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4.1 Medical Microbiology > Gastrointestinal Tract Infections - STEC, C. diff, Norovirus > Flashcards

Gastrointestinal Tract Infections - STEC, C. diff, Norovirus Flashcards

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1
Q

What are the two E. Coli strains we are most concerned with, what genes encode these?

A

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

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2
Q

How is STEC transmissed

A

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

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3
Q

What are the three mobile genetic elements of STEC

A

Phages
Genomic islands
Plasmid

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4
Q

Talk about genomic islands in STEC

A

LEE pathogenicity island
- integrated into the bacterial chromosome
- associated with pathogenicity but not found in all strains

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5
Q

Talk about plasmids in STEC

A

plasmids encode a haemolysin
There are found in O157

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6
Q

Talk about bacteriophages in STEC

A

This is where the shiga toxin is found
This bacteriophage integrates itself into the bacterial chromosome
Everytime the organism replicates it produces the toxin

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7
Q

What are the symptoms of O157:H7

A

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

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8
Q

What is clinically diagnostic of HUS

A

Any person with acute renal failure and either:
Microangiopathic haemolytic anaemia
Thrombocytopenia

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9
Q

How do we diagnose STEC in the lab?

A

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

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10
Q

Comment on VTEC rates in ireland vs rest of europe

A

We are the second worst in europe only to Denmark
Up until recent years we had consistently been the worst

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11
Q

What are some reasons why STEC is so common in Ireland?

A

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

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12
Q

Talk about trends in STEC in Ireland over the years

A

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

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13
Q

Talk about trends in STEC in Ireland over the years

A

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

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14
Q

How have our detection methods for STEC changed?

A

We used to just use CTSMAC but moved over to molecular methods

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15
Q

How have our detection methods for STEC changed?

A

We used to just use CTSMAC but moved over to molecular methods

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16
Q

What are the most common STEC serogroups in ireland

A

O26
O157
O145

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17
Q

Comment on the trends in different STEC serogroups over time in Ireland

A

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

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18
Q

Talk about the sesonal distribution in STEC 026 vs o157

A

o26 peaks in summer while O157 peaks in autumn
- we dont know why this happens, no obvious reason for this

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19
Q

Talk about STEC outbreaks in Ireland

A

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

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20
Q

Why is diagnosis of STEC challenging?

A

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

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21
Q

Where is the reference lab for VTEC/STEC?

A

Cherry orchard

22
Q

How do we detect VTEC in the lab

A

EntericBio RT-Gastro Panel
Film Array GI panel
xTAG

23
Q

Talk about C. difficile

A

A major HCAI patogen
A spore forming anaerobe
Toxin producing
Causes a spectrum of disease

24
Q

What are the two main risk factors for C. difficile?

A

Antibiotic use
Direct correlation with age

25
Q

What is different about the lab diagnostics of C. diff versus VTEC

A

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

26
Q

What antibiotic treatments are most associated with C. diff?

A

Clindamycins
Cephalosporins
And now the fluoroquinolones, particuluarly the newer ones e.g. levofloxacin

27
Q

Talk about C. diff infection, where do you get it, incidence, mortality

A

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

28
Q

Why is it thought that the C. diff mortality rate is increasing?

A

increasing virulence
Increasing resistance
Increasing host vulnerability - people living for longer
Changing risk factors

29
Q

What kind of resistance are we concerned with in C. diff

A

Not really concerned with the actual resistance but more sore its conferrred persistance in the hospital enviroment

30
Q

Talk about C diff in the community

A

Incidence of CAI is increasing
Over the last few years about 20% of cases have been CAI

31
Q

Compare asymptomatic C. diff to symptomatic C. diff, how does it affect the host differently

A

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

32
Q

Talk about the clinical manifestation of C diff

A

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

33
Q

Talk about the 5 year trends in C. diff

A

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

34
Q

Where are C. diff outbreaks seen

A

Vast majority are in acute hospital
High in long term care facilities
Few in childcare facilities
Community acquired increasing

35
Q

How has C. diff diagnosis in the lab changed over the years?

A

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

36
Q

What genes are we looking for in C. diff?

A

tcdA and tcdB genes which encode toxin A and B

37
Q

What is the 2 step algorithm for detection of C. diff?

A

1 = screen for toxin gene
2 = confirm toxin protein in sample

38
Q

What is the a common method of screening for C. diff in a sample?

A

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

39
Q

How are C. diff cases confirmed, how do we know the gene is actually producing the target?

A

EIA
Tells us if toxin is present in sample
Gene has been translated etc into protein

40
Q

Talk about viral gastrointestinal disease

A

Historically under reported
Incidence has increase with the ability to diagnose
Recently emerged as the most common reported cause of food-borne disease

41
Q

Why is viral gastrointestinal disease so under-reported?

A

Causes mild illness - people dont bother going to doctor
No routine reliable detection methods
Early clinical samples required - usually sample not suitable

42
Q

Compare the frequency of viral food-borne disease to the two most frequent bacterial casues

A

66.7% of cases are viral
14.2 are campylobacter
9.7 are salmonella

43
Q

What are human enteric viruse

A

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

44
Q

What are the most frequent enteric viruses in infants?

A

Rotavirus A
- large decrease since introduction of vaccine in 2016
Adenovirus 40,41
Coxsackie A24 virus

45
Q

What are the most common enteric viruses in children and adults

A

Norovirus
Calicivurus astrovirus???
Rotavirus B
Reovirus

46
Q

Talk about human noroviruses (HuNoV)

A

Calciviridea family???
Five genera:
- Most concerned with Sapovirus and Norovirus
Multiple genogroups:
- GI, GII etc
Many genotypes

47
Q

Talk about the transmission of norovirus

A

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

48
Q

Talk about how norovirus outbreaks often affect C. diff numbers

A

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

49
Q

Talk about norovirus outbreaks in ireland

A

We get well over 100 outbreaks a year
70% of norovirus cases are related to outbreaks
33% in nursing homes
26% in hospitals

50
Q

Talk about incidence of rotavirus

A

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

51
Q

Laboratory detection of GI viruses

A

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

4.1 Medical Microbiology (30 decks)

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