usda vetnet update - aphl
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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
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