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Chapter 28 : Present and Future Surveillance of Antimicrobial Resistance in Animals: Principles and Practices

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Abstract:

There is broad consensus internationally that surveillance of the levels of antimicrobial resistance (AMR) occurring in various systems underpins strategies to address the issue. The key reasons for surveillance of resistance are to determine (i) the size of the problem, (ii) whether resistance is increasing, (iii) whether previously unknown types of resistance are emerging, (iv) whether a particular type of resistance is spreading, and (v) whether a particular type of resistance is associated with a particular outbreak. The implications of acquiring and utilizing this information need to be considered in the design of a surveillance system.

Citation: Simjee S, McDermott P, Trott D, Chuanchuen R. 2018. Present and Future Surveillance of Antimicrobial Resistance in Animals: Principles and Practices, p 595-618. In Schwarz S, Cavaco L, Shen J (ed), Antimicrobial Resistance in Bacteria from Livestock and Companion Animals. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.ARBA-0028-2017
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Figures

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Figure 1

MIC distribution for a hypothetical bacterial species targeted in antimicrobial resistance surveillance programs. Arrows indicate the epidemiological cutoff value (ECOFF) established according to EUCAST recommendations, separating the wild type (no resistance determinants) from the non-wild type (presumed resistance determinants that could be verified by whole-genome sequencing analysis), and the clinical breakpoint. Susceptible, resistant, and intermediate value columns are indicated ( ).

Citation: Simjee S, McDermott P, Trott D, Chuanchuen R. 2018. Present and Future Surveillance of Antimicrobial Resistance in Animals: Principles and Practices, p 595-618. In Schwarz S, Cavaco L, Shen J (ed), Antimicrobial Resistance in Bacteria from Livestock and Companion Animals. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.ARBA-0028-2017
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References

