Prediction of Phenotypic Antimicrobial Resistance Profiles From Whole Genome Sequences of Non-typhoidal Salmonella enterica

Surveillance of antimicrobial resistance (AMR) in non-typhoidal Salmonella enterica (NTS), is essential for monitoring transmission of resistance from the food chain to humans, and for establishing effective treatment protocols. We evaluated the prediction of phenotypic resistance in NTS from genotypic profiles derived from whole genome sequencing (WGS). Genes and chromosomal mutations responsible for phenotypic resistance were sought in WGS data from 3,491 NTS isolates received by Public Health England’s Gastrointestinal Bacteria Reference Unit between April 2014 and March 2015. Inferred genotypic AMR profiles were compared with phenotypic susceptibilities determined for fifteen antimicrobials using EUCAST guidelines. Discrepancies between phenotypic and genotypic profiles for one or more antimicrobials were detected for 76 isolates (2.18%) although only 88/52,365 (0.17%) isolate/antimicrobial combinations were discordant. Of the discrepant results, the largest number were associated with streptomycin (67.05%, n = 59). Pan-susceptibility was observed in 2,190 isolates (62.73%). Overall, resistance to tetracyclines was most common (26.27% of isolates, n = 917) followed by sulphonamides (23.72%, n = 828) and ampicillin (21.43%, n = 748). Multidrug resistance (MDR), i.e., resistance to three or more antimicrobial classes, was detected in 848 isolates (24.29%) with resistance to ampicillin, streptomycin, sulphonamides and tetracyclines being the most common MDR profile (n = 231; 27.24%). For isolates with this profile, all but one were S. Typhimurium and 94.81% (n = 219) had the resistance determinants blaTEM-1, strA-strB, sul2 and tet(A). Extended-spectrum β-lactamase genes were identified in 41 isolates (1.17%) and multiple mutations in chromosomal genes associated with ciprofloxacin resistance in 82 isolates (2.35%). This study showed that WGS is suitable as a rapid means of determining AMR patterns of NTS for public health surveillance.

[1]  Gemma C. Langridge,et al.  Patterns of genome evolution that have accompanied host adaptation in Salmonella , 2014, Proceedings of the National Academy of Sciences.

[2]  S. Nakamura,et al.  Quinolone resistance-determining region in the DNA gyrase gyrA gene of Escherichia coli , 1990, Antimicrobial Agents and Chemotherapy.

[3]  N Woodford,et al.  The role of whole genome sequencing in antimicrobial susceptibility testing of bacteria: report from the EUCAST Subcommittee. , 2017, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

[4]  P. Ashton,et al.  Public health surveillance in the UK revolutionises our understanding of the invasive Salmonella Typhimurium epidemic in Africa , 2017, Genome Medicine.

[5]  Haruo Watanabe,et al.  Characterization of drug resistant Salmonella enterica serotype Typhimurium by antibiograms, plasmids, integrons, resistance genes and PFGE. , 2010, Journal of microbiology and biotechnology.

[6]  K. Nagy,et al.  The European Union summary report on antimicrobial resistance in zoonotic and indicator bacteria from humans, animals and food in 2015 , 2017, EFSA journal. European Food Safety Authority.

[7]  W. Gaastra,et al.  Antimicrobial Resistance, Class 1 Integrons, and Genomic Island 1 in Salmonella Isolates from Vietnam , 2010, PloS one.

[8]  I. Karunasagar,et al.  Antimicrobial-resistant genes associated with Salmonella spp. isolated from human, poultry, and seafood sources , 2014, Food science & nutrition.

[9]  E. Threlfall,et al.  Increasing incidence of resistance to trimethoprim and ciprofloxacin in epidemic Salmonella typhimurium DT104 in England and Wales. , 1997, Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin.

[10]  Zhemin Zhou,et al.  Multilocus Sequence Typing as a Replacement for Serotyping in Salmonella enterica , 2012, PLoS pathogens.

