Bacteriology

Koch’s postulates

I. the microorganism must be present in every case of the disease
(not in healthy animals)
II. the microorganism must be isolated from the diseased host and
grown in pure culture
III.the specific disease must be reproduced when a pure culture of
the microorganism is inoculated into a healthy susceptible host
IV.the microorganism must be recoverable from the experimentally
infected host and shown to be identical to the original causative
agent.

Virulence gene postulates

Gene should be in virulent strain & not in non-virulent strain. Disrupting gene should make it non-virulent. Introduction should cause disease.

Cycle of infection

Encounter → Entry → Spread → Evade → Multiply & Damage → Disperse

Ingress

Bacteria enter via open source (mouth)

Penetration

Bacteria enter via newly made orafice

Iatrogenic

Infections caused by medical examination or treatment.

Type 3 secretion system

A needle-like protein appendage used by certain bacteria to inject effector proteins directly into host cells.

Adhesins

Surface molecules on bacteria that facilitate attachment to host cells.

S.aureus defences

Inhibit opsonization, kill phagocyte, resist lysosome action.

Virulence factors: Coagulase, Hyaluronidase, Protein A, Heamolysins, Staphylokinase, Lipase, Protease

Mycobacterium TB defences

Inhibit IFN-Y activation of macrophages, hibit lysosome fusion

Strep.pyogenes defences

Hyaluronic acid capsule - inhibit phagocytosis, produce toxins to damage host tissues.

Leukocidins - kill phagocytes and destroy immune cells.

Degradation of host tissue:

• Hyaluronidase (connective tissue)
• Streptokinase (clots)
• Streptodornase (DNA)
• Protease
• Adhesins
• Anti-opsonic factors

Infection risk factors

Genetics (leprosy susceptibility), Sex bias (UTIs), Stress, Age extremes, poor nutrition, overcrowding, violent exercise, lifestyle (diet, smoking…), hygeine.

Direct detection

Establish microbe at particular site. Determines: therapy response, epidemiology info.

Use microscopy to detect whole organism, or detect components (Ag/DNA test)

Doesn’t show treatment susceptability, serotypes.

Indirect detection

Provide definite ID + sertotyping + susceptability via culture.

Must use correct media + conditions. Some bacteria not cultivatable.

Selective media

Contain components that are inhibitory to specific microorganisms.

Like: antibiotics, chemicals (NaCl, Bile salts).

Indicator media

Indicates a certain property of the bacteria.

Like: sugar fermentation on MacConkey agar.

Bacterial ID

Confirming specific bacteria using growth on selective and/or indicator media and further testing:

Gram stain: Chemical process that distinguishes between bacterial cell walls that retain crystal violet, and those that do not, when stained and washed
with acetone. G+ = purple G-= pink

Haemolysis types for Streptococcus.spp

Oxidase test for G- bacilli

Catalase for S.aureus or not

MALDI-TOF - Bacterial mass spectrometer

Susceptability testing

Measure zone of inhibition - Against known breakpoint zone sizes to give; sensitive (s),
intermediate (I) or resistant (R).

Commercial e-tests - give minimum inhibitory concentration.

Breakpoint plates - Positive or negative for growth on media containing a specific
concentration of antibiotic

Immunological testing

Antibody detection:

IgM detection, rise in Ab titre, seroconversion - specific Abs developing when immune response occurs. IFN-Y detection in mTB.

Useful for non-cultivatable organisms. But can only use if patient can make Abs, and too slow for treatment response.

Biofilms

Structured aggregate of bacteria in polymeric matrix.

Function to capture, concentrate and conserve resources & protection.

Composed of 10-30% bacteria & 70-90% extracellular polymeric substance (mainly exopolysaccharide)

Biofilm formation

Stages: Initial attachment → Irreversible attachment → Maturation 1 & 2 → Dispersion

Triggers:

Dessication, antibiotics, high cell density → quorum sensing → Production and detection of signalling molecules: N-acyl homoserine lactones, oligopeptides, autoinducer-2 → Trigger gene expression (surface attachment genes…) → EPS production

Emergent properties

Properties or behaviours that arise
in a complex system that are not predictable from study of the individual components

Emergent properties of Biofilms

Slower growth, change in gene expression, resistance to antibiotics (physical/genetic), resistance to immune response, increased spontaneous mutation, increased HGT

Oral biofilms

Gingivitis - plaque biofilm causing gum inflammation.

