Comprehensive resistome analysis reveals the prevalence of NDM and MCR-1 in Chinese poultry production

Nature Microbiology

Volumn 2, Issue , 2017, Pages

  Wang, Yang ^a   Zhang, Rongmin ^a   Li, Jiyun ^a   Wu, Zuowei ^b   Yin, Wenjuan ^a   Schwarz, Stefan ^c,d   Tyrrell, Jonathan M ^e   Zheng, Yongjun ^a   Wang, Shaolin ^a   Shen, Zhangqi ^a   Liu, Zhihai ^a   Liu, Jianye ^a   Lei, Lei ^a   Li, Mei ^a,e   Zhang, Qidi ^f   Wu, Congming ^a   Zhang, Qijing ^b   Wu, Yongning ^g   Walsh, Timothy R ^e   Shen, Jianzhong ^a  

^a CHINA AGRICULTURAL UNIVERSITY   (China)

^b IOWA STATE UNIVERSITY   (United States)

^c FREIE UNIVERSITÄT BERLIN   (Germany)

^d FEDERAL RESEARCH INSTITUTE FOR ANIMAL HEALTH   (Germany)

^e UNIVERSITY HOSPITAL OF WALES   (United Kingdom)

^f QINGDAO AGRICULTURAL UNIVERSITY   (China)

^g CHINA NATIONAL CENTER FOR FOOD SAFETY RISK ASSESSMENT   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIINFECTIVE AGENT; BETA LACTAMASE; COLISTIN; ESCHERICHIA COLI PROTEIN; MCR-1 PROTEIN, E COLI;

ANIMAL; ANTIBIOTIC RESISTANCE; BACTERIAL GENOME; BIRD; CARBAPENEM-RESISTANT ENTEROBACTERIACEAE; CHICKEN; CHINA; DIPTERA; DOG; DRUG EFFECT; ESCHERICHIA COLI; ESCHERICHIA COLI INFECTION; GENETICS; HIGH THROUGHPUT SEQUENCING; ISOLATION AND PURIFICATION; MICROBIAL SENSITIVITY TEST; MICROBIOLOGY; MULTIDRUG RESISTANCE; PREVALENCE; WILD ANIMAL;

ANIMALS; ANIMALS, WILD; ANTI-BACTERIAL AGENTS; BETA-LACTAMASES; BIRDS; CARBAPENEM-RESISTANT ENTEROBACTERIACEAE; CHICKENS; CHINA; COLISTIN; DIPTERA; DOGS; DRUG RESISTANCE, BACTERIAL; DRUG RESISTANCE, MULTIPLE, BACTERIAL; ESCHERICHIA COLI; ESCHERICHIA COLI INFECTIONS; ESCHERICHIA COLI PROTEINS; GENOME, BACTERIAL; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MICROBIAL SENSITIVITY TESTS; PREVALENCE;

EID: 85011655568     PISSN: None     EISSN: 20585276     Source Type: Journal    
DOI: 10.1038/nmicrobiol.2016.260     Document Type: Article

References (36)

