Emergence of monophasic Salmonella Typhimurium in

the US: Looking through the Minnesota VDL

KeyholeSeptember 19, 2016

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!

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

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 )

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%)

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

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

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

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!

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

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

10 years of swine-Salmonellainteractions 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

Serotypes over time at the VDL

21%

15%

12%7%

7%5%

4%

29%

Looking for comparators: the NARMS data

0

2

4

6

8

10

12

14

16

18

20

% P

reva

lenc

e

NARMS: 2006-2013, n=947

0

5

10

15

20

25

% P

reva

lenc

e

VDL: 2006-2015, n=2570

Associated with (likely) clinical case in 34% of the cases

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)

Trend at the MIC level?

• MICs recorded against enrofloxacin

Not all Salmonella are the same

• Also in terms of AMR!

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

S. Typhimurium and S. monophasic recovered at the VDL

2014-2015

(n=51)(n=171)

(n=201)

*Swine (276/431)

Variability compared withother monophasics?

VDL

Clade I

Clade II

(n=94)(n=422)

VDL

*VDL (51/516)

Significance of subdivision? AMR

ASSuT

Carriage of Qnr resistance genes

No ASSuT

*Swine (121/516)

13/51 MVDL were R-Enrofloxacin

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

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)

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