Periodontitis - progression of gingivitis leading to teeth + joining tissue inflammation

Wound biofilms

Polymicrobial biofilms that slow down healing process. Debridlement used to treat rather than antibiotics

Device biofilms

Facilitated by host coating it in inflammatory molecules which bacteria bind to → surface conditioning occurs to form biofilm.

Surgical removal usually required

Staphylococcal biofilms

Occur with S.aureus / S.epidermidis. Microbial Surface Components that
Recognize Adhesive Matrix Molecules Mediate adhesion to cell and surfaces
coated with host plasma proteins: Fibronectin, Fibrinogen, Collagen, Laminin, Vitronectin

Cystic fibrosis

Defect in CFTR gene - affects chloride transport → Secretions lack water → Lungs fill with thick mucus → opportunistic biofilm made from Pseudomonas aeruginosa

Antibiofilm compounds

Type I - cell killers - disrupt membranes

Type II - matrix killers - disrupt matrix so antibiotics can work

Cystitis

Inflammation of the bladder

Pyelonephritis

Kidney parenchyma infection

Urethritis

Inflammation of urethra

UTI

Infection typically caused by a single bacterial pathogen. Usually a member of the patient’s enteric/skin microbiota. Most frequently ascending infections. Commonly causing: urethritis, pyelonephritis, cystitis

Communnity acquired - 80% E.coli

Hospital acquired - Gram-negative bacteria other than Escherichia coli, commonly include Klebsiella spp., Enterobacter spp., Serratia spp. and Pseudomonas aeruginosa.

UTI defences

Urine: Urine flow, Osmolarity, pH, organic acids, prostatic secretions.

Urinary tract mucosa: Defensins/antimicrobial peptides, Glycosaminoglycan (restricts adherence), Tamm-Horsfall protein (inhibits fimbriae action), IgA, Lactoferrin (iron sequestration)

UTI risk factors

Sex - anatomy + pregancy

Age - Reduced expression of Tamm-Horsfall protein. Prostatitis/prostatic hypertrophy (increased retention). Microbiota changes in women (pH)

Structural abnormalities (retention of urine): Urethral valves, Stenosis of ureters/urethra, Vesicoureteral reflux, Calculi (stones)

Diabetes - increased glucose in urine

Bladder UTI

Adhesion - Type 1 pili binds mannosylated uroplakins → invasion

Formation of intracellular bacterial communities for protection and further invasion

Cell damage/death - eveals transiontal cells & releases iron + nutrients

Kidney UTI

P (pap) pili are required for adhesion and IgA suppression in pyelonephritis

Bladder UTI (Proteus)

Proteus introduced from catheterisation. Urease produced → increases pH → crystals (struvite) forms, making biofilm

UTI diagnosis

Compare urine samples from catheter/midstream.

Dipstick: Nitrate - bacteria detection. Leukocytes - pyuria (pus in urine). Blood & haem products in urine.

Semi-quantitation: Microscopy, laminar flow, flow cytometry.

Quantitation: Gram staining, selective media, MALDI-TOF, susceptability testing

UTI treatment

Uncomplicated cystitis: Antibiotic treatment: Nitrofurantonin, Fosfomycin, Fluoroquinolone, B-lactams.

Pyelonephritis: Amioglycosides, Carbapenams, Same as normal minus nitrofurantoin

UTI prevention

Methenamine → formeldahyde causes decrease in urine pH.

Restriction of spermicides in contraception - reduces microbiota disruption.

Topical estrogens - reverse pre-menopausal microbiota → Decrease pH

STIs

Close sexual contact required for
transmission (or via contaminated blood
products). Most bacterial causes are very vulnerable to temperature change/desiccation

STI Risk factors

Age - 16-24

Institutionalisation

Sexual lifestyle - partners, travel, MSM, use of contraceptives

Gonorrhoea

Caused by Neisseria gonorrhoeae (intracellular). 2nd most common STI.
-Incidence peaks in males 20-24, females 16-19
-Sex bias on symptom presentation

Gonorrhoea symptoms

Discharge of pus from urethra/vagina/rectum
-‘Burning’ sensation
-Testicular/scrotal pain (epididymitis)
-Anal itching/bleeding
-Sore throat (oral inoculation)
-Non-genital complications

Symptoms are indistinguishable from
non-gonococcal urethritis (Chlamydia trachomatis)

Gonorrhoea complications

Disseminated infection: Arthritis-dermatitis syndrome, Meningitis/osteomyelitis/sepsis.

