NATIONAL SALMONELLA, SHIGELLA & LISTERIA REFERENCE
LABORATORY OF IRELAND
(HUMAN HEALTH)
ANNUAL REPORT FOR 2011
NATIONAL SALMONELLA, SHIGELLA & LISTERIA REFERENCE LABORATORY
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Introduction
The National Salmonella Reference Laboratory was established in 2000 with support
from the Department of Health and Children to provide reference services related to
human health. It is a public service laboratory which currently operates with 2 full
time scientific staff representing a reduction from 3 staff working in the service until
2011. The service operates from the Department of Bacteriology at the Clinical
Science Institute, NUIGalway. The NSSLRL website is at
http://www.nuigalway.ie/salmonella_lab/. The reference laboratory uses a number of
phenotypic methods (serotyping, antibiotic-resistance testing and phage typing) and
molecular methods (pulse-field gel electrophoresis (PFGE) and multi-locus variable
number tandem repeat analysis (MLVA) to precisely characterise Salmonella isolates.
This process can be considered as genetic fingerprinting of Salmonella. The goal of
this genetic fingerprinting is to assist relevant agencies in protecting public health by
identifying and interrupting chains of transmission of Salmonella infection. In
addition the NSSLRL provides typing services for Shigella species and Listeria
monocytogenes.
As outlined in previous annual reports a particular phenomenon that has become
prominent in Ireland and Europe in recent years is the increase in the number of
isolates that represent a monophasic variant of S. Typhimurium. Cells of S.
Typhimurium, as with most other serovars of Salmonella, have genes for 2 different
types of flagellar antigens (called phase 1 flagella and phase 2 flagella).
In S.
Typhimurium the phase 1 flagellar antigen is “i" and the phase 2 flagellar antigen is
“2”.
There is a process of genetic switching (variation between 2 “phases”) in
Salmonella so that a culture of S. Typhimurium comprises a mixture of individual
cells some of which are expressing “i" and some of which are expressing “2”.
There
2
are variants of S. Typhimurium that only have the capacity to express one type of
flagellar antigen (monophasic variants) so that all cells in the culture express a single
common flagellar antigen. Such monophasic variants have long been recognised but
have been observed more commonly in recent years and are now an established
feature of Salmonella biology. This change may be substantially related to successful
dissemination of a specific clonal group (Scientific Opinion on monitoring and
assessment of the public health risk of “Salmonella Typhimurium like” strains; EFSA
Journal 2010;8(10):1826).
The Laboratory is committed to providing a high quality and timely service and has
achieved accreditation to the ISO15189 standard from the Irish National
Accreditation Board (INAB).
The continued success of the laboratory is entirely
dependent on the support of the staff in the laboratories that submit isolates for
typing. My colleagues and I appreciate that the preparation, packing and dispatch of
isolates is a significant burden and would like to thank you for your support over the
years.
I would also like to acknowledge the support of all those agencies with whom we work
closely to ensure that the service we provide works as information for action. In
particular I would like to thank Galway University Hospitals, NUI Galway, the Food
Safety Authority of Ireland, the Health Protection Surveillance Centre and colleagues
in Public Health Departments and Environmental Health Departments throughout
the country and to acknowledge the work of colleagues in the National Reference
Laboratory Salmonella (Food, Feed and Animal Health)1.
If you have any comments or questions arising from the report please feel free to
contact me at the email address given below.
Martin Cormican
Director National Salmonella, Shigella & Listeria Reference Laboratory
martin.cormican@hse.ie
1. The Annual Report of National Reference Laboratory Salmonella (Food, Feed
and Animal Health is available at
3
http://www.agriculture.gov.ie/media/migration/animalhealthwelfare/labservice/nrl
/AMRAnnualReport2010.pdf
Salmonella
In 2011, 854 isolates were submitted to the National Salmonella, Shigella & Listeria
Reference Laboratory. When non-Salmonella, QC, contaminants and duplicate isolates
were removed a total of 701 Salmonella isolates were typed. This represents a 12%
decrease in the number of isolates received in 2010.
There were 320 human clinical isolates, including 291 faecal isolates, 23 from blood
(including 8 S. Typhi and 3 S.Paratyphi A), 2 other invasive isolates, and 4 urine isolates.
