4/18/2008

Paula J. Fedorka-Cray, PhDResearch Leader, Antimicrobial Resistance Research Unit

Athens, GA706-546-3685

paula.cray@ars.usda.gov

USDA VetNet Update

Preliminary data; subject to change; not for public distribution

Acknowledgements

ARSDr. Charlene JacksonBeth McGlincheyCarolina HallCheryl GreshamRobert BellLindsay NashJovita HaroJodie Plumblee

FSISDr. Bill CrayDr. Neelum NarangDr. Jeoff LevineDr. Lynda KelleyDr. Adrienne DunhamDr. Kristen HoltDr. NeenaAnandaraman

CDCPulseNet Database Team

Preliminary data; subject to change; not for public distribution

USDA VetNetPFGE program complementary to CDC PulseNetIsolates originate from animal species

Primarily major food animal groupsEstablished: 2004 in the USDA-ARS-BEAR unitAll VetNet staff trained and certified by CDC

Preliminary data; subject to change; not for public distribution

USDA VetNetFood borne pathogen

Non-typhoidal SalmonellaCampylobacter added in 2005C. difficile added in 2007E. coli 0157:H7 added in 2008

Historical isolatesAlso starting non-0157:H7

Database moved from CDC to RRC in 2006Currently only analyzing gels done in house

Preliminary data; subject to change; not for public distribution

Has VetNet really arrived?

YES!!!!

*Linked with CDC

Preliminary data; subject to change; not for public distribution

USDA VetNet ObjectivesAnalyze PFGE patterns of isolates submitted from the animal arm of the National Antimicrobial Resistance Monitoring System (NARMS)Compare USDA VetNet and CDC PulseNet PFGE patternsUse comparative data for surveillance and investigation of foodborne illness outbreaks as well as carriage/disease within animals

Preliminary data; subject to change; not for public distribution

VetNet database managers

Salmonella – Beth McGlincheyCampylobacter – Carolina HallC. difficile – Cheryl GreshamE. coli – Carolina HallMRSA??Listeria??

Preliminary data; subject to change; not for public distribution

Salmonella DatabaseStarted May 2004Isolates from slaughter, diagnostic, and on-farm sourcesPrimarily 1 enzyme cuts

All isolates are assigned a VetNet pattern nameStarting with the top 30 serotypes of PHLIS

VN patterns are compared to PN patterns

If a match occurs, both patterns are listed

As of April 10, 2008 database contained:

14,466 isolates4,139 unique XbaIpatterns

217 serotypesLimited BlnI patterns

Preliminary data; subject to change; not for public distribution

Why a separate database?CDC names outbreak strains 1st

All animal associated strains named immediatelyNot all VetNet patterns have comparable PulseNet pattern matchesTrack emerging patterns on the animal side

Animal healthHuman health

Preliminary data; subject to change; not for public distribution

Salmonella database timelineJune 2007

Compared VetNet Salmonella patterns to PulseNet patterns; captured PN pattern names in databaseSalmonella cluster searches looking for animal illness outbreaksSalmonella VetNet isolates matching CDC clusters

CDC epis notifiedJuly 2007

FSIS has need for PFGE data Implementation of new Salmonella regulations

FSIS-OSEL accessed VetNet Salmonella database

Preliminary data; subject to change; not for public distribution

Salmonella database timeline

January 2008Notified PulseNet of VetNet matches to ongoing Salmonella clusters in real time

March 2008PulseNet database managers provided with Salmonella VetNet logins

Preliminary data; subject to change; not for public distribution

Top Salmonella VN Patterns

ARS-XbaI-pattern Serotype No. of IsolatesJGPX01.0003 ARS Kentucky 879JEGX01.0003 ARS Enteritidis 384JGPX01.0001 ARS Kentucky 320JF6X01.0015 ARS Heidelberg 298JEGX01.0002 ARS Enteritidis 279JGPX01.0342 ARS Kentucky 261JJPX01.0023 ARS Newport 198TDKX01.0004 ARS Hadar 192JPXX01.0003 ARS Typhimurium 174JF6X01.0011 ARS Heidelberg 146

diagnostic and slaughter isolates (n = 14,466)

Blue = match to PN top 10 pattern

Preliminary data; subject to change; not for public distribution

How can we use the data?Can sort by

Animal/product typeRegionSerotypeTimeAntibiogram

Predictive?Common patterns?Emerging pattern?

