Salmonella enterica Serotype 4,[5],12:i:-in Swine in the United States Midwest: An Emerging Multidrug-Resistant Clade

Clinical Infectious Diseases

Volumn 66, Issue 6, 2018, Pages 877-885

  Elnekave, Ehud ^a   Hong, Samuel ^a   Mather, Alison E ^b   Boxrud, Dave ^c   Taylor, Angela J ^c   Lappi, Victoria ^c   Johnson, Timothy J ^d   Vannucci, Fabio ^d   Davies, Peter ^a   Hedberg, Craig ^e   Perez, Andres ^a   Alvarez, Julio ^a  

^a UNIVERSITY OF MINNESOTA   (United States)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^c MINNESOTA DEPARTMENT OF HEALTH   (United States)

^d UNIVERSITY OF MINNESOTA   (United States)

^e UNIVERSITY OF MINNESOTA   (United States)

Author keywords

AMR; MDR; Monophasic; Pig; Quinolones

Indexed keywords

AMPICILLIN; CEFTIOFUR; CEFTRIAXONE; CIPROFLOXACIN; ENROFLOXACIN; STREPTOMYCIN; SULFONAMIDE; TETRACYCLINE DERIVATIVE; ANTIINFECTIVE AGENT; QUINOLONE DERIVATIVE; VIRULENCE FACTOR;

ANTIBIOTIC RESISTANCE; ARTICLE; GENETIC HETEROGENEITY; LIVESTOCK; NONHUMAN; PHYLOGENETIC TREE; PRIORITY JOURNAL; SALMONELLA ENTERICA; SALMONELLA ENTERICA SEROVAR TYPHIMURIUM; SINGLE NUCLEOTIDE POLYMORPHISM; WHOLE GENOME SEQUENCING; ANIMAL; ANIMAL SALMONELLOSIS; DRUG EFFECT; EUROPE; GENETIC VARIATION; GENETICS; GENOTYPE; ISOLATION AND PURIFICATION; MICROBIAL SENSITIVITY TEST; MICROBIOLOGY; MULTIDRUG RESISTANCE; PHENOTYPE; PIG; SEROTYPE; UNITED STATES;

ANIMALS; ANTI-BACTERIAL AGENTS; DRUG RESISTANCE, MULTIPLE, BACTERIAL; EUROPE; GENETIC VARIATION; GENOTYPE; MICROBIAL SENSITIVITY TESTS; MIDWESTERN UNITED STATES; PHENOTYPE; QUINOLONES; SALMONELLA ENTERICA; SALMONELLA INFECTIONS, ANIMAL; SALMONELLA TYPHIMURIUM; SEROGROUP; SWINE; VIRULENCE FACTORS; WHOLE GENOME SEQUENCING;

EID: 85043461204     PISSN: 10584838     EISSN: 15376591     Source Type: Journal    
DOI: 10.1093/cid/cix909     Document Type: Article

References (40)

