Wk7 - clinical microbiology 2 Flashcards
Bacterial GI infection agents include two categories according to the mechanism by which they cause illness
Direct infection – bacterial pathogens develop in the gut after ingestion of contaminated food.
incubation time of at least 8-12h before symptoms develop
Examples: Salmonella, Campylobacter, pathogenic E.coli
Intoxication (poisoning) - bacterial pathogens grow in foods and produce toxins
Relative short incubation time (as short as few hours) because of preformed toxin in food
Examples: Bacillus cereus, Staphylococcus aureus
Clinical terminology - diarrhoea
Abnormal frequency and/or fluid stool
Usually indicates small bowel disease
Causes fluid and electrolyte loss
Severity varies widely from milk-limiting to severe/fatal - virulence of organism, degree of compromise of the host
Clinical terminology - gastroenteritis
Nausea, vomiting, diarrhoea and abdominal discomfort
Clinical terminology - dysentery
Inflammatory disorder of the large bowel
Blood and pus in faeces
Pain, fever and abdominal cramps
Clinical terminology - enterocolitis
Inflammatory process affecting small and large bowel
manifestations of GI infection within GI tract (GIT) and outwith GIT
Within GI tract:
Toxic effects e.g. cholera
Inflammation due to microbial invasion e.g. shigellosis
Outwith GIT
Systemic effect of toxins e.g. STEC
Invasive infection of GIT with wider dissemination e.g. metastatic salmonella infection
Barriers to GI infection
Mouth - lysozyme
Stomach - acid pH
Small intestine - mucous, bile, secretory IgA, lymphoid tissue (peyer’s patches), epithelial turnover, normal flora
Large intestine - epithelial turnover, normal flora
Normal GIT flora
Lower GIT has very rich microbial flora (microbiome)
Each gram of faeces contains 100,000,000,000 microbes
1kg in weight of bacteria in the gut (most are anaerobes)
99% anaerobes
Still many important facultative organsisms particularly Enterobacteriaceae e.g. E.coli, Proteus spp
Protective and metabolic function
Sources of GI infection
Many GI infections are zoonotic - symptomatic animals (e.g. Salmonella Dublin), asymptomatic shedders (e.g. reptiles and salmonella carriage, E.coli 0157 in cattle)
Human carriers important for some (Typhoid - invasive infection - becomes incorporated into gut flora - can be passed easily to others)
Environmental sources - contamination of soil and produce e.g. Listeria, E.coli 0157
Transmission of GI infection
Faecal-oral - any means by which infectious organisms from human/animal faeces can gain access to GIT of another susceptible host
3F’s:
Food - contamination - farm to fork, cross contamination - distribution chain or domestic kitchen
Fluids - water, contaminated juices etc.
Fingers - importance of washing hands - after toileting, before and after preparing or consuming food and drinks
Person-to-person transmission - infectious dose (some have high dose e.g. e.coli, some have low dose e.g. norovirus), ability to contaminate and persist in the environment
Diagnosis of GI infection
History - can get useful clues - vomiting, abdo pain, diarrhoea, travel history, food history, blood in stools
Laboratory diagnosis of GI infection
10^10 organisms of normal gut flora per gram of faeces
Looking for a needle in a haystack so need to use various methods
Enrichment broth - contains nutrients that promote growth of the pathogen
Selective media - suppress growth of background flora while allowing growth of the pathogen
Differential media - distinguishes mixed microorganisms growing in presence of specific nutrients combined with an indicator that changes colour.