S.Typhimurium (n = 87) and its monophasic variant 4,5,12:i:- (n = 28) and S.Enteritidis (n
= 58) predominated (Table 2). There was marked seasonal variation with the highest
number of isolates occurring in months June to October. This coincides with the warmer
months of the year and with the peak season for foreign travel (Fig.1) and may be related in
part to one or both of these factors.
In some cases more than one isolate was received from a patient.
For example we may
have received an invasive isolate (e.g. from a blood culture) and an isolate from faeces
from the same patient. Where invasive and faecal isolates come from the same patient,
only the invasive isolate is recorded to avoid duplication. The average turnaround time for
human isolates was 6 days (range 0-22 days). The number of human Salmonella isolates
received is now just over half that observed when the laboratory was established in 2000
(Table 1).
4
Table 1:
Number of Salmonella isolates received in NSSLRL
Year Human
Non-human
2011
320
381
2010
364
559
2009
364
368
2008
447
815
2007
457
653
2006
430
308
2005
357
494
2004
420
650
2003
486
634
2002
394
540
2001
508
574
2000
636
214
Table 2:
Top 17 serotypes of Human Isolates (inc typhoidal)
Serotype
Frequency
%
Typhimurium
87
27
1
4,5,12:i:-
28
8.7
Enteritidis
58
18
Typhi
13
4
Newport
10
3
Stanley
9
2.8
Heidelberg
9
2.8
Concord
7
2.2
Braenderup
7
2.2
Infantis
6
1.9
Saintpaul
5
1.6
Agona
5
1.6
5
Mbandaka
5
1.6
Kentucky
4
1.2
Umbilo
4
1.2
Paratyphi A
3
0.9
Montevideo
3
0.9
Others
57
17.8
Total
320
100
1
This antigenic formula is that of S. Typhimurium except that the phase 2 antigen is not
expressed. These isolates are generally referred to as monophasic S. Typhimurium.
Figure 1
Seasonal Variation in numbers of Salmonella isolates 1
50
45
40
35
30
25
20
15
10
5
0
Total
Ent
Typ/4,5.12:i
FT
r
n
b
Ja Fe Ma
r
y
Ap M a
n
Ju
l
t
v
c
Ju Aug Sep Oc No De
1. The line “Foreign Travel” describes the number of cases of salmonellosis for which an association with
recent foreign travel was reported to NSSLRL. Reporting of recent foreign travel is likely to be incomplete.
It is important to note that there is always an interval gap between the time of onset of
symptoms and date of isolate receipt in the NSSLRL. This includes time taken for patient
to access doctor, taking and transporting the sample to the primary laboratory, isolation of
Salmonella, and referral to NSSLRL.
6
Salmonellosis non-typhoidal
S.Typhimurium and its monophasic variant.
S.Typhimurium 4,5,12;i:2 and its monophasic variant (4,5,12;i:-) together accounted for
35.7% of all cases of Salmonella. Phage type DT104 was the most common (23.5%) phage
type among human isolates in 2011. Phage types DT193 accounted for 20%, DT120/120
low 8.7%, phage type Untypable* 8.7%, DT8 7.8% and DT12 accounted for 5.2% of the
total number of S.Typhimurium/4,5,12:i:- isolates. The proportion of isolates accounted for
by phage type DT104b was low (3.5%) compared to recent years (2010 (11%), 2009
(12%), 2008 (20%), 2007 (12%)).
* Does not react with typing phages.
S.Enteritidis
S.Enteritidis accounted for 18% of all cases of Salmonella. The predominant phage types
were PT1 (17%), RDNC* (17%), PT21 (10.3%), PT4 (8.6%) and PT8 (8.6%).
* Reacts with phages but Does Not Conform to a recognised pattern.
Salmonellosis Typhi and Paratyphi
Thirteen isolates of S.Typhi and 3 isolates of S.Paratyphi A were received. A history of
recent travel was recorded for 11 of the S.Typhi isolates; 6 to the Indian subcontinent, 3 to
Africa, 1 to the Philippines and 1 to Afghanistan. All of the S.Paratyphi A isolates were
associated with reported travel to the Indian subcontinent.
Antimicrobial resistance
Fifty-two percent of isolates (n = 168) were susceptible to all antimicrobial agents tested.
Thirty one percent of isolates (n = 98) were multi-drug resistant (three or more different
classes of antibiotics). Of the 31% of multi-drug resistant isolates, 31% (n=30) had the
profile of resistance to ampicillin, chloramphenicol, streptomycin, sulphonamide and
tetracycline (ACSSuT) and were mainly S.Typhimurium DT104 or closely related phage
types. This group of S. Typhimurium DT104 has accounted for a high proportion of
multidrug-resistant Salmonella isolates for some years now.
