseudomonal
1st
Generation
Generation
rd
3 Generation
2nd
Drugs
Sides effects
Penicillins
Benzylpenicillin, penicillin G, Rash
Phenoxymethypenicillin,
Anaphylaxis
penicillin
Nausea/vomiting
Amoxicillin
Flucloxacillin, Co-amoxiclav
Interactions/
Containdications
Reduced efficacy of COC
Hypersensitivity
Tazocin
Cephalosporins
Cefelexin
C. Difficile
Bleeding
Cefuroxime
Thrombophlebitis
Cefotaxime, Ceftazidime,
Ceftriaxone
Glycopeptides
Vancomycin, Teicopanin
Ototoxicity
Nephrotoxicity
Thrombophlebitis
Carbapenems
Imipenem, Meropenem
Nausea/vomiting
Seizures
Aminoglycosides
Gentamicin, Streptomycin
Nephrotoxicity
Ototoxicity
Thrombophlebitis
Tetracyclines
Tetracycline, Doxycycline
Teeth/bone deposits
Macrolides
Eryhtromycin, Clarithromycin Nausea/vomiting
Cholestatic jaundice
Quinolones
Ciprofloxacin, Ofloxacin
GI disurbance
Tendon damage
Metronidazole
Nitromidazoles
GI disturbance
Antabuse reaction
with
alcohol
Hypersensitivity (10% who
are allergic to penicillin will
also be allergic)
Loop diuretics ↑
ototoxicity, Cyclosporin or
Aminoglycosides ↑
nephrotoxicity
Pregancy, MG
Loop diuretics or
cyclosporine ↑
nephrotoxicity
Antagonise
anitcholinesterases
Renal impairement
Absorption affected by
Ca2+, Iron tablets, Mg2+
CP450 inhibitor, Stop
statins
CP450 inhibitor Epilepsy
(lower seizure threshold)
Hx of tendon damage
Hepatic impairement, Hx of
tendon damage,
↑phenytoin levels,
↑warfarin levels
Anti-Mycobacterium Drugs
Drug
Rifampicin
Indications
Tuberculosis, Leprosy
Contact prophylaxis in meningitis
Isoniazed
Tuberculosis
Pyrazinamide
Ethambutol
Tuberculosis
Tuberculosis (if isoniazid
resistance is likley)
Adverse effects
Deranged LFTs
Orange secretions
CP450 inducer
Peripheral neuropathy (Rx pyridoxine), Hepatotoxicity
Hepatocellular toxicity
Retrobulbar neuritis (< 8 weeks
therapy)
Infections by Organ system
Cerbral Infections
Disease
Organisms
Cerebral
Local infection: Bacterial
Abscess
(strep milleri, bacteroides,
staph) or fungal
Metastatic infection:
pneumonia, infective
endocarditis
Encephalitis
Meningitis
Bacterial: secondary to
meningitis
Viral: Herpes simplex,
rabies
Fungal: histoplasma,
cryptococcus
Protozoal: toxoplasma,
plasmodium
Viral: Enteroviruses
Bacterial: N. meningitidis,
Group B strep, Gram -ve
bacilli, Listeria Fungal:
Cryptoccous, candida
Features/Ix
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
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.
Inflammation of the meninges
Stiff neck, headache, fever,
photophobia, non-blanching
rash, vomiting, confusion, joint
pain, seizures
Ix: LP
Treatment
Aerobes - cephalosporin
Anaerobes – metronidazole
+ dexamethasone +/- antifungal
? Surgery to reduce
pressure
Mostly due to herpes
simplex so use acyclovir I.V.
Emergency:
1.2 g benzypenicillin IM
Cefotaxime 2g 6-hourly IV
+/- ampicillin for Listeria
Contacts – rifampicin or
ciprofloxacin
Vaccination
Lung Infctions
Disease Organisms
CAP
Typicals (85%)
S. pneumoniae, H. influenza,
staph. aureus (elderly), M.
catarrhalis (smoking), Klebsiella
(alcoholic)
Atypicals (15%)
Mycoplasma, Legionella
Zoonoes: Chlamydia, Coxiella,
bordetella
HAP
AP
TB
Viruses:
Influenza A & B, Varicella and
Herpes pneumonitis
Gram -ve, few Gram +ve
Klebsiella, Serratia,
Enterobacter, Pseudomonas
Nearly always Gram -ve
organisms from the gut
Mycobacterium tuberculosis
Features/Ix
General symptoms, Cough
+/- sputum, SoB, Pleuritic
chest pain
Reduced air entry, Dullness
to percussion, Tactile vocal
fremitus, Bronchial
breathing, Crackles coarse
Treatment
Typicals - β lactams,
Amoxicillin, Cefuroxime
Atypicals – Macrolides,
Clarithromycin/Erythromycin
Anti-virals - amantadine +/neuraminidase inhibitors
Chest X-ray: Consolidation
Gram +ve - Vancomycin,
Gram –ve – Ceftazidime,
Gentamicin
Cefuroxime and
metronidazole
AFB on Ziehl-Neelson staining Rifampicin, Isoniazed,
Culture up to 7 weeks!