Salmonella will stain black, Shigella will stain pink
Microbiology of campylobacter
Curved Gram-negative bacilli
Microaerophilic and thermophilic (42oC)
Culture on Campylobacter selective agar
C. jejuni most important species
Epidemiology of campylobacter
Commonest bacterial foodborne infection in the UK
¨ Large animal reservoir (poultry, cattle, sheep, rodents & wild birds)
¨ Infection transmitted via contaminated food (esp. poultry), milk or water
¨ Marked seasonal peaks of infection in May & September
¨ Person-to person spread rare
¨ Large point source outbreaks uncommon (doesn’t multiply in food)
¨ ~70% of raw retail fresh (not frozen) chicken is contaminated with
Campylobacter
Pathogenesis of campylobacter
Inflammation, ulceration & bleeding in small and large bowel due to bacterial
invasion
¨ Bacteraemia can occur (extremes of age, immunocompromised)
¨ Rarely causes post-infectious demyelination syndrome (Guillain-Barre),
characterised by ascending paralysis
Clinical aspects of campylobacter
Incubation 2-5 days ¨ Bloody diarrhoea ¨ Cramping abdominal pain ¨ Vomiting is not usually a feature ¨ Fever ¨ Duration 2-10 days
Treatment of campylobacter
Fluid replacement is sufficient in most cases
¨ Clarithromycin for severe/persistent disease
¨ Quinolone (e.g. ciprofloxacin) or aminoglycoside (e.g. gentamicin) for invasive
disease
Control points for campylobacter
Reduction of contamination in raw, retail poultry meat
Adequate cooking
Microbiology of salmonella
Gram-negative bacilli
¨ Member of the Enterobacteriaceae
¨ Nomenclature confusing
n Majority of human infection caused by single species Salmonella enterica
n > 2000 serotypes defined on basis of lipopolysaccharide “O” antigens of the cell wall
and flagellar protein “H” antigens (Kauffmann-White scheme)
n Commonly referred to as if they are species in their own right e.g. Salmonella enterica
serovar Dublin is written as Salmonella Dublin.
¨ Non-lactose fermenters
¨ XLD plates most commonly used in clinical labs
Epidemiology of salmonella
Found in a wide range of warm and cold blooded animals
¨ Only S. Typhi & S. Paratyphi, the causal organisms of enteric fever (typhoid &
paratyphoid, do not have an animal reservoir
¨ Acquired via contaminated food, especially pork, poultry & other meat and
milk/dairy products
¨ Waterborne infection less common
¨ Large foodborne outbreaks can occur (can multiply in foodstuffs)
¨ Secondary spread via person-to-person transmission may be a feature
¨ Seasonal peaks in summer and autumn
Pathogenesis of salmonella
Diarrhoea due to invasion of epithelial cells in the distal small intestine, and
subsequent inflammation
¨ Bacteraemia can occur (extremes of age, immunocompromised)
¨ Distant organs may become seeded to establish metastatic foci of infection e.g.
osteomyelitis, septic arthritis, meningitis etc.
Clinical aspects of salmonella
Incubation 12-72 hours ¨ Watery diarrhoea ¨ Vomiting is common ¨ Fever can occur, and is usually associated with more invasive disease ¨ Duration 2-7 days
Treatment of salmonella
Fluid replacement is sufficient in most cases
¨ Antibiotics reserved for severe infections and bacteraemia
n Beta-lactams, quinolones or aminoglycosides may be used
¨ Antibiotics and antimotility agents prolong excretion of salmonellae in the faeces
Specific control points for salmonella
The introduction of immunisation of poultry flocks lead to a dramatic reduction in
S.Enteritidis in the UK
Microbiology of shigella
Gram-negative bacilli
¨ Member of the Enterobacteriaceae
¨ 4 species
n Shigella sonnei associated with milder infections
n Shigella boydii & S.flexneri associated with more severe disease
n Shigella dysenteriae associated with most severe disease
¨ Non-lactose fermenters (useful in differential media)
¨ XLD plates most commonly used in clinical labs
Wpidemiology of shigella
Mainly associated with diarrhoeal disease in children
¨ S.dysenteriae in developing world
¨ Humans are only reservoir
¨ Large outbreaks can occur
¨ Does not persist in the environment (unlike V.cholerae)
¨ Person-to-person spread via faecal-oral route is most important
n Associated with low infectious dose
¨ Contaminated food and water less important
¨ Recent outbreaks associated with MSM
Pathogenesis of shigella
Organisms attach to and colonise mucosal epithelium of terminal ileum & colon
¨ Systemic invasion is not a feature
¨ S.dysenteriae produces a potent protein exotoxin (Shiga toxin) which not only
damages intestinal epithelium, but in some patients targets glomerular
endothelium causing renal failure as part of haemolytic-uraemic syndrome (HUS)
Clinical aspects of shigela
Dysentery ¨ Incubation 1-3 days ¨ Duration 2-7 days ¨ Initially watery diarrhoea followed by bloody diarhoea ¨ Marked, cramping abdominal pain ¨ Vomiting is uncommon ¨ Fever is usually present
Treatment of shigella
Usually self-limiting
