USDA VetNet Update. Paula J. Fedorka-Cray, PhD Research Leader, Antimicrobial Resistance Research Unit Athens, GA
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1 USDA VetNet Update Paula J. Fedorka-Cray, PhD Research Leader, Antimicrobial Resistance Research Unit Athens, GA /18/2008
2 Acknowledgements ARS Dr. Charlene Jackson Beth McGlinchey Carolina Hall Cheryl Gresham Robert Bell Lindsay Nash Jovita Haro Jodie Plumblee CDC FSIS Dr. Bill Cray PulseNet Database Team Dr. Neelum Narang Dr. Jeoff Levine Dr. Lynda Kelley Dr. Adrienne Dunham Dr. Kristen Holt Dr. Neena Anandaraman
3 USDA VetNet PFGE program complementary to CDC PulseNet Isolates originate from animal species Primarily major food animal groups Established: 2004 in the USDA-ARS- BEAR unit All VetNet staff trained and certified by CDC
4 USDA VetNet Food borne pathogen Non-typhoidal Salmonella Campylobacter added in 2005 C. difficile added in 2007 E. coli 0157:H7 added in 2008 Historical isolates Also starting non-0157:h7 Database moved from CDC to RRC in 2006 Currently only analyzing gels done in house
5 Has VetNet really arrived? YES!!!! *Linked with CDC
6 USDA VetNet Objectives Analyze PFGE patterns of isolates submitted from the animal arm of the National Antimicrobial Resistance Monitoring System (NARMS) Compare USDA VetNet and CDC PulseNet PFGE patterns Use comparative data for surveillance and investigation of foodborne illness outbreaks as well as carriage/disease within animals
7 VetNet database managers Salmonella Beth McGlinchey Campylobacter Carolina Hall C. difficile Cheryl Gresham E. coli Carolina Hall MRSA?? Listeria??
8 Salmonella Database Started May 2004 Isolates from slaughter, diagnostic, and on-farm sources Primarily 1 enzyme cuts All isolates are assigned a VetNet pattern name Starting 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 isolates 4,139 unique XbaI patterns 217 serotypes Limited BlnI patterns
9 Why a separate database? CDC names outbreak strains 1 st All animal associated strains named immediately Not all VetNet patterns have comparable PulseNet pattern matches Track emerging patterns on the animal side Animal health Human health
10 Salmonella database timeline June 2007 Compared VetNet Salmonella patterns to PulseNet patterns; captured PN pattern names in database Salmonella cluster searches looking for animal illness outbreaks Salmonella VetNet isolates matching CDC clusters CDC epis notified July 2007 FSIS has need for PFGE data Implementation of new Salmonella regulations FSIS-OSEL accessed VetNet Salmonella database
11 Salmonella database timeline January 2008 Notified PulseNet of VetNet matches to ongoing Salmonella clusters in real time March 2008 PulseNet database managers provided with Salmonella VetNet logins
12 Top Salmonella VN Patterns diagnostic and slaughter isolates (n = 14,466) Blue = match to PN top 10 pattern ARS-XbaI-pattern Serotype No. of Isolates JGPX ARS Kentucky 879 JEGX ARS Enteritidis 384 JGPX ARS Kentucky 320 JF6X ARS Heidelberg 298 JEGX ARS Enteritidis 279 JGPX ARS Kentucky 261 JJPX ARS Newport 198 TDKX ARS Hadar 192 Typhimurium 174 JF6X ARS Heidelberg 146
