NATIONAL SALMONELLA, SHIGELLA & LISTERIA REFERENCE
LABORATORY OF IRELAND
(HUMAN HEALTH)
ANNUAL REPORT FOR 2010
NATIONAL SALMONELLA, SHIGELLA & LISTERIA REFERENCE LABORATORY
1
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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 with 3 full time scientific staff.
It
operates from the Department of Bacteriology at the Clinical Science Institute, NUI
Galway.
The NSRL website is at http://www.nuigalway.ie/salmonella_lab/.
The
reference laboratory uses a number of phenotypic methods (serotyping, antibioticresistance testing and phage typing) and molecular methods (pulse-field gel
electrophoresis (PFGE) and multi-locus variable number tandem repeat analysis
(MLVA) to precisely characterise isolates of Salmonella, Shigella and Listeria spp.
This process can be considered as genetic fingerprinting of food-borne bacteria. The
goal of this genetic fingerprinting is to assist relevant agencies in protecting public
health by identifying and interrupting chains of transmission of food-borne bacteria.
A particular phenomenon that has become very prominent in Ireland 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 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 relatively uncommon. This situation has changed quite
2
dramatically in recent years with increasing numbers of monophasic S. Typhimurium
in Ireland and throughout Europe.
of significant research.
The biological basis for this change is the subject
The growth of this phenomenon in Ireland is referred to in
this report.
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 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 Reference Laboratory
martin.cormican@hse.ie
An extract from the 2010 Annual Report of National Reference Laboratory
Salmonella (Food, Feed and Animal Health) is available at
http://www.agriculture.gov.ie/media/migration/animalhealthwelfare/labservice/nrl/N
RL%20Spring%202011%20Newsletter.pdf
3
Salmonella
In 2010, 1070 isolates were submitted to the National Salmonella Reference Laboratory.
When non-Salmonella, QC contaminants and duplicate isolates were removed a total of
923 Salmonella isolates were typed. This represents a 26% increase in the number of
isolates received in 2009.
There were 364 human clinical isolates, including 334 faecal isolates, 22 from blood
(including 6 S.Typhi, 2 S.Paratyphi A and 1 S.Paratyphi B), 3 other invasive isolates, and 5
urine isolates. S.Typhimurium (n = 113) and its monophasic variant 4,5,12:i:- (n = 19) and
S.Enteritidis (n = 70) predominated (Table 2). There was marked seasonal variation with
the highest number of isolates occurring in months May to November. 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
testing was 6.3 days (range 2-32 days). An equal number of Salmonella isolates from
humans were received in the NSRL in 2010 and 2009 (Table 1).
Table 1:
Number of Salmonella isolates received in NSRL
Year Human
Non-human
2010
364
559
2009
364
368
2008
447
815
2007
457
653
2006
430
308
2005
357
494
2004
420
650
2003
486
634
4
2002
394
540
2001
508
574
2000
636
214
Table 2:
Top sixteen serotypes of Human Isolates (including Typhi and
Paratyphi)
Serotype
Frequency
%
Typhimurium
113
31
1
4,5,12:i:-
19
5.2
Enteritidis
70
19.2
Infantis
17
4.7
Newport
8
2.2
Typhi
8
2.2
Braenderup
7
1.9
Dublin
7
1.9
Saintpaul
7
1.9
Montevideo
7
1.9
Java
7
1.9
2
3
0.8
Stanley
5
1.4
Concord
5
1.4
Paratyphi A
4
1.1
Virchow
4
1.2
Others
73
19.8
Total
364
100
1
4,5,12:b:-
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.
2
Isolates with this antigenic formula are most likely monophasic variants of S. Java, i.e.
phase 2 antigen is not expressed.
5
Seasonal Variation in Salmonella isolates 1
Figure 1
60
no. of isolates
50
Total
Salmonella
40
Enteritidis
30
20
Typhimurium/
4,5,12:i:-
10
Foreign Travel
Dec
Nov
Oct
Sep
Aug
Jul
Jun
May
Apr
Mar
Feb
Jan
0
Month of receipt in NSRL
1. The line “Foreign Travel” describes the number of cases of salmonellosis for which an association with
recent foreign travel was reported to NSRL. Reporting of recent foreign travel is likely to be incomplete.
