Prevalence and molecular epidemiology of ESBL and carbapenemase producing Enterobacteriaceae along the food chain

Transcription

1 Prevalence and molecular epidemiology of ESBL and carbapenemase producing Enterobacteriaceae along the food chain Roger Stephan Institute for food safety and hygiene University of Zurich Switzerland

2 Agenda Background Impact of antibiotic resistance Extended-spectrum β-lactamase (ESBL) Different studies Meat chain (poultry meat chain) Vegetables Conclusions

3 Antimicrobial resistance: global report on surveillance 2014

4 Dissemination of ARM Davies et al MMBR 74:

5 b-lactam antibiotics:(targeting the cell wall synthesis) β-lactamases 2/3 of human anti-infectious therapies worldwide are still based on b-lactams!

6 4. Generation: Cefepime Cefpirome 1. Generation: Cephalothin Cefaloridin ESBLs (plasmid encoded) bla CTX-M bla TEM bla SHV Basic structure BSBLs 3. Generation: Cefotaxime Ceftriaxon Ceftazidime 2. Generation: Cefamandole Cefuroxime

7 34/ 586 (5.8%) Characteristics of ESBL-producers: All Escherichia coli 70.6 % CTX-M group 1 (14 CTX-M-15, 10 CTX-M-1) 20.5 % CTX-M group 9 (7 CTX-M-14) 6 % CTX-M group 2 (2 CTX-M-2) 3% SHV-ESBL (1 SHV-12) Totally 15 strains positive for additional TEM-1 Geser, N., et al. (2012). Antimicrobial Agents and Chemotherapy

8 Agenda Background Impact of antibiotic resistance Extended-spectrum β-lactamase (ESBL) Different studies Meat chain (poultry meat chain) Vegetables Conclusions

9 Meat chain: preharvest level Fecal samples pigs (15% positive) calfs (25% positive) cows (2% positive) poultry flocks (63% positive) Geser, N., et al. (2012). BMC Veterinary Research

10 Meat chain: postharvest level 80 samples at retail level 36 samples Swiss meat (19.4% positive) 44 imported meat (59% positiv) prevalence: 41.3% Denmark (n=5): 20% Germany (n=13): 39% Hungary (n=5): 60% Italy (n=8): 100% Solovenia (n=6): 67% Argentina (n=2): 100% ESBL types: bla CTX-M1 bla SHV-12 bla TEM-52 Zogg, AL., et al. (2016). Schweizer Archiv für Tierheilkunde

11 Poultry pyramide abroad ESBL Nukleusherden Nucleus flocks bla CTX-M-1 ESBL CH breeder Eltern ere Fattening Mastherden flocks Chicken , 660kb 50.9% GC content IncI1-type Broiler breeder Broilers 1 day old broiler breeders: ESBL + meconium: ESBL + broilers: ESBL + Zurfluh, K., et al. (2014). Frontiers in Microbiology

12 Geser, N., et al. (2012). BMC Veterinary Research

13 bla CTX-M1 harbouring plasmids mainly IncI1,IncN, IncF types with plasmid of IncI1/ST3 predominating in isolates from chicken and from humans. Zurfluh, K., et al. (2014). Frontiers in Microbiology

14 bla CTX-M1 harbouring IncI1/ST3 plasmids Wang et al. (2014). J Antimicrob Chemotherapy; Wang, J. et al. (2015). Frontiers in Microbiology

15 Agenda Background Impact of antibiotic resistance Extended-spectrum β-lactamase (ESBL) Different studies Meat chain (poultry meat chain) Vegetables Conclusions

16 Ready-to-eat salads (Swiss production) 238 samples (5 % positive) Nüesch, M., et al. (2015). Journal of Food Protection

17 Ready-to-eat salads (Swiss production) S. fonticola K. ascorbata bla ESBL chromosomally encoded Normal plant flora Nüesch, M., et al. (2015). Journal of Food Protection

18 Imported vegetables (Dominican Republic, India, Thailand and Vietnam) 169 samples (25.4% positive) Zurfluh, K., et al. (2015). Applied and Environmental Microbiology

