Microbiology Flashcards
What are HAI?
Infections which occur within a certain period from contact with healthcare
~8% of patients in hospitals have an HAI in UK
Worldwide: 3.5-10.5% of hospitalised pts in industrialised countries; ~>25% in developing nations
We can categorise it based on organism:
- –MRSA
- –C. difficile
- –E. coli
- –MSSA
- –R Gram negs
- –Yeasts / Candida
Or by syndrome:
- Catheter associated BSI
- Urinary cath assocd UTI
- Surgical site infection
- Vent assocd pneumonia
- Antibiotic assocd diarrhoea
What is the impact of HAI?
Cost
- Enormous – social / clinical / economic
- UK: £1 Billion a year*
- probable underestimate, very outdated, but often quoted
- In 2004 DH estimate 300,000 HAI per year
Preventable?
- Probably 15-30%
- Financial incentives to prevent – non reimbursement
- US leading the way
- UK and others following
- Unintended consequences
Perceptions of HAI
- dirty hospitals
- poor staff practise
- affects pts who attended hospital for unrelated problems
What are the different types of HAI?
They come from the microbiome of patients and staff, as well as the environment
What are the key strategies for infection control?
Reducing the number of bugs:
- On equipment: sterilisation of equipment prior to operation
- On environment: cleaning = dilution / reduction but not eradication
- On patient: washing, skin preparation pre-op, prophylaxis for contaminated procedures
- On staff hands: hand cleaning after contact any surface
- On staff skin: ??
Reducing number of resistant bugs:
- Screen patients – segregate those with organism detected from those in whom not detected
- for certain organisms, evidence of organism burden reduction with topical suppression
Reduce transmission of bugs:
- Staff - understand and use hand cleaning
- Staff - cleaning environment and equipment
- Staff - reduce use of broadest spectrum antibiotics and of unnecessary antibiotics
- Systems - better design of surfaces with preventing adherence and transmission in mind
What are surgical site infections and what affects them?
3 things that affect SSI:
Host defence, wound environment and pathogens
What are the challenges for outbreak control measures?
- §Improved screening and isolation, impact of delays to typing results
- §Laboratory and epidemiological investigations
- §Internal and external communications. Coordinating briefing and discussions with external stakeholders.
- §Input from other Trusts addressing CRE
- §Hand hygiene and equipment focus, ward based adherence monitors
- §Environmental cleaning and disinfection, attention to pillows and mattresses, HPV usage
- §External reviews and visits of clinical areas
- §Antimicrobial usage and stewardship
- §Expediting discharges
How are HAIs changing over time?
- •Invasive procedures
- •Prosthetic and implantable devices
- •Obesity
- •Diabetes
- •Extremes of age
- •Immunosuppression
- •Emerging organisms/ resistance
Hospital environment
- •Environmental hygiene and cleaning
- eg C. difficile, Norovirus, Acinetobacter outbreaks
- chlorine agents; use of vapourised Hydrogen peroxide
- •Control of environmental sources
- Water: Legionella- cooling towers; Pseudomonas – all water; unusual Mycobacteria – all water
- Building works – Aspergillus
- •Negative pressure isolation – protection of others from an infectious patient with airborne infection
- •Positive pressure isolation – protection of transplant patients from organisms from outside the room
Resistance:
- •Widespread, prolonged use of antibiotics
- •Broad spectrum antibiotics
- •MRSA / VISA / VRE
- •ESBL
- •Multi-resistant / pan-resistant gram negatives
What is gastroenteritis and diarrhoea?
- Gastroenteritis - A rapid onset diarrhoeal illness, lasting less than 2 weeks ¡with diarrhoea (loose and unformed stool) three or more times a day or at least 200 g of stool which is either viral or bacterial in aetiology
- Diarrhoea – loose, or watery stool at least 3x in 24hrs: acute (less than 14d due to viral/bacterial), persistent (14-29d), chronic (>30d due to parasites and non-infectious aetiology should be excluded)
¡Small bowel diarrhea- often watery, associated with crampy abdominal pain and of large volume with bloating and gas. Accompanying fever and blood or inflammatory cells in the stool are rare.
¡Large bowel diarrhea –small volume painful stool which occur often with blood, mucus and inflammatory cells found in the stools and an accompanying fever.
What are the risk factors for gastroenteritis?
- Food bourne
- Exposure related – outbreak situation; travel hx (resource poor setting, cruise, recreational water facilities); occupational/healthcare exposure (c. diff); animal contacts (petting zoos/farms); reptiles (salmonella types with snakes and turtles) or other house pets with diarrhoea; institution/childcare facility
- Host related – immunosuppressed, young children/elderly; men who have sex with men; haemochromatosis; ano-genital/oral-anal/digital anal contact; haemochromatosis or haemoglobinopathies
What is the epidemiology of gastroenteritis?
- Underreporting of GI infections
- Incidence of bacterial GE is less than viral GE and varies in countries and rural vs urban settings
- Most are self limiting <24 hours, patients do not seek healthcare
- Developing countries-outbreaks, cholera especially in war torn countries with no access to clean drinking water and sanitation
- Most vulnerable groups: Infants, elderly, men who have sex with men, immunocompromised
- Reportable: Campylobacter, Salmonella, Shigella, E.Coli 0157, Listeria, Norovirus
What are the mechanisms of disease in gastroenteritis?