It is important to note that there is always an interval between the time of onset of
symptoms and date of isolate receipt in the NSRL. This includes time taken for patient to
seek medical attention, taking and transporting the sample to the primary laboratory,
isolation of Salmonella, and referral to NSRL.
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
36% of all cases of Salmonella. Phage type DT8 was the most common (21%) phage type
among human isolates in 2010. This was driven by a single outbreak associated with
consumption of duck eggs. Phage types DT104 accounted for 20%, DT104b 11% and
DT193 accounted for 14% of the total number of S.Typhimurium/4,5,12:i:- isolates. Apart
from DT8 the predominance of phage type DT104 and related phage types are similar to
recent years.
6
S.Enteritidis
S.Enteritidis accounted for 19% of all cases of Salmonella. The predominant phage types
were PT14b (24%), PT1 (20%), PT4 (13%), PT21 (9%) and PT8 (6%). The increase in
PT14b was primarily caused by an outbreak (n = 9) of nalidixic acid resistant PT14b.
Salmonella Typhi and Paratyphi
Eight isolates of S.Typhi, 4 isolates of S.Paratyphi A and 1 isolate of S.Paratyphi B were
received. A history of recent travel was recorded for all of the S.Typhi isolates; 7 to the
Indian subcontinent and 1 to Guinea (West Africa). Two of the S.Paratyphi A isolates were
associated with reported travel to the Indian subcontinent, while 1 isolate had foreign travel
to Asia with country not stated. A history of travel to South America (country not stated)
was recorded for the S.Paratyphi B isolate.
Antimicrobial resistance
Fifty-two percent of isolates (n = 189) were susceptible to all antimicrobial agents tested.
Thirty percent of isolates (n = 109) were multi-drug resistant (three or more different
classes of antibiotics). Of the 30% of multi-drug resistant isolates, 24% (n=26) 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. All were
from patients with a history of foreign travel including 5 S.Concord isolates from children
adopted from Ethiopia. The association of ESBL producing S. Concord with 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 NSRL participated was
published in 2009.
Other ESBL producing isolates included those from patients with travel history to Thailand
(S.Typhimurium and 4,5,12:i:-), Poland (S.Enteritidis PT4), India (S.Worthington), and
Morocco (S.Typhimurium). One AmpC producing isolate was received, a S.Newport, from
a patient with no reported history of foreign travel.
7
Two isolates of Salmonella resistant to ciprofloxacin were detected. These were both
S.Kentucky, one with travel history to East Africa, and the other with no report of foreign
travel. Resistance to ciprofloxacin is rare among Salmonella but a ciprofloxacin-resistant
clone of S. Kentucky has arisen and spread from North Africa in the last decade. In
addition 61 isolates resistant to nalidixic acid and with reduced susceptibility to
ciprofloxacin were detected; an increase from 50 in 2009.
Travel related infection
A history of recent foreign travel was recorded in 40% (147) of human cases of infection
(Table 3), Ireland was noted as the country of infection in 38.5% (140) of cases while 21%
(77) had no country of infection recorded. Spain was the most commonly recorded travel
destination (recorded in 24 cases) with S. Enteritidis (n = 15) accounting for the majority of
these cases. More than half (61%) of S.Enteritidis isolates were associated with foreign
travel compared to 19% for S.Typhimurium and its monophasic variant combined.
Although NSRL 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.
