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Carbapenems belong to the group of last resort antibiotics in human medicine. Therefore, the emergence of growing numbers of carbapenemase-producing bacteria in food-producing animals or the environment is worrying and an important concern for the public health sector. In the present study, a set of 45 Enterobacteriaceae isolated from German retail seafood (clams and shrimps), sampled in 2016, were investigated by real-time PCR for the presence of carbapenemase-producing bacteria. One (ST10), isolated from a Venus clam () harvested in the Mediterranean Sea (Italy), contained the carbapenemase gene as part of the variable region of a class I integron. Whole-genome sequencing indicated that the integron was embedded in a Tn3-like transposon that also contained the fluoroquinolone resistance gene S1. Additional resistance genes such as the extended-spectrum beta-lactamase and the AmpC gene were also present in this isolate. Except , all resistance genes were located on an IncY plasmid. These results confirm previous observations that carbapenemase-producing bacteria have reached the food chain and are of increasing concern for public health.


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  1. World Health Organization (WHO). Critically important antimicrobials for human medicine. 3rd revision 2011. Geneva: WHO; 2012. Available from: http://apps.who.int/iris/bitstream/10665/77376/1/9789241504485_eng.pdf
  2. Woodford N, Wareham DW, Guerra B, Teale C. Carbapenemase-producing Enterobacteriaceae and non-Enterobacteriaceae from animals and the environment: an emerging public health risk of our own making? J Antimicrob Chemother. 2014;69(2):287-91.  https://doi.org/10.1093/jac/dkt392  PMID: 24092657 
  3. Fischer J, Rodríguez I, Schmoger S, Friese A, Roesler U, Helmuth R, et al. Escherichia coli producing VIM-1 carbapenemase isolated on a pig farm. J Antimicrob Chemother. 2012;67(7):1793-5.  https://doi.org/10.1093/jac/dks108  PMID: 22454489 
  4. Fischer J, Rodríguez I, Schmoger S, Friese A, Roesler U, Helmuth R, et al. Salmonella enterica subsp. enterica producing VIM-1 carbapenemase isolated from livestock farms. J Antimicrob Chemother. 2013;68(2):478-80.  https://doi.org/10.1093/jac/dks393  PMID: 23034713 
  5. European Commission. Commission implementing decision 2013/652/EU on the monitoring and reporting of antimicrobial resistance in zoonotic and commensal bacteria. Official Journal of the European Union. Luxembourg: Publications Office of the European Union. 14.11.2013; L303. Available from: http://eur-lex.europa.eu/legal-content/EN/TXT/PDF/?uri=OJ:L:2013:303:FULL&from=EN
  6. Morrison BJ, Rubin JE. Carbapenemase producing bacteria in the food supply escaping detection. PLoS One. 2015;10(5):e0126717.  https://doi.org/10.1371/journal.pone.0126717  PMID: 25966303 
  7. Zurfluh K, Poirel L, Nordmann P, Klumpp J, Stephan R. First detection of Klebsiella variicola producing OXA-181 carbapenemase in fresh vegetable imported from Asia to Switzerland. Antimicrob Resist Infect Control. 2015;4(1):38.  https://doi.org/10.1186/s13756-015-0080-5  PMID: 26448862 
  8. Rubin JE, Ekanayake S, Fernando C. Carbapenemase-producing organism in food, 2014. Emerg Infect Dis. 2014;20(7):1264-5.  https://doi.org/10.3201/eid2007.140534  PMID: 24960459 
  9. Páll E, Niculae M, Kiss T, Şandru CD, Spînu M. Human impact on the microbiological water quality of the rivers. J Med Microbiol. 2013;62(Pt 11):1635-40.  https://doi.org/10.1099/jmm.0.055749-0  PMID: 23813274 
  10. Kumaran S, Deivasigamani B, Alagappan K, Sakthivel M, Karthikeyan R. Antibiotic resistant Esherichia coli strains from seafood and its susceptibility to seaweed extracts. Asian Pac J Trop Med. 2010;3(12):977-81.  https://doi.org/10.1016/S1995-7645(11)60013-8 
  11. Rogers C, Basurco B, editors. The use of veterinary drugs and vaccines in Mediterranean aquaculture. Zaragoza: Centre International de Hautes Etudes Agronomiques Méditerranéennes (CIHEAM); 2009. 223 p. Available from: http://om.ciheam.org/option.php?IDOM=387