Ten extended spectrum beta-lactamase (ESBL) producing isolates were detected. Most
were from patients with a history of foreign travel including 7 S.Concord isolates from
children adopted from Ethiopia. The association of ESBL producing S. Concord with
7
children adopted from Ethiopia has been noted in a number of countries and a report of an
international collaborative study on this phenomenon in which NSSLRL participated was
published in 2009. Given the multi drug resistant nature of these isolates it may be
appropriate to consider screening infants adopted from Ethiopia for carriage and measures
to ensure that parents of these children are aware of the potential for carriage of these
organism. Other ESBL producing isolates included those from patients with travel histories
to Thailand (S.Stanley) and India (S.Worthington). An AmpC producing S. Typhimurium
isolate was received from a patient with no history of foreign travel.
Three isolates of Salmonella resistant to ciprofloxacin were detected. Two of these were
S.Kentucky, one with travel history to India and the other to Jordan. Resistance to
ciprofloxacin (based on widely used interpretive criteria up to and including 2011) is rare
among Salmonella but a ciprofloxacin-resistant S. Kentucky clonal group has arisen and
spread from North Africa in the last decade. A S.Infantis isolate with resistance to
ciprofloxacin was received from a patient who had no history of foreign travel.
In addition 43 isolates resistant to nalidixic acid and with reduced susceptibility to
ciprofloxacin were detected; a decrease from 61 in 2010. It is worth noting that the issue of
interpretive criteria for resistance to ciprofloxacin for Salmonella has been controversial for
a number of years and some would regard all those isolates with reduced susceptibility as
resistant.
Travel related infection
A history of recent foreign travel was recorded in 43.1 % (n = 138) of human cases of
infection (Table 3), Ireland was noted as the country of infection in 40.6 % (n = 130) of
cases while 16.2 % (n = 52) had no country of infection recorded. Turkey, India, Thailand
and Spain were the most commonly recorded travel destinations. S.Enteritidis accounted
for the majority of isolates associated with travel to Turkey and Spain while S.Stanley was
strongly associated with travel to Asia (Thailand, Vietnam & Cambodia). Two-thirds (67.2
%) of S.Enteritidis isolates were associated with foreign travel compared to 15.6 % for
S.Typhimurium and its monophasic variant combined. Although NSSLRL does not have
access to data on the number of Irish people who travel to each country it is likely that the
number of cases associated with each country is at least in part accounted for by the
popularity of the country as a holiday destination.
8
Table 3:
Foreign travel history for Salmonella isolates
Continent
Country
Number
Europe (n = 50)
Turkey
14
Spain
12
UK
7
Bosnia
4
Poland
3
Germany
2
Russia
2
France
1
Hungary
1
Lithuania
1
Malta
1
Portugal
1
Slovakia
1
Africa (n = 38)
Tanzania
8
Ethiopia
7
Nigeria
7
Ghana
4
Cameroon
2
Kenya
2
Sudan
2
Algeria
1
Egypt
1
Malawi
1
South Africa
1
Sudan/Kenya
1
Uganda
1
9
Australasia (n = 45)
India
14
Thailand
13
Pakistan
4
Bangladesh
3
China
2
Vietnam
2
Asia *
1
Afghanistan
1
Cambodia
1
Jordan
1
Middle East
1
Nepal
1
Philippines
1
Americas (n = 3)
Brazil
1
Mexico
1
USA
1
Foreign travel Country unknown (n = 2)
* Country not stated
Clusters
Twenty-four clusters of cases involving 76 isolates were identified in 2011.
S.Typhimurium/S.4,[5],12:i:- was involved in 12 clusters while S.Enteritidis was implicated
in 3 clusters.
Nine of the clusters were family outbreaks, i.e. all patients affected were from one family,
while 5 outbreaks were associated with foreign travel (all patients had travelled to same
country). This included a S.Heidelberg outbreak associated with travel to Tanzania.
10
A point source outbreak involving two Salmonella strains, S.Newport (n = 3) and
S.4,[5],12:i:- (n = 2) was linked to a golf society outing in the East of the country.