/content/book/10.1128/9781555819804.chap28
1. Anderson ES . 1968. Drug resistance in Salmonella typhimurium and its implications. BMJ 3 : 333 339.[CrossRef][PubMed]
2. UK Joint Committee of Houses of Parliament . 1969. Report on the use of antibiotics in animal husbandry and veterinary medicine (‘Swann Report’). Her Majesty’s Stationery Office, London.[PubMed]
3. Wray C,, McLaren IM,, Beedell YE . 1993. Bacterial resistance monitoring of salmonellas isolated from animals, national experience of surveillance schemes in the United Kingdom. Vet Microbiol 35 : 313 319.[CrossRef]
4. Pocurull DW,, Gaines SA,, Mercer HD . 1971. Survey of infectious multiple drug resistance among Salmonella isolated from animals in the United States. Appl Microbiol 21 : 358 362.
5. Martel JL,, Coudert M . 1993. Bacterial resistance monitoring in animals: the French national experiences of surveillance schemes. Vet Microbiol 35 : 321 338.[CrossRef]
6. Cohen ML,, Tauxe RV . 1986. Drug-resistant Salmonella in the United States: an epidemiologic perspective. Science 234 : 964 969.[CrossRef][PubMed]
7. DuPont HL,, Steele JH . 1987. Use of antimicrobial agents in animal feeds: implications for human health. Rev Infect Dis 9 : 447 460.[CrossRef][PubMed]
8. Tollefson L,, Angulo FJ,, Fedorka-Cray PJ . 1998. National surveillance for antibiotic resistance in zoonotic enteric pathogens. Vet Clin North Am Food Anim Pract 14 : 141 150.[CrossRef]
9. Aarestrup FM,, Bager F,, Jensen NE,, Madsen M,, Meyling A,, Wegener HC . 1998. Resistance to antimicrobial agents used for animal therapy in pathogenic-, zoonotic- and indicator bacteria isolated from different food animals in Denmark: a baseline study for the Danish Integrated Antimicrobial Resistance Monitoring Programme (DANMAP). APMIS 106 : 745 770.[CrossRef][PubMed]
10. Moyaert H,, de Jong A,, Simjee S,, Thomas V . 2014. Antimicrobial resistance monitoring projects for zoonotic and indicator bacteria of animal origin: common aspects and differences between EASSA and EFSA. Vet Microbiol 171 : 279 283.[CrossRef][PubMed]
11. Shaban RZ,, Simon GI,, Trott DJ,, Turnidge J,, Jordan D . 2014. Surveillance and reporting of antimicrobial resistance and antibiotic usage in animals and agriculture in Australia. Report to the Department of Agriculture, Griffith University and University of Adelaide, Australia.
12. Pagel SW,, Gautier P . 2012. Use of antimicrobial agents in livestock. Rev Sci Tech 31 : 145 188.[CrossRef][PubMed]
13. Weir M,, Rajić A,, Dutil L,, Uhland C,, Bruneau N . 2012. Zoonotic bacteria and antimicrobial resistance in aquaculture: opportunities for surveillance in Canada. Can Vet J 53 : 619 622.[PubMed]
14. Brudeseth BE,, Wiulsrød R,, Fredriksen BN,, Lindmo K,, Løkling KE,, Bordevik M,, Steine N,, Klevan A,, Gravningen K . 2013. Status and future perspectives of vaccines for industrialised fin-fish farming. Fish Shellfish Immunol 35 : 1759 1768.[CrossRef][PubMed]
15. DANMAP . 2016. DANMAP 2015. Use of Antimicrobial Agents and Occurrence of Antimicrobial Resistance in Bacteria from Food Animals, Food and Humans. https://www.danmap.org/.
16. DANMAP . 2012. DANMAP 2011. Use of Antimicrobial Agents and Occurrence of Antimicrobial Resistance in Bacteria from Food Animals, Food and Humans. https://www.danmap.org/.
17. Liu YY,, Wang Y,, Walsh TR,, Yi LX,, Zhang R,, Spencer J,, Doi Y,, Tian G,, Dong B,, Huang X,, Yu LF,, Gu D,, Ren H,, Chen X,, Lv L,, He D,, Zhou H,, Liang Z,, Liu JH,, Shen J . 2016. 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.[CrossRef]
18. Guerra B,, Fischer J,, Helmuth R . 2014. An emerging public health problem: acquired carbapenemase-producing microorganisms are present in food-producing animals, their environment, companion animals and wild birds. Vet Microbiol 171 : 290 297.[CrossRef][PubMed]
