Gastrointestinal Tract Infections - STEC, C. diff, Norovirus Flashcards
What are the two E. Coli strains we are most concerned with, what genes encode these?
VTEC = verotoxigneic E. Coli
- encoded by vtx1 and vtx2
- verotoxins encoded on bacteriophages
EHEC = Eneterhaemorrhagic E. Coli
- encoded by vtx1, vtx2, eae
- causes haemorrhagic colitis
How is STEC transmissed
STEC is associated with cattle
Minced meat -> faecal contamination, bacteria gets into meet, undercooked meat e.g. burgers ets
Small infectious dose -> can contaminate water sources, outbreaks associated with outdoor water sports ets
Cross contamination with ready to eat foods such as sprouts
Unpasteurised apple juice whereby fruit fell into animal faeces and werent washed properly
Person to person spread particularly in younger kids with poor hygiene
What are the three mobile genetic elements of STEC
Phages
Genomic islands
Plasmid
Talk about genomic islands in STEC
LEE pathogenicity island
- integrated into the bacterial chromosome
- associated with pathogenicity but not found in all strains
Talk about plasmids in STEC
plasmids encode a haemolysin
There are found in O157
Talk about bacteriophages in STEC
This is where the shiga toxin is found
This bacteriophage integrates itself into the bacterial chromosome
Everytime the organism replicates it produces the toxin
What are the symptoms of O157:H7
Intestinal symptoms:
- can be asymptomatic
- watery diarrhoea
- haemorrhagic colitis
NB: often starts as watery diarrhea but moves towards bloody
Systemic
- Haemolitic Uremic Syndrome
NB: multi-system involvement, high mortality associated with development of HUS
What is clinically diagnostic of HUS
Any person with acute renal failure and either:
Microangiopathic haemolytic anaemia
Thrombocytopenia
How do we diagnose STEC in the lab?
One of the three:
- isolation of E. Coli strain that produces verotoxin or harbours vt1 or vt2 genes
- direct detection of vt1 or vt2 genes nucleic acid (without strain isolation)
- detection of free verotoxin in faeces
Comment on VTEC rates in ireland vs rest of europe
We are the second worst in europe only to Denmark
Up until recent years we had consistently been the worst
What are some reasons why STEC is so common in Ireland?
In ireland we have a lot of household outbreaks, especially in rural areas
Families using the same water source
Often from drinking untreted well water
Cattle run off -> untreated water
Talk about trends in STEC in Ireland over the years
Numbers increasing year on year in Ireland
STEC in Ireland wayyy above EU average
Significant increase from 2011/2012
- due to introduction of molecular methods (explains some of increase but not all)
Very high in 0-4 yr olds
Talk about trends in STEC in Ireland over the years
Numbers increasing year on year in Ireland
STEC in Ireland wayyy above EU average
Significant increase from 2011/2012
- due to introduction of molecular methods (explains some of increase but not all)
Very high in 0-4 yr olds
How have our detection methods for STEC changed?
We used to just use CTSMAC but moved over to molecular methods
How have our detection methods for STEC changed?
We used to just use CTSMAC but moved over to molecular methods
What are the most common STEC serogroups in ireland
O26
O157
O145
Comment on the trends in different STEC serogroups over time in Ireland
When we were exclusively using CTSMAC agar O157 was the most common as we were missing a lot of other serogroups with this agar
Since moving to more molecular methods O26 is now the most common STEC
Over the years we have had an increase in some of the lesser known serogroups of VTEC
NB: O157 not the most common but is the most researched
Talk about the sesonal distribution in STEC 026 vs o157
o26 peaks in summer while O157 peaks in autumn
- we dont know why this happens, no obvious reason for this
Talk about STEC outbreaks in Ireland
The majority of outbreaks are family outbreaks and not general outbreaks
Most are associated with childcare facilities -> quickly spreads amongst children
Very few associated with halthcare
-> CAI not a HCAI
Why is diagnosis of STEC challenging?
Wide range of presenting features from mild diarrhoea to HUS
Large number of serogroups implicated in disease all with varing virulence factors
Lack of clear phenotypic distinguishing characteristics to separate STEC from other pathotypes of E. Coli
Safety -> cat 3 organism -> really low infectious dose -> containment level lab
Lack of standardisation both nationally and internationally
Where is the reference lab for VTEC/STEC?
Cherry orchard
How do we detect VTEC in the lab
EntericBio RT-Gastro Panel
Film Array GI panel
xTAG
Talk about C. difficile
A major HCAI patogen
A spore forming anaerobe
Toxin producing
Causes a spectrum of disease
What are the two main risk factors for C. difficile?
Antibiotic use
Direct correlation with age
What is different about the lab diagnostics of C. diff versus VTEC
Detection of the toxin alone is not enough for C. diff diagnosis
- People can be colonised with C. diff without being infected by it
- babies have a high carriage rate due to hospital environment
What antibiotic treatments are most associated with C. diff?