The outbreak of S.Typhimurium phage type DT8 that began in August 2009 continued
through 2010 and 2011. This phage type is associated with ducks and several of the cases
were linked epidemiologically with ducks or consumption of duck eggs. However the
number of DT8 isolates from human cases typed in the NSSLRL decreased from 28 in
2010 to 9 in 2011. This suggests that the control procedures put in place are working,
leading to reduced burden of human infection from this source.
The NSSLRL liaises with the European Centre for Disease Control (ECDC) in the
investigation of outbreaks that may have an international dimension, e.g. the S. Heidelberg
outbreak associated with travel to Tanzania.
Evidence of Links between S. Typhimurium in Humans, Food and Animals.
Multi locus variable number tandem repeat analysis (MLVA) is a relatively new
technology that allows for very fine discrimination between isolates that appear very
closely related by other methods including PFGE. This precise discrimination has proved
a useful technique in showing persuasive evidence of links between human S.Typhimurium
clusters and individual cases and recent food and animals sources.
Table 4 illustrates
evidence of links between human infection and food /food animal types. In some cases the
link is complete from animal, to animal related food product and to human cases.
The importance of using standardised and readily comparable methods for “fingerprinting”
human, food and animal isolates of Salmonella not just within Ireland but across Europe
and the world is illustrated by this body of work over the past year.
11
Table 4
MLVA profiles of human and food/animal isolates
Isolate no.
Source
Phage type
Resistance
MLVA profile
Typhimurium
(n = 9)
Human
DT8
none
2-10-NA-12-212*
(n =15)
Duck/Poultry
DT8
Not tested
2-9-NA-12-212*
(n = 3)
Bovine
DT8
none
2-9-NA-12-212
* Or closely related patterns, e.g. 2-9-NA-13-212
(n = 2)
Human
Untypable
none
2-15-17-11-212
(n = 3)
Bovine
Untypable
none
2-15-17-11-212
(n = 1)
Human
Untypable
none
2-16-17-11-212
(n = 1)
Greyhound
Untypable
none
2-16-17-11-212
(n = 1)
Equine
Untypable
none
2-16-17-11-212
(n = 1)
Swine
Untypable
none
2-16-17-11-212
(n = 1)
Bovine
Untypable
none
2-16-17-11-212
(n = 1)
Environmental
Untypable
none
2-16-17-11-212
(n = 2)
Human
DT120
ASSuT
3-11-10-NA-211
(n = 2)
Swine
DT120
ASSuT
3-11-10-NA-211
(n = 8)
Human
DT104
ACSSuT
3-14-14-14-311*
(n = 5)
Bovine
DT104
ACSSuT
3-14-14-14-311*
* Or closely related patterns, i.e. 3-14-15-14-311 or 3-14-16-14-311
(n = 1)
Human
DT104b
ACSSuTTm 3-15-6-12-311
(n = 1)
Swine
DT104b
Not tested
3-15-6-12-311
(n = 1)
Human
DT104b
ACSSuT
3-5-8-14-311
(n = 1)
Swine
DT104b
Not tested
3-5-8-14-311
12
4,[5],12:i:(n = 8)
Human
DT193
ASSuT
3-13-10-NA-211*
(n = 10)
Bovine
DT193
ASSuT
3-13-10-NA-211*
(n = 8)
Swine
DT193
ASSuT
3-13-10-NA-211*
(n = 1)
Chicken
DT193
ASSuT
3-13-10-NA-211
* Or closely related patterns, i.e. 3-13-8-NA-211, or 3-13-9-NA-211
(n = 2)
Human
DT120
ASSuT/Tm
3-11-11-NA-211
(n = 2)
Human
DT193
ASSuT
3-11-11-NA-211
(n = 1)
Swine
DT120
ASSuT
3-11-11-NA-211
(n = 2)
Bovine
DT120
Not tested
3-11-12-NA-211
(n = 1)
Human
DT193
T
3-11-9-NA-211
(n = 1)
Swine
DT193
Not tested
3-11-9-NA-211
(n = 1)
Bovine
DT193
Not tested
3-11-9-NA-211
(n = 1)
Human
DT120low
ASSuTNa
5-9-19-12-211
(n = 2)
Swine
DT120low
ASSuTNa
5-9-19-12-211
Animal Contact
A history of animal contact was recorded for 52 patients with salmonellosis including
contact with turtles, lizards, snakes, fish, pet birds, horses, dogs and farm animals (Table
5). Dogs were the most common contact animal (n = 25) while contact with cats was less
common (n = 7).