19. Johnson TJ . 2017. Carbapenemase-producing Enterobacteriaceae in swine production in the United States: impact and opportunities. Antimicrob Agents Chemother 61 : e02348-16.[PubMed]
20. El Garch F,, de Jong A,, Simjee S,, Moyaert H,, Klein U,, Ludwig C,, Marion H,, Haag-Diergarten S,, Richard-Mazet A,, Thomas V,, Siegwart E . 2016. Monitoring of antimicrobial susceptibility of respiratory tract pathogens isolated from diseased cattle and pigs across Europe, 2009–2012: VetPath results. Vet Microbiol 194 : 11 22.[CrossRef][PubMed]
21. Michael GB,, Kadlec K,, Sweeney MT,, Brzuszkiewicz E,, Liesegang H,, Daniel R,, Murray RW,, Watts JL,, Schwarz S . 2012. ICEPmu1, an integrative conjugative element (ICE) of Pasteurella multocida: structure and transfer. J Antimicrob Chemother 67 : 91 100.[CrossRef][PubMed]
22. Michael GB,, Kadlec K,, Sweeney MT,, Brzuszkiewicz E,, Liesegang H,, Daniel R,, Murray RW,, Watts JL,, Schwarz S . 2012. ICEPmu1, an integrative conjugative element (ICE) of Pasteurella multocida: analysis of the regions that comprise 12 antimicrobial resistance genes. J Antimicrob Chemother 67 : 84 90.[CrossRef][PubMed]
23. Lubbers BV,, Hanzlicek GA . 2013. Antimicrobial multidrug resistance and coresistance patterns of Mannheimia haemolytica isolated from bovine respiratory disease cases: a three-year (2009–2011) retrospective analysis. J Vet Diagn Invest 25 : 413 417.[CrossRef][PubMed]
24. Bossé JT,, Li Y,, Fernandez Crespo R,, Chaudhuri RR,, Rogers J,, Holden MT,, Maskell DJ,, Tucker AW,, Wren BW,, Rycroft AN,, Langford PR, the BRaDP1T Consortium . 2016. ICEApl1, an integrative conjugative element related to ICEHin1056, identified in the pig pathogen Actinobacillus pleuropneumoniae. Front Microbiol 7 : 810.[CrossRef][PubMed]
25. Jahanbakhsh S,, Smith MG,, Kohan-Ghadr HR,, Letellier A,, Abraham S,, Trott DJ,, Fairbrother JM . 2016. Dynamics of extended-spectrum cephalosporin resistance in pathogenic Escherichia coli isolated from diseased pigs in Quebec, Canada. Int J Antimicrob Agents 48 : 194 202.[CrossRef]
26. Smith M,, Do TN,, Gibson JS,, Jordan D,, Cobbold RN,, Trott DJ . 2014. Comparison of antimicrobial resistance phenotypes and genotypes in enterotoxigenic Escherichia coli isolated from Australian and Vietnamese pigs. J Glob Antimicrob Resist 2 : 162 167.[CrossRef][PubMed]
27. Walther B,, Monecke S,, Ruscher C,, Friedrich AW,, Ehricht R,, Slickers P,, Soba A,, Wleklinski CG,, Wieler LH,, Lübke-Becker A . 2009. Comparative molecular analysis substantiates zoonotic potential of equine methicillin-resistant Staphylococcus aureus. J Clin Microbiol 47 : 704 710.[CrossRef][PubMed]
28. Larsen J,, Stegger M,, Andersen PS,, Petersen A,, Larsen AR,, Westh H,, Agersø Y,, Fetsch A,, Kraushaar B,, Käsbohrer A,, Feβler AT,, Schwarz S,, Cuny C,, Witte W,, Butaye P,, Denis O,, Haenni M,, Madec JY,, Jouy E,, Laurent F,, Battisti A,, Franco A,, Alba P,, Mammina C,, Pantosti A,, Monaco M,, Wagenaar JA,, de Boer E,, van Duijkeren E,, Heck M,, Domínguez L,, Torres C,, Zarazaga M,, Price LB,, Skov RL . 2016. Evidence for human adaptation and foodborne transmission of livestock-associated methicillin-resistant Staphylococcus aureus. Clin Infect Dis 63 : 1349 1352.[CrossRef][PubMed]
29. Platell JL,, Johnson JR,, Cobbold RN,, Trott DJ . 2011. Multidrug-resistant extraintestinal pathogenic Escherichia coli of sequence type ST131 in animals and foods. Vet Microbiol 153 : 99 108.[PubMed]
30. Platell JL,, Cobbold RN,, Johnson JR,, Heisig A,, Heisig P,, Clabots C,, Kuskowski MA,, Trott DJ . 2011. Commonality among fluoroquinolone-resistant sequence type ST131 extraintestinal Escherichia coli isolates from humans and companion animals in Australia. Antimicrob Agents Chemother 55 : 3782 3787.[CrossRef][PubMed]