Pelvic inflammatory disease: Salpingitis (infection of fallopian tubes), Tubo-ovarian abscesses, Ectopic pregnancy, Sterility.

In men: Orchitis, Epididymitis, Sterility

Ophthalmia neonatorum

N. gonorrhoeae pathogenesis

Adhesion via type IV pili & Opa protein for tight adherence.

Uptake via transcytosis.

Induction of large quantities of PMNLs
(polymorphonuclear lymphocytes): peptidoglycan fragments, lipopolysaccharides, outer.mem. vesicles.

Pathogen resists: PMNLs, complement, IgA activity (via protease).

Damage, caused by: Inflammation, products of PMNLs + Toxic effects of OMVs & LOS

Gonorrhoea diagnosis

Take swab or urine sample (low sensitivity for women).

Nucleic acid amplification technology (NAAT). Or culture & microscopy from swab

Gonorrhoea treatment

Current treatment = high dose (1g)
ceftriaxone (injection). Oral cefixime &
azithromycin can be used as an
alternative.

Use contact tracing.

non-gonococcal/specific infection

Typically caused by Chlamydia trachomatis - intracellular parasite.

Most common STI in the UK
-Incubation 1-3 weeks
-50% males 80% females remain asymptomatic
-10-40% women develop pelvic inflammatory disease
Symptoms/complications typically indistinguishable
from those of gonorrhoea
Co-infection with N. gonorrhoeae can occur

Chlamidya lifecycle

T3SS Injects invasion effectors - internalisation & anti-apoptotic factors. T3SS injects early effectors - blocks lysosomal fusion & recruits exocytic vesicles. → Transition to reticulate body (metabolically active) + replication →
Synthesis of invasion effectors and transition to elementary body for release

Chlamydia diagnosis

Swap or urine sample taken (low sensitivity in women). NAAT or cell culture (only on swab) performed.

Chlamydia treatment

Doxycycline 100mg twice daily for 7 days. Or, Azithromycin 1g single dose (followed up with 500mg once daily for 2
days).

Doxycycline associated with greater
clinical cure rates. Fewer compliance problems with azithromycin. AMR rare.

Mycoplasma genitalium

Alternative cause of non-gonococcal urethritis. Similar presentation to chlamydia/gonorrhoea. Slow uptake on NAAT. Treated with moxifloxacin

Syphillis

Caused by T. pallidum pallidum.

Manifests in 3 stages:

Primary - painless chancre (ulcer) forms. Secondary (6-8 wks) - malaise, rash, Condylomata lata (wart). Tertiary (3-30 yrs) - Gumma, Cardiovascular/ meningovascular lesions, insanity.

Syphillis diagnosis

Serological testing: Treponemal Abs - remain + for life. Non-treponemal - decline after treatment. Infection can be missed in lag phase.

Treatment:
Benzathine/procaine penicillin
(IM injection)

Bacterial vaginosis

Reduction in the dominant
lactobacilli in the vagina &
increase in other organisms
(Gardnerella vaginalis &
Bacteroides spp.)

Risk factors include multiple sexual partners
Diagnosis - ‘clue cells’ and the ‘whiff test

Folliculitis

Superficial hair follicle infection by S.aureus or Pseudomonas aeruginosa (hot tub folliculitis).

Bacterial buildup → spot lesions

Furuncle

Deep foliculitis of one follicle - infects root

Carbuncle

Furuncle collection subcutaneously, extends to subcutaneous fat. Can’t treat with antibiotics.

Impetigo

Superficial skin infection by group A Strep/S.aureus. Common in kids.

Initially disrupts corneal layer → access subcorneal keratinocytes → crust lesions form.

