Antimicrobial Resistance: Do we know everything? Dr. Sid Thakur Assistant Professor Swine Health & Production CVM, NCSU

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1 Antimicrobial Resistance: Do we know everything? Dr. Sid Thakur Assistant Professor Swine Health & Production CVM, NCSU

2 Research Focus Antimicrobial Resistance On farm, Slaughter, Retail, Human Sample & Environment Pathogen detection, Phenotypic & Genotypic Characterization Global Epidemiology Develop Sensitive and Rapid Detection Tests Microarray Real-time PCR Molecular Characterization: Mechanisms of resistance Transfer of resistance Virulence genes

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4 Antimicrobial Resistance: Lost in Translation!!! Are bacterial pathogens smarter than humans?

5 Pathogen Evolution: How good bacteria go bad Difference between good and bad pathogen Few genes encoded on plasmids or chromosome E. coli (commensal) : E. coli O157: H7 (HUS) Stephens & Murray, Current Biology, 2001 Raskin et al., Cell, 2006

6 EID Global Trends EID are dominated by zoonoses (60.3 %) Zoonotic Wildlife Drug Resistant Jones et al., Nature, 2008

7 Emergence of a new AR NDM-1 All the (New patients Delhi had metallo- a travel β- Lactamase) history to Escherichia India coli within and Klebsiella the past pneumoniae one year Dec 2009 in India; Pakistan, US, UK, Japan, Brazil International Travel mechanism in India Number of cases by Country Sweden (Dec 2009): 1 st report India (March 2010): 1 st report USA (June 2010): 3 cases India (June 2010): More cases UK (Aug 2010): 37 cases Canada (Aug 2010): 1 st report Japan (Sept 2010): 1 report

8 Antibiotics Antimicrobials: Farm to Table Fungicides Food Tissue Treatments Sanitizers Disinfectants Plant Agriculture Food Tissue Treatments Sanitizers Disinfectants Food retail Home Aquaculture Food Processing Personal hygiene products Humans Animal Agriculture Sanitizers Food Service Biocides Food Grade Preservatives Antimicrobial soaps/lotions Disinfectants Sanitizers Disinfectants Food Tissue Treatments

9 Back to susceptible population: Is it so simple? Treatment Antimicrobial Exposure Antimicrobial Susceptible Treatment Antimicrobial Resistant Environment Treatment Antimicrobial Resistant Antimicrobial Resistant

10 Reservoirs of Antimicrobial Resistance determinants Focus is on the commodity Food animals, produce, humans Role of Environment Limited research conducted Need to focus more on the environment Study environmental reservoirs Food animals: Farm environment (lagoon, truck, lairage) Produce: Water for irrigation, birds, manure Humans: Hospital environment, community

11 Soil Antibiotic Resistosome Vanessa et al., Science, 2006

12 Bacteria subsisting on antibiotics Dantas et al., Science, 2008

13 Role of trucks in Pathogen dissemination All in all out swine production system Breeding/Farrowing Nursery Finishing Four truck wash systems were selected that service one integrated system. Samples obtained from each wash station 10 trucks pre-wash, 5 swabs from each 10 trucks post-wash, 5 swabs from each Fecal samples were also collected on farm, at slaughter (Cecal content & MLN) & lairage Applied Environmental Microbiology, 2009

14 % Positive % Positive Role of Truck Wash in Pathogen Dissemination A = recycled water and Virkon-S B = recycled water and phenol C = fresh water, soap, and phenol D = recycled water and phenol Truck Wash Truck Wash Campylobacter Salmonella Prevalence - Pre - and Pre Post and Wash Post Wash Salmonella and Campylobacter isolates 100 at farm were different from those isolated at the slaughter plant (Cecal content and MLN) Isolates from the Cecum and MLN were 50 similar to those isolated from the truck floor Truck Wash A A Truck Wash BB Truck Truck Wash C Truck Truck Wash D Pre Pre Wash Post Post Wash

15 Plasmid exchange in Salmonella positive pigs S. Typhimurium S. Muenchen kb kb Ch. Pl Ch. Pl -6.5 kb AKSSuT -4.3 kb ACKSSuT Conjugation Analysis Southern Hybridization apha1-iab probe -2.3 kb -2.0 kb Gebreyes and Thakur, AEM, 2005