31. Ewers C,, Bethe A,, Stamm I,, Grobbel M,, Kopp PA,, Guerra B,, Stubbe M,, Doi Y,, Zong Z,, Kola A,, Schaufler K,, Semmler T,, Fruth A,, Wieler LH,, Guenther S . 2014. CTX-M-15-D-ST648 Escherichia coli from companion animals and horses: another pandemic clone combining multiresistance and extraintestinal virulence? J Antimicrob Chemother 69 : 1224 1230.[CrossRef][PubMed]
32. Vangchhia B,, Abraham S,, Bell JM,, Collignon P,, Gibson JS,, Ingram PR,, Johnson JR,, Kennedy K,, Trott DJ,, Turnidge JD,, Gordon DM . 2016. Phylogenetic diversity, antimicrobial susceptibility and virulence characteristics of phylogroup F Escherichia coli in Australia. Microbiology 162 : 1904 1912.[CrossRef][PubMed]
33. Iwamoto M,, Reynolds J,, Karp BE,, Tate H,, Fedorka-Cray PJ,, Plumblee JR,, Hoekstra RM,, Whichard JM,, Mahon BE . 2017. Ceftriaxone-resistant nontyphoidal Salmonella from humans, retail meats, and food animals in the United States, 1996–2013. Foodborne Pathog Dis 14 : 74 83.[PubMed]
34. Jiu Y,, Zhu S,, Khan SB,, Sun M,, Zou G,, Meng X,, Wu B,, Zhou R,, Li S . 2016. Phenotypic and genotypic resistance of Salmonella isolates from healthy and diseased pigs in China during 2008–2015. Microb Drug Resist 23 : 651 659.[PubMed]
35. Lin D,, Chen K,, Wai-Chi Chan E,, Chen S . 2015. Increasing prevalence of ciprofloxacin-resistant food-borne Salmonella strains harboring multiple PMQR elements but not target gene mutations. Sci Rep 5 : 14754.[CrossRef][PubMed]
36. Clewell DB,, Weaver KE,, Dunny GM,, Coque TM,, Francia MV,, Hayes F, . 2014. Extrachromosomal and mobile elements in Enterococci: transmission, maintenance, and epidemiology. In Gilmore MS,, Clewell DB,, Ike Y,, Shankar N (ed), Enterococci: from Commensals to Leading Causes of Drug Resistant Infection. [Internet.] Massachusetts Eye and Ear Infirmary, Boston, MA.
37. Al-Tawfiq JA,, Laxminarayan R,, Mendelson M . 2017. How should we respond to the emergence of plasmid-mediated colistin resistance in humans and animals? Int J Infect Dis 54 : 77 84.[CrossRef][PubMed]
38. Kluytmans JA,, Overdevest IT,, Willemsen I,, Kluytmans-van den Bergh MF,, van der Zwaluw K,, Heck M,, Rijnsburger M,, Vandenbroucke-Grauls CM,, Savelkoul PH,, Johnston BD,, Gordon D,, Johnson JR . 2013. Extended-spectrum β-lactamase-producing Escherichia coli from retail chicken meat and humans: comparison of strains, plasmids, resistance genes, and virulence factors. Clin Infect Dis 56 : 478 487.[CrossRef]
39. Mitchell NM,, Johnson JR,, Johnston B,, Curtiss R III,, Mellata M . 2015. Zoonotic potential of Escherichia coli isolates from retail chicken meat products and eggs. Appl Environ Microbiol 81 : 1177 1187.[CrossRef][PubMed]
40. Abraham S,, Jordan D,, Wong HS,, Johnson JR,, Toleman MA,, Wakeham DL,, Gordon DM,, Turnidge JD,, Mollinger JL,, Gibson JS,, Trott DJ . 2015. First detection of extended-spectrum cephalosporin- and fluoroquinolone-resistant Escherichia coli in Australian food-producing animals. J Glob Antimicrob Resist 3 : 273 277.[CrossRef][PubMed]
41. Doi Y,, Hazen TH,, Boitano M,, Tsai YC,, Clark TA,, Korlach J,, Rasko DA,, Chattaway MA,, DoNascimento V,, Wain J,, Helmuth R,, Guerra B,, Schwarz S,, Threlfall J,, Woodward MJ,, Coldham N,, Doi Y,, Hazen TH,, Boitano M,, Tsai YC,, Clark TA,, Korlach J,, Rasko DA . 2014. Whole-genome assembly of Klebsiella pneumoniae coproducing NDM-1 and OXA-232 carbapenemases using single-molecule, real-time sequencing. Antimicrob Agents Chemother 58 : 5947 5953.[CrossRef]