Staphylococcal scalded skin syndrome (SSSS)

S.aureus infection produces exfoliating exotoxin, causing vast skin exfoliation. Risk of fluid/electrolyte imbalance & secondary infection.

<6 y.o most susceptable, but more fatal in adults

Erysipelas

Superficial cellulitis by Group A Strep. Makes red lesions on face/lower extremities.

Cellulitis

Infection of skin & underlying tissues by: S.aureus, Group A Strep & P.aeruginosa (Fournier’s Gangrene).

Can lead to sepsis due to rapid development.

Necrotising fasciitis

Severe infection of soft tissues - superficial & deep fascia. Caused by Group A Strep → cellulitis → fluid accumulation → impairs blood flow → tissue destruction rapidly.

Treated with amputation/excision.

Gangrene

Infection of deep tissues by Clostridium spp. causing myonecrosis. Arises in areas with poor blood flow.

C perfringens (gas gangrene): Alpha toxin – phospholipase
• Rapid metabolism = gas
• Extremely rapid spread
• Surgical intervention required

Anthrax

Caused by Bacillus antraxis - G+ve sporing bacteria found in soil/faeces.

Cutaneous anthrax:

Rare ulcerative skin lesion with central necrosis & black ‘eshar’.

Rickettsial infection

Rickettsia spp. - Obligate intracellular pathogens. Transmitted by fleas/ticks/mites/lice.
• Epidemic typhus - Rickettsia prowazekii - Skin rash resembling that of typhoid. Transmitted by Pediculus corporis
• Endemic typhus - Rickettsia typhi
• Scrub typhus - Orientia tsutsugamushi
• Rocky mountain spotted fever -Rickettsia rickettsi

Cat/dog bites

Injury causing Pasturella multocida or Capnocytophaga canimorus infection.

Rat bites

Injury causing Spirillum minus/Streptobacillus moniliformis infection

Human bite

Injury causing infection of oral commensal bacteria or Eikeella corrodens

Lyme disease

Disease caused by Borellia burgdorferi infection from Ixodes tick bite.

Symptoms:

• Fever
• Muscle pain
• Headache
• ‘Target shaped’ rash

Osteomyelitis

Bone infection with symptoms of: Pain/swelling/redness/warmth around
affected area.

Caused by: S. aureus, S. pyogenes, M. tuberculosis, Actinomyces israelii, Kingella kingae, T. pallidum

Arthritis

Swollen/painful/red joints – warm to
the touch. Caused by immunological reaction (reactive/rheumatoid) or infection (septic).

Causative agents:
• Staphylococcus aureus
• Coagulase-negative
staphylococi
• Salmonella enterica
• Haemophilus influenzae
• N. gonorrhoeae
• S. pyogenes (rheumatic
fever)

Oral infection

Opportunistic infection from
commensal oral microbiotia, causing: gingivitis, dental caries, abcesses, peridontal infection.

Or, Infection from primary pathogens:
• HSV
• Oral thrush
• Syphilitic lesions
• AIDS-associated lesions

Dental caries

Tooth decay due to bacteria -polymicrobial, but mainly Strep.mutans with biofilm secretions.

Treated by removal + fillings. Prevented with fluoride.

Can cause: apical/brain abcesses, osteomyelitis, sinusitis.

Gut commensals

Benefits for metabolism, resistance, Ab induction. Heavily affected by diet/antibiotics.

Obligate anaerobic bacteria, e.g. Bacteroides, outnumber the facultatively anaerobic coliforms, such as
E. coli by at least 100:1.

Gastroentiritis causes

Bacterial:
- Salmonella,
- Shigella,
- E coli
- Campylobacter
- Vibrio cholerae
- Clostridium difficile
- Staph aureus
- Bacillus cereus

Parasitic (protozoa):
- Entamoeba hist.
- Giardia lamblia
- Cryptosporidium

Viral:
- Norovirus
- Rotavirus

Cholera toxin

Binding onto epithelial cells → Retrograde endocytosis of toxin protiens → Targets G-Proteins → Triggers cAMP → Opens Cl- channels → H2O efflux into intestinal lumen → diarrhoea

Salmonella

Divided into typhoidal/non-typohidal.