5* 3

4

1

2

*Gu= Guam, VI= US Virgin Islands, MIS=Mariana Islands

Preliminary data; subject to change; not for public distribution

VN patterns-source and yearSource 2004 (n=2,397) 2005 (n=2,842) 2006 (n=2,350) 2007 (n=1,848)

No. of isolates 593 328 383 414Braenderup JBPX01.0002 ARS Montevideo JIXX01.0015 ARS Cerro JCGX01.0002 ARS Dublin JDXX01.0002 ARS

Agona JABX01.0099 ARS Cerro JCGX01.0002 ARS Montevideo JIXX01.0027 ARS Montevideo JIXX01.0006 ARSAnatum JAGX01.0034 ARS Agona JABX01.0014 ARS Montevideo JIXX01.0015 ARS Montevideo JIXX01.0015 ARSCerro JCGX01.0002 ARS Meleagridis JHXX01.0001 ARS Anatum JAGX01.0053 ARS Cerro JCGX01.0002 ARS

No. of isolates 1,269 1,976 1,364 958Kentucky JGPX01.0003 ARS Kentucky JGPX01.0003 ARS Kentucky JGPX01.0003 ARS Kentucky JGPX01.0003 ARSKentucky JGPX01.0001 ARS Kentucky JGPX01.0001 ARS Enteritidis JEGX01.0003 ARS Enteritidis JEGX01.0003 ARSKentucky JGPX01.0342 ARS Kentucky JGPX01.0342 ARS Kentucky JGPX01.0001 ARS Heidelberg JF6X01.0015 ARS

Heidelberg JF6X01.0015 ARS Heidelberg JF6X01.0015 ARS Enteritidis JEGX01.0002 ARS Enteritidis JEGX01.0002 ARSNo. of isolates 298 298 295 204

Adelaide TDAX01.0001 ARS Derby JDPX01.0028 ARS Anatum JAGX01.0070 ARS Typhimurium JPXX01.0003 ARSAnatum JAGX01.0005 ARS Saintpaul JN6X01.0035 ARS Heidelberg JF6X01.0115 ARS Adelaide TDAX01.0004 ARS

Typhimurium JPXX01.0003 ARS Derby JDPX01.0005 ARS Hadar TDKX01.0005 ARS Hadar TDKX01.0005 ARSDerby JDPX01.0005 ARS Adelaide TDAX01.0001 ARS Derby JDPX01.0028 ARS Derby JDPX01.0005 ARS

No. of isolates 5 15 11 10Give JEXX01.0003 ARS Derby JDPX01.0004 ARS Newport JJPX01.0323 ARS Agona JABX01.0038 ARS

Heidelberg JF6X01.0011 ARS Muenster TDSX01.0062 ARS Senftenberg JMPX01.0078 ARS Derby JDPX01.0099 ARSSenftenberg JMPX01.0008 ARS Agona JABX01.0217 ARS Zanzibar ZANX01.0002 ARS Heidelberg JF6X01.0015 ARS

Urbana JQGX01.0001 ARS Anatum JAGX01.0008 ARS Derby JDPX01.0039 ARS Infantis JFXX01.0085 ARSNo. of isolates 232 225 297 262

Heidelberg JF6X01.0010 ARS Hadar TDKX01.0004 ARS Hadar TDKX01.0004 ARS Hadar TDKX01.0004 ARSIIIa 18:z4,z23:- RXKX01.0001 ARS IIIa 18:z4,z23:- RXKX01.0001 ARS Hadar TDKX01.0025 ARS Hadar TDKX01.0011 ARS

Reading JLGX01.0001 ARS Saintpaul JN6X01.0023 ARS Reading JLGX01.0034 ARS Hadar TDKX01.0035 ARSSaintpaul JN6X01.0023 ARS Reading JLGX01.0001 ARS Heidelberg JF6X01.0010 ARS Saintpaul JN6X01.0030 ARS

Predominant patterns

Year (n=total number of isolates for year)