Pyrazinamide, Ethambutol
Mantoux - Does not
distinguish vaccinated and
infected/Not reliable in HIV
GI Infections
Disease
Throat
Infections
Upset Tummy
Hepatitis A
Hepatitis B
Hepatitis C
Organisms
Herpes
Tonsillitis
Glandular fever
Candidiasis
Bacteria - staph. aureus,
bacillus cereus, lostridium,
listeria
Viruses - Rota virus,
Noraviruses, Adenovirus,
Hepatitis A
Protozoa - Entamoeba
histolytica, Giardia lamblia
Cryptosporidium
Features/Ix
Treatment
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
Faeco-oral spread
Incubation: few weeks
Acute never chronic
Systemic symptoms +
jaundice
Elevated AST/ALT
Spread through sex, blood
products, vertical
Incubation - up to 6 months
Acute or chronic
Increased risk of cirrhosis and
HCC
Support with fluids,
loperamide
As for Hep. B - but blood
spread most common
Acute or chronic
Complications of chronicity 30% cirrhosis, 5%
hepatocellular carcinoma
Antibiotics for neonates,
elderly and
immunocompromised
(Ciprofloxacin)
Treat protozoals with
metronidazole
Interferon alpha,
lamuvudine (NRTI) or
adefovir
Only a 40% success rate
Vaccination for certain
groups
Transplantation
Peginterferon alpha
Sexually Transmitted Infections
Disease
Organisms
Chlamydia
Chlamydia
trachomatis
Gonorrhoea
Gram -ve intracellular
cocci
NSU
Syphilis
LGV
HSV
HPV
Treponema pallidum
Lymphogranuloma
venereum caused by
L1/L2/L3 variant of
Chlamydia
Type I - cold sores,
gingivostomatitis
Type II - genital sores
Features/Ix
Incubation a few weeks
Clear mucoid discharge
Mucopurulent cervicitis
Asymptomatic (80% female, 50%
male)
Dx requires: Urine, Endocervical
swab
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
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
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)
Painless ulcerative papule
Heals to give painful
lymphadenopathy/buboes
Ciprofloxacin/ofloxacin
3rd gen cephalosporin ceftriaxone
Single dose azithromycin
Complication - epidydimoorchitis, reactive arthritis
2.4 MU penicillin
Doxycycline
Topical or systemic acyclovir
Low Grade (types 6/11) - painless
warts
High Grade (types 16/18/31/32) CIN/AIN
HIV


Treatment
Single dose of azithromycin
A retrovirus with an RNA genoma
Relies on reverse transcriptase to integrate into genome
Podophyllin extract
Cryotherapy



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)
o Screening test
 Viral load (PCR)
o Very sensitive and definitive test
o Initial baseline plasma viral load predict time for active disease to appear
Monitoring
 Viral load
 CD4+ T cell counts
 HIV-resistance tests
o Expensive tests that look at resistance to anti-retroviral medication
Therapies
 “HAART”
o Reverse transcriptase inhibitors
o Protease inhibitors
Type
NNRTs - nucleoside
analogues
Drug
Zidovudine (AZT)
Didanosine (DDI)
Zalcitabine (DDC)
Lamivudine (3TC)
Abacavir
NNRTI - non-nucleoside
analogue
Nevirapine
Efavirenz
Protease Inhibitors
Saquinavir
Efavirenz
Indinavir
Side Effects
Myelotoxicity -anaemia and neutropenia
Muscle wasting
Pancreatitis
Peripheral neuropathy
Peripheral neuropathy
Well tolerated so used first line
May cause SJS so required screening before
using
May cause SJS
Enzyme inducer
Popular at present - O.D. dosing
25% develop minor skin rash
Deranged LFTs
Perioral hyperaesthesia
Kidney stones
Urinary Tract Infections
Disease
Organisms
Simple Cystitis
E.coli, proteus,
staphylococcus
saprophyticus,
Pyelonephritis
Klebsiella,
Enterococcus
Skin Infections
Disease
Cellulitis
Infected eczema
Dermatophytosis
Organisms
Staph. and strep.
Impetigo -Usually
caused by Strep.
pyogenes
Eczema herpeticum Caused by HSV 1 & II
Trichophyton and
microsporum are most
common
Features/Ix
Dysuria, Frequency,
Suprapubic pain, urgency
Systemic sx, Loin pain and
tenderness
Treatment
Trimethoprim, amoxicillin,
nitrofurantoin, cephalosporin
Requires IV antibiotics Cefuroxime + Gentamicin
Men and children require
urography post-infection
Features/Ix
Infection and inflammation of
connective tissue underlying skin
Often following minor skin
trauma
Superficial bacterial skin
infection common in kids
Serious
Widespread vesicular rash
A group of skin infections caused
by dermatophytes
- Tinea corporis
- Tinea crucris
- Tinea pedis
- Onychomycosis
Treatment
Flucloxacillin + coamoxiclav
Topical fusidic acid,
mupirocin
oral if severe
Topical and oral aciclovir
Cotrimazole (Imidazole)
Miconazole (Imidazole)
Terbinafide (Allylamines)
Tropical Infections
Disease
Organisms
Malaria
P. falciparum
P. vivax
P. ovale
P. malariae
Features/Ix
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?)
Leptospirosis
Lyme Disease
Spirochaete - Borreli
burgorferi
Schistosomiasis
Schistosomal
cerceriae
Trypanosomiasis
Trypanosomal
protozoans
Leishmaniasis
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
Ticks on infected deer/mice
Localised early disease: erythema
chronic migrans + minor systemic
Disseminated disease: systemic
disease (arthritis, carditis, neurol
symptoms)
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
2 types:
• African (Sleeping sickness) Gambiense/rhodesiense
• American (Chagas disease) - Cruzi
Baghdad boil, kala azar, dum-dum
fever
Spread by sandflies
Cutaneous (skin sores) or Visceral
(hepatosplenomegaly, anaemia)
Treatment
Prophylaxis
Avoid getting bitten nets, repellants etc.
Treatment
P. Falciparium - quinine +
tetracycline
Non-falciparium chloroquine + primaquine
Erythromycin
Erythromycin
Priziquantel
Amphotericin or
Miltefosine