3 types of disease:
Secretory diarrhoea - toxin production: cholera toxin, superantigens
Inflammatory diarrhoea
Enteric fever
inflammatory is exudative and enteric fever has interstitial inflammation
What is the method of disease of cholera?
Cholera toxin -
cAMP: opens Cl channel at the apical membrane of enterocytes
>> efflux of Cl to lumen; loss of H2O and electrolytes
Efflux of water and ions which the body can’t keep up with replacing
What are examples of superantigens?
In secretoy diarrhoea - toxin production: superantigens are produced
Superantigens bind directly to T-cell receptors and MHC molecules; outside the peptide binding site
>> massive cytokine production by CD4 cells ie systemic toxicity and suppression of adaptive response
What is the difference in mechanism of disease between inflammatory diarrhoea and enteric fever?
Host responses in bacteraemia:
Inflammatory (exudative ) diarrhoea Vs Enteric fever; interstitial inflammation
How can we diagnose gastroenteritis?
- Stools taking shape of container tested with culture dependent or independent methods with PCR
- Enteric fever – blood and stool tested with culture dependent and independent methods, bone marrow, duodenal fluid and urine also tested
- Stools for microscopy and culture requested where enteric infection suspected
- Stools for bac/viral/parasitic infection tested irrespective of blood in the stool, inflammatory markers or presence of fever or systemic syx if there is suspicion of an outbreak and if tested with molecular methodology, should be followed by culture for public
- Can also tx based on the clinical feature -> each feature is specifically associated with a specific pathogen
What are the extraintestinal manifestations of gastroenteritis and their causative organisms?
•Aortitis, osteomyelitis, deep tissue infections
–Salmonella, Yersinia
•Haemolytic anaemia
–Campylobacter Yersinia
•Glomerulonephritis
–Shigella, camp, Yersinia
•HUS
–STEC, shigella dysenteriae type 1
•Erythema nodosum
–Yersinia, camp salmonella shigella
•Reactive arthritis
–Salmonella, shigella, camp, Yersinia, giardia, cyclospora
•Meningitis
–Listeria, salmonella
What is Staph aureus?
- •1/3 population chronic carriers, 1/3 transient
- •Spread by skin lesions on food handlers
- •Catalase, coagulase positive Gram positive coccus
- •Appears in tetrads, clusters on Gram stain
- •Yellow colonies on blood agar
- Produces enterotoxin, an exotoxin that can act as a superantigen in the GI tract, releasing IL1 and IL2
- Causing prominent vomiting and watery, non bloody diarrhoea
- Don’t treat, self limited
What is Bacillus cereus?
Gram positive rod - spore forming
Found commonly in reheated fried rice
- •Heat stable emetic toxin -not destroyed by reheating
- •Heat labile diarrhoeal toxin - food is not cooked to a high enough temperature
and
- •watery non bloody diarrhoea; self limited
- •Rare cause of bacteremia in vulnerable population
- •Can cause cerebral abscesses
What are clostridia?
Clostridium botulinum : botulism
- •Source : canned or vacuum packed food (honey / infants)
- •Ingestion of preformed toxin (inactivated by cooking)
- •Blocks Ach release from peripheral nerve synapses
- •Treatment with antitoxin
Clostridium pefringens : food poisoning
- •Source : reheated food (meat) like Cosmos
- •Normal flora of colon but not small bowel, where the enterotoxin acts (superantigen)
- •Incubation 8-16hrs
- •Watery diarrhoea, cramps,little vomiting lasting 24hrs
Clostridium difficile: pseudomembranous colitis
- •3%, 30% of hospitalised patients
- •It isn’t an invasive disease and non-toxin producing strains don’t cause disease but can colonise the gut and asyx shedders of spores can act as reservoir to infection
- •2 toxins: A enterotoxin, B is cytotoxin
- •A causes inflammation with intestinal fluid secretion and damage to mucosa
- •B more potent than A and is a virulence factor
- •Antibiotic related colitis (any but.. mainly cephalosporins, cipro and clindamycin)
- •Infection control and preventions precautions required
- Treatment : (PO) metronidazole, vancomycin, stop antibiotics where possible
What is listeria monocytogenes?
- •Outbreaks of febrile gastroenteritis
- •ß haemolytic, aesculin positive with tumbling motility
- •Source : refrigerated food (“cold enhancement”),i.e. unpasteurised dairy, vegetables
- •Grows at 4 ºC
- •GI: watery diarrhoea, cramps, headache, fever, little vomiting
- •Perinatal infection, immunocompromised patients
- •Treatment : ampicillin
What are enterobacteriacae and give an example organism?