Table 3:
Foreign travel history for Salmonella isolates
Continent
Country
Number
Europe (n = 54)
Spain
24
Turkey
8
UK
5
Poland
4
Malta
3
Italy
2
Bulgaria
1
France
1
Germany
1
Lithuania
1
Greece
1
8
Croatia
1
Croatia/Bosnia
1
The Netherlands
1
Africa (n = 36)
Ethiopia
6
Nigeria
6
Tunisia
6
Egypt
4
Morocco
3
S.Africa
1
Algeria
1
Chad
1
Ghana
1
Guinea
1
Sudan
1
Zambia
1
Tanzania
1
Tanzania/Zanzibar
1
Mauritius
1
Mauritius/Africa
1
Australasia (n = 51)
Thailand
16
India
9
Indonesia
4
Pakistan
3
Bangladesh
3
Phillipines
2
UAE
2
Vietnam
2
Cambodia
2
Asia *
2
Nepal
1
9
Bahrain
1
Australia
1
Australia/Malaysia
1
Malaysia/Thailand
1
Maldives/Dubai
1
Americas (n = 6)
Carribean/USA
2
USA
1
Mexico
1
South America *
1
Dominican Republic 1
* Country not stated
Clusters
Twenty-six clusters of cases involving 106 isolates were identified in 2010. S.Typhimurium
was involved in 13 clusters while S.Enteritidis was implicated in 3 clusters.
Eight of the clusters were family outbreaks, i.e. all patients affected were from one family,
while four outbreaks were associated with foreign travel (all patients had travelled to same
country).
A point source outbreak involving a S.Infantis strain was linked to a self-catered
confirmation party and turkey was the suspected vehicle. Fourteen of thirty people were
sick after the event while 9 S.Infantis isolates were received in the NSRL.
Detailed subtyping detected a S.Montevideo outbreak (n = 5) occurring in the East of the
country. PFGE proved useful in distinguishing sporadic cases from the outbreak strain.
The outbreak of S.Typhimurium phage type DT8 that began in August 2009 continued in
2010. A total of 28 DT8 isolates from human cases were typed in the NSRL in 2010. This
10
phage type is associated with ducks and several of the cases were linked epidemiologically
with ducks or consumption of duck eggs. The UK has also seen a similar outbreak which is
also linked to ducks. The NSRL has liased with the Central Veterinary Research
Laboratory, the Food Safety Authority of Ireland, the Health Protection Surveillance Centre
and other agencies in the investigation and control of this outbreak and a detailed account is
in preparation in association with other partners involved in managing this issue.
The NSRL liaises with the European Centre for Disease Control (ECDC) in the
investigation of outbreaks that may have an international dimension. The UK declared an
outbreak of S.Bareilly involving 224 isolates since August 2010 linked to the consumption
of beansprouts. The NSRL typed a S.Bareilly isolate with an indistinguishable pulsed field
profile. This patient had travelled to London in September and had eaten beansprouts.
An outbreak of S.Enteritidis PT14b with resistance to nalidixic acid in which the first cases
were seen here in November 2009 continued until March 2010 (11 cases in 2009 and 9
cases in 2010). A similar increase in isolation of this strain in the UK was considered to be
associated with consumption of Spanish eggs.
(http://www.hpa.org.uk/NewsCentre/NationalPressReleases/2010PressReleases/100914coo
perationcurtailedsalmonellaoutbreak/). Irish isolates have been provided to colleagues in
the UK to assist in further research on this strain.
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
molecular and other laboratory 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. Interpretation is not always straightforward as illustrated in
footnotes 5 and 6.
11
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.
Table 4
MLVA profiles of human, food and animal S. Typhimurium isolates
Isolate no.