Turkey Predominant patterns

Bovine Predominant patterns

Chicken Predominant patterns

Ready to eat product Predominant

patterns

Porcine

Preliminary data; subject to change; not for public distribution

Can VN be used to predict emerging PN clusters

MAYBE!0710CAJJP-1c

Newport JJPX01.0422 PNNewport JJPX01.0028 ARS

YES!!0801MLJIX-1c

Montevideo JIXX01.0081 PNMontevideo JIXX01.0006 ARS

Preliminary data; subject to change; not for public distribution

History of Newport Pattern JJPX01.0028 ARS

VetNet DatabaseJJPX01.0422 is indistinguishable from VetNet pattern JJPX01.0028 ARS

First diagnostic isolate in 2001First slaughter isolate in March 2005

Accounts for 0.98% of Newport isolates in VetNet database

3 diagnostic cattle isolates7 slaughter ground beef isolates1 slaughter cow/bull isolate1 slaughter steer/heifer isolate3 resistance patterns

8: Amo, Amp, Fox, Tio, Chl, Str, Sul, Tet3: Amo, Amp, Fox, Tio, Str, Sul, Tet1: Chl, Str, Sul, Tet

PulseNet DatabaseFirst isolate with this pattern uploaded in May 2006

58 isolatesAccounts for 0.23% of Newport isolates in PulseNet databasePattern seen in AZ, CA, ID, NC, NV, OR

Preliminary data; subject to change; not for public distribution

JJPX01.0422 PN/JJPX01.0028 ARS Occurrences in VetNet and PulseNet

0

5

1015

20

25

2004

-03

2004

-06

2004

-09

2004

-12

2005

-03

2005

-06

2005

-09

2005

-12

2006

-03

2006

-06

2006

-09

2006

-12

2007

-03

2007

-06

2007

-09

2007

-12

2008

-03

Date

No.

of I

sola

tes

VetNet PulseNetDiagnostic

isolates

Preliminary data; subject to change; not for public distribution

History of Montevideo Pattern JIXX01.0006 ARS

VetNet DatabaseJIXX01.0081 is indistinguishable from VetNet pattern JIXX01.0006 ARS

First slaughter isolate in April 2004First diagnostic isolate in June 2004

Accounts for 7.02% of Montevideo isolates in VetNet database

33 ground beef slaughter isolates1 diagnostic cattle isolate

PulseNet DatabaseFirst isolate with this pattern uploaded in March 2003

53 isolatesAccounts for 1.06% of Montevideo isolates in PulseNet databasePattern seen in AZ, CA, GA, HI, IL, MD, MN, MO, ND, NM, NY, OH, OR, PA, TX, WA, WI

Preliminary data; subject to change; not for public distribution

JIXX01.0081PN/JIXX01.0006 ARS Occurrences in VetNet and PulseNet

012345678

2003

-03

2003

-06

2003

-09

2003

-12

2004

-03

2004

-06

2004

-09

2004

-12

2005

-03

2005

-06

2005

-09

2005

-12

2006

-03

2006

-06

2006

-09

2006

-12

2007

-03

2007

-06

2007

-09

2007

-12

2008

-03

Date

No.

of I

sola

tes

VetNet PulseNet

Diagnostic isolate

Increase

Preliminary data; subject to change; not for public distribution

JPXX01.0003 ARS/JPXX01.0003 PN

•Most common Typhimurium/Typhimurium var. O 5- pattern in VetNet database

• 60 slaughter isolates are pattern JPXX01.0003 ARS (21 = Typhimurium; 39 = Typhimurium var. O 5-)

• In pattern JPXX01.0003 ARS there are 9 different resistance profiles

antibio

AMO

X/C

A

AMPC

CFO

X

CHL

GEN

KAN

NAL

STR

SSS

TET

TIO

Typhimurium var. O 5 - (Copenhagen)TyphimuriumTyphimurium var. O 5 - (Copenhagen)Typhimurium var. O 5 - (Copenhagen)TyphimuriumTyphimurium var. O 5 - (Copenhagen)Typhimurium var. O 5 - (Copenhagen)Typhimurium var. O 5 - (Copenhagen)Typhimurium var. O 5 - (Copenhagen)TyphimuriumTyphimuriumTyphimurium var. O 5 - (Copenhagen)

Typhimurium var. O 5 - (Copenhagen)Typhimurium var. O 5 - (Copenhagen)Typhimurium var. O 5 - (Copenhagen)Typhimurium var. O 5 - (Copenhagen)TyphimuriumTyphimuriumTyphimurium var. O 5 - (Copenhagen)Typhimurium var. O 5 - (Copenhagen)TyphimuriumTyphimurium var. O 5 - (Copenhagen)TyphimuriumTyphimuriumTyphimuriumTyphimurium