  12. Food and Agriculture Organization of the United Nations (FAO). The state of world fisheries and aquaculture. Contributing to food security and nutrition for all. Rome: FAO; 2016. Available from: http://www.fao.org/3/a-i5555e.pdf
  13. Rahiman KMM, Hatha AAM, Selvam ADG, Thomas AP. Relative prevalence of antibiotic resistance among heterotrophic bacteria from natural and culture environments of freshwater rawn, Macrobrachium Rosenbergii. J World Aquacult Soc. 2016;47(4):470-80.  https://doi.org/10.1111/jwas.12287 
  14. Boss R, Overesch G, Baumgartner A. Antimicrobial resistance of Escherichia coli, Enterococci, Pseudomonas aeruginosa, and Staphylococcus aureus from raw fish and seafood imported into Switzerland. J Food Prot. 2016;79(7):1240-6.  https://doi.org/10.4315/0362-028X.JFP-15-463  PMID: 27357045 
  15. Sperling L, Alter T, Huehn S. Prevalence and antimicrobial resistance of Vibrio spp. in retail and farm shrimps in Ecuador. J Food Prot. 2015;78(11):2089-92.  https://doi.org/10.4315/0362-028X.JFP-15-160  PMID: 26555534 
  16. Roschanski N, Friese A, von Salviati-Claudius C, Hering J, Kaesbohrer A, Kreienbrock L, et al. Prevalence of carbapenemase producing Enterobacteriaceae isolated from German pig-fattening farms during the years 2011-2013. Vet Microbiol. 2017;200:124-9.  https://doi.org/10.1016/j.vetmic.2015.11.030  PMID: 26654218 
  17. Poirel L, Naas T, Nicolas D, Collet L, Bellais S, Cavallo JD, et al. Characterization of VIM-2, a carbapenem-hydrolyzing metallo-beta-lactamase and its plasmid- and integron-borne gene from a Pseudomonas aeruginosa clinical isolate in France. Antimicrob Agents Chemother. 2000;44(4):891-7.  https://doi.org/10.1128/AAC.44.4.891-897.2000  PMID: 10722487 
  18. Clermont O, Christenson JK, Denamur E, Gordon DM. The Clermont Escherichia coli phylo-typing method revisited: improvement of specificity and detection of new phylo-groups. Environ Microbiol Rep. 2013;5(1):58-65.  https://doi.org/10.1111/1758-2229.12019  PMID: 23757131 
  19. Guerra B, Junker E, Miko A, Helmuth R, Mendoza MC. Characterization and localization of drug resistance determinants in multidrug-resistant, integron-carrying Salmonella enterica serotype Typhimurium strains. Microb Drug Resist. 2004;10(2):83-91.  https://doi.org/10.1089/1076629041310136  PMID: 15256022 
  20. Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S, Lund O, et al. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother. 2012;67(11):2640-4.  https://doi.org/10.1093/jac/dks261  PMID: 22782487 
  21. Carattoli A, Zankari E, García-Fernández A, Voldby Larsen M, Lund O, Villa L, et al. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother. 2014;58(7):3895-903.  https://doi.org/10.1128/AAC.02412-14  PMID: 24777092 
  22. Joensen KG, Scheutz F, Lund O, Hasman H, Kaas RS, Nielsen EM, et al. Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli. J Clin Microbiol. 2014;52(5):1501-10.  https://doi.org/10.1128/JCM.03617-13  PMID: 24574290 
  23. Larsen MV, Cosentino S, Rasmussen S, Friis C, Hasman H, Marvig RL, et al. Multilocus sequence typing of total-genome-sequenced bacteria. J Clin Microbiol. 2012;50(4):1355-61.  https://doi.org/10.1128/JCM.06094-11  PMID: 22238442 
  24. Wirth T, Falush D, Lan R, Colles F, Mensa P, Wieler LH, et al. Sex and virulence in Escherichia coli: an evolutionary perspective. Mol Microbiol. 2006;60(5):1136-51.  https://doi.org/10.1111/j.1365-2958.2006.05172.x  PMID: 16689791 
  25. Clinical and Laboratory Standards Institute (CLSI). Performance standards for antimicrobial disk susceptibility tests. Approved standard—eleventh edition. M02-A11. 32. Wayne, PA: CLSI; 2012.
  26. Clinical and Laboratory Standards Institute (CLSI). Performance standards for antimicrobial susceptibility testing. Twenty-Fourth Informational Supplement. M100-S24. ISBN:1562388975. Wayne, PA: CLSI; 2014.