[11]  J. Wain,et al.  Changes in causes of acute gastroenteritis in the United Kingdom over 15 years: microbiologic findings from 2 prospective, population-based studies of infectious intestinal disease. , 2012, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[12]  Shaohua Zhao,et al.  WGS accurately predicts antimicrobial resistance in Escherichia coli. , 2015, The Journal of antimicrobial chemotherapy.

[13]  M. Mulvey,et al.  Characterization of Variant Salmonella Genomic Island 1 Multidrug Resistance Regions from Serovars Typhimurium DT104 and Agona , 2002, Antimicrobial Agents and Chemotherapy.

[14]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[15]  C. Chiu,et al.  High Rate of Reduced Susceptibility to Ciprofloxacin and Ceftriaxone among Nontyphoid Salmonella Clinical Isolates in Asia , 2009, Antimicrobial Agents and Chemotherapy.

[16]  J. R. Johnson,et al.  Predicting antimicrobial susceptibilities for Escherichia coli and Klebsiella pneumoniae isolates using whole genomic sequence data , 2013, The Journal of antimicrobial chemotherapy.

[17]  E. Kristiansson,et al.  Computational discovery and functional validation of novel fluoroquinolone resistance genes in public metagenomic data sets , 2017, BMC Genomics.

[18]  Ole Lund,et al.  Genotyping using whole-genome sequencing is a realistic alternative to surveillance based on phenotypic antimicrobial susceptibility testing. , 2013, The Journal of antimicrobial chemotherapy.

[19]  Aamir Fazil,et al.  The global burden of nontyphoidal Salmonella gastroenteritis. , 2010, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

[20]  T. Dallman,et al.  Comparison of phenotypic and WGS‐derived antimicrobial resistance profiles of Shigella sonnei isolated from cases of diarrhoeal disease in England and Wales, 2015 , 2017, The Journal of antimicrobial chemotherapy.

[21]  A. Kapil,et al.  Re-emergence of chloramphenicolsensitive Salmonella typhi , 1999, The Lancet.

[22]  F. Aarestrup,et al.  Establishing streptomycin epidemiological cut-off values for Salmonella and Escherichia coli. , 2012, Microbial drug resistance.

[23]  G. Dougan,et al.  Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype. , 2009, Genome research.

[24]  M. Tobin-D'Angelo,et al.  Salmonellosis outcomes differ substantially by serotype. , 2008, The Journal of infectious diseases.

[25]  Gemma C. Langridge,et al.  WGS for surveillance of antimicrobial resistance: a pilot study to detect the prevalence and mechanism of resistance to azithromycin in a UK population of non-typhoidal Salmonella. , 2016, The Journal of antimicrobial chemotherapy.

[26]  J. Funk,et al.  Genetic and phenotypic characterization of the bla(CMY) gene from Escherichia coli and Salmonella enterica isolated from food-producing animals, humans, the environment, and retail meat. , 2009, Foodborne pathogens and disease.

[27]  K. Hopkins,et al.  Mechanisms of quinolone resistance in Escherichia coli and Salmonella: recent developments. , 2005, International journal of antimicrobial agents.

[28]  N. Woodford,et al.  Resistance to third-generation cephalosporins in human non-typhoidal Salmonella enterica isolates from England and Wales, 2010-12. , 2014, The Journal of antimicrobial chemotherapy.

[29]  J. J. Borrego,et al.  Analysis of the mechanism of quinolone resistance in nalidixic acid-resistant clinical isolates of Salmonella serotype Typhimurium. , 1997, Journal of medical microbiology.

[30]  Neil Woodford,et al.  Antimicrobial resistance in Shiga toxin-producing Escherichia coli serogroups O157 and O26 isolated from human cases of diarrhoeal disease in England, 2015 , 2017, The Journal of antimicrobial chemotherapy.

[31]  J. Crump,et al.  Global Burden of Invasive Nontyphoidal Salmonella Disease, 2010 , 2015, Emerging infectious diseases.