Sourced from infected food → enter intestinal epithelia via endocytosis → Disrupt junctions between cells of intestine wall → enter macrophages - typohidal uses to disseminate in body via mononuclear phagocyte system.

Uses type III secretion system.

E.coli

Adheres to cell membrane by Tir embedding into membrane. So intimin adheres to Tir protein for constant bond.

O157 - produces Shiga toxin → large fluid buildups → diarrhoea

C.difficle

Bacteria producing A, B & Binary toxins that induce diarrhoea, toxic megacolon & pseudomembranous colitis. Spores are extremely hardy and can survive heat, UV light, dessication, radiation and most cleaning agents

Toxin mechanism:

glycosyltransferases modify small GTPases → apoptosis → chemokines made → tight junctions of epithelia degraded → fluid accumulation → diarrhoea

Use of antibiotics increases risk, as reduces normal flora. Reoccurrence common.

Campylobacter spp.

Sourced from raw meat/milk/untreated water. Penetrates intestinal mucosa via adhesion, internalidation & translocation. produces a cytolethal distending toxin, arrest cell division in G2 phase

Bacteraemia

Prescence of bacteria in blood

Septicaemia

Bacteria in blood causing symptoms. Caused by Gram-positive & Gram-negative bacteria & Candida albicans.

Newborns vulnearble to Listeria monocytogenes & Group B streptococcus.

DIagnosed with blood culture and CO2 (colourimetric) detection

Treated with empirical chemotherapy of: aminoglycosides, B-lactams, metronidazole

Sepsis

Organ failure due to bacterai in the blood

Plague

Disease caused by Yersinia pestis. Transmitted by droplets, contact, faecal-oral & vector.

Bubonic/pneumonic forms develop by infecting lymph nodes

Endotoxic shock

Bacteria emit Lipid A toxin (LPS component) → vasodilation → hypotension (warm shock) → peripheral blood vessels constrict (cold shock). Can cause disseminated intravascular coagulation - more bleeding as less coagulants.

Results in multiple organ failure, necrosis & death

Toxic shock syndrome (Exotoxic shock)

Toxin produced by S.aureus TSS T1 toxin. Nonspecifically binds MHCIIs to FCRs → cytokine storm occurs

Endocarditis

Infection of heart lining - mainly valves - where biofilms develop.

Pathology - pyogenic (pus) brain abcesses → stroke. Vegetation. Roth spots.

Early prosthetic valve endocarditis

<1yr post surgery. Occurs from contamination in surgery of: Coagulase- staph, S.aureus & diptheriodes (Cornyebacterium spp.)

Late prosthetic valve endocarditis

>1yr. Caused by: Viridans Strep, Enterococci, Coagulae- Staph. 100% without treatment

Vegetations

Caused by valve damage → change in blood flow → microcolonies develop → fibrin deposition → Become friable → septic emboli (spread).

Treated with bacteriocidal antibiotcs & surgery.

Major Duke criteria

Criteria to diagnose infective endocarditis (IE) 2x blood culture for + organisms known to cause IE.

Minor duke criteria

Risk factors - IV drug use, heart condition

Symptoms - fever, Janeway lesions, Roth’s spots

+ve blood culture

+diagnosis = 2 major/ 1 major 3 minor/ 5 minor

Mycotic aneurysm

Infection causing inflammation and damage and arterial wall leakage → bulging → aneurysm

Suppurative thrombophlebitis

Infection causing inflammation of vein wall → clots form → microbial colonisation.

Common in IV catheterisation

Upper airway defences

Air filtration, coughing, epigloting reflex, mucociliary clearance, secretory IgA.

Impaired by: tracheotomy, alcohol, foreign body, tumour, abnormal secretions, endotracheal intubation

Acute pharyngitis & tonsillitis

40-80% infections are viral
15-30% infections caused by Group A
streptococci (e.g. S. pyogenes)
• Other bacteria:
• Mycoplasma pneumoniae
• Chlamydophila pneumoniae
• Corynebacterium diphtheriae
• Neisseria gonorrhoeae

Treated with B-lactams or Macrolides

Diagnosed with symptom scoring and serotyping of swab.

Post streptococcal glomerulonephritis

Acute inflammation of kidney glomeruli → Blocks renal immune complexes → Hypersensitivity reaction