Microbiology Revision

Mark Eveleigh

Section Outline

1. Bacteria

2. Viruses

3. Eukaryotic organisms

4. Immunisation

Section 1: Bacteria

Bacteria

• Have no nucleus and few organelles• Thick peptidoglycan cell wall = Gram

positive• Thin cell wall = Gram negative

Groups of bacteria

• Gram positive cocci• Gram positive bacilli• Gram negative cocci• Gram negative bacilli• Obligate intracellular organisms

Gram positive cocci: Staphylococci

• S. aureus– Common commensal– MRSA– Skin and soft-tissue infections, LRTI,

meningitis, osteomyelitis, endocarditis, TSS, septicaemia

• S. epidermis– Normal commensal– Skin and soft tissue infections, prosthesis and

line infections

Gram positive cocci: Streptococci

• S. pyogenes– Pharyngitits, impetigo, erysipelas, scarlet fever,

necrotizing fascitits, TSS, septicaemia, Rheumatic fever, post-streptococcal glomerulonephritis

• S. pneumoniae– Pneumonia, otitis media, meningitis,

septicaemia, peritonitis

• S. viridans– Endocarditis

• S. mutans– Dental caries

Gram positive cocci: Enterococci

• E. faecalis– UTI, wound infections, septicaemia, SBE– VRE

• E. faecium– UTI, wound infections, septicaemia– VRE

Gram positive bacilli: Anaerobes

• Clostridium– C. botulinum

• Botulism– C. perfringens

• Gas gangrene– C. difficile

• Diarrhoea, pseudomembranous colitis– C. tetani

• tetanus

• Actinomyces israelli– Subcutaenous infections especially around the

jaw

Gram positive bacilli: Aerobes

• Bacillis anthracis– Cutaneous infection, fever, organomegaly,

systemic involvement leading to haemorrhage

• Corynebacterium diptheriae– Tonsillitis, fauces pseudomembrane,

lymphadenopathy

• Listeria monocytogenes– Pneumonia, meningoencephalitis, ataxia, rash,

stillbirth

Gram negative diplococci: Neisseria

• N. meningitidis– Only infects humans– Meningitis– Septcaemia

• N. gonorrhoeae– Urethral discharge, proctitis, pharangitis,

Reiter’s, endocarditis, ophthalmia neonatorum, infertility

Gram negative diplococci: Moraxella

• M. catarrhalis– Pneumonia, infective exacerbations of COPD,

otitis media, sinusitis, septicaemia

Gram negative bacilli: Anaerobes

• Mycobacterium– M. tuberculosis

• Pulmonary (1o), miliary, meningeal, genitourinary, bone (Pott’s), skin (lupus vulgaris), peritoneal, pericarditis

– M. bovis• Rarely TB in humans from cattle

– M. leprae• Tuberculoid (ineffective immune response)

or lepromatous (vigourous immune response)

– M. avium intracellulare• Usually only in immunocompromised

Gram negative bacilli: Anaerobes

• Helicobacter pylori– Ulcers, MALTomas, GORD

• Spirochaetes– Treponema pallidum

• Primary (chancre), secondary (systemic features e.g. condylomata lata), tertiary (gummas) and quaternary syphillis

– Leptospira interrogans• Tropical granulomatous ulcers

– Borrelia burgdorferi• Lyme disease (erythema chronicum

migrans)

Gram negative bacilli: Enterbacteriaceae

• Escheria coli– Neonatal meningitis, pneumonia, UTI,

diarrhoea (HUS in 0157 strain), osteomyelitis, endocarditis, soft-tissue infection, septic arthritis, septicaemia

• Shigella– Travellers diarrhoea

• Salmonella– Similar to E. coli– Typhoid, parathyoid, UTI, septicaemia,

aneurysm infection, osteomyelitis

Gram negative bacilli: Enterbacteriaceae

• Klebsiella– Common commensals– Pneumonia, UTI, line/prosthesis infections,,

meningitis, osteomyelitis, endocarditis

• Enterobacter– Normal commensals– Soft-tissue infections, UTIs, endocarditis

• Proteus– UTI, struvite nephrolithosis

• Yersinia– Plague (pestis), enterocolitis, mesenteric

lymphadenitis (enterocolitica)

