Emergence of Monophasic Salmonella Typhimurium in the US: Looking through the Minnesota VDL Keyhole - Dr. Julio Alvarez, from the 2016 Allen D. Leman Swine Conference, September 17-20, 2016, St. Paul, Minnesota, USA. More presentations at http://www.swinecast.com/2016-leman-swine-conference-material

1. Emergence of monophasic
Salmonella Typhimurium in
the US: Looking through
the Minnesota VDL
Keyhole
September 19, 2016

2. The world today
• Dynamic context  problems (diseases)
arising and fainting
• Big data era  information bias?
– We are now much more capable of keeping track
of changes
– Always good?  Infoxication: discriminate
between data and information!

3. Salmonella… a moving target
• A challenging bug to tackle!
– One of the most common and economically important
zoonotic diseases in the world
– Multiple hosts, multiple reservoirs!
• Food animals (poultry, swine, cattle…)
• Exotic companion animals
• Food and feed contamination
– Stable incidence over time

4. One bacteria… multiple names!
• Two species (S. enterica), six subspecies (S. enterica subsp. enterica),
over 2,500 serotypes (<100 concerning)
• Some host-pathogen adaptation (certain serotypes)
• Reporting issues (sampling, typing...)  hard to establish baseline
situation (in reservoirs)
• Dynamic situation
 Artifacts
 True variations
Salmonella in swine (Foley et al., 2008) Salmonella in humans (CDC, 2016 )

5. Salmonella I 4,5,12:i:-?
• S. Typhimurium variant (S. I 4,5,12:i:1,2) 
does not express phase 2 flagella
• Rarely reported before the 90s
(underreporting?)
• “Emerging” since then!
– US: among the top five serotypes from human
clinical cases since 2011 (>5%, 474% increase since
2002) (CDC)
– Europe: 3rd most common serotype (>7%)

6. Origin?
• Traditionally linked to S. Typhimurium
• Animal source?
– Poultry, cattle, companion animals..
– And pigs (and pork products)
• 3rd most frequent serovar in Europe in 2011
• Not picked up in NARMS data (sample size?)
• Causative agent of several large foodborne
outbreaks

7. So what is a S. I 4,5,12:i:-?
• Multiple ways of defining it (PFGE, MLST, phage
typing)  ≈S. Typhimurium
• Still… variability on profiles (Spanish clone vs.
European clone)  multiple independent emergence
events?
• The AMR layer of complexity: ASSuT strains

8. Can Veterinary Diagnostic
Laboratories help?
• Were in fact used as sources of information in the past!
(NARMS 1996-2006)
• Discontinued due in part to selection bias
– Representative of sick animals (food chain)
– Uncertainty about true status of the animals (other processes?)
– Biased (partial) reality

9. Still…
• Sick animals are part of herd (at one point)
– May represent source of exposure for other animals
– Can help to describe (part of the) real situation in the
farm
• So we hypothesize that analysis
of VDL data may help us to
better understand evolution of
Salmonella serotypes over time
in pigs, and detect differences in
trends…check the weather!
– Careful not to overestimate!

10. What we know about data
quality… in data from the VDL
• Reasons for submission?
• Origin of the sample?
• Clinical significance of isolates?
• Selection of antibiotics for susceptibility
testing

11. Objective
• To explore the usefulness of the (MN)
VDL data to detect changes in the
ecology (predominant serotypes, AMR
profiles) of Salmonella in swine
• Model can be expanded to other targets

12. 10 years of swine-Salmonella
interactions at the VDL
• 2006-2015
– 2,644 isolates recovered from 1,832 farms
(180-384 isolates per year, mean=281)
– 2,537 isolates (85% from tissue, 15% fecal)
– 2,513 serotyped isolates  79 serotypes
Exclusion of repeated serotype-AMR from the
same farm within one month, no AMR data

13. Serotypes over time at the
VDL
21%
15%
12%
7%
7%
5%
4%
29%

14. Looking for comparators: the
NARMS data
0
2
4
6
8
10
12
14
16
18
20
%Prevalence
NARMS: 2006-2013, n=947
0
5
10
15
20
25
%Prevalence
VDL: 2006-2015, n=2570
Associated with (likely) clinical
case in 34% of the cases

15. General AMR trends? ↓ AMR (<8% annual change)
• Ampicillin
• Ceftiofur
• Florfenicol
• Oxytetracycline
No trend
• Gentamicin
• Neomycin
• Sulfadimethoxine
• Trimethoprim-Sul
↑ AMR (99% annual)
• Enrofloxacin
70%
66%
37%
30%
51%
37%
89%
82%
1%
18%
Enrofloxacin is licensed for
its use in swine (apr 2008)

16. Trend at the MIC level?
• MICs recorded against enrofloxacin

17. Not all Salmonella are the same
• Also in terms of AMR!

18. Where do these come from?
• The question:
“Is this one successful clone or multiple clones
emerging from S. Typhimurium strains?”
– 2014-2015 monophasic swine (48) and non swine (3) isolates and 179
S. Typhimurium (47.5% swine) / 201 var. 5- (71% swine) recovered
from food animals at the VDL (2003-2012)
– 2014-2015 monophasic swine isolates and 465 (15.6% swine)
monophasic strains recovered from elsewhere
WGS

19. S. Typhimurium and S. monophasic
recovered at the VDL
2014-2015
(n=51)
(n=171)
(n=201)
*Swine (276/431)

20. Variability compared with
other monophasics?
VDL
Clade I
Clade II
(n=94)
(n=422)
VDL
*VDL (51/516)

21. Significance of subdivision? AMR
ASSuT
Carriage of Qnr resistance genes
No ASSuT
*Swine (121/516)
13/51 MVDL were R-Enrofloxacin

22. So in summary…
• Analysis of (MN)VDL data has revealed that:
1. Frequency of isolation of S. I 4,5,12:i:- from swine clinical
samples has increased since 2011(3rd in 2015)
2. S. I 4,5,12:i:- strains recovered from swine clinical samples
are not closely related with other S. Typhimurium strains
circulating in food animals
3. S. I 4,5,12:i:- strains are divided in two clades, with most
(US) swine isolates located in clade II, and human cases
located in both clades
4. R to enrofloxacin in swine clinical Salmonella isolates has
been increasing since 2008; in at least a subset of isolates
it is mediated by plasmid-borne qnr genes

23. Next steps
• Why is S. I 4,5,12:i:- becoming a
predominant strain?
• What is the mechanism behind the
increase in Enrofloxacin-resistance in
other serotypes?
• How can we combine data on AMR with
information on clinical significance and
antimicrobial use? (USDA, FDA funded
efforts)

24. Acknowledgements
• The ones doing the work!
– Samuel Hong, BSc
– Ehud Elnekave, DVM, PhD
– Shivdeep Singh, DVM
• Drs. Rovira, Davies, Perez and
Vannucci (UMN)
• Minnesota Veterinary Diagnostic
Laboratory
• Minnesota Department of Health
(D. Boxrud)
• STEMMA Lab
• Funding
– MnDrive Initiative