Science for Defra: excellence in the application of evidence

Transcription

1 Science for Defra: excellence in the application of evidence Defra Science Showcase Session 6 Animal health and food and farming Chair: Professor James Wood

2 2050: >65%+ New paradigms to solve the aquaculture disease crisis Source: Worldfish.org 1975: <10% Now: 50% Prof. Grant D. Stentiford, Pathology and Microbial Systematics Theme,

3 Disease is the #1 issue in limiting yield, reducing profit and preventing investment Extensive losses Infamous pathogens Pandemic spread Emergence rate is high Deficit in trained professionals/ah investment Dispersed industry. 90% in

4 Decentralise diagnostics Centralise data Close the gap between farmer, scientist, policy maker Simple and quick Pond-side testing Remote locations Smartphone app Poverty alleviation. Food. Trade Centralised

5 Next generation thinking Digital pathology for networking and training Pathogen genomics for diagnostics/therapy edna/microbiomes for early warning Host genetics for resilience Reduce impact of disease to promote insurability of

6 When you have 5

7 Molecular characterisation of colistin resistance in bacteria isolated from food animals. Dr. Muna Anjum Molecular Lead: Antimicrobial Resistance and Enteric Pathogens, Department of Bacteriology

8 The colistin outbreak Colistin is a last resort antibiotic with limited usage in humans due to its toxicity. It is authorised for usage in animals for treatment of gastrointestinal infections, and was first authorised in the UK in 2004 for veterinary medicine. Until recently all reported polymyxin resistance mechanisms have been chromosomally mediated, involving for example SNPs in genes encoding two component regulatory systems (e.g. pmrab, phopq), resulting in modification of lipid A. Liu et al 2015 reported the first case of a plasmid-mediated colistin resistance mechanism, designated mcr-1, in E. coli and Klebsiella pneumoniae. 8

9 Usage levels reported in 2011:

10 Occurrence of mcr-1 in animals in GB: The mcr-1 E. coli was detected on two pig farms in GB through anonymised surveillance of 387 caecal samples collected in 2015 from pigs at slaughter from 313 different herds, thus 0.6% of those pig herds sampled were positive.** mcr-1 E. coli was also detected on 2/105 (1.9%) of pig farms from which archived E. coli isolates from veterinary diagnostic investigations in 2015/16 were available.** *(Anjum et al, 2016, Journal of Antimicrobial Chemotherapy) *(Duggett et al, 2016, Journal of Antimicrobial Chemotherapy)

11 Characterising of mcr-1 isolates by WGS using SeqFinder (Duggett et al, JAC 2016). Isolate and origin Inc-types present Estimated size of mcr-1 containing plasmid (kb)** Similarity to phnshp45 (%) Maximum similarity to publicly available mcr-1 plasmids (%) Colistin resistance genes Other AMR genes Virulence genes E4 # O139:K Veterinary submission 4 IncX4, IncIFIB(K), repb, po111, IncI1, IncX1, IncFIA(HI1), IncA/C pmra*, pmrb*, phop*, phoq*, etk* and mcr-1 aada2, aac3-iva, aph4-ia, aph3-ib, aph6-id, blatem-1, blalat-1, cml, dfra12, sul1, sul2, tet(a), gyra* cfaa-d, ecpa-e, ecpr, fimf-i, hlye, iss Clinical isolate ^ O149:H Veterinary submission Inc1, IncX4, IncFII(pCoo), IncFIB(AP001918), IncFIC(FII), IncY phop*, phoq*, pmra*, etk* and mcr-1 aada1b, ant3-ia, dfra1, folp*, sul2 aec15-19, aec22-27, aec29-32, asta9, cah, eaeh, ecpa-e, ecpr, ehab, elta-b, espl4, espr1, faec- E, faeg-j, fimf-g, hlya-e, ibeb-c, ItcA, stb1, shf PO155 ^ -:H surveillance study Incl1, Col8282, po111, IncX mcr-1 aac3-iva, aada2, ant3-ia, aph3-ib, aph4-ia, aph6-id, blatem-1, cml, dfra12, inuf, sul2, teta aec19, aec32, asta ecpa-b, ecpd- E, ecpr, espl1, espl4, espx5, fimb-c, fimf-g, fimi, hlye, iss, iuca, sita-c PO169 ^ -:H surveillance IncX1, IncI2, IncFII(pCoo), IncB/O/K/Z acrr*, phop* and mcr-1 blatem-1, gyra*, qnrs1, teta aec31-32, ecpa-e, ecpr, espr1, fima-c, fime-i, hlye, ibec, iss, mchf, tia 11

12 Comparison of mcr-1 plasmids from animal isolates in GB to human clinical and food isolates. (Duggett et al, JAC 2016) 12

13 Conclusion First reporting of mcr-1 in enteric bacteria from animals in GB, indicating surveillance was a good mechanism for detection. The isolates are MDR but mcr-1 harbours no other AMR gene, so spread of mcr-1 plasmid is not leading to MDR. Scanning of archived isolates indicated prevalence of mcr-1 was low (0.6%) in healthy pigs in GB. Plasmid comparison showed GB mcr-1 plasmids are quite diverse with high similarity to mcr-1 plasmid in isolates from human, food, animals from various countries, indicating that this is a global epidemic with a worldwide spread. 13

14 Acknowledgement APHA colleagues: Nick Duggett Manal AbuOun Miranda Kirchner Ellie Saywers Luke Randall Sarah Evans Fabrizio Lemma Richard Smith Rob Davies Susanna Williamson Camilla Brena Richard Ellis Francesca Martelli Javier Nunez-Garcia Robert Horton Chris Teale Jon Rogers 14