Source
Phage type
Resistance
MLVA profile
28 Isolates
Human
DT8
none
2-10-NA-12-2121,2
119 Isolates
Duck3
DT8
none
2-10-NA-12-2122,4
MS100758
Human
Untypable
none
2-15-17-11-212
MS100800
Human
Untypable
none
2-15-17-11-212
(N = 3)
Bovine faeces
Untypable
none
2-15-17-11-212
MS1008045
Dairy product
Untypable
none
2-15-17-11-212
Group 1
Group 2
Group 3
MS100796
Human(Typhimurium) DT120
ASSuT
3-11-10-NA-211
MS100926
Human (4,5,12:i:-)
ASSuT
3-11-10-NA-211
(N = 4)
Bovine faeces (4,5,12:i:-) DT193
ASSuT
3-11-10-NA-211
MS100185
Human
DT104
ACSSuT
3-13-15-14-311
MS100504
Bovine faeces
DT104
Not tested
3-13-15-14-311
MS100054
Human (4,5,12:i:-)
DT193
ASSuT
3-13-9-NA-211
MS100080
Human (4,5,12:i:-)
DT193
ASSuT
3-13-9-NA-211
MS1006866
Human (4,5,12:i:-)
DT193
ACSSuTCazCtx 3-13-9-NA-211
MS1006427
Human (4,5,12:i:-)
U323
ASSuT
3-13-9-NA-211
MS100911
Human (Typhimurium) DT120
none
3-13-9-NA-211
(N = 2)
Bovine faeces(4,5,12:i:-) DT193
ASSuT
3-13-9-NA-211
DT193
Group 4
Group 5
12
(N = 2)
Chicken (4,5,12:i:-)
DT193
ASSuT
3-13-9-NA-211
(N = 6)8
Swine (4,5,12:i:-)
Untypable
ASSuT
3-13-9-NA-211
MS100018
Human (4,5,12:i:-)
U311
ASSuT
3-14-10-NA-211
(N = 18)9,10
Swine
U311
ASSuT
3-14-10-NA-211
MS101008
Human
DT104b
ACSSuTTm 3-14-6-11-311
MS101024
Human
DT104b
ACSSuTTm 3-14-6-11-311
MS101047
Human
DT104b
ACSSuTTm 3-14-6-11-311
MS101048
Human
DT104b
ACSSuTTm 3-14-6-11-311
MS100342
Swine faeces
DT104b
ACSSuT
MS100513
Human
DT104b
ACSSuTTm 3-14-6-12-311
MS100167
Bovine
DT104b
ACSSuT
3-14-6-13-311
(N = 5) 12
Swine
DT104b
ASu
3-14-6-12-311
MS100891
Human
DT104
SSu
3-15-17-11-311
MS100908
Human
DT104
SSu
3-15-17-11-311
MS100914
Bovine faeces
DT104
SSu
3-15-17-11-311
MS100220
Human
DT104b
ACSSuT
3-15-6-13-311
(N = 5) 13
Swine
DT104b14
ACSSuT
3-15-6-12-311
(N = 2) 13
Swine
DT1214
ACSSuT
3-15-6-12-311
MS100534
Human
DT104b
ACSSuT
3-16-5-12-311
MS100645
Bovine faeces
DT104b
ACSSuT
3-16-5-12-311
Group 6
Group 7
3-14-6-11-311
Group 8 11
Group 9
Group 10
Group 11
13
1. A small number of isolates exhibited antimicrobial resistance as follows, 2 resistant to streptomycin, 1
resistant to ampicillin and 1 resistant to Ampicillin, sulphonamide and trimethoprim
2. A small number of isolates showed a degree of variation in the MLVA pattern for example, 2-9-NA-12212
3. In addition there was a single isolate each of S. Typhimurium DT8 from feline and bovine sources
4. A small number of isolates exhibited antimicrobial resistance as follows, 2 resistant to streptomycin, 1
resistant to streptomycin, sulphonamide, tetracycline and trimethoprim
5. This isolate was from a previously opened product and post-opening contamination was suspected.
6. History of recent travel to Thailand – it is unlikely that these strains are epidemiologically related – this
could reflect convergence of unrelated strains on a common MLVA profile
7. History of recent travel to Spain – it is unlikely that these strains are epidemiologically related – this could
reflect convergence of unrelated strains on a common MLVA profile.
8. Group 5 included porcine sponge (n=5) and pig meat (n=1).
9. There were in addition a number of isolates other then U311 with indistinguishable MLVA profile as
follows; (a) phage untypable (ASSuT), (b) DT193 (ASSuT) and (c) DT104 (ACSSuT). These isolates may
be related to this group.
10. Group 6 included swine (n=7) and pork (n=11).
11. Likely to be closely related to Group 7.
12. Group 8 included swine (n=3), swine food (n=1) and sausages (n=1).
13. Group 10 included swine animals (n=4) and swine meat (n=3).
14. Phage types DT104, DT104b and DT12 are closely related
Animal Contact
A history of animal contact was recorded for 75 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 = 34) while contact with cats was less
common (n = 11).
As dogs and cats are very common companion animals contact with
these animals is not persuasive evidence of a link between the infection and the animal
species. However in some cases typing of isolates from patients and individual animals
they had contact with, e.g. lizards (S.Oranienburg and S.subsp.IV 48:g,z51) showed them to
be indistinguishable.