¨ Fluid replacement is usually sufficient
¨ Some cases of S.dysenteriae infection will require treatment of renal failure
Specific control points for shigella
Only found in humans, so good standards of sanitation and personal hygiene are
key measures
Vibrio cholerae micorbiology
Comma-shaped Gram-negative bacilli
¨ Serotypes defined on basis of “O” antigens. Important serotypes: -
n Serotype O1
¨ Classical
¨ El Tor (less severe disease, more carriage, better persistence in environment)
n Serotype O139
¨ Sucrose-fermenter. Thiosulphate-bile sucrose selective/differential
medium
Epidemiology of vibrio cholerae
Cause of epidemic and pandemic cholera
¨ Endemic in parts of SE Asia, Africa, South America
¨ Can live in fresh water
¨ Only infects humans. Asymptomatic human reservoir
¨ Spreads via contaminated food or water
¨ Direct person-to-person transmission uncommon
Pathogenesis of vibrio cholerae
Flagellae and mucinase facilitate penetration of intestinal mucous
¨ Attachment to mucosa by specific receptors
¨ Diarrhoea due to production of a potent protein exotoxin
Clinical aspects of vibrio cholerae
Severe, profuse, non-bloody, watery diarrhoea (rice
water stool)
¨ Profound fluid loss & dehydration precipitates
hypokalaemia, metabolic acidosis, hypovolaemic
shock and cardiac failure
¨ Untreated mortality 30-40%
Treatment of vibrio cholerae
Prompt oral or intravenous rehydration is lifesaving
(mortality reduced to <1%)
¨ Tetracycline antibiotics may shorten duration of
shedding
Specific control point
No animal reservoir
¨ Clean drinking water supply and proper sanitation are
key preventative measures
Other pathogenic vibrio species - associated with vibrio cholerae
Vibrio parahaemolyticus is a halophilic organism that
can cause diarrhoeal disease associated with
contaminated fish and shellfish in warm coastal
waters
Overview of e.coli
Gram-negative bacilli ¨Members of the Enterobacteriaceae n Important component of gut flora of man and animals n Some strains possess virulence factors which enable them to cause infections ¨Six different diarrhoeagenic groups of E.coli n Enteropathogenic E. coli (EPEC) n Enterotoxigenic E. coli (ETEC) n Enterohaemorrhagic E. coli (EHEC) n Enteroinvasive E.coli (EIEC) n Entero-aggregative E.coli (EAEC) n Diffuse aggregative E.coli (DAEC)
Microbiology of enteropathogenic E.coli (EPEC)
No differential media available
¨ Test selection of colonies using polyvalent antisera for common
EPEC “O” types
¨ Not routinely done
Epidemiology of EPEC
Sporadic cases & outbreaks of diarrhoea in infants & children
¨ Cause of some cases of “traveller’s” diarrhoea
Pathogenesis of EPEC
Initial adherence via pili, followed by formation of characteristic
“attatching & effacing” lesion mediated by intimin protein and Tir
(translocated intimin receptor) with disruption of intestinal microvilli
Clinical aspects of EPEC
Incubation 1-2 days
¨ Duration 1-several weeks
¨ Watery diarrhoea with abdominal pain and vomiting
¨ Often accompanied by fever
Microbiology of ETEC
No differential media available
¨ Test liquid cultures for production of toxins by immunoassays
¨ Not routinely done
Epidemiology of ETEC
The major bacterial cause of diarrhoea in infants & children in
developing world
¨ The major cause of “travellers” diarrhoea
Pathogenesis of ETEC
Diarrhoea due to action of 1 or 2 plasmid-encoded toxins
n Heat-labile (LT). Structural and functional analogue of cholera toxin
n Heat-stable (ST). Produced in addition to or instead of LT. Similar
mode of action
Clinical aspects of ETEC
Incubation 1-7 days
¨ Duration 2-6 days
¨ Watery diarrhoea with abdominal pain and vomiting
¨ No associated fever
Microbiology of EHEC
More than 100 serotypes
¨ Best known is E.coli O157:H7
¨ O157 is a non-sorbitol fermenter. Sorbitol MacConkey agar (SMAC)
Epidemiology of EHEC
Outbreaks & sporadic cases worldwide (~250 cases/year in Scotland)
¨ Large animal reservoirs (esp. cattle & sheep)
¨ Persistent in environment
¨ Consumption of contaminated food, water and dairy products & direct environmental contact
with animal faeces e.g. petting zoos
¨ Secondary person-to-person spread important (associated with low infectious dose)
pathogenesis of EHEC
Attaching and effacing lesion (similar to EPEC)
¨ Production of Shiga-like toxins. Structural and functional analogue of Shigella dysenteriae
toxin (sometimes strains called STEC [shiga-toxin producing EC] or VTEC [verotoxinproducing
EC] because toxins are toxic for cultured vero cells
Clinical aspects of EHEC
Incubation 1-7 days
¨ Duration 5-10 days
¨ Bloody diarrhoea with abdominal pain and vomiting
¨ No associated fever
¨ Haemolytic uraemic syndrome (5-10% of cases)
n Microangiopathic haemolytic anaemia
n Thrombocytopaenia
n Acute renal failure
¨ Commonest cause of acute renal failure in children in the UK
What species are the key causes of diarrhoea in children in the developing world?