Clindamycins
Cephalosporins
And now the fluoroquinolones, particuluarly the newer ones e.g. levofloxacin
Talk about C. diff infection, where do you get it, incidence, mortality
Causes 25-30% of antibiotic associated diarrheae
-> the rest of these probably caused by antibiotic themselves
Most common cause of healthcare associated infectious bacterial diarrhea
Hospital outbreaks are common and cost the Health service millions
Incidence has doubled since the 1990s
Mortality is increasing
Increase in CAI
Why is it thought that the C. diff mortality rate is increasing?
increasing virulence
Increasing resistance
Increasing host vulnerability - people living for longer
Changing risk factors
What kind of resistance are we concerned with in C. diff
Not really concerned with the actual resistance but more sore its conferrred persistance in the hospital enviroment
Talk about C diff in the community
Incidence of CAI is increasing
Over the last few years about 20% of cases have been CAI
Compare asymptomatic C. diff to symptomatic C. diff, how does it affect the host differently
Non toxigenic C. diff = asymptomatic carriage
Toxigenic C. diff but patient IgG to toxin = asymptomatic carriage
Toxigenic C. diff but no immune response = symptomatic C. diff
Talk about the clinical manifestation of C diff
No symptoms if only colonised
Can cause recurrent diarrhoeal illenss, abdominal pain, feve etc lasting months
Can cause Pseudomembraneous colitis and toxic megacolon which often requires surgical intervention and can be lifethreatening
Talk about the 5 year trends in C. diff
Cases highest before covid in 2019, dip during covid, numbers increasing to what it was prior to covid now
- relatively steady numbers though - hasnt really changed i.e. numbers match pre-covid stats
Where are C. diff outbreaks seen
Vast majority are in acute hospital
High in long term care facilities
Few in childcare facilities
Community acquired increasing
How has C. diff diagnosis in the lab changed over the years?
In the 1970s - bacterial culture on CCFA agar
Tissue culture in 1970s/1980s
Mid 80s = latex agglutination
1990s = ELISA for toxins A and B
2008 = Algorithm testing for Ag and toxins A and B
2009 = Molecular tests for tcdB and tcdA
What genes are we looking for in C. diff?
tcdA and tcdB genes which encode toxin A and B
What is the 2 step algorithm for detection of C. diff?
1 = screen for toxin gene
2 = confirm toxin protein in sample
What is the a common method of screening for C. diff in a sample?
GHD antigen test
- An EIA, enzyme test
- looks for antibodies against the toxin
-confirmed with molecular detection of genes through PCR or EIA on sample to confirm toxins presence
How are C. diff cases confirmed, how do we know the gene is actually producing the target?
EIA
Tells us if toxin is present in sample
Gene has been translated etc into protein
Talk about viral gastrointestinal disease
Historically under reported
Incidence has increase with the ability to diagnose
Recently emerged as the most common reported cause of food-borne disease
Why is viral gastrointestinal disease so under-reported?
Causes mild illness - people dont bother going to doctor
No routine reliable detection methods
Early clinical samples required - usually sample not suitable
Compare the frequency of viral food-borne disease to the two most frequent bacterial casues
66.7% of cases are viral
14.2 are campylobacter
9.7 are salmonella
What are human enteric viruse
Obligate intracellular parasites
They require live cells to replicate
They have a smiple structure
They have an RNA genome
They are very small
They are transmitted by humans mostly by faeces but norovirus can be transmitted throug vomitus
They are highly transmissible
They are difficult to study and detect
What are the most frequent enteric viruses in infants?
Rotavirus A
- large decrease since introduction of vaccine in 2016
Adenovirus 40,41
Coxsackie A24 virus
What are the most common enteric viruses in children and adults
Norovirus
Calicivurus astrovirus???
Rotavirus B
Reovirus
Talk about human noroviruses (HuNoV)
Calciviridea family???
Five genera:
- Most concerned with Sapovirus and Norovirus
Multiple genogroups:
- GI, GII etc
Many genotypes
Talk about the transmission of norovirus
Frequently implicated in hospital settings and nursing homes - projectile vomiting
These outbreaks cause challenges when ereadicating the source and a financial burden
Person-to-person transmission in hospital settings
Often spreads between patients and staff
Talk about how norovirus outbreaks often affect C. diff numbers
Norovirus is highly contagious and causes projectile vomiting
Staff usualy get a lot better at hand hygiene etc when there is a norovirus outbreak
This has a knockk on affect on c. diff numbers - improved hand hygiene preventing spread
Talk about norovirus outbreaks in ireland
We get well over 100 outbreaks a year
70% of norovirus cases are related to outbreaks
33% in nursing homes
26% in hospitals
Talk about incidence of rotavirus
There has been a massive decrease in rotavirus numbers since the introduction of the Rotarix vaccine in December 2016
Number were over 4000 in 2015 and fell as low as 158 in 2020 (covid) but remain at 560 in 2023
Laboratory detection of GI viruses
Multiplex PCR for viral gastrointestinal pathogens (NVRL) - introduced in September 2014
Since October 2014 stool samples from children <5 years of age could be used and only adults were tested for norovirus
EntericBio and BD Max gastro panels
-> recenly validated a new panel for norovirus GI and GII
Multiplex panels are available on the BioFire Film Array and the xtag GPP