TyphimuriumTyphimurium var. O 5 - (Copenhagen)Typhimurium var. O 5 - (Copenhagen)Typhimurium var. O 5 - (Copenhagen)TyphimuriumTyphimurium var. O 5 - (Copenhagen)TyphimuriumTyphimurium var. O 5 - (Copenhagen)Typhimurium var. O 5 - (Copenhagen)Typhimurium var. O 5 - (Copenhagen)TyphimuriumTyphimuriumTyphimurium var. O 5 - (Copenhagen)Typhimurium var. O 5 - (Copenhagen)Typhimurium var. O 5 - (Copenhagen)Typhimurium var. O 5 - (Copenhagen)

Typhimurium var. O 5 - (Copenhagen)Typhimurium var. O 5 - (Copenhagen)Typhimurium var. O 5 - (Copenhagen)Typhimurium var. O 5 - (Copenhagen)Typhimurium var. O 5 - (Copenhagen)Typhimurium var. O 5 - (Copenhagen)Typhimurium var. O 5 - (Copenhagen)TyphimuriumTyphimuriumTyphimuriumTyphimurium var. O 5 - (Copenhagen)TyphimuriumTyphimurium var. O 5 - (Copenhagen)Typhimurium

Typhimurium var. O 5 - (Copenhagen)Typhimurium var. O 5 - (Copenhagen)Typhimurium var. O 5 - (Copenhagen)Typhimurium var. O 5 - (Copenhagen)

JPXX01.0003 ARSJPXX01.0003 ARSJPXX01.0003 ARSJPXX01.0003 ARSJPXX01.0003 ARSJPXX01.0003 ARSJPXX01.0003 ARSJPXX01.0003 ARSJPXX01.0003 ARSJPXX01.0003 ARSJPXX01.0003 ARSJPXX01.0003 ARS

JPXX01.0003 ARSJPXX01.0003 ARSJPXX01.0003 ARSJPXX01.0003 ARSJPXX01.0003 ARSJPXX01.0003 ARSJPXX01.0003 ARSJPXX01.0003 ARSJPXX01.0003 ARSJPXX01.0003 ARSJPXX01.0003 ARSJPXX01.0003 ARSJPXX01.0003 ARSJPXX01.0003 ARS

JPXX01.0003 ARSJPXX01.0003 ARSJPXX01.0003 ARSJPXX01.0003 ARSJPXX01.0003 ARSJPXX01.0003 ARSJPXX01.0003 ARSJPXX01.0003 ARSJPXX01.0003 ARSJPXX01.0003 ARSJPXX01.0003 ARSJPXX01.0003 ARSJPXX01.0003 ARSJPXX01.0003 ARSJPXX01.0003 ARSJPXX01.0003 ARS

JPXX01.0003 ARSJPXX01.0003 ARSJPXX01.0003 ARSJPXX01.0003 ARSJPXX01.0003 ARSJPXX01.0003 ARSJPXX01.0003 ARSJPXX01.0003 ARSJPXX01.0003 ARSJPXX01.0003 ARSJPXX01.0003 ARSJPXX01.0003 ARSJPXX01.0003 ARSJPXX01.0003 ARS

JPXX01.0003 ARSJPXX01.0003 ARSJPXX01.0003 ARSJPXX01.0003 ARS

Region 1Region 5Region 1Region 3Region 3Region 2Region 3Region 5Region 6Region 1Region 1Region 1

Region 2Region 1Region 2Region 1Region 5Region 1Region 1Region 3Region 5Region 3Region 5Region 5Region 1Region 5

Region 1Region 2Region 2Region 3Region 5Region 6Region 2Region 1Region 1Region 2Region 2Region 2Region 2Region 2Region 2Region 1

Region 1Region 2Region 2Region 2Region 2Region 4Region 2Region 5Region 2Region 4Region 4Region 4Region 2Region 1

Region 4Region 4Region 2Region 1

Ground beefGround beefGround beefMarket hogYoung chickenYoung chickenGround beefGround turkeyMarket hogGround beefGround beefMarket hog

Market hogMarket hogMarket hogGround beefGround beefGround beefGround beefGround beefGround beefGround beefGround beefGround beefGround beefGround turkey

