Whole-Genome Sequencing for Detecting Antimicrobial Resistance in Nontyphoidal Salmonella

Abstract

b Laboratory-based in vitro antimicrobial susceptibility testing is the foundation for guiding anti-infective therapy and monitoring antimicrobial resistance trends. We used whole-genome sequencing (WGS) technology to identify known antimicrobial resistance determinants among strains of nontyphoidal Salmonella and correlated these with susceptibility phenotypes to evaluate the utility of WGS for antimicrobial resistance surveillance. Six hundred forty Salmonella of 43 different serotypes were selected from among retail meat and human clinical isolates that were tested for susceptibility to 14 antimicrobials using broth microdilution. The MIC for each drug was used to categorize isolates as susceptible or resistant based on Clinical and Laboratory Standards Institute clinical breakpoints or National Antimicrobial Resistance Monitoring System (NARMS) consensus interpretive criteria. Each isolate was subjected to whole-genome shotgun sequencing, and resistance genes were identified from assembled sequences. A total of 65 unique resistance genes, plus mutations in two structural resistance loci, were identified. There were more unique resistance genes (n ‫؍‬ 59) in the 104 human isolates than in the 536 retail meat isolates (n ‫؍‬ 36). Overall, resistance genotypes and phenotypes correlated in 99.0% of cases. Correlations approached 100% for most classes of antibiotics but were lower for aminoglycosides and beta-lactams. We report the first finding of extended-spectrum ␤-lactamases (ESBLs) (bla CTX-M1 and bla SHV2a ) in retail meat isolates of Salmonella in the United States. Whole-genome sequencing is an effective tool for predicting antibiotic resistance in nontyphoidal Salmonella, although the use of more appropriate surveillance breakpoints and increased knowledge of new resistance alleles will further improve correlations.

Establishing Genotypic Cutoff Values To Measure Antimicrobial Resistance in Salmonella

“…An additional 81 Salmonella isolates from retail meats isolated from 2002 to 2011 were included in this study based on the presentation of rare MICs, resulting in a total of 1,738 isolates (see Materials and Methods). This builds on a prior analysis we had conducted in which we compared resistance genotypes and phenotypes for 640 Salmonella isolates (12). In this study, we measured the correlation of specific MICs with the presence of resistance genes as defined in the ResFinder database (17).…”

“…A total of 1,738 Salmonella isolates were isolated in the United States from 40 states from retail meat (1,297), food animal (337), and human (104) sources; these included 640 isolates from a prior analysis (12). Retail meat isolates were from 2002 to 2015, food animal isolates from 2014, and human isolates from 2011 to 2012.…”

“…For most bacteria, the evidence for using WGS to infer antimicrobial susceptibility data is sparse, although some studies have shown a high correlation between resistance phenotypes and the presence of resistance genes or resistance-associated mutations. This agreement has been best demonstrated with enteric bacteria, including Escherichia coli, Campylobacter spp., and nontyphoidal Salmonella (8)(9)(10)(11)(12). In addition, other DNAbased methods have been used to detect resistance determinants and even guide therapy for infections caused by Mycobacterium tuberculosis, Staphylococcus aureus, HIV, and other pathogens (13)(14)(15).…”

Whole-Genome Sequencing of Drug-Resistant Salmonella enterica Isolates from Dairy Cattle and Humans in New York and Washington States Reveals Source and Geographic Associations

“…Our study reported here demonstrates that in silico AMR gene predictions are highly correlated with phenotypic resistance in Salmonella enterica Typhimurium, Newport, and Dublin, as AMR genotype correlated with AMR phenotype with an overall sensitivity and specificity of 97.2 and 85.2%, respectively. The ability to predict AMR phenotype from WGS data with high sensitivity and specificity has previously been observed in Salmonella enterica isolated from humans and retail meats (27) and S. Typhimurium from swine (28), as well as in other organisms, including Staphylococcus aureus (29,30) Campylobacter spp. (31), and Mycobacterium tuberculosis (30).…”

Impact of whole genome sequencing in Public Health reference laboratories

“…Overall, correlation between the extrapolated genotype and phenotype is promising and the epidemiological information generated on genetic mechanisms is valuable 8,9 . Reports suggest that inferring antibiotic resistance from genotype results in an overestimation of resistance, possibly due to the presence of silent genes or poorly understood mechan- That is, facilitating the appropriate antimicrobial management of gonorrhoea in an era of increasing resistance to prevent treatment failure, timely provision of an accurate diagnosis to inform appropriate treatment, and providing molecular insights to better understand gonococcal transmission (Table 1).…”