19 E. coli K. pneumoniae E. cloacae E. aerogenes C. sakazakii CTX-M-1 CTX-M-3 CTX-M-15 CTX-M-55 CTX-M-14 CTX-M-27 CTX-M-65 CTX-M-63 SHV-2 SHV-2a SHV-12 AM10 AMC30 CF30 CTX30 NA30 CIP5 GM10 K30 S10 SMZ TMP5 Te10 C30 Institute for Food Safety and Hygiene Imported vegetables (Dominican Republic, India, Thailand and Vietnam) Origin Sample ID Vegetable Species MLST/CC E.coli Phylogroup Dominican Republic India Thailand Vietnam ESBL DR06 Bitter cucumber ST131 B2 ESBL DR24 Bitter cucumber ST661 ESBL DR45 Chilli ST405/CC405 D ESBL DR13 Curry leaves ST307 ESBL DR26 Curry leaves ST38/CC38 D ESBL DR47T ST1742 Curry leaves ESBL DR47B ST1656 B1 ESBL DR23 Egg plant ST45 ESBL DR27 Egg plant ST147 ESBL DR31 Egg plant ESBL DR09 Green Chilli ST307 ESBL DR28 Small Chilli ST167 /CC10 A 52SK1 Cucumber ESBL H238 V ST410/CC 23 A Curry leaves ESBL H238 T ST1739 E37SK2 ST155/CC155 B1 Curry leaves E37SK2.1 ST4681 B1 19SK1 Curry leaves ST SK1 ST152 Curry Leaves 46SK2 ST1881 B1 E48t ST1740 Green Chilli C48SK3gb ST37 E3SK2 Okra (marrow) ST38/CC38 D E49SK1b ST155/CC155 B1 E49SK2b ST443/CC205 B1 Okra E49t ST997 C49b 28SK1 Okra 37SK1 Okra ST4682 B1 54SK1 Okra 54SK2 ST4684 B1 49SK1 ST244 Parwal beans 49SK2 ST641/CC86 A 45SK1 Peppermint ST15 ESBL H226 T nd ESBL H226 B Cha-om (acacia) ST167/CC10 A ESBL H226 L ST393/CC 31 D 23SK1 ST58/CC155 B1 Coriander 23SK2 ST48/CC10 A ESBL H241 B ST4680 B1 Curry leaves ESBL H241 T ST17 ESBL H239 V ST4679 B1 Garlic chives ESBL H239T ST SK1 ST226/CC226 A Green Chilli 33SK2 ST458 25SK1 Lemongrass ST SK1 Sweet basil ST76 E5 Yard long beans ST3696 A 21SK1 Yard long beans ESBL H242 Water mimosa ST37 ESBL H227 Water spinach ST16 2SK1 Basil leaves ST4683 B1 6SK1 Ceylon spinach ST37 E26SK1 Curry leaves ST10/CC10 A 13SK1 Egg plant 40SK1 ST36 Holy Basil 40SK2 ST58/CC155 B1 15SK1 Lemongrass ST45 E25 Soy sprouts ST208 41SK1 Yard long beans ESBL(s) Zurfluh, K., et al. (2015). Applied and Environmental Microbiology Antibiotic resistance profile Figure 1: Source data, identity, distribution of sequence types, clonal complexes, bla genes and antibiotic susceptibility patterns of ESBL-producing Enterobacteriaceae isolated from fresh vegetables imported from the Dominican Republic, India, Thailand and Vietnam. Colors of squares categorizing ESBLs: Light orange, CTX-M-group 1; dark orange, CTX-M-group 9; red, CTX-M-group 8. Blue, SHVenzymes. Colors of squares categorizing antibiotic resistance profiles: Pink, reisistant; yellow, intermediate; green, susceptible. Abbreviations: MLST, multilocus sequence type; CC, clonal complex; AM, Escherichia coli Klebsiella pneumoniae Enterobacter cloacae CTX-M-15 CTX-M-14 CTX-M-55 bla ESBL Plasmid encoded /transferable Human associated Contaminated water Good agriculture practice!