42. de Been M,, Lanza VF,, de Toro M,, Scharringa J,, Dohmen W,, Du Y,, Hu J,, Lei Y,, Li N,, Tooming-Klunderud A,, Heederik DJ,, Fluit AC,, Bonten MJ,, Willems RJ,, de la Cruz F,, van Schaik W . 2014. Dissemination of cephalosporin resistance genes between Escherichia coli strains from farm animals and humans by specific plasmid lineages. PLoS Genet 10 : e1004776.[CrossRef][PubMed]
43. Jorgensen JH,, Ferraro MJ . 2009. Antimicrobial susceptibility testing: a review of general principles and contemporary practices. Clin Infect Dis 49 : 1749 1755.[CrossRef][PubMed]
44. Lubbers BV,, Turnidge J . 2015. Antimicrobial susceptibility testing for bovine respiratory disease: getting more from diagnostic results. Vet J 203 : 149 154.[CrossRef][PubMed]
45. CLSI . 2011. Generation, presentation and application of antimicrobial susceptibility test data for bacteria of animal origin. https://clsi.org/standards/products/veterinary-medicine/documents/vet05/.
46. Silley P . 2012. Susceptibility testing methods, resistance and breakpoints: what do these terms really mean? Rev Sci Tech 31 : 33 41.[CrossRef][PubMed]
47. European Food Safety Authority . 2012. Technical specifications for the analysis and reporting of data on antimicrobial resistance (AMR) in the European Union Summary Report. Parma, Italy.
48. World Health Organization . 2002. Surveillance Standards for Antimicrobial Resistance. WHO, Geneva, Switzerland.
49. European Food Safety Authority--Working Group on Developing Harmonised Schemes for Monitoring Antimicrobial Resistance in Zoonotic Agents . 2008. Harmonised monitoring of antimicrobial resistance in Salmonella and Campylobacter isolates from food animals in the European Union. Clin Microbiol Infect 14 : 522533.[PubMed]
50. Regula G,, Lo Fo Wong DMA,, Ledergerber U,, Stephan R,, Danuser J,, Bissig-Choisat B,, Stärk KDC . 2005. Evaluation of an antimicrobial resistance monitoring program for Campylobacter in poultry by simulation. Prev Vet Med 70 : 29 43.[CrossRef][PubMed]
51. Agersø Y,, Aarestrup FM . 2013. Voluntary ban on cephalosporin use in Danish pig production has effectively reduced extended-spectrum cephalosporinase-producing Escherichia coli in slaughter pigs. J Antimicrob Chemother 68 : 569 572.[CrossRef][PubMed]
52. Parmley EJ,, Pintar K,, Majowicz S,, Avery B,, Cook A,, Jokinen C,, Gannon V,, Lapen DR,, Topp E,, Edge TA,, Gilmour M,, Pollari F,, Reid-Smith R,, Irwin R . 2013. A Canadian application of One Health: integration of Salmonella data from various Canadian surveillance programs (2005–2010). Foodborne Pathog Dis 10 : 747 756.[CrossRef][PubMed]
53. Gilbert JM,, White DG,, McDermott PF . 2007. The US national antimicrobial resistance monitoring system. Future Microbiol 2 : 493 500.[CrossRef][PubMed]
54. FDA . 2016. National Antimicrobial Resistance Monitoring System - Enteric Bacteria (NARMS): NARMS Integrated Report 2014. Rockville, Maryland: U.S. Department of Health and Human Services, Food & Drug Administration. Available at: http://www.fda.gov/AnimalVeterinary/SafetyHealth/AntimicrobialResistance/NationalAntimicrobialResistanceMonitoringSystem/default.htm.
55. Kahlmeter G . 2014. Defining antibiotic resistance-towards international harmonization. Ups J Med Sci 119 : 78 86.[CrossRef][PubMed]
56. Zankari E,, Hasman H,, Cosentino S,, Vestergaard M,, Rasmussen S,, Lund O,, Aarestrup FM,, Larsen MV . 2012. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother 67 : 2640 2644.[CrossRef][PubMed]
57. McArthur AG,, Waglechner N,, Nizam F,, Yan A,, Azad MA,, Baylay AJ,, Bhullar K,, Canova MJ,, De Pascale G,, Ejim L,, Kalan L,, King AM,, Koteva K,, Morar M,, Mulvey MR,, O’Brien JS,, Pawlowski AC,, Piddock LJV,, Spanogiannopoulos P,, Sutherland AD,, Tang I,, Taylor PL,, Thaker M,, Wang W,, Yan M,, Yu T,, Wright GD . 2013. The comprehensive antibiotic resistance database. Antiƒmicrob Agents Chemother 57 : 3348 3357.[CrossRef][PubMed]