In some cases typing of isolates from patients and individual animals they had contact with,
e.g. S.Braenderup isolates from 2 siblings and water and samples from the turtle tank, had
indistinguishable PFGE patterns.
Other strong links included single cases of S.Pomona and S.Litchfield and turtle contact; a
case of S.Bredeney and snake contact; contact with lizards and cases of S.Monschaui,
S.Enteritidis PT8 and S.subsp. II 6,7:m,t. There was 1 case of S.Typhimurium DT135
13
linked to pet birds. This strain was linked with pet canaries in previous years. However the
same strain has also been isolated from cattle.
Although public information on the risk (particularly to children) of contact with reptiles
has been circulated it appears that this may not be reaching relevant sections of the
population or may not have resulted in modification of risk behaviour.
It may be
appropriate to consider if further steps to limit exposure of children to risk of salmonellosis
from contact with reptiles and other exotic pets is appropriate. In total 14 isolates of
Salmonella (approx. 4.4 % of all human cases) were associated with contact with exotic
animals, predominately reptiles.
Among people that had a recorded history of living on farms or working with farm animals
(n = 15), S.Typhimurium/4,5,12:i:- predominated (n =9).
Many of the patients that had a history of animal contact also had other risk factors, e.g.
recent history of foreign travel, consumption of particular food products such as duck eggs,
etc. It is important to note that Salmonella is primarily a foodborne disease and only a
certain percentage of these animal contacts resulted in the patients infections.
14
Table 5:
Animal contact history or strains associated with animal contact
NSSLRL no. Source
Sub1. Strain
Animal Contact
Exotic animals
MS110111
Human
I
Braenderup
Turtle
MS110204
Human
I
Braenderup
Turtle
MS110163
Human
I
Litchfield
Turtle
MS110571
Human
I
Pomona
Turtle
MS110661
Human
I
Bredeney
Snake
MS110623
Human
I
Monschaui
Lizard
MS110111
Human
I
Enteritidis PT8
Lizard
MS110579
Human
I
II 6,7:m,t:-
Bearded dragon
MS110344
Human
I
Typhimurium RDNC
Safari
MS110168
Human
I
4,[5],12:i:- DT193
Parrot
MS110203
Human
I
Saintpaul
Aviary-birds
MS110576
Human
I
Enteritidis PT22
Budgie, chickens
MS110652
Human
I
Typhimurium DT135
Pet birds
MS110544
Human
I
Typhimurium DT135
Ferrets
Farm or Food animals (including horses)
MS110166
Human
I
Tennessee
Sheep,Hens
MS110183
Human
I
Dublin
Farm, Dogs, Cats
MS110348
Human
I
4,[5],12:i:- DT193
Horses, dogs
MS110046
Human
I
4,12:-:2
Chickens, Pigeons
MS110528
Human
I
Typhimurium DT8
Ducks, Hens, Cows
MS110563
Human
I
Typhimurium U302
Hens, Dogs
MS110606
Human
I
Typhimurium DT120
Hens
MS110626
Human
I
4,[5],12:i:- DT193
Hens, Duck eggs
MS110657
Human
I
Enteritidis PT4
Cows
MS110741
Human
I
Typhimurium Untypable
Cattle, Sheep
MS110747
Human
I
Newport
Chicken, Dog
MS110796
Human
I
Typhimurium DT104
Calves, Dogs
15
MS110438
Human
I
Typhimurium Untypable
Pet farm
MS110212
Human
I
4,[5],12:i:- DT193
Puppy (diarrhoea)1
MS110682
Human
I
4,[5],12:i:- DT120
Dog
MS110043
Human
I
Typhimurium DT120
Dog- boxers
MS110375
Human
I
Typhimurium DT104
Dog
MS110631
Human
I
Typhimurium Untypable
Dog
MS110752
Human
I
Typhimurium DT1
Dog
MS110753
Human
I
Typhimurium DT193
Dog, handled pet food
MS110024
Human
I
Agona
Dog
MS110279
Human
I
Mbandaka
Dog
MS110305
Human
I
Mbandaka
Dog
MS110309
Human
I
Mbandaka
Dog
MS110310
Human
I
Mbandaka
Dog
MS110527
Human
I
Stanley
Dog
MS110175
Human
I
Enteritidis PT8
Dog
MS110663
Human
I
Enteritidis PT14b
Dog
MS110678
Human
I
Enteritidis RDNC
Dog
MS110490
Human
I
Enteritidis PT14c
Dog, Cat
MS110746
Human
I
Typhimurium DT104
Dog, Kittens
MS110075
Human
I
Typhimurium DT104
Dogs, Ducks
MS110217
Human
I
IV
Cat
MS110383
Human
I
Napoli
Cat
MS110533
Human
I
Enteritidis RDNC
Cat
MS110761
Human
I
Typhimurium DT104b
Cat
Domestic pets
50:g,z51
1. Sub = Subspecies. There are over 2500 Salmonella serotypes of which approximately
60% belong to subspecies I. These account for about 99% of human infections. Subspecies
I is present in both warm and cold blooded animals while the other Salmonella subspecies
are generally associated with cold-blooded animals.