20 E. coli K. pneumoniae E. cloacae E. aerogenes C. sakazakii CTX-M-1 CTX-M-3 CTX-M-15 CTX-M-55 CTX-M-14 CTX-M-27 CTX-M-65 CTX-M-63 SHV-2 SHV-2a SHV-12 AM10 AMC30 CF30 CTX30 NA30 CIP5 GM10 K30 S10 SMZ TMP5 Te10 C30 Institute for Food Safety and Hygiene Imported vegetables (Dominican Republic, India, Thailand and Vietnam) Origin Sample ID Vegetable Species MLST/CC E.coli Phylogroup Dominican Republic India Thailand Vietnam ESBL DR06 Bitter cucumber ST131 B2 ESBL DR24 Bitter cucumber ST661 ESBL DR45 Chilli ST405/CC405 D ESBL DR13 Curry leaves ST307 ESBL DR26 Curry leaves ST38/CC38 D ESBL DR47T ST1742 Curry leaves ESBL DR47B ST1656 B1 ESBL DR23 Egg plant ST45 ESBL DR27 Egg plant ST147 ESBL DR31 Egg plant ESBL DR09 Green Chilli ST307 ESBL DR28 Small Chilli ST167 /CC10 A 52SK1 Cucumber ESBL H238 V ST410/CC 23 A Curry leaves ESBL H238 T ST1739 E37SK2 ST155/CC155 B1 Curry leaves E37SK2.1 ST4681 B1 19SK1 Curry leaves ST SK1 ST152 Curry Leaves 46SK2 ST1881 B1 E48t ST1740 Green Chilli C48SK3gb ST37 E3SK2 Okra (marrow) ST38/CC38 D E49SK1b ST155/CC155 B1 E49SK2b ST443/CC205 B1 Okra E49t ST997 C49b 28SK1 Okra 37SK1 Okra ST4682 B1 54SK1 Okra 54SK2 ST4684 B1 49SK1 ST244 Parwal beans 49SK2 ST641/CC86 A 45SK1 Peppermint ST15 ESBL H226 T nd ESBL H226 B Cha-om (acacia) ST167/CC10 A ESBL H226 L ST393/CC 31 D 23SK1 ST58/CC155 B1 Coriander 23SK2 ST48/CC10 A ESBL H241 B ST4680 B1 Curry leaves ESBL H241 T ST17 ESBL H239 V ST4679 B1 Garlic chives ESBL H239T ST SK1 ST226/CC226 A Green Chilli 33SK2 ST458 25SK1 Lemongrass ST SK1 Sweet basil ST76 E5 Yard long beans ST3696 A 21SK1 Yard long beans ESBL H242 Water mimosa ST37 ESBL H227 Water spinach ST16 2SK1 Basil leaves ST4683 B1 6SK1 Ceylon spinach ST37 E26SK1 Curry leaves ST10/CC10 A 13SK1 Egg plant 40SK1 ST36 Holy Basil 40SK2 ST58/CC155 B1 15SK1 Lemongrass ST45 E25 Soy sprouts ST208 41SK1 Yard long beans ESBL(s) Zurfluh, K., et al. (2015). Applied and Environmental Microbiology Antibiotic resistance profile Figure 1: Source data, identity, distribution of sequence types, clonal complexes, bla genes and antibiotic susceptibility patterns of ESBL-producing Enterobacteriaceae isolated from fresh vegetables imported from the Dominican Republic, India, Thailand and Vietnam. Colors of squares categorizing ESBLs: Light orange, CTX-M-group 1; dark orange, CTX-M-group 9; red, CTX-M-group 8. Blue, SHVenzymes. Colors of squares categorizing antibiotic resistance profiles: Pink, reisistant; yellow, intermediate; green, susceptible. Abbreviations: MLST, multilocus sequence type; CC, clonal complex; AM, Escherichia coli Klebsiella pneumoniae Epidemic colones: E. coli B2:ST131 E. coli D:ST405 E. coli D:ST38 K. pneumoniae ST15 K. pneumoniae ST147 EAEC E. coli D:ST38

21 Imported vegetables (Thailand and Vietnam) bla OXA , 000kb IncX3-type Zurfluh, K., et al. (2015). Antimicrobial Resistance and Infection Control

22 New dimension...

23 Imported vegetables (Thailand and Vietnam) Zn 2+, Cu 2+ mcr-1 209, 401kb IncHI1-type Zurfluh, K., et al. (2016). Antimicrobial Agents and Chemotherapy

24 Isolate from poultry meat imported from Italy bla ESBL MDR-region of this plasmid includes two class 1 integrons carrying transposons In641 and In369 mcr-1!!!!! IncH2 type + sulphonamide + trimethoprim + tetracycline + aminoglycosides + chloramphenicol + macrolide efflux pump + tellurite + quaternary ammonium compounds Zurfluh, K., Stephan, R. (2016). AAC, in press.

25 Conclusions Food chain is an important transmission route for ESBL-producing Enterobacteriaceae Food animals are healthy carriers especially poultry Vegetables are a hidden reservoir for ESBL producers The spread of ESBL-producing Enterobacteriaceae along the food chain is mainly based on epidemic plasmids rather than epidemic clones mcr-1 harbouring ESBL producers, a new threat along the food chain

26 Acknowledgements Helga Abgottspon Christine Gallati Nadine Geser Herbert Hächler Magdalena Nüesch-Inderbinen Annatina Romagna Katrin Zurfluh Seamus Fanning Karen Power Juan Wang