1. World population projected to reach 9. 7 billion by 2050. United Nations (29 July 2015); http://www. un. org/en/development/desa/news/population/2015-report. html
2. Walsh, T. R., Wu, Y. N. China bans colistin as a feed additive for animals. Lancet Infect. Dis. 16, 1102-1103 (2016).
3. Kumarasamy, K. K., et al. Emergence of a new antibiotic resistance mechanism in India, Pakistan, and the UK: a molecular, biological, and epidemiological study. Lancet Infect. Dis. 10, 597-602 (2010).
4. Munoz-Price, L. S., et al. Clinical epidemiology of the global expansion of Klebsiella pneumoniae carbapenemases. Lancet Infect. Dis. 13, 785-796 (2013).
5. Chen, Y., Zhou, Z., Jiang, Y., Yu, Y. Emergence ofNDM-1-producing Acinetobacter baumannii in China. J. Antimicrob. Chemother. 66, 1255-1259 (2011).
6. Wang, X., et al. High rate of New Delhi metallo-lactamase 1-producing bacterial infection in China. Clin. Infect. Dis. 56, 161-162 (2013).
7. Zhu, J., et al. Outbreak of NDM-1-producing Klebsiella pneumoniae ST76 and ST37 isolates in neonates. Eur. J. Clin. Microbiol. Infect. Dis. 35, 611-618 (2016).
8. Woodford, N., Wareham, D. W., Guerra, B., Teale, C. Carbapenemaseproducing Enterobacteriaceae and non-Enterobacteriaceae from animals and the environment: an emerging public health risk of our own making? J. Antimicrob. Chemother. 69, 287-291 (2014).
9. Michael, G. B., et al. Emerging issues in antimicrobial resistance of bacteria from food-producing animals. Future Microbiol. 10, 427-443 (2015).
10. Poirel, L., Stephan, R., Perreten, V., Nordmann, P. The carbapenemase threat in the animal world: the wrong culprit. J. Antimicrob. Chemother. 69, 2007-2008 (2014).
11. Falagas, M. E., Karageorgopoulos, D. E., Nordmann, P. Therapeutic options for infections with Enterobacteriaceae producing carbapenem-hydrolyzing enzymes. Future Microbiol. 6, 653-666 (2011).
12. Halaby, T., Al Naiemi, N., Kluytmans, J., van der Palen, J., Vandenbroucke-Grauls, C. M. Emergence of colistin resistance in Enterobacteriaceae after the introduction of selective digestive tract decontamination in an intensive care unit. Antimicrob. Agents Chemother. 57, 3224-3229 (2013).
13. Liu, Y. Y., et al. Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study. Lancet Infect. Dis. 16, 161-168 (2016).
14. McGann, P., et al. Escherichia coli harboring mcr-1 and blaCTX-M on a novel IncF plasmid: first report of mcr-1 in the USA. Antimicrob. Agents Chemother. 60, 4420-4421 (2016).
15. Schwarz, S., Johnson, A. P. Transferable resistance to colistin: a new but old threat. J. Antimicrob. Chemother. 71, 2066-2070 (2016).
16. Espedido, B. A., Dimitrijovski, B., van Hal, S. J., Jensen, S. O. The use of wholegenome sequencing for molecular epidemiology and antimicrobial surveillance: identifying the role of IncX3 plasmids and the spread of blaNDM-4-like genes in the Enterobacteriaceae. J. Clin. Pathol. 68, 835-838 (2015).
17. Zhang, R. M., Wang, Y., et al. Characterization of NDM-1-producing carbapenemase in Acinetobacter spp., E. coli isolates from diseased pigs. Front. Agr. Sci. Eng. 2, 223-229 (2015).
18. Zhi, C., Lv, L., Yu, L. F., Doi, Y., Liu, J.-H. Dissemination of the mcr-1 colistin resistance gene. Lancet Infect. Dis. 16, 292-293 (2016).
19. Hassan, B., Carvalho, M., Mushtaq, A., et al. Environmental Dissemination of MDRB Carrying blaNDM and blaCTX-M-15 in Hospital Environment, Drinking Water, Birds and Insects (ECCMID, 2015).
20. Wang, Y., et al. Multidrug resistance gene cfr in methicillin-resistant coagulasenegative staphylococci from chickens, ducks, and pigs in China. Int. J. Med. Microbiol. 303, 84-87 (2013).
21. Poirel, L., Walsh, T. R., Cuvillier, V., Nordmann, P. Multiplex PCR for detection of acquired carbapenemase genes. Diagn. Microbiol. Infect. Dis. 70, 119-123 (2011).
22. M100-S25: Performance Standards for Antimicrobial Susceptibility Testing; Twenty-Fifth Informational Supplement (Clinical and Laboratory Standards, 2015).
23. Breakpoint Tables for Interpretation of MICs and Zone Diameters v. 6. 0 (European Committee on Antimicrobial Susceptibility Testing, 2016); http://www. eucast. org/clinical-breakpoints/
24. PlasmidFinder 1. 3 (Center for Genomic Epidemiology, accessed 10 June 2016); https://cge. cbs. dtu. dk/services/PlasmidFinder/
25. Fang, L., et al. Co-spread of metal and antibiotic resistance within ST3-IncHI2 plasmids from E. coli isolates of food-producing animals. Sci. Rep. 6, 25312 (2016).
26. Yamaguchi, Y., Park, J. H., Inouye, M. Toxin-antitoxin systems in bacteria and archaea. Annu. Rev. Genet. 45, 61-79 (2011).
27. Clermont, O., Bonacorsi, S., Bingen, E. Rapid and simple determination of the Escherichia coli phylogenetic group. Appl. Environ. Microbiol. 66, 4555-4558 (2000).
28. Treangen, T. J., Ondov, B. D., Koren, S., Phillippy, A. M. The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome Biol. 15, 524 (2014).
29. Wirth, T., et al. Sex and virulence in Escherichia coli: an evolutionary perspective. Mol. Microbiol. 60, 1136-1151 (2006).
30. Tang, J., Hanage, W. P., Fraser, C., Corander, J. Identifying currents in the gene pool for bacterial populations using an integrative approach. PLoS Comput. Biol. 5, e1000455 (2009).
31. Corander, J., Marttinen, P., Siren, J., Tang, J. Enhanced Bayesian modelling in BAPS software for learning genetic structures of populations. BMC Bioinformatics 9, 539 (2008).
32. Cheng, L., Connor, T. R., Siren, J., Aanensen, D. M., Corander, J. Hierarchical and spatially explicit clustering of DNA sequences with BAPS software. Mol. Biol. Evol. 30, 1224-1228 (2013).
33. Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792-1797 (2004).
34. Price, M. N., Dehal, P. S., Arkin, A. P. Fasttree 2-approximately maximum-likelihood trees for large alignments. PLoS ONE 5, e9490 (2010).
35. Huson, D. H., Scornavacca, C. Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks. Syst. Biol. 61, 1061-1067 (2012).
36. Huson, D. H., et al. Dendroscope: an interactive viewer for large phylogenetic trees. BMC Bioinformatics 8, 460 (2007).