58. Gupta SK,, Padmanabhan BR,, Diene SM,, Lopez-Rojas R,, Kempf M,, Landraud L,, Rolain JM . 2014. ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes. Antimicrob Agents Chemother 58 : 212 220.[CrossRef][PubMed]
59. Tyson GH,, McDermott PF,, Li C,, Chen Y,, Tadesse DA,, Mukherjee S,, Bodeis-Jones S,, Kabera C,, Gaines SA,, Loneragan GH,, Edrington TS,, Torrence M,, Harhay DM,, Zhao S . 2015. WGS accurately predicts antimicrobial resistance in Escherichia coli. J Antimicrob Chemother 70 : 2763 2769.[CrossRef][PubMed]
60. Stoesser N,, Batty EM,, Eyre DW,, Morgan M,, Wyllie DH,, Del Ojo Elias C,, Johnson JR,, Walker AS,, Peto TE,, Crook DW . 2013. Predicting antimicrobial susceptibilities for Escherichia coli and Klebsiella pneumoniae isolates using whole genomic sequence data. J Antimicrob Chemother 68 : 2234 2244.[CrossRef][PubMed]
61. Zankari E,, Hasman H,, Kaas RS,, Seyfarth AM,, Agersø Y,, Lund O,, Larsen MV,, Aarestrup FM . 2013. Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing. J Antimicrob Chemother 68 : 771 777.[CrossRef][PubMed]
62. Zhao S,, Tyson GH,, Chen Y,, Li C,, Mukherjee S,, Young S,, Lam C,, Folster JP,, Whichard JM,, McDermott PF . 2015. Whole-genome sequencing analysis accurately predicts antimicrobial resistance phenotypes in Campylobacter spp. Appl Environ Microbiol 82 : 459 466.[CrossRef][PubMed]
63. Mcdermott PF,, Tyson GH,, Kabera C,, Chen Y,, Li C,, Folster JP,, Ayers SL,, Lam C,, Tate HP,, Zhao S . 2016. The use of whole genome sequencing for detecting antimicrobial resistance in nontyphoidal Salmonella. Antimicrob Agents Chemother. 60 : 5515 5520.[PubMed]
64. Gordon NC,, Price JR,, Cole K,, Everitt R,, Morgan M,, Finney J,, Kearns AM,, Pichon B,, Young B,, Wilson DJ,, Llewelyn MJ,, Paul J,, Peto TE,, Crook DW,, Walker AS,, Golubchik T . 2014. Prediction of Staphylococcus aureus antimicrobial resistance by whole-genome sequencing. J Clin Microbiol 52 : 1182 1191.[CrossRef][PubMed]
65. Zhao S,, Mukherjee S,, Chen Y,, Li C,, Young S,, Warren M,, Abbott J,, Friedman S,, Kabera C,, Karlsson M,, McDermott PF . 2015. Novel gentamicin resistance genes in Campylobacter isolated from humans and retail meats in the USA. J Antimicrob Chemother 70 : 1314 1321.[CrossRef][PubMed]
66. Pal C,, Bengtsson-Palme J,, Rensing C,, Kristiansson E,, Larsson DG . 2014. BacMet: antibacterial biocide and metal resistance genes database. Nucleic Acids Res 42( D1) : D737 D743.[CrossRef][PubMed]
67. Tyson GH,, Li C,, Ayers S,, McDermott PF,, Zhao S . 2016. Using whole-genome sequencing to determine appropriate streptomycin epidemiological cutoffs for Salmonella and Escherichia coli. FEMS Microbiol Lett 363 : 363.[CrossRef][PubMed]
68. Kaye KS,, Pogue JM,, Tran TB,, Nation RL,, Li J . 2016. Agents of last resort: polymyxin resistance. Infect Dis Clin North Am 30 : 391 414.[CrossRef][PubMed]
69. Hu Y,, Liu F,, Lin IY,, Gao GF,, Zhu B . 2016. Dissemination of the mcr-1 colistin resistance gene. Lancet Infect Dis 16 : 146 147.[CrossRef]
70. Stoesser N,, Mathers AJ,, Moore CE,, Day NP,, Crook DW . 2016. Colistin resistance gene mcr-1 and pHNSHP45 plasmid in human isolates of Escherichia coli and Klebsiella pneumoniae. Lancet Infect Dis 16 : 285 286.[CrossRef]
71. Hasman H,, Hammerum AM,, Hansen F,, Hendriksen RS,, Olesen B,, Agersø Y,, Zankari E,, Leekitcharoenphon P,, Stegger M,, Kaas RS,, Cavaco LM,, Hansen DS,, Aarestrup FM,, Skov RL . 2015. Detection of mcr-1 encoding plasmid-mediated colistin-resistant Escherichia coli isolates from human bloodstream infection and imported chicken meat, Denmark 2015. Euro Surveill 20 : 20.[CrossRef][PubMed]