14
Other strong links included a family outbreak of S. Newport and pet turtles; single cases of
S.Muenchen and a serovar 4,5,12:i:- (monophasic Typhimurium) DT191A associated with
turtle contact; contact with lizards and cases of S.Itami, S.Muenchen, S.Muenster and
S.subsp. IV 45:g,z51. There were also 2 cases of S.Typhimurium DT135 linked to pet
canaries. This strain was also linked with pet canaries in previous years. However an
indistinguishable 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 19 isolates of
Salmonella (approx. 5.2 % 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 = 24), S.Typhimurium/4,5,12:i:- predominated (n =15), especially the DT104 phage
group (n = 6). Three patients with S.Typhimurium DT8 had contact with ducks.
In the
absence of more detailed analysis this must be interpreted with caution however it is
noteworthy particularly as S. Typhimurium is more closely associated with acquisition in
Ireland than the other major serovar S. Enteritidis.
Many of the patients that had a history of animal contact also had other risk factors, e.g.
recent history of foreign travel or consumption of particular food products such as duck
eggs. 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.
15
Table 5:
Animal contact history or strains associated with animal contact
NSRL no.
Source
Sub1. Strain
Animal Contact
MS100327
Human
I
Newport
Turtle
MS100400
Human
I
Newport
Turtle
MS100722
Human
I
Muenchen
Turtle
MS100035
Human
I
4,5,12:i:- DT191A
Turtle
MS100244
Human
I
Itami
Lizards, Corn snake
MS101025
Human
I
Muenchen
Lizard
MS100175
Human
I
Typhimurium DT10
Lizard
MS100790
Human
IV
45:g,z51
Lizard
MS100020
Human
I
Oranienburg
Lizard
MS100021
Human
I
Oranienburg
Lizard
I
Oranienburg
-
MS100044 1 Lizard faeces I
Oranienburg
-
MS100150
Human
I
Oranienburg
Lizard
MS100375
Human
I
Muenster
Bearded dragon (lizard)
MS100501
Human
IV
48:g,z51
Lizard
MS100425 2 Lizard
IV
48:g,z51
-
MS100901
Human
I
Typhimurium DT135
Canaries
MS101012
Human
I
Typhimurium DT135
Canary, cats, dogs
MS100050
Human
II
13,23:g,s,t
Bird
MS100011
Human
I
Enteritidis PT1
Zoo
MS100102
Human
I
Enteritidis PT13a
Octopus
MS101023
Human
I
Enteritidis PT21
Bird
MS100397
Human
I
Java
Fish aquarium
MS100647
Human
II 1
42:r:-
None
Exotic animals
MS100043 1 Lizard hide
Farm or Food animals (including horses)
MS100428
Human
I
Dublin
Cattle
MS100503
Human
I
Dublin
Cattle- farmer
16
MS100793
Human
I
Dublin
Farmer
MS100358
Human
I
4,5,12:i:- DT193
Vet assistant, pets
MS100291
Human
I
4,5,12:i:- DT193
Ponies, cats
MS100348
Human
I
Typhimurium DT104
Horses, cattle, dogs
MS100562
Human
I
Typhimurium DT104
Cattle, dogs
MS100578
Human
I
Typhimurium DT104
Chickens
MS100581
Human
I
Typhimurium DT104
Lives on farm
MS100636
Human
I
Typhimurium DT104
Horses
MS100891
Human
I
Typhimurium DT104
Meat worker
MS100105
Human
I
Typhimurium DT120
Horse, dog, rabbit
MS100911
Human
I
Typhimurium DT120
Horses, dogs
MS100749
Human
I
Typhimurium DT8
Duck, dog, horse
MS100860
Human
I
Typhimurium DT8
Ducks, hens, goat
MS100894
Human
I
Typhimurium DT8
Ducks, hens, goat
MS100523
Human
I
Typhimurium PT untypable Horses, dogs
MS100758
Human
I
Typhimurium PT untypable Father has contact with
Human
I