Gram negative bacilli

• Haemophilus influenzae– Meningitis, epiglottitis, pneumonia, septic

arthritis, cellulitis

• Pseudomonas aeruginosa– Pneumonia, UTI, skin infections, bacteraemia

• Brucella– Zoonosis– Indolent infection causing malaise,

organomegaly, diarrhoea, constipation, other non-specific features

– Complications osteomyelitis, meningoencephalitis, abscesses

Gram negative bacilli

• Bordetella pertussis– Whooping cough, pneumonia

• Campylobacter jejuni– Zoonosis– Enteritis– Systemic in immunocompromised

• Vibrio cholera– Epidemic diarrhoea

Obligate intracellular pathogens

• Chlamydia– C. trachomatis

• Cervicitis, salpingitis, conjunctivitis, neonatal pneumonia, PID

– C. psittaci• Pneumonia after bird exposure

– C. pneumonia• Pneumonia, URTIs

• Legionella pneumophilia– Atypical Pneumonia

• Mycoplasma pneumoniae– Atypical pneumonia

Obligate Intracellular Pathogens

• Rickettsia– Coxiella burnetti

• Q fever from cattle/sheep reservoir– Bartonella bacilliformis

• Infects RBCs from sandflies– Bartonella henselea

• Cat-scratch fever– Bartonella quintana

• Lice– Ehrlichia chaffeensis

• Tick-borne– Typhus

• Causes widespread vasculitis

Section 2: Viruses

Viruses

• Infectious sub-microscopic agent• Not really ‘life’ by most definitions• Either DNA or RNA• Replicate inside host cells: have no

capacity to replicate by themselves• Growing appreciation of role in cancers

Groups of Viruses

• DNA viruses– Single-stranded– Double-stranded

• RNA viruses– Single-stranded– Double-stranded– Retroviruses

DNA: single stranded

• Erythrovirus (formerly parvovirus)– Fifth disease– 1st phase: ‘slapped cheek’ appearance– 2nd phase: extensor morbilliform eruption– 3rd phase: rash fades to reticulate pattern– Joint involvement more common in adults

DNA: double-stranded

• Papillomavirus– Viral warts, cervical cancer

• Adenovirus– URTI/LRTI, viral meningitis

• Variola– smallpox

• Vaccinia– cowpox

• Orf– Cutaneous pustules caught from sheep

• Molluscum contagiosum– ‘pearly’ papules

DNA: double-stranded

• Human herpesviridae– HHV1: (HSV1) predominantly oral, lies latent in

neuron– HHV2: (HSV2) predominantly genital, lies latent

in neuron– HHV3: (varicella) chicken-pox and shingles, lies

latent in neuron– HHV4: (EBV) mononucleosis, Burkitt’s

lymphoma, post-transplant, hairy-leukoplakia, lies latent in B-cells

– HHV5: (CMV) retinitis– HHV6: (Sixth disease) roseola infantum– HHV8: Kaposi sarcoma-associated herpesvirus

RNA: Positive single-stranded

• Rhinovirus– Coryza

• Rubella– Usually benign but can cause arthropathy– Congenital infection causes deafness,

microcephaly, cataracts, cardiac defects

• Alphavirus– May cause encephalitis

• Flavirus– Yellow fever, hepatitis C, dengue

• Coronavirus– LRTI/URTI, SARS

RNA: Positive single-stranded

• Enterovirus– Coxsackie A

• Meningitis, gastroenteritis– Coxsackie B

• Pericarditis, Bornholm disease– Polio

• Abortive, non-paralytic or paralytic poliomyelitis

– Echovirus• Meningitis

– Hepatitis A

RNA: Negative single-stranded

• Influenza– Types A and B– Subtypes of A based on (H)aemagglutinin and

(N)euroaminidase– 4 day incubation, droplet spread– Complications bronchitis, LRTI, sinusitis, otitis

media, encephalitis, pericarditis, Reye’s syndrome

• Parainfluenza– Seasonal LRTI/URTI in children e.g. croup

RNA: Negative single-stranded

• Mumps– Parotitis, orchitits, meningoencephalitis,

deafness

• Measles– Coryza, conjunctivitis, Koplik spots– Complications otitis media, LRTI and SSPE

• Respiratory syncitial virus– Bronchiolitis

• Lassa• Lymphocytic-choriomengitis virus• Rabies

RNA: retroviruses

• HIV– 2 subtypes HIV-1 and HIV-2– Infects CD4+ T-cells– Seroconversion after 2-6 weeks– AIDS develops once CD4 count <200x106

– Complications opportunistic infection, HIV-encephalopathy, AIDS-dementia, Kaposi’s sarcoma, oral hairy leukoplakia, non-Hodgkin’s lymphoma, retinitis

• Human T-Lymphotropic virus– T-cell leukaemia/lymphoma

Section 3: Eukaryotes

Eukaryotes

• Protista• Fungi• Animalia

Protista: flagellates

• Trypanosoma– T. gambiense

• African Sleeping sickness (slow, wasting)– T. rhodesiense

• African Sleeping sickness (rapid, progressive)

– T. cruzi• Chagas disease (S. america)

• Trichomonas– Vaginitis (‘fishy’, thin discharge, STI)