72. McGann P,, Snesrud E,, Maybank R,, Corey B,, Ong AC,, Clifford R,, Hinkle M,, Whitman T,, Lesho E,, Schaecher KE . 2016. Escherichia coli harboring mcr-1 and blaCTX-M on a novel IncF plasmid: first report of mcr-1 in the United States. Antimicrob Agents Chemother 60 : 4420 4421.[CrossRef][PubMed]
73. Suzuki S,, Ohnishi M,, Kawanishi M,, Akiba M,, Kuroda M . 2016. Investigation of a plasmid genome database for colistin-resistance gene mcr-1. Lancet Infect Dis 16 : 284 285.[CrossRef]
74. Lesho E,, Clifford R,, Onmus-Leone F,, Appalla L,, Snesrud E,, Kwak Y,, Ong A,, Maybank R,, Waterman P,, Rohrbeck P,, Julius M,, Roth A,, Martinez J,, Nielsen L,, Steele E,, McGann P,, Hinkle M . 2016. The challenges of implementing next generation sequencing across a large healthcare system, and the molecular epidemiology and antibiotic susceptibilities of carbapenemase-producing bacteria in the healthcare system of the U.S. Department of Defense. PLoS One 11 : e0155770.[CrossRef][PubMed]
75. Carattoli A,, Zankari E,, García-Fernández A,, Voldby Larsen M,, Lund O,, Villa L,, Møller Aarestrup F,, Hasman H . 2014. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother 58 : 3895 3903.[CrossRef][PubMed]
76. Chen Y,, Mukherjee S,, Hoffmann M,, Kotewicz ML,, Young S,, Abbott J,, Luo Y,, Davidson MK,, Allard M,, McDermott P,, Zhao S . 2013. Whole-genome sequencing of gentamicin-resistant Campylobacter coli isolated from U.S. retail meats reveals novel plasmid-mediated aminoglycoside resistance genes. Antimicrob Agents Chemother 57 : 5398 5405.[CrossRef][PubMed]
77. Wang J,, Stephan R,, Power K,, Yan Q,, Hächler H,, Fanning S . 2014. Nucleotide sequences of 16 transmissible plasmids identified in nine multidrug-resistant Escherichia coli isolates expressing an ESBL phenotype isolated from food-producing animals and healthy humans. J Antimicrob Chemother 69 : 2658 2668.[CrossRef][PubMed]
78. Seiler C,, Berendonk TU . 2012. Heavy metal driven co-selection of antibiotic resistance in soil and water bodies impacted by agriculture and aquaculture. Front Microbiol 3 : 399.[CrossRef][PubMed]
79. Larsen MV,, Cosentino S,, Lukjancenko O,, Saputra D,, Rasmussen S,, Hasman H,, Sicheritz-Pontén T,, Aarestrup FM,, Ussery DW,, Lund O . 2014. Benchmarking of methods for genomic taxonomy. J Clin Microbiol 52 : 1529 1539.[CrossRef][PubMed]
80. Salipante SJ,, SenGupta DJ,, Cummings LA,, Land TA,, Hoogestraat DR,, Cookson BT . 2015. Application of whole-genome sequencing for bacterial strain typing in molecular epidemiology. J Clin Microbiol 53 : 1072 1079.[CrossRef][PubMed]

Tables

Generic image for table
Table 1

Antimicrobial classes and agents registered for human and veterinary use that are often screened in antimicrobial resistance surveillance programs

Citation: Simjee S, McDermott P, Trott D, Chuanchuen R. 2018. Present and Future Surveillance of Antimicrobial Resistance in Animals: Principles and Practices, p 595-618. In Schwarz S, Cavaco L, Shen J (ed), Antimicrobial Resistance in Bacteria from Livestock and Companion Animals. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.ARBA-0028-2017
Generic image for table
Table 2

Microorganisms of interest in AMR monitoring programs focused on both zoonotic foodborne pathogens and commensals in healthy livestock and major animal pathogens

Citation: Simjee S, McDermott P, Trott D, Chuanchuen R. 2018. Present and Future Surveillance of Antimicrobial Resistance in Animals: Principles and Practices, p 595-618. In Schwarz S, Cavaco L, Shen J (ed), Antimicrobial Resistance in Bacteria from Livestock and Companion Animals. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.ARBA-0028-2017

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