1
Also has hens
16
Non-Human isolates
In 2011, 381 isolates of Salmonella of non-human origin were submitted to the NSSLRL.
This represents a decrease of 38 % in the number of non-human isolates received in 2010.
The majority of isolates were from swine (n = 202), bovine (n = 74) and poultry (n = 38)
sources. S.Typhimurium/4,5,12;i:- (n = 322) were the most prevalent serovars (Table 6).
Table 6
Top ten serotypes among non-human isolates
Serotype
Frequency
%*
Typhimurium
53
14.0
4,5,12:i:-
23
6.0
246
64.5
11
2.8
Dublin
8
2.1
Kentucky
6
1.6
Infantis
4
1.0
Enteritidis
3
0.8
Braenderup
3
0.8
Montevideo
3
0.8
Senftenberg
3
0.8
Others
18
4.7
Total
381
100
Not serotyped
Mbandaka
1
* Approximate figures
1
These are Typhimurium/4,5,12:i:- isolates received from CVRL for phage typing only.
17
Salmonella serotypes and correlation with Human Infection
S.Typhimurium
S.Typhimurium and its monophasic variant 4,5,12;i:- accounted for 84.5% of all nonhuman isolates and were isolated from a variety of sources predominantly swine (n = 194)
but also including poultry (n = 25) and bovine (n = 62) sources. Phage types DT193 (n =
85), Untypable (n = 24), DT104b (n = 20), DT120/DT120 low (n = 19), U302 (n = 16), and
DT104 (n = 7) were the most common phage types from swine. Phage types DT104b (n =
14), DT193 (n = 14), DT104 (n = 9) and Untypable (n = 8) were the most common phage
type among bovine isolates. As illustrated in Table 4 (above) there is evidence from
molecular typing of a significant link between isolates from pigs and pig products and also
with cattle and human infection.
Salmonella Enteritidis.
Three S.Enteritidis isolates were received from non-human sources in the NSSRL in 2011,
2 from poultry and 1 from bovine sources. It is of interest that S. Enteritidis is rarely
detected from poultry or poultry products in Ireland but that S. Enteritidis is the first or
second most common serovar isolated from human infections each year. In this context it
is worth noting that a history of travel outside of Ireland is reported in relation to 65.5 % of
S. Enteritidis cases compared with only 13.9 % of S. Typhimurium/4,5,12:i:- cases in 2011.
Sources of Isolates
Swine
A total of 5 serovars accounted for the 203 isolates received from swine with
S.Typhimurium and its monophasic variant 4,5,12:i:- (n = 194) accounting for the majority
of isolates.
Poultry
A total of 38 isolates comprising 7 serovars were received from poultry sources. As with
swine S.Typhimurium and its monophasic variant 4,5,12:i:- (n = 25) was the most common
serovar received. S.Typhimurium isolates were from a variety of poultry sources including
18
duck, chicken, turkey and geese while the S. Infantis (n = 3), S. Kentucky (n = 3) and S.
Java (n = 2) isolates were from chickens.
Isolates of all of these serovars were associated with human infections (S. Infantis (n = 6),
S. Kentucky (n = 4) and S. Java (n = 1) in 2011.
Bovine
A total of 74 isolates were received from bovine sources and again S.Typhimurium and its
monophasic variant 4,5,12:i:- accounted for the majority of isolates (n = 62) with DT193 (n
= 14), DT104b (n = 14), DT104 (n = 9) and Untypable (n = 8) being the most common
phage types. There were also 7 S. Dublin isolates (and 2 human cases).