13 How can we use the data? Can sort by Animal/product type Region Serotype Time Antibiogram Predictive? Common patterns? Emerging pattern? *Gu= Guam, VI= US Virgin Islands, MIS=Mariana Islands 5*
14 VN patterns-source and year Year (n=total number of isolates for year) Source 2004 (n=2,397) 2005 (n=2,842) 2006 (n=2,350) 2007 (n=1,848) No. of isolates Bovine Chicken Porcine Ready to eat product Turkey Braenderup JBPX ARS Montevideo JIXX ARS Cerro JCGX ARS Dublin JDXX ARS Predominant Agona JABX ARS Cerro JCGX ARS Montevideo JIXX ARS Montevideo JIXX ARS patterns Anatum JAGX ARS Agona JABX ARS Montevideo JIXX ARS Montevideo JIXX ARS Cerro JCGX ARS Meleagridis JHXX ARS Anatum JAGX ARS Cerro JCGX ARS No. of isolates 1,269 1,976 1, Kentucky JGPX ARS Kentucky JGPX ARS Kentucky JGPX ARS Kentucky JGPX ARS Predominant Kentucky JGPX ARS Kentucky JGPX ARS Enteritidis JEGX ARS Enteritidis JEGX ARS patterns Kentucky JGPX ARS Kentucky JGPX ARS Kentucky JGPX ARS Heidelberg JF6X ARS Heidelberg JF6X ARS Heidelberg JF6X ARS Enteritidis JEGX ARS Enteritidis JEGX ARS No. of isolates Adelaide TDAX ARS Derby JDPX ARS Anatum JAGX ARS Typhimurium Predominant Anatum JAGX ARS Saintpaul JN6X ARS Heidelberg JF6X ARS Adelaide TDAX ARS patterns Typhimurium Derby JDPX ARS Hadar TDKX ARS Hadar TDKX ARS Derby JDPX ARS Adelaide TDAX ARS Derby JDPX ARS Derby JDPX ARS No. of isolates Give JEXX ARS Derby JDPX ARS Newport JJPX ARS Agona JABX ARS Predominant Heidelberg JF6X ARS Muenster TDSX ARS Senftenberg JMPX ARS Derby JDPX ARS patterns Senftenberg JMPX ARS Agona JABX ARS Zanzibar ZANX ARS Heidelberg JF6X ARS Urbana JQGX ARS Anatum JAGX ARS Derby JDPX ARS Infantis JFXX ARS No. of isolates Predominant patterns Heidelberg JF6X ARS Hadar TDKX ARS Hadar TDKX ARS Hadar TDKX ARS IIIa 18:z4,z23:- RXKX ARS IIIa 18:z4,z23:- RXKX ARS Hadar TDKX ARS Hadar TDKX ARS Reading JLGX ARS Saintpaul JN6X ARS Reading JLGX ARS Hadar TDKX ARS Saintpaul JN6X ARS Reading JLGX ARS Heidelberg JF6X ARS Saintpaul JN6X ARS
15 Can VN be used to predict emerging PN clusters MAYBE! 0710CAJJP-1c Newport JJPX PN Newport JJPX ARS YES!! 0801MLJIX-1c Montevideo JIXX PN Montevideo JIXX ARS
16 History of Newport Pattern JJPX ARS VetNet Database JJPX is indistinguishable from VetNet pattern JJPX ARS First diagnostic isolate in 2001 First slaughter isolate in March 2005 Accounts for 0.98% of Newport isolates in VetNet database 3 diagnostic cattle isolates 7 slaughter ground beef isolates 1 slaughter cow/bull isolate 1 slaughter steer/heifer isolate 3 resistance patterns 8: Amo, Amp, Fox, Tio, Chl, Str, Sul, Tet 3: Amo, Amp, Fox, Tio, Str, Sul, Tet 1: Chl, Str, Sul, Tet PulseNet Database First isolate with this pattern uploaded in May isolates Accounts for 0.23% of Newport isolates in PulseNet database Pattern seen in AZ, CA, ID, NC, NV, OR
17 JJPX PN/JJPX ARS Occurrences in VetNet and PulseNet Date Diagnostic isolates VetNet PulseNet No. of Isolates
18 History of Montevideo Pattern JIXX ARS VetNet Database JIXX is indistinguishable from VetNet pattern JIXX ARS First slaughter isolate in April 2004 First diagnostic isolate in June 2004 Accounts for 7.02% of Montevideo isolates in VetNet database 33 ground beef slaughter isolates 1 diagnostic cattle isolate PulseNet Database First isolate with this pattern uploaded in March isolates Accounts for 1.06% of Montevideo isolates in PulseNet database Pattern seen in AZ, CA, GA, HI, IL, MD, MN, MO, ND, NM, NY, OH, OR, PA, TX, WA, WI