Ground turkeyMarket hogMarket hogMarket hogMarket hogMarket hogMarket hogMarket hogMarket hogMarket hogMarket hogMarket hogMarket hogMarket hogMarket hogMarket hog

Market hogMarket hogMarket hogMarket hogMarket hogMarket hogMarket hogSteer/heiferTurkeyTurkeyYoung chickenYoung chickenYoung chickenYoung chicken

Young chickenYoung chickenYoung chickenYoung chicken

AMOX/CA, AMPC, CFOX, CHL, STR, SSS, TET, TIOMM

M

M

M

M

MM

M

KAN, NAL

AMPC, CHL, KAN, SSS, TET

STR, SSSAMPC, CHL, SSS, TETAMPC, CHL, STR, SSS, TET

AMPC, CHL, GEN, STR, SSS, TETPan-susceptible

AMPC, CHL, KAN, STR, SSS, TET

Are all isolates created equal?

Preliminary data; subject to change; not for public distribution

Campylobacter DatabaseStarted December 2005Isolates from broiler slaughter sources

Other species availablePrimarily 1 enzyme cuts, SmaI

All isolates assigned a VetNet pattern name

Start comparing VN and PN patterns Salmonella database serves as the model

As of April 20081670 total isolates

Cj – 1122 (67%)Cc – 548 (33%)

814 unique patterns (12/07)

Cj – 534 (66%)Cc – 280 (34%)

Preliminary data; subject to change; not for public distribution

C. coli

C. jejuni

C. jejuni

C. jejuni

C. jejuni

C. jejuni

C. jejuni

C. jejuni

C. jejuni

C. jejuni

DBBS16.0003 ARS

DBRS16.0023 ARS

DBRS16.0049 ARS

DBRS16.0036 ARS

DBRS16.0005 ARS

DBRS16.0044 ARS

DBRS16.0054 ARS

DBRS16.0108 ARS

DBRS16.0064 ARS

DBRS16.0120 ARS

34

16

16

15

14

14

14

14

13

11

Most common patterns

Species Pattern Name No. Isolates

Preliminary data; subject to change; not for public distribution

C. difficile DatabaseStarted in 2007Isolates from swine and cattle sources Subtyping

PFGEPCR ribotypingToxinotyping

~700 isolates ~300 completed

Preliminary data; subject to change; not for public distribution

Dice (Opt:1.10%) (Tol 1.1%-1.1%) (H>0.0% S>0.0%) [0.0%-100.0%]Ribotyping

100

90807060

Ribotyping

Isolates are from same farm

8 Pulsotypes

Preliminary data; subject to change; not for public distribution

E. coli DatabaseStarted in 2007O157:H7 primarily from cattle

historicalnon-O157

Swine, broilers, cattle2 enzymes

XbaIBlnI

259 O157:H7 isolates54 completed

non-O157:H7 Thousands of isolates

Preliminary data; subject to change; not for public distribution

2008 plansInclusion in the NARMS reportNew database?

MRSA?Expand collaboration with CDC, FSIS, and FDATo initiate collaboration with state veterinary labs

Accept tiff filesName patterns with state extensionsCompare with VN and PN patternsReport back to states

Preliminary data; subject to change; not for public distribution

What’s the vision!!And they thought they were so smart!

If I’m Flipper is she

MOOPER!??

I

Preliminary data; subject to change; not for public distribution

Summary reports and interactive feature on website

Preliminary data; subject to change; not for public distribution

Food Borne DiseasesIt’s often difficult, and contentious, to accurately determine where pathogens, including resistant pathogens, FIRST emerge or what the source might be in food borne outbreaks

Aka the chicken or the egg theoryRequires collaborations and a willingness to look outside of the box

Preliminary data; subject to change; not for public distribution

AcknowledgementsPaula Fedorka-CrayCharlene JacksonMarcia HeadrickBenny BarrettLeena JainSonya HerbertStephanie Carter

Roxanne ReevesJovita HaroTakiyah Ball Cheryl GreshamCarolina HallJennifer MurphyThe NARMS Working Group

I wonder if it’s cooked right?I hope they washed

their hands!

I thought we were

having beef!!

BEAR WEBSITE http://www.ars.usda.gov/main/site

_main.htm?modecode=66120508