Facultative anaerobes, glucose/lactose fermenters (LF), oxidase negative
Escherichia coli :
- •Traveller’s diarrhoea
- •Source: food/water contaminated with human faeces
- •Enterotoxins :
- -Heat labile stimulates adenyl cyclase and cAMP
- -Heat stable stimulates guanylate cyclase
- -Act on the jejeunum, ileum not on colon
Types of e. coli
- •Enterotoxigenic ETEC; toxigenic, main cause of traveller’s diarrhoea
- •Enteropathogenic EPEC; pathogenic, infantile diarrhoea
- •Enteroinvasive EIEC; invasive, dysentery
- •Enterohaemorrhagic EHEC; haemorrhagic O157:H7 EHEC: shiga- like verocytotoxin causes HUS
- •Avoid antibiotics – not beneficial for toxin process
-
What are salmonellae bacteria?
- Non lactose fermenters,
- H2S producers,
- TSI agar,
- XLD agar,selenite F broth
- Antigens:
- -cell wall O (groups A-I)
- -flagellar H
- -capsular Vi (virulence, antiphagocytic)
•Three species :
- -S. typhi (and paratyphi)
- -S.enteritidis
- -S.cholerasuis
What are shigellae bacteria?
- Non lactose fermenters, non H2S producers, non motile
- Antigens:
- -cell wall O antigens,
- -polysaccharide (groups A-D) : S.sonnei, S.dysenteriae,
S.flexneri (MSM)
- •The most effective enteric pathogen (low ID 10-100)
- •No animal reservoir
- •No carrier state
•Dysentery
- invading cells of mucosa of distal ileum and colon
- producing enterotoxin (Shiga toxin)
- Abdo pain and watery diarrhoea
Avoid antibiotics (ciprofloxacin if required)
What are vibrios?
•Curved, comma shaped, late lactose fermenters, oxidase positive.
Treat with doxycycline
Vibrio cholerae
- •O1 group: epidemics, biotypes El Tor, Cholerae and serotypes Ogawa, Inaba, Hikojima
- •Non O1 group: sporadic or non pathogens
- •Transmitted by contamination of water and food from human faeces ( shellfish, oysters, shrimp)
- •Colonisation of small bowel and secretion of enterotoxin with A and B subunit, causing persistent stimulation of adenylate cyclase
- •Causes massive diarrhoea (rice water stool) without inflammatory cells
- •Treat the losses
•Vibrio parahaemolyticus
- -Ingestion of raw or undercooked seafood (ie oysters),
- -major cause of diarrhoea in Japan..or when cruising in the Carribean.. ,
- -self limited for 3 days
- -cholerae : grows in salty 8.5% NaCl..
•Vibrio vulnificus
- can cause diarrhea, but isolated from blood and tissues of septic patients
- cellulitis in shellfish handlers
- fatal septicaemia with D+V in HIV patients
What are campylobacter?
- •Curved, comma or S shaped
- •Microaerophilic
- •C.jejuni at 42 ºC
- •oxidase pos ,motile
- •Self limiting but symptoms can last for weeks (20 days)
- •Transmited via contaminated food and water with animal faeces
- •Only treat if immunocompromised (macrolide)
- •Transmitted via contaminated food and water with animal faeces ( poultry, meat,unpast. milk)
- •Watery foul smelling diarrhoea, bloody stool, fever and severe abdo pain
- •Loose stools occur >10x a day, bloody from 2/3rd day forwards
- •? Enterotoxin (watery diarrhoea) ? Invasion (+/- blood)
- •Treat with erythromycin or cipro if in the first 4-5days
- •GBS syndrome, reactive arthritis, Reiter’s ..
What is Yersinia enterocolitica?
Non lactose fermenter, prefers 4ºC “cold enrichment”
Transmitted via food contaminated with domestic animals excretions
enterocolitis
mesenteric adenitis
associated with reactive arthritis , Reiter’s
What is entamoeba histolytica?
- motile trophozoite in diarrhoea
- non motile cyst in nondiarrhoeal illness
- Killed by boiling, removed by water filters
- 4 nuclei
- No animal reservoir
Ingestion of cysts >> trophos in ileum >> colonize cecum, colon >> “flask shaped” ulcer
- -dysentery, flatulence, tenesmus
- -chronic : wt loss,+/- diarrhoea
- -liver abscess
Diagnosis
- -stool micro (wet mount, iodine and trichrome )
- -serology in invasive disease
Treat : metronidazole + paromomycin in luminal disease
What is Giardia lamblia?
- trophozoite “pear shaped”
- 2 nuclei
- 4 flagellas and a suction disk
- Ingestion of cyst from fecally contaminated water,food
- •Excystation at duodenum
- •tropho attaches
- •no invasion
- •malabsorption of protein and fat
- At risk: Travellers, hikers, day care, mental hospitals, MSM
- foul smelling non bloody diarrhoea, cramps, flatulence, no fever
- Diagnosis : stool micro, ELISA, “string test”
- Treatment :metronidazole
What is cryptosporidium parvum?
Parasite
- Infects the jejunum
- Severe diarrhoea in the immunocomromised
- Oocysts seen in stool by modified Kinyoun acid fast stain
Treatment : reconstitution of immune system
What is norovirus?
- outbreaks
- Low ID (18-1000 viral particles)
- Environmental resilience (0-60 ºC)
- No long term immunity
- GII.4 currently predominant strain