Antimicrobial Resistance
Antimicrobial susceptibility testing was performed on 111 of the 381 non-human isolates
(270 were referred for phage typing only). Of the isolates tested 41% (n = 46) were
susceptible to all antimicrobial agents tested while 41% (n = 46) were multi-drug resistant
(three or more different classes of antibiotics). Twelve percent of isolates tested had the
profile of resistance to ampicillin, chloramphenicol, streptomycin, sulphonamide and
tetracycline (ACSSuT) and most of these typed as S.Typhimurium DT104 or closely
related phage types.
A S. Kentucky isolate from poultry was resistant to third generation cephalosporins and
was identified as a possible AmpC procucer. None of the isolates were resistant to
ciprofloxacin; however 7 isolates exhibited resistance to nalidixic acid and reduced
susceptibility to ciprofloxacin as discussed earlier in this report.
Laboratory Contamination
False-positive Salmonella results due to laboratory cross-contamination are a serious
problem for laboratories and can be difficult to detect. Cross contamination in a laboratory
can result in inappropriate diagnosis of patient infection or in unfounded concerns
regarding the safety of a food product. Detailed subtyping of isolates by the NSSLRL
helps in detection and confirmation of laboratory contamination incidents (Role of
Subtyping in Detecting Salmonella Cross Contamination in the Laboratory; BMC
Microbiology: 9; 155).
19
The NSSLRL recognised 2 such incidents (4 isolates) with Salmonella in 2011. One of the
incidents involved contamination of food samples with the laboratory positive control
strain, S.Nottingham. The other contamination incident occurred with human clinical
samples where the contaminating isolate arose from another patient’s sample.
We would like to reiterate our request that all laboratories involved in testing Salmonella
from any source use Salmonella Nottingham NCTC 7382 as their positive control.
20
Other Testing:
Listeria monocytogenes
Fig. 2 Pulse Field Gel Electrophoresis image of L.monocytogenes isolates digested
with ApaI
The NSSLRL received 60 Listeria monocytogenes isolates in 2011. These included 6
human clinical isolates; 4 from blood cultures and 2 from CSF. Three of the isolates from
humans typed as serotype 4b while 3 typed as serotype 1/2.
Pulsed field gel electrophoresis (PFGE) with ApaI and AscI was performed on the
L.monocytogenes isolates. Two of the human 4b isolates, MQ110050 and MQ120054 had
similar AscI and ApaI patterns to each other and to isolates from human and ready to eat
(RTE) foods from previous years.
Three isolates from swine products (MQ110071-73) had indistinguishable PFGE profiles
with human (2007-09) and swine product (2010) isolates from previous years with AscI.
However PFGE following digestion with ApaI showed some variations between the
isolates. An isolate from pork sausage (MQ110003) had indistinguishable AscI PFGE
profiles from that of a human (2005-09) and swine product (2010) isolates from previous
years while their ApaI patterns were indistinguishable or very similiar.
21
Among the serotype 1/2 isolates the PFGE patterns of MQ110039 was similar (AscI 100%
and ApaI >95%) to 2 isolates from humans from 2008. Isolate MQ110004 had a PFGE
pattern that matched those of isolates from a number of different food sources as well as
from human cases from 2006-11. MQ110049 had similar PFGE AscI and ApaI PFGE
profiles to human case from 2012 and food isolates from 2009 and 2011.
The majority of the food isolates serotyped as 1/2 (n = 49), while 5 isolates were serotype
4b (4 from swine and 1 from smoked salmon).
The NSSLRL is working with colleagues in food and veterinary microbiology in Ireland
and with colleagues in Europe to build a library of typing data that may help to identify
sources of human infection. A critical limiting factor is the availability of human isolates
for typing.
The total number of human clinical isolates in Ireland per year is very small
therefore it is critical that all such isolates are available for typing and we appeal for all
isolates to be forwarded for typing.
22
Shigella species
Fig. 3
Pulse Field Gel Electrophoresis image of S.sonnei digested with XbaI
Dice (Opt:0.50%) (Tol 1.5%-1.5%) (H>0.0% S>0.0%) [0.0%-98.3%]
100
98
96
94
92
90
88
PFGE-XbaI
86
84
PFGE-XbaI
MH110009 Belgium
MH110038
MH110025 Ireland
MH110027 Ireland
MH110022 Ireland
MH110024 Ireland
MH110007 Kenya
MH110014
MH110003 South America
MH110028 Sudan
MH110033 Gambia
MH110041
MH110006 Gambia
MH110004 Yes-Unknown
MH110015 India
MH110002 Ireland
MH110016 India
MH110019 Lebanon
MH110005 Ireland
MH110018
A total of 41 isolates were referred to the NSSLRL in 2011 for Shigella typing. When nonShigella, QC and duplicate isolates were removed a total of 30 Shigella isolates were typed.