  27. Zurfluh K, Power KA, Klumpp J, Wang J, Fanning S, Stephan R. A novel Tn3-like composite transposon harboring blaVIM-1 in Klebsiella pneumoniae spp. pneumoniae isolated from river water. Microb Drug Resist. 2015;21(1):43-9.  https://doi.org/10.1089/mdr.2014.0055  PMID: 25098892 
  28. European Food Safety Authority (EFSA). Scientific opinion on carbapenem resistance in food animal ecosystems. EFSA J. 2013;11(12):3501. . Available from: https://www.efsa.europa.eu/en/efsajournal/pub/3501 https://doi.org/10.2903/j.efsa.2013.3501 
  29. Nordmann P, Naas T, Poirel L. Global spread of carbapenemase-producing Enterobacteriaceae. Emerg Infect Dis. 2011;17(10):1791-8.  https://doi.org/10.3201/eid1710.110655  PMID: 22000347 
  30. Lutgring JD, Limbago BM. The problem of carbapenemase-producing-carbapenem-resistant-Enterobacteriaceae detection. J Clin Microbiol. 2016;54(3):529-34.  https://doi.org/10.1128/JCM.02771-15  PMID: 26739152 
  31. Hirsch EB, Tam VH. Detection and treatment options for Klebsiella pneumoniae carbapenemases (KPCs): an emerging cause of multidrug-resistant infection. J Antimicrob Chemother. 2010;65(6):1119-25.  https://doi.org/10.1093/jac/dkq108  PMID: 20378670 
  32. Falcone M, Mezzatesta ML, Perilli M, Forcella C, Giordano A, Cafiso V, et al. Infections with VIM-1 metallo-beta-lactamase-producing enterobacter cloacae and their correlation with clinical outcome. J Clin Microbiol. 2009;47(11):3514-9.  https://doi.org/10.1128/JCM.01193-09  PMID: 19741074 
  33. Falcone M, Perilli M, Mezzatesta ML, Mancini C, Amicosante G, Stefani S, et al. Prolonged bacteraemia caused by VIM-1 metallo-beta-lactamase-producing Proteus mirabilis: first report from Italy. Clin Microbiol Infect. 2010;16(2):179-81.  https://doi.org/10.1111/j.1469-0691.2009.02781.x  PMID: 19624511 
  34. Weisenberg SA, Morgan DJ, Espinal-Witter R, Larone DH. Clinical outcomes of patients with Klebsiella pneumoniae carbapenemase-producing K. pneumoniae after treatment with imipenem or meropenem. Diagn Microbiol Infect Dis. 2009;64(2):233-5.  https://doi.org/10.1016/j.diagmicrobio.2009.02.004  PMID: 19345034 
  35. Adams-Sapper S, Nolen S, Donzelli GF, Lal M, Chen K, Justo da Silva LH, et al. Rapid induction of high-level carbapenem resistance in heteroresistant KPC-producing Klebsiella pneumoniae. Antimicrob Agents Chemother. 2015;59(6):3281-9.  https://doi.org/10.1128/AAC.05100-14  PMID: 25801565 
  36. Perilli M, Bottoni C, Pontieri E, Segatore B, Celenza G, Setacci D, et al. Emergence of blaKPC-3-Tn4401a in Klebsiella pneumoniae ST512 in the municipal wastewater treatment plant and in the university hospital of a town in central Italy. J Glob Antimicrob Resist. 2013;1(4):217-20.  https://doi.org/10.1016/j.jgar.2013.07.002  PMID: 27873616 
  37. Poirel L, Barbosa-Vasconcelos A, Simões RR, Da Costa PM, Liu W, Nordmann P. Environmental KPC-producing Escherichia coli isolates in Portugal. Antimicrob Agents Chemother. 2012;56(3):1662-3.  https://doi.org/10.1128/AAC.05850-11  PMID: 22203588 
  38. Kittinger C, Lipp M, Folli B, Kirschner A, Baumert R, Galler H, et al. Enterobacteriaceae isolated from the river Danube: antibiotic resistances, with a focus on the presence of ESBL and carbapenemases. PLoS One. 2016;11(11):e0165820.  https://doi.org/10.1371/journal.pone.0165820  PMID: 27812159 
  39. Zurfluh K, Hächler H, Nüesch-Inderbinen M, Stephan R. Characteristics of extended-spectrum β-lactamase- and carbapenemase-producing Enterobacteriaceae Isolates from rivers and lakes in Switzerland. Appl Environ Microbiol. 2013;79(9):3021-6.  https://doi.org/10.1128/AEM.00054-13  PMID: 23455339 