• Giardia lamblia– Chronic infestation in duodenum/jejunum

Protista: flagellates

• Leishmania– L. major and L. tropica

• Cutaneous leishmaniasis causing ulcer at site of sandfly bite

– L. brasiliensis• Mucocutaneous leishmaniasis

– L. donovani, L. chagasi and L. infantum• Visceral leishmaniasis or kala-azar• dry, warty, hyperpigmented skin lesions• Hypersplenism and lymphadenopathy• High untreated mortality

Protista: Amoeboids

• Entamoeba histolytica– Dysentery, liver abscess, invasive disease

• Cryptosporidium– Uncomplicated diarrhoea– Severe resistant form in immunocompromised

Protista: Sporozoa

• Plasmodium– P. falciparum

• Severe malaria• Complications cerebral malaria, metabolic

acidosis, anaemia, hypoglycaemia, pulmonary oedema, hyperparasitaemia

– P. malaria• Benign, but may cause glomerulonephritis

– P. vivax and P. ovale• Benign, but can lie dormant in liver

• Toxoplasma– Cat host– Congenital defects in pregnancy

Fungi

• Dermatophytes– Trichophyton, Microsporum and Dermatophyton

• Superficial skin and nail infections

• Histoplasma capsulatum– LRTI, retinitis, disseminated disease

• Malassezia furfur– Pityriasis versicolor (macular ‘tan’ rash)

• Cryptococcus neoformans– Meningitis, LRTI in immunocompromised

• Pneumocystis jiroveci– Pneumonia in immunocompromised

Fungi

• Aspergillus– A. fumigatus

• Asthma, ABPA, aspergilloma, invasive aspergillosis

– A. flavus• ABPA, aspergillosis, HCC

– A. clavatus• EAA in association with malt

• Candida albicans– Oral and vaginal thrush, systemic infection in

immunocompromised

Animalia: helminths

• Nematodes– Necator americanus and Ankylostoma

duodenale• Iron deficiency anaemia in Asia, Africa and

Americas– Stongyloides stercoralis

• Cutaenous larva migrans in subtropics– Toxocara canis

• Visceral larva migrans and blindness– Enterobius vermicularis

• Anal itch common in temperate climates– Ascaris lumbricoides

• Migrates to biliary tree

Animalia: helminths

• Cestodes– Taenia

• T. solium– From pork

• T. saginata– From beef

– Neurocysticerosis• Seizures, hemiplegia, hydrocephalus

– Diphyllobothrium latum• Fish tapeworm

– Echinococcus granulosus• Caused by ingesting eggs of parasite (dog)

Animalia: helminths

• Trematodes– Schistosoma

• S. mansoni and S. japonicum– From water-snail vectors– Inflammation and scarring due to type

IV hypersensitivity to eggs– Fasciola hepatica

• Hepatic fibrosis from sheep, snails and water

– Paragonimus westermani• Pulmonary infestation from crabs/ crayfish

– Clonorchis and Opisthorchis• Cholangi -tis/-iocarcinoma, cholecystitis

Section 4: Immunisation

Immunisation

• Active stimulates the body’s own immune system to respond

• Passive is the provision of pre-formed antibodies

• Vaccines may be live, attenuated, dead or toxins

• Adjuvants are often added to stimulate an immune response, often aluminium or bacterial cell-wall compounds

UK immunisation scheduleAge Vaccine

2 months Diptheria, tetanus, pertussis, polio, Hib, pneumococcus

3 months Diptheria, tetanus, pertussis, polio, Hib, meningitis C

4 months Diptheria, tetanus, pertussis, polio, Hib, pneumococcus, meningitis C

12 months Hib, meningitis C

13 months MMR, pneumococcus

3 years Diptheria, tetanus, pertussis, polio, MMR

12 years (♀ only) HPV 16+18

18 years Diptheria, tetanus, polio

*Non-standard vaccinations include hepatitis B and TB (BCG) if specific need identified

UK immunisations

• For travellers• Yellow fever, typhoid, tetanus, polio, rabies

(pre-exposure), meningococcus, Japanese encephalitis, tick-borne encephalitis, hepatitis A and hepatitis B

• Exact vaccines will depend on location, activity and perceived risk pertaining to travel

Live versus inactivatedLive vaccines Inactivated vaccines

Measles Diptheria (toxoid)

Mumps Tetanus (toxoid)

Rubella Pertussis

Polio (oral) Polio (injection)

Typhoid (oral) Meningococcus C

TB (BCG) Haemophilus influenzae B

Yellow fever Pneumococcus

HPV (Cervarix)

Hepatitis A

Hepatitis B

Typhoid (injection)

Influenza

Japanese encephalitis

Tick-borne encephalitis

Rabies