These included 20 S.sonnei and 10 S.flexneri. The S.flexneri isolates were further divided
into 1 S.flexneri 1a, 5 S.flexneri 2a, 1 S.flexneri 3a, 1 S.flexneri 3b, and 2 S.flexneri 6.
Ninety percent of isolates (n = 27) were multi-drug resistant (three or more different classes
of antibiotics). No ESBL producing Shigella isolates were received in the NSSLRL in 2011
while 4 isolates were resistant to ciprofloxacin. The ciprofloxacin resistant isolates
included 2 Shigella sonnei, 1 of whom had travelled to India, and 2 S.flexneri isolates, one
with history of travel to India and the other to Spain.
Eighteen patients had a recorded history of recent foreign travel, including Europe (n = 4),
Africa (n = 5), Australasia (n = 6) and the Americas (n = 2). Seven patients had Ireland
recorded as their country of infection while there were no details for six patients.
23
Table 7:
Foreign travel history for Shigella isolates
Continent
Country
Number
Gambia
2
Kenya
1
Morocco
1
Sudan
1
Spain
3
Belgium
1
Africa (n = 5)
Europe (n = 4)
Australasia (n = 6)
India
3
Thailand
1
Lebanon
1
Timor-Leste
1
Americas (n = 2)
South America
Panama
1
1
There was one family outbreak (n = 3) of Shigella sonnei in 2011.
24
NSSLRL Publications and Presentations 2011
Oral Presentations
You are what you Eat. Irish Society of Clinical Microbiology, Dublin. Feb 2011.
Salmonella enterica serovar Enteritidis biofilm formation on 5 surfaces found in food
processing environments. Queens University Belfast, UK. Apr 2011.
National Salmonella, Shigella & Listeria Reference Laboratory - Come Dine with Me.
Oxoid, LIP, Fannin Seminar. Galway. Oct 2011.
How to kill a Salmonella Biofilm. British Society for Antimicrobial Chemotherapy –
Antimicrobial Resistance Mechanisms Workshop. Birmingham, UK. Nov 2011.
Poster Presentations
Differences in the biofilm properties of laboratory adapted and recent isolates of
Salmonella enterica. Society for General Microbiology, Harrogate, UK. Apr 2011
Variation in Salmonella enterica Serovars Ability to Establish a Biofilm. American Society
for Microbiology, New Orleans, Louisiana, USA. May 2011.
Salmonella enterica biofilm: older biofilms are different. Federation of Infections Society,
Manchester, UK. Nov 2011.
Papers
Fox, E., De Lappe, N., Garvey, P., McKeown, P., Cormican, M., Leonard, N., and
K.Jordan. PFGE analysis of Listeria monocytogenes isolates of clinical, animal, food and
environmental origin from Ireland J Med Microbiol April 2012 61:540-547
Prendergast, D.M, O’Grady, D., Fanning, S., Cormican, M., De Lappe, N., Egan, J.,
Mannion, C., Fanning, J., and M.Gutierrez. Application of multiple locus variable number
of tandem repeat analysis (MLVA), phage typing and antimicrobial susceptibility testing to
25
subtype Salmonella enterica serovar Typhimurium isolated from pig farm, pork
slaughterhouses and meat producing plants in Ireland. Food Microbiol Aug 2011 28:10871094
Boyle, F., Healy, G., Hale, J., Kariuki, S., Cormican, M., and D.Morris. Characterisation of
a novel extended-spectrum B-lactamase phenotype from OXA-1 expression in Salmonella
Typhimurium strains from Africa and Ireland. Diagn Microbiol Infect Dis. Aug 2011 70
(4):549-53
Nicolay, N., Thornton, L., Cotter, S., Garvey, P., Bannon, O., McKeown, P., Cormican, M.,
Fisher, I., Little, C., Boxall, N., De Pinna, E., Peters, T.M., Cowden, J., Salmon, R., Mason,
B., Irvine, N., Rooney, P., and D.O’Flanagan. Salmonella enterica serovar Agona
European outbreak associated with a food company. Epidemiol Infect Aug 2011
139(8):1272-80.
26