16 DANMAP Data-2011 DANMAP, 2011

17 S. Typhimurium Antimicrobial Resistance profile: Pigs DANMAP, 2011

18 S. Typhimurium AR: Pigs, pork and human cases DANMAP, 2011

19 Campylobacter jejuni: Antimicrobial Resistance DANMAP, 2011

20 FQ consumption: Humans DANMAP, 2011

21 DANMAP 2011 Report: Key Highlights DANMAP, 2011

22 NARMS Retail meat (Poultry) Antimicrobial Resistance Data C. jejuni CIP/NAL

23 Are resistant pathogens are better fit to survive in vivo? No Fluoroquinolone (FQ) selection pressure in this model FQ sensitive C. jejuni FQ resistant C. jejuni FQ sensitive and FQ resistant C. jejuni FQ sensitive C. jejuni FQ resistant C. jejuni FQ resistant C. jejuni Luo, et al., PNAS, 2005

24 USDA-NIFA Study Antibiotic Exposed Use of antimicrobials Intensive Indoor Antibiotic-free (ABF) No use of antimicrobials Extensive Outdoor VS Salmonella, Campylobacter & Clostridium

25 Sampling Scheme Conventional Farm ( All-in -All-out) 10 cohorts (35 pigs/cohort) Environment samples ( n=5 each) at farm Farrowing Truck Nursery Truck Finishing Truck 8 days old 6,10 weeks 16,26 weeks Feed Water Swab Lagoon Soil Truck Environment samples Slaughter ( n=5 each) at Slaughter Lairage Kill Floor Pre-Evis Post-Evis Chilling Lairage Truck MLN, Carcass Swab Carcass Swab

26 Antimicrobial Free System Farrowing Nursery-- Finishing Truck Slaughter Post evis MLN Post chill 8 cohorts 35 pigs/cohort Rotate on new land Environment at Farm and Slaughter water, feed, swabs, soil (n=5 each) water, feed, swabs, soil (n=5 each) water, feed, swabs, soil (n=5 each) Lariage Truck (n=5 each)

27 Pig v/s Environment Swine Environment ABF Conventional 80 ABF Conventional Resistance % Resistance % AZI CIP ERY GEN TET FFN NAL TEL CLI MDR 0 AZI CIP ERY GEN TET FFN NAL TEL CLI MDR Antimicrobials Antimicrobials AZI = azithromycin, ERY = erythromycin, CIP = ciprofloxacin, GEN = gentamicin, TET = tetracycline, FFN = florfenicol, NAL = nalidixic acid, TEL = telithromycin, CLI = clindamycin; Macarena and Thakur, Applied Environmental Microbiology, 2012

28 Key Outcomes Campylobacter and C. difficile Antimicrobial Exposed Antimicrobial free (ABF) Pig Antimicrobial Resistant Strains Antimicrobial Resistant Strains Environment

29 C. coli Population Tree ST-1186 ST-5776 ST-1068 ABF pigs and carcass ABF env at farm and slg. Conv pigs and carcass Conv env at farm and slg. ST-854

30 Phylogenetics ST-5248 Prod. System Unique STs ABF 14 Conventional 32 ST-5764 Clustering of STs Conventional system ABF system Macarena and Thakur, PLOS ONE, 2012 ST-5770, ST- 1827, ST-1109, ST-5772

31 Clostridium difficile AR Profile 100 Farm ABF CONVENTIONAL 100 Environment ABF CONVENTIONAL Resistance % Resistance % TET AMP MET ERY CIP VAN MDR 0 TET AMP MET ERY CIP VAN MDR Antimicrobials Antimicrobials AMP: Ampicillin; CIP: Ciprofloxacin; ERY: Erythromycin; MET: Metronidazole; TET: Tetracycline; VAN: Vancomycin; MDR: Multidrug Resistance Susick and Thakur, Veterinary Microbiology, 2012

32 Salmonella Serotypes A total of 1090 Salmonella isolates 24 different Salmonella serotypes

33 Ecological Niche Farm Salmonella Farm Campylobacter Slaughter S. Typhimurium AR Pattern: SSuT S. Typhimurium AR Pattern: ACSSuT A; Ampicillin C: Chloramphenicol S: Streptomycin Su: Sulfamethoxazole T: Tetracycline Carcass

34 Salmonella Genotypic Similarity PFGE pattern Antimicrobials Serotype Farm Stage Sample type A-Antimicrobial Free System; C- Conventional System

35 Salmonella environmental transmission from swine manure 5 plots Sprayer/ effluent Lagoon Day 0, Before Application 10 Lagoon 5 Effluent 25* Soil SAMPLE COLLECTION Day 0, After Application 25 Soil samples Day 7 25 Soil samples Day Soil samples *5 replicates for the five 1m 2 plots, 20m apart

36 Preliminary Results Salmonella Prevalence % Before D0 D7 D14 Before D0 D7 D14 Farm1 Farm2

37 Summary Move away from a generalized discussion on antimicrobial resistance solution Pathogen ecological niche: specific environment Renew focus on the role of environment Antimicrobial resistance is a global problem

38 Questions (