Enteritidis PT4
Horses,Cows, dogs, cats
MS100489
Human
I
Enteritidis PT4
Cattle
MS100036
Human
I
Enteritidis PT14b
Horses, Dogs
MS100543
Human
I
London
Pigs
MS100186
Human
I
Nima
Cattle- calving
MS100019
Human
I
Saintpaul
Hens, Dogs
MS100003
Human
I
Enteritidis PT1
Dog
MS100088
Human
I
Enteritidis PT14b
Hamster
MS100756
Human
I
Enteritidis PT14c
Dog
MS100410
Human
I
Typhimurium DT104
Dog, cat
MS100454
Human
I
Typhimurium DT104
Dogs
MS100670
Human
I
Typhimurium DT104
Dogs
MS100691
Human
I
Typhimurium DT104
Dogs
MS100653
Human
I
Typhimurium DT104
Dog, cat
horses
MS100075
and hens
Domestic pets
17
MS100757
Human
I
Typhimurium DT104
Dog, cat
MS100100
Human
I
Typhimurium DT104b
Dog
MS100538
Human
I
Typhimurium DT8
Dogs
MS100058
Human
I
Typhimurium DT8
Dog, cat
MS100085
Human
I
Typhimurium DT8
Cat
MS100695
Human
I
Typhimurium DT8
Cats
MS100910
Human
I
Typhimurium DT8
Dog
MS100702
Human
I
Typhimurium DT2
Dog
MS100754
Human
I
Typhimurium PT untypable Dog
MS100406
Human
I
4,5,12:i:- PT untypable
Dog
MS100436
Human
I
4,5,12:i:- DT193
Pets
MS100443
Human
I
Kentucky
Dogs
MS100611
Human
I
Kentucky
Rabbit
MS101046
Human
I
Senftenberg
Dogs
MS100740
Human
I
Infantis
Dogs
MS100332
Human
I
Umbilo
Dogs
MS100594
Human
I
Javiana
Dogs
MS100741
Human
I
Panama
Dog
MS100755
Human
I
Unnamed (4,12:-:-)
Dog
MS100806
Human
I
Saintpaul
Dog
MS100698
Human
I
Newport
Dog, cat
MS100013
Human
I
Hadar
Cat
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
Isolates from pet lizard of patients MS110020 & MS110021.
2
Isolate from pet lizard of patient MS100501
18
Non-Human isolates
In 2010, 559 isolates of Salmonella of non-human origin were submitted to the NSRL. This
represents an increase of 52% on the number of non-human isolates received in 2009. The
majority of isolates were from swine (n = 193) and poultry (n = 221) while there were 65
isolates from bovine sources. S.Typhimurium/4,5,12;i:- (n = 381) and S.Kentucky (n = 63)
were the most prevalent serovars (Table 6). The increase in the S.Typhimurium isolates
tested was due to the investigation of the duck-associated DT8 outbreak.
Table 6
Top fifteen serotypes among non-human isolates
Serotype
Frequency
Typhimurium
%3
222
39.7
49
8.8
110
19.7
Kentucky
63
11.3
Dublin
18
3.2
Mbandaka
10
1.8
Virchow
7
1.3
Tennessee
6
1.0
Montevideo
6
1.0
Agona
4
0.7
Derby
4
0.7
Oranienburg
4
0.7
Livingstone
3
0.5
Ohio
3
0.5
50
8.9
1
4,5,12:i:-
2
Not serotyped
Others
Total
559
100
1
Most likely monophasic variants of S. Typhimurium
2
These are S. Typhimurium or 4,5,12:i:- (monophasic S. Typhimurium) isolates received
from CVRL for phage typing only.
3
Approximate figures.
19
Salmonella serotypes and correlation with Human Infection
S.Typhimurium
S.Typhimurium and its monophasic variant 4,5,12;i:- accounted for 68.2% of all nonhuman isolates and were isolated from a variety of sources predominantly swine (n = 172)
but also including poultry (n = 141) and bovine (n = 39) sources. Phage types DT104b (n =
33), DT193 (n = 32), Untypable (n = 22), U311 (n = 25), U302 (n = 21), DT120/DT120
low (n = 12) and DT104 (n = 8), were the most common phage types from swine. Phage
type DT104 (n = 18) was 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.