[32]  P. Ashton,et al.  Detection of the plasmid-mediated mcr-1 gene conferring colistin resistance in human and food isolates of Salmonella enterica and Escherichia coli in England and Wales. , 2016, The Journal of antimicrobial chemotherapy.

[33]  L. Ng,et al.  Characterization of Canadian cefoxitin-resistant non-typhoidal Salmonella isolates, 2005-06. , 2009, The Journal of antimicrobial chemotherapy.

[34]  M. Rahman,et al.  Decline in epidemic of multidrug resistant Salmonella Typhi is not associated with increased incidence of antibiotic-susceptible strain in Bangladesh , 2002, Epidemiology and Infection.

[35]  A. Carattoli,et al.  IncA/C Plasmid Carrying blaNDM-1, blaCMY-16, and fosA3 in a Salmonella enterica Serovar Corvallis Strain Isolated from a Migratory Wild Bird in Germany , 2015, Antimicrobial Agents and Chemotherapy.

[36]  S. Magnet,et al.  Activation of the Cryptic aac(6′)-IyAminoglycoside Resistance Gene of Salmonella by a Chromosomal Deletion Generating a Transcriptional Fusion , 1999, Journal of bacteriology.

[37]  A. B. CiusnE,et al.  Typhoid fever. , 1967, The Journal of the Arkansas Medical Society.

[38]  Claire Jenkins,et al.  Identification of Salmonella for public health surveillance using whole genome sequencing , 2016, PeerJ.

[39]  A. Carattoli,et al.  Characterization of plasmids harbouring qnrS1, qnrB2 and qnrB19 genes in Salmonella. , 2009, The Journal of antimicrobial chemotherapy.

[40]  C. Chiu,et al.  Increasing ceftriaxone resistance in Salmonella isolates from a university hospital in Taiwan. , 2005, The Journal of antimicrobial chemotherapy.

[41]  V. Miriagou,et al.  Multidrug and Broad-Spectrum Cephalosporin Resistance among Salmonella enterica Serotype Enteritidis Clinical Isolates in Southern Italy , 2002, Journal of Clinical Microbiology.

[42]  Gemma C. Langridge,et al.  Distinct Salmonella Enteritidis lineages associated with enterocolitis in high-income 1 settings and invasive disease in low-income settings , 2016 .

[43]  N. Beeching,et al.  A retrospective study of secondary bacteraemia in hospitalised adults with community acquired non-typhoidal Salmonella gastroenteritis , 2013, BMC Infectious Diseases.

[44]  M. Gazouli,et al.  Spread of a Salmonella typhimurium Clone Resistant to Expanded-Spectrum Cephalosporins in Three European Countries , 1999, Journal of Clinical Microbiology.

[45]  Shaohua Zhao,et al.  Whole-Genome Sequencing for Detecting Antimicrobial Resistance in Nontyphoidal Salmonella , 2016, Antimicrobial Agents and Chemotherapy.

[46]  K. Hopkins,et al.  Plasmid-mediated quinolone resistance determinant qnrS1 found in Salmonella enterica strains isolated in the UK. , 2007, The Journal of antimicrobial chemotherapy.

[47]  P. Ashton,et al.  Comparison of phenotypic and WGS-derived antimicrobial resistance profiles of Salmonella enterica serovars Typhi and Paratyphi , 2018, The Journal of antimicrobial chemotherapy.

[48]  J. A. Frost,et al.  Increasing spectrum of resistance in multiresistant Salmonella typhimurium , 1996, The Lancet.

[49]  Shaohua Zhao,et al.  Establishing Genotypic Cutoff Values To Measure Antimicrobial Resistance in Salmonella , 2016, Antimicrobial Agents and Chemotherapy.

[50]  F. Weill,et al.  Highly drug-resistant Salmonella enterica serotype Kentucky ST198-X1: a microbiological study. , 2013, The Lancet. Infectious diseases.