19 JIXX PN/JIXX ARS Occurrences in VetNet and PulseNet Diagnostic isolate Date VetNet PulseNet Increase No. of Isolates
20 Are all isolates created equal? /JPXX PN Most common Typhimurium/Typhimurium var. O 5- pattern in VetNet database 60 slaughter isolates are pattern (21 = Typhimurium; 39 = Typhimurium var. O 5-) In pattern there are 9 different resistance profiles MKAN, NAL M AMOX/CA, AMPC, CFOX, CHL, STR, SSS, TET, TIO M AMPC, CHL, KAN, SSS, TET M AMPC, CHL, KAN, STR, SSS, TET M AMPC, CHL, GEN, STR, SSS, TET M Pan-susceptible M STR, SSS M AMPC, CHL, SSS, TET M AMPC, CHL, STR, SSS, TET antibio AMOX/CA AMPC CFOX CHL GEN KAN NA L STR SSS TET TIO Region 5 Region 3 Region 3 Region 3 Region 5 Region 6 Region 5 Region 3 Region 5 Region 3 Region 5 Region 5 Region 5 Region 3 Region 5 Region 6 Region 4 Region 5 Region 4 Region 4 Region 4 Region 4 Region 4 Young chicken Young chicken Ground turkey Ground turkey Ground turkey Steer/heifer Turkey Turkey Young chicken Young chicken Young chicken Young chicken Young chicken Young chicken Young chicken Young chicken
21 Campylobacter Database Started December 2005 Isolates from broiler slaughter sources Other species available Primarily 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 total isolates Cj 1122 (67%) Cc 548 (33%) 814 unique patterns (12/07) Cj 534 (66%) Cc 280 (34%)
22 Most common patterns Species Pattern Name No. Isolates C. coli C. jejuni C. jejuni C. jejuni C. jejuni C. jejuni C. jejuni C. jejuni C. jejuni C. jejuni DBBS ARS DBRS ARS DBRS ARS DBRS ARS DBRS ARS DBRS ARS DBRS ARS DBRS ARS DBRS ARS DBRS ARS
23 C. difficile Database Started in 2007 Isolates from swine and cattle sources Subtyping PFGE PCR ribotyping Toxinotyping ~700 isolates ~300 completed
24 Ribotyping Dice (Opt:1.10%) (Tol 1.1%-1.1%) (H>0.0% S>0.0%) [0.0%-100.0%] Ribotyping Isolates are from same farm 8 Pulsotypes
25 E. coli Database Started in 2007 O157:H7 primarily from cattle historical non-o157 Swine, broilers, cattle 2 enzymes XbaI BlnI 259 O157:H7 isolates 54 completed non-o157:h7 Thousands of isolates
26 2008 plans Inclusion in the NARMS report New database? MRSA? Expand collaboration with CDC, FSIS, and FDA To initiate collaboration with state veterinary labs Accept tiff files Name patterns with state extensions Compare with VN and PN patterns Report back to states
27 I What s the vision!! If I m Flipper is she MOOPER!?? And they thought they were so smart!
28 Summary reports and interactive feature on website
29 Food Borne Diseases It 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 theory Requires collaborations and a willingness to look outside of the box
30 BEAR WEBSITE _main.htm?modecode= Acknowledgements Paula Fedorka- Cray I hope they washed Charlene Jackson their hands! Marcia Headrick Benny Barrett Leena Jain Sonya Herbert Stephanie Carter I wonder if it s cooked right? Roxanne Reeves Jovita Haro Takiyah Ball Cheryl Gresham Carolina Hall Jennifer Murphy having beef!! The NARMS Working Group I thought we were
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