1. Kirk MD, Pires SM, Black RE, et al. World Health Organization estimates of the global and regional disease burden of 22 foodborne bacterial, protozoal, and viral diseases, 2010: a data synthesis. PLoS Med 2015; 12:e1001921.
2. Scallan E, Hoekstra RM, Angulo FJ, et al. Foodborne illness acquired in the United States-major pathogens. Emerg Infect Dis 2011; 17:7-15.
3. Switt AI, Soyer Y, Warnick LD, Wiedmann M. Emergence, distribution, and molecular and phenotypic characteristics of Salmonella enterica serotype 4, 5, 12:i:-. Foodborne Pathog Dis 2009; 6:407-15.
4. Echeita MA, Herrera S, Usera MA. Atypical, fljB-negative Salmonella enterica subsp. enterica strain of serovar 4, 5, 12:i:-appears to be a monophasic variant of serovar Typhimurium. J Clin Microbiol 2001; 39:2981-3.
5. de la Torre E, Zapata D, Tello M, et al. Several Salmonella enterica subsp. enterica serotype 4, 5, 12:i:-phage types isolated from swine samples originate from sero-type Typhimurium DT U302. J Clin Microbiol 2003; 41:2395-400.
6. Centers for Disease Control and Prevention. Foodborne Diseases Active Surveillance Network (FoodNet): FoodNet 2015 surveillance. Report (final data). Atlanta, GA: Centers for Disease Control and Prevention, 2017.
7. Centers for Disease Control and Prevention (CDC). National Salmonella Surveillance Annual Report, 2013. Atlanta, Georgia: US Department of Health and Human Services, CDC, 2016.
8. Laorden L, Herrera-León S, Martínez I, et al. Genetic evolution of the Spanish multidrug-resistant Salmonella enterica 4, 5, 12:i:-monophasic variant. J Clin Microbiol 2010; 48:4563-6.
9. Petrovska L, Mather AE, AbuOun M, et al. Microevolution of monophasic Salmonella Typhimurium during epidemic, United Kingdom, 2005-2010. Emerg Infect Dis 2016; 22:617-24.
10. Mossong J, Marques P, Ragimbeau C, et al. Outbreaks of monophasic Salmonella enterica serovar 4, [5], 12:i:-in Luxembourg, 2006. Euro Surveill 2007; 12:E11-2.
11. Alcaine SD, Soyer Y, Warnick LD, et al. Multilocus sequence typing supports the hypothesis that cow-and human-associated Salmonella isolates represent distinct and overlapping populations. Appl Environ Microbiol 2006; 72:7575-85.
12. Agasan A, Kornblum J, Williams G, et al. Profile of Salmonella enterica subsp. enterica (subspecies I) serotype 4, 5, 12:i:-strains causing food-borne infections in New York City. J Clin Microbiol 2002; 40:1924-9.
13. Centers for Disease Control and Prevention (CDC). Reports of selected Salmonella outbreak investigations. Available at: https://www.cdc.gov/salmonella/outbreaks.html. Accessed 1 February 2017.
14. Hauser E, Tietze E, Helmuth R, et al. Pork contaminated with Salmonella enterica serovar 4, [5], 12:i:-, an emerging health risk for humans. Appl Environ Microbiol 2010; 76:4601-10.
15. Soyer Y, Moreno Switt A, Davis MA, et al. Salmonella enterica serotype 4, 5, 12:i:-, an emerging Salmonella serotype that represents multiple distinct clones. J Clin Microbiol 2009; 47:3546-56.
16. Lucarelli C, Dionisi AM, Filetici E, Owczarek S, Luzzi I, Villa L. Nucleotide sequence of the chromosomal region conferring multidrug resistance (R-type ASSuT) in Salmonella Typhimurium and monophasic Salmonella Typhimurium strains. J Antimicrob Chemother 2012; 67:111-4.
17. García P, Malorny B, Rodicio MR, et al. Horizontal acquisition of a multidrug-re-sistance module (R-type ASSuT) is responsible for the monophasic phenotype in a widespread clone of Salmonella serovar 4, [5], 12:i:. Front Microbiol 2016; 7:680.
18. Clinical and Laboratory Standards Institute. Performance standards for anti-microbial susceptibility testing: twenty-fifth informational supplement. Wayne, PA: Clinical and Laboratory Standards Institute, 2015.
19. Hong S, Rovira A, Davies P, et al. Serotypes and antimicrobial resistance in Salmonella enterica recovered from clinical samples from cattle and swine in Minnesota, 2006 to 2015. PLoS One 2016; 11:e0168016.