EPEC and ETEC
severity may be related to underlying malnutrition
Treatment of E.coli infections
Adequate rehydration
¨Antibiotics not indicated, and in the case of EHEC
may increase risk of HUS
¨Antimotility agents also increase HUS risk
Staph aureus microbiology
Gram-positive cocci
¨ Grow well on routine media
¨ Testing for enterotoxins not routinely performed
Epidemiology and pathogenesis of staph aureus
50% of S.aureus produce enterotoxins (types A-E)
¨ Heat stable and acid-resistant protein toxins
¨ Food is contaminated by human carriers
¨ Especially cooked meats, cakes and pastries
¨ Bacteria multiply at room temperature and produce toxins
Clinical aspects of staph aureus
Incubation 30 minutes – 6 hours
¨ Duration 12 – 24 hours
¨ Profuse vomiting and abdominal cramps
¨ No fever and no diarrhoea
Treatment of staph aureus
Self-limiting disease
Control of staph aureus
Hygienic food preparation to minimise contamination
¨ Refrigerated storage
Bacillus cereus microbiology
Aerobic, spore-forming Gram-positive bacilli
¨ Not routinely tested for
Epidemiology and pathogenesis of bacillus cereus (inc. the 2 types of disease)
Spores & vegetative cells contaminate wide range of foodstuffs
¨ 2 types of disease: -
¨ Emetic disease
n Typically associated with fried rice
n Spores survive initial boiling
n If rice is bulk cooled and stored prior to frying, the spores germinate, multiply and re-sporulate
n Protein enterotoxin produced during sporulation
n Heat stable toxin survives further frying
¨ Diarrhoeal disease
n Spores in food survive cooking, germinate and organisms multiply in food
n Ingested organisms produce a heat-labile toxin in the gut with similar mode of action to cholera toxin
Clinical aspects of bacillus cereus
Emetic disease n Incubation 30 minutes - 6 hours n Duration 12 -24 hours n Profuse vomiting with abdominal cramps and watery diarrhoea n No fever ¨ Diarrhoeal n Incubation 8 -12 hours n Duration 12 -24 hours n Watery diarrhoea with cramping abdominal pain, but no vomiting n No fever
Treatment of bacillus cereus
Self-limiting disease
Microbiology of clostridium perfringens
Anaerobic, spore-forming Gram-positive bacilli
¨ Not routinely tested for
Epidemiology and pathogenesis of clostridium perfringens
Spores & vegetative cells ubiquitous in soil and animal gut
¨ Contaminated foodstuff (usually meat products)
¨ Often involves bulk-cooking of stews, meat pies
¨ Spores survive cooking, germinate and organisms multiply in cooling food
¨ Food inadequately re-heated to kill organisms
¨ Organisms ingested & sporulate in large intestine with production of enterotoxin
Clinical aspects of clostridium perfringens
Incubation 6 - 24 hours
¨ Duration 12 – 24 hours
¨ Watery diarrhoea and abdominal cramps
¨ No fever and no vomiting
Treatment of clostridium perfringens
Self-limiting disease
Control of clostridium perfringens
Rapid chilling/freezing of bulk-cooked foods
¨ Thorough re-heating before consumption
Microbiology of clostridium botulinum
Anaerobic, spore-forming Gram-positive bacilli
¨ Laboratory diagnosis based upon toxin detection
Epidemiology and pathogenesis of clostridium botulinum
Very uncommon in UK
¨ Spores & vegetative cells ubiquitous in soil and animal GIT
¨ Produces powerful heat-labile protein neurotoxin (types A, B & E cause human disease)
¨ Foodborne botulism- pre-formed toxin in food. Commonly associated with improperly processed
canned foods
¨ Infant botulism- organisms germinate in gut of babies fed honey containing spores, and toxins
are produced in gut
¨ Wound botulism- organisms implanted in wound produce toxin
¨ Absorbed toxins spread via bloodstream and enter peripheral nerves where they cause
neuromuscular blockade at the synapses