No S.Enteritidis isolates were received from non-human sources in the NSRL in 2010. 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. In this context it is worth noting that a history of travel outside of Ireland is
reported in relation to 61% of cases S. Enteritidis compared with only 19% of S.
Typhimurium/4,5,12:i:-.
Sources of Isolates
Swine
A total of 9 serovars accounted for the 193 isolates received from swine with
S.Typhimurium/ 4,5,12:i:- (n = 172) accounting for the majority of isolates.
Poultry
A total of 221 isolates comprising 13 serovars were received from poultry sources.
S.Typhimurium/ 4,5,12:i:- (n = 141) and S. Kentucky were the most common serovars (n =
56) and most isolates were susceptible to all antimicrobial agents tested. The vast majority
of the S.Typhimurium isolates were from ducks while the S. Kentucky isolates were mainly
from chickens. S.Virchow was also a common serovar from poultry sources (n = 7). There
20
were 4 human cases of S.Virchow in 2010 but no specific product was implicated in these
infections.
Bovine
A total of 65 isolates were received from bovine sources. S.Typhimurium/4,5,12:i:accounted for the majority of isolates (n = 39) with DT104 (n = 18) being the most
common phage type. There were also 14 S.Dublin isolates. There were 7 human cases of
S.Dublin. No specific product was implicated in these infections but 3 were farmers.
Antimicrobial Resistance
Antimicrobial susceptibility testing was performed on 437 of the 559 non-human isolates
(122 were referred for phage typing only). Fifty-six percent of isolates were susceptible to
all antimicrobial agents tested. Thirty-four percent were multi-drug resistant (three or more
different classes of antibiotics). Ten percent of isolates 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.
None of the non-human isolates were resistant to third generation cephalosporins or
ciprofloxacin; however 26 isolates exhibited resistance to nalidixic acid and reduced
susceptibility to ciprofloxacin.
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 NSRL helps in
detection and confirmation of laboratory contamination incidents (Role of Subtyping in
Detecting Salmonella Cross Contamination in the Laboratory; BMC Microbiology: 9; 155).
The NSRL assisted in recognising 9 such incidents (14 isolates) with Salmonella in 2010
with 3 of the incidents involving the laboratory positive control strain, S.Nottingham, and 1
incident involving a S.Alachua control isolate. Two of the S.Nottingham incidents involved
food laboratories while the other involved a human clinical sample. The S.Alachua incident
21
occurred in a food laboratory. There was an incident of S.Enteritidis contamination (4
isolates) involving an external quality assessment sample in another laboratory.
Four contamination incidents 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.
22
Listeria monocytogenes
Fig. 2 Dendrogram of L. monocytogenes 4b isolates digested with AscI
Dice (Opt:1.50%) (Tol 1.5%-1.5%) (H>0.0% S>0.0%) [0.0%-100.0%]
100
95
90
PFGE-AscI
85
80
PFGE-AscI
MQ100005
Swine
MQ100011
Sausage
MQ100022
Sausage- Swine
MQ100019
Sliced cooked ham
MQ100007
Goats cheese starter
MQ100018
CSF
MQ100015
Ice cream from machine
MQ100016
Blood culture
MQ100030
Cooked duck
The NSRL received 30 Listeria monocytogenes isolates and 1 Listeria innocua isolate in
2010. These included 4 human clinical isolates; 3 from blood cultures and 1 from CSF.
Two of the isolates from humans typed as serotype 4b while 2 typed as serotype 1/2.
Pulsed field gel electrophoresis (PFGE) with ApaI and AscI was performed on the
L.monocytogenes isolates. Comparison of the serotype 4b patterns showed that MQ100016
matched human and food isolates from this and previous years (2004-10) with both AscI
and ApaI.
MQ100018 was an unusual profile that was similar (AscI 100% and ApaI 90%) to an
isolate from goats cheese.
This is not a basis for concluding that goats cheese was the
vehicle of infection in this instance.