20. McKinney W. Data structures for statistical computing in Python. In: van der Voort S, Millman J, eds. Proceedings of the 9th Python in Science Conference, Austin, Texas, 28 June 28-3 July. 2010:51-6.
21. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient align-ment of short DNA sequences to the human genome. Genome Biol 2009; 10:R25.
22. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312-3.
23. Letunic I, Bork P. Interactive Tree of Life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res 2016; 44:W242-5.
24. Tritt A, Eisen JA, Facciotti MT, Darling AE. An integrated pipeline for de novo assembly of microbial genomes. PLoS One 2012; 7:e42304.
25. McDermott PF, Tyson GH, Kabera C, et al. Whole-genome sequencing for detect-ing antimicrobial resistance in nontyphoidal Salmonella. Antimicrob Agents Chemother 2016; 60:5515-20.
26. Chiaretto G, Zavagnin P, Bettini F, et al. Extended spectrum beta-lactamase SHV-12-producing Salmonella from poultry. Vet Microbiol 2008; 128:406-13.
27. Alcaine SD, Sukhnanand SS, Warnick LD, et al. Ceftiofur-resistant Salmonella strains isolated from dairy farms represent multiple widely distributed subtypes that evolved by independent horizontal gene transfer. Antimicrob Agents Chemother 2005; 49:4061-7.
28. Altschul SF, Gish W, Miller W, Myers E W, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403-10.
29. Jacoby GA. Mechanisms of resistance to quinolones. Clin Infect Dis 2005; 41(suppl 2):S120-6.
30. Abouzeed YM, Baucheron S, Cloeckaert A. ramR mutations involved in efflux-mediated multidrug resistance in Salmonella enterica serovar Typhimurium. Antimicrob Agents Chemother 2008; 52:2428-34.
31. Olliver A, Vallé M, Chaslus-Dancla E, Cloeckaert A. Role of an acrR mutation in multidrug resistance of in vitro-selected fluoroquinolone-resistant mutants of Salmonella enterica serovar Typhimurium. FEMS Microbiol Lett 2004; 238:267-72.
32. Larsson A. AliView: a fast and lightweight alignment viewer and editor for large datasets. Bioinformatics 2014; 30:3276-8.
33. Cornish-Bowden A. Nomenclature for incompletely specified bases in nucleic acid sequences: recommendations 1984. Nucleic Acids Res 1985; 13:3021-30.
34. Krull A, Kreuder A, Arruda B, Burrough E, Schwartz K, Sahin O. Increased frequency of isolation of multi-drug resistant Salmonella I 4, [5], 12:i:-from swine with histologic lesions consistent with salmonellosis. Presented at: American Association of Veterinary Laboratory Diagnosticians Annual Conference; 13-19 October 2016; Greensboro, NC.
35. Pires AF, Funk JA, Bolin C. Risk factors associated with persistence of Salmonella shedding in finishing pigs. Prev Vet Med 2014; 116:120-8.
36. Beceiro A, Tomás M, Bou G. Antimicrobial resistance and virulence: a successful or deleterious association in the bacterial world? Clin Microbiol Rev 2013; 26:185-230.
37. Crump JA, Sjölund-Karlsson M, Gordon MA, Parry CM. Epidemiology, clinical presentation, laboratory diagnosis, antimicrobial resistance, and antimicrobial management of invasive Salmonella infections. Clin Microbiol Rev 2015; 28:901-37.
38. Food and Drug Administration. NADA 141-068 in the approved animal drug products (Green Book). Available at: https://www.fda.gov/AnimalVeterinary/Products/ApprovedAnimalDrugProducts/FOIADrugSummaries/ucm056920. htm. Accessed 29 September 2017.
39. Cummings KJ, Rodriguez-Rivera LD, Norman KN, Ohta N, Scott HM. Identification of a plasmid-mediated quinolone resistance gene in Salmonella isolates from Texas dairy farm environmental samples. Zoonoses Public Health 2017; 64:305-7.
40. Taylor AJ, Lappi V, Wolfgang WJ, et al. Characterization of foodborne outbreaks of Salmonella enterica serovar Enteritidis with whole-genome sequencing single nucleotide polymorphism-based analysis for surveillance and outbreak detection. J Clin Microbiol 2015; 53:3334-40.