Clinical aspects of clostridium botulinum
Neuromuscular blockade results in flaccid paralysis & progressive muscle weakness
¨ Involvement of muscles of chest/diaphragm causes respiratory failure
¨ High mortality if untreated
Treatment of clostridium botulinum
Urgent intensive supportive care due to difficulties breathing and swallowing
Antitoxin
Control of clostridium botulinum
Proper manufacturing controls in canning industry
¨ Hygienic food preparation
¨ Proper cooking
¨ Refrigerated storage
Microbiology of clostridium difficile
Anaerobic, spore-forming Gram-positive bacilli
¨ Spores resistant to heat, drying, disinfection, alcohol
¨ Clinical features due to production of potent toxins (A+B)
¨ Laboratory diagnosis based two-step algorithm
Epidemiology and pathogenesis of c.diff
Spores & vegetative cells ubiquitous in environment
¨ Carriage
n 3-5% in adults in community
n May rise to 30% in hospitalised patients
n Asymptomatic carriage rates may be very high in infants
¨ Infection requires disruption of the normal “protective” gut flora
n Most commonly due to antibiotic therapy
n Can also be due to cytotoxic therapy
n Proton pump inhibitor use may be an additional risk factor
¨ Predominantly affects the elderly
¨ Major cause of healthcare associated infections
Clinical aspects of c.diff
Mild to severe with abdominal pain
¨ Severe cases may develop pseudomembranous colitis
¨ Fulminant cases may progress to colonic dilatation and perforation
¨ Severe cases may be fatal
¨ Relapses are common and may be multiple
Treatment of c.diff
Stop precipitating antibiotics
¨ Oral metronidazole (mild [0 severity markers]). Oral vancomycin (severe [≥ 1 severity markers or
no improvement after 5 days metronidazole])
¨ Refractory recurrent disease may require faecal transplant
Control of c.diff
Antimicrobial stewardship
n Remember that any antibiotic therapy will disturb the normal gut flora to some extent
¨ Avoid/stop unnecessary antimicrobial treatment
n Restrictive antibiotic formularies to minimise use of “high risk” antibiotics
¨ Cephalosporins
¨ Fluoroquinolones
¨ Clindamycin
¨ Co-amoxyclav
¨ Infection Prevention & Control measures
n Source isolation
n Hand hygiene
n Use of Personal Protective Equipment (PPE)
¨ Cleaning/disinfection with hypochlorite disinfectants
Microbiology of listeria monocytogenes
Gram-positive coccobacilli
¨ Selective culture media available for culture from suspect foods
¨ Standard laboratory for blood and CSF samples
Epidemiology & pathogenesis of listeria
Widespread among animals and the environment
¨ Pregnant women, elderly and immunocompromised
¨ Overall number of cases small, but mortality high
¨ Infection associated with contaminated foods, especially unpasteurised milk and soft cheeses, pate, cooked
meats, smoked fish, and coleslaw
¨ Outbreaks occur associated with contaminated ready to eat foods and produce
¨ Can multiply at 4oC
¨ Invasive infection from GIT results in systemic spread via bloodstream
Clinical aspects of listeria
Median incubation period 3 weeks
¨ Duration of illness 1-2 weeks
¨ Initial flu-like illness, with or without diarrhoea
¨ Majority of cases present with severe systemic infection
n Septicaemia
n Meningitis
Treatment of listeria
Intravenous antibiotics (usually Ampicillin and synergistic gentamicin) is required
Control of listeria
Susceptible groups should avoid high risk foods
¨ Observe use by dates
¨ Wash raw fruit and vegetables and avoid cross contamination
Microbiology of h.pylori
Gram-negative spiral shaped bacilli
¨ Microaerophilic. Urease-positive
¨ Diagnosis by detection of faecal antigen or urea “breath test”. Serum antibody tests mainly
of use in epidemiological surveys of past or current infection.