  40. Montezzi LF, Campana EH, Corrêa LL, Justo LH, Paschoal RP, da Silva IL, et al. Occurrence of carbapenemase-producing bacteria in coastal recreational waters. Int J Antimicrob Agents. 2015;45(2):174-7.  https://doi.org/10.1016/j.ijantimicag.2014.10.016  PMID: 25499185 
  41. Oteo J, Diestra K, Juan C, Bautista V, Novais A, Pérez-Vázquez M, et al. Extended-spectrum beta-lactamase-producing Escherichia coli in Spain belong to a large variety of multilocus sequence typing types, including ST10 complex/A, ST23 complex/A and ST131/B2. Int J Antimicrob Agents. 2009;34(2):173-6.  https://doi.org/10.1016/j.ijantimicag.2009.03.006  PMID: 19464856 
  42. Aibinu I, Odugbemi T, Koenig W, Ghebremedhin B. Sequence type ST131 and ST10 complex (ST617) predominant among CTX-M-15-producing Escherichia coli isolates from Nigeria. Clin Microbiol Infect. 2012;18(3):E49-51.  https://doi.org/10.1111/j.1469-0691.2011.03730.x  PMID: 22192452 
  43. Blaak H, van Hoek AH, Hamidjaja RA, van der Plaats RQ, Kerkhof-de Heer L, de Roda Husman AM, et al. Distribution, numbers, and diversity of ESBL-producing E. coli in the poultry farm environment. PLoS One. 2015;10(8):e0135402.  https://doi.org/10.1371/journal.pone.0135402  PMID: 26270644 
  44. Simões RR, Poirel L, Da Costa PM, Nordmann P. Seagulls and beaches as reservoirs for multidrug-resistant Escherichia coli. Emerg Infect Dis. 2010;16(1):110-2.  https://doi.org/10.3201/eid1601.090896  PMID: 20031053 
  45. Varela AR, Macedo GN, Nunes OC, Manaia CM. Genetic characterization of fluoroquinolone resistant Escherichia coli from urban streams and municipal and hospital effluents. FEMS Microbiol Ecol. 2015;91(5):91.  https://doi.org/10.1093/femsec/fiv015  PMID: 25764463 
  46. Brahmi S, Touati A, Cadière A, Djahmi N, Pantel A, Sotto A, et al. First description of two sequence type 2 Acinetobacter baumannii isolates carrying OXA-23 carbapenemase in Pagellus acarne fished from the Mediterranean Sea near Bejaia, Algeria. Antimicrob Agents Chemother. 2016;60(4):2513-5.  https://doi.org/10.1128/AAC.02384-15  PMID: 26787693 
  47. Janecko N, Martz SL, Avery BP, Daignault D, Desruisseau A, Boyd D, et al. Carbapenem-resistant Enterobacter spp. in retail seafood imported from Southeast Asia to Canada. Emerg Infect Dis. 2016;22(9):1675-7.  https://doi.org/10.3201/eid2209.160305  PMID: 27533255 
  48. Mangat CS, Boyd D, Janecko N, Martz SL, Desruisseau A, Carpenter M, et al. Characterization of VCC-1, a novel Ambler class A carbapenemase from Vibrio cholerae isolated from imported retail shrimp sold in Canada. Antimicrob Agents Chemother. 2016;60(3):1819-25.  https://doi.org/10.1128/AAC.02812-15  PMID: 26824956 
  49. Aschbacher R, Pagani L, Doumith M, Pike R, Woodford N, Spoladore G, et al. Metallo-β-lactamases among Enterobacteriaceae from routine samples in an Italian tertiary-care hospital and long-term care facilities during 2008. Clin Microbiol Infect. 2011;17(2):181-9.  https://doi.org/10.1111/j.1469-0691.2010.03225.x  PMID: 20345467 
  50. Riccio ML, Pallecchi L, Fontana R, Rossolini GM. In70 of plasmid pAX22, a bla(VIM-1)-containing integron carrying a new aminoglycoside phosphotransferase gene cassette. Antimicrob Agents Chemother. 2001;45(4):1249-53.  https://doi.org/10.1128/AAC.45.4.1249-1253.2001  PMID: 11257042 

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