Among the serotype 1/2 isolates the PFGE patterns of MQ100029 matched those of isolates
from mushrooms, beef, pork and swine from 2006-09 and were very similar to a human
case from 2009 (L07-029).
23
The majority of the food isolates serotyped as 1/2 (n = 19), while 7 isolates were serotype
4b.
The NSRL 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.
typing.
A critical limiting factor is the availability of human isolates for
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.
24
Shigella species
Fig. 3
Dendrogram of PFGE 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
86
84
PFGE-XbaI
82
80
78
PFGE-XbaI
MH100009
SSuTTm
MH100010
SSuTTm
MH100011
SSuTTm
MH100015
SSuTTm
MH100030
Cameroon
SSuTTm
MH100048
Egypt
SSuTTm
MH100021
Nigeria
SSuTTm
MH100025
TmNaCp
MH100027
TmNaCp
MH100012
SSuTTmNaCp
MH100026
India
SSuTTmNaCp
MH100033
India
SSuTTmNaCp
MH100017
MH100018
SSuTTm
South America
MH100037
MH100016
AST
ASSuTTm
India
SSuTTmNa
A total of 49 isolates were referred to the NSRL in 2010 for Shigella typing. When nonShigella, QC and duplicate isolates were removed a total of 39 Shigella isolates were typed.
These included 17 S.sonnei, 18 S.flexneri, 3 S.boydii and 1 Shigella unidentifiable (did not
react with any Shigella antisera). The S.flexneri isolates were further divided into 1
S.flexneri 1a, 3 S.flexneri 1b, 1 S.flexneri 1c, 2 S.flexneri 2a, 3 S.flexneri 3a, 2 S.flexneri 3b,
3 S.flexneri 4c, and 3 S.flexneri 6.
Ninety-seven percent of isolates (n = 38) were multi-drug resistant (three or more different
classes of antibiotics). A S.boydii isolate, where the patient had a history of recent travel to
Egypt, was an ESBL producer while 9 isolates were resistant to ciprofloxacin. The
ciprofloxacin resistant isolates included 6 Shigella sonnei, 2 of whom had travelled to
India, and 2 S.flexneri 6 isolates, also with history of travel to India.
A combination of pulsed field gel electrophoresis and antimicrobial susceptibility testing
proved useful in outbreak detection and investigation. There were 2 suspected Shigella
sonnei outbreaks in 2010.
25
Nineteen patients had a recorded history of recent foreign travel, including Africa (n = 10),
Australasia (n = 7) and the Americas (n = 2). Nine patients had Ireland recorded as their
country of infection while there were no details for 11 patients.
Table 7:
Foreign travel history for Shigella isolates
Continent
Country
Number
Africa (n = 10)
Egypt
4
Nigeria
2
Cameroon
1
Ethiopia
1
Africa *
2
Australasia (n = 7)
India
5
China
1
Pakistan
1
Americas (n = 2)
South America
Haiti
1
1
* Country not stated
26
NSRL Publications and Presentations 2010
Poster Presentations
Comparative Genomic Analysis of Salmonella enterica Serovar Enteritidis Typing Phages
SETP3, SETP7 and SETP13.
I3S Conference, Saint-Malo, France. June 2010.
Papers
Nicolay, N., Garvey, P., DeLappe,N., Cormican,M., and P. McKeown. Completeness
and timeliness of Salmonella notifications in Ireland in 2008: a cross sectional study.
BMC Public Health. 2010. v.10: 568.
Garvey, P., McKeown, P., DeLappe, N., and M.Cormican. Number of shigellosis cases
in Ireland remain low. Epi-Insight. 2010. v.11: Issue 1.
Garvey, P., Skally, M., McKeown, P., DeLappe, N., Doran, G., Ward, J., and
M.Cormican. Indigenous salmonellosis low in Ireland. Epi-Insight. 2010. v.11: Issue 3.
Boyle, F., Morris, D., O Connor,J., DeLappe, N., Ward, J., and M.Cormican. First
Report of Extended-Spectrum –-Lactamase-Producing Salmonella enterica Serovar
Kentucky Isolated from Poultry in Ireland. AAC. 2010. v.54: p.551-553.
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.;.
2010 Oct 18: 1-9.
27