Epidemiology and pathogenesis of h.pylori
One of the most common bacterial infections in the world
n 70% prevalence in developing world; 30-40% in developed world
¨ Thought to be faecal-oral or oral-oral
¨ Humans are the only reservoir
¨ Infection acquired in childhood and persists life long unless treated
¨ Pathogenesis is complex involving cytotoxin production, and a range of factors to promote
adhesion and colonisation
Clinical aspects of h.pylori
Infection is asymptomatic unless peptic ulceration develops
¨ Now established as cause of >90% of duodenal ulcers, and 70-80% of gastric ulcers
¨ Gastric cancer risk
Treatment of h.pylori
Combined treatment with a proton pump inhibitor and combinations of antibiotics such as
clarithromycin and metronidazole eradicates carriage and facilitates ulcer healing
GI infections in developed world vs developing world
Developed world:
Large economic burden
Mainly associated with foodborne infection
Pathogens have important animal reservoirs
Developing world:
High mortality - particularly in children <5 years old
Mainly a problem of lack of clean water and poor sanitation
Viral gastroenteritis =
Inflammation of the stomach and intestines caused by virus(es)
People at higher risk of gastroenteritis
Children under age of 5
Old age people - especially in nursing homes
Immunocompromised people
Important viruses that cause gastroenteritis
Norovirus Sappovirus Rotavirus (the above 3 = Calciviridae) Adenovirus 40 & 41 Astrovirus
What people does norovirus/sappovirus (Calciviridae) cause gastroenteritis in?
Can affect all ages and healthy individuals but often most serious in young and elderly
What people does rotavirus/adenovirus/astrovirus cause gastroenteritis in?
Affects mainly children under 2 years old, elderly and immunocompromised
Structural features of norovirus
Family: Calciviridae
Non-enveloped (so can survive longer), single stranded RNA virus
Five genotypes - only 3 affect humans (GI, GII and GIV)
Genotypes divided into at least 32 genotypes
Most common in the UK is the GII-4 strain
Transmission of norovirus
Person to person (faecal-oral, aerolised e.g. by toilet flush, fomites)
Food borne (most commonly in shellfish)
Water
Infectious dose is very small (10-100 virions)
Can affect all ages
24-48 hour incubation period
Can shed virus for up to 3 weeks after infection
Clinical features of norovirus
Can be asymptomatic (not common) Vomiting Diarrhoea Nausea Abdominal cramps Headache, muscle aches (viral symptoms) Fever (minority) Dehydration in young and elderly
Usually lasts 12-60 hours
Complications of norovirus
Significant proportion of childhood hospitalisation (cant manage fluid balance - become dehydrated)
In elderly increased post infection complications (dehydration, AKI, inc. potassium levels)
Chronic diarrhoea and virus shedding in both solid organ transplant patients and bone marrow trasnplant patients - shedding for up to 2 years
Treatment of norovirus
Symptomatic therapy - oral and or IV fluids; antispasmodics; analgesics; antipyretics
(might use immunoglobulins for immunocompromised patients
Immunity against norovirus
Although antibodies are developed to norovirus, immunity only lasts 6-14 weeks (when the virus re-circulates next year can become infected again).
Due to the incomplete understanding of immunity and the fact norovirus can’t be cultured there have been issues with creating a vaccine
Reports have shown a link between the expression of human histo-blood antigens (HBGAs) and the susceptibility to norovirus infection.
Infection control of norovirus
Isolation or cohorting
Exclude symptomatic staff until symptom free for 48 hours
Do not ove patients
Do not admit new patients
Thorough cleaning of the ward/hospital/cruise ship/bus - dilute hypochlorite or hot soapy water
hand hygiene - contaminated hands are probably the single most common vector for the spread of norovirus
Rotavirus - structural features
Family: Reoviridae Double stranded, non-enveloped RNA virus 5 predominant strains, G1-4, G9 G1 acounts for >70% infections Stable in environment and fairly resistant to hand washing
