Neuert, Saskia, Nair, Satheesh, Day, Martin R, Doumith, Michel, Ashton, Philip M, Mellor, Kate C, Jenkins, Claire, Hopkins, Katie L, Woodford, Neil, de Pinna, Elizabeth et al (show 2 more authors)
(2018)
Prediction of Phenotypic Antimicrobial Resistance Profiles From Whole Genome Sequences of Non-typhoidal <i>Salmonella enterica</i>.
FRONTIERS IN MICROBIOLOGY, 9 (MAR).
592-.
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Prediction of Phenotypic Antimicrobial Resistance Profiles From Whole Genome Sequences of Non-typhoidal iSalmonella enterica.pdf - Open Access published version Download (484kB) | Preview |
Abstract
Surveillance of antimicrobial resistance (AMR) in non-typhoidal <i>Salmonella enterica</i> (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%, <i>n</i> = 59). Pan-susceptibility was observed in 2,190 isolates (62.73%). Overall, resistance to tetracyclines was most common (26.27% of isolates, <i>n</i> = 917) followed by sulphonamides (23.72%, <i>n</i> = 828) and ampicillin (21.43%, <i>n</i> = 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 (<i>n</i> = 231; 27.24%). For isolates with this profile, all but one were <i>S</i>. Typhimurium and 94.81% (<i>n</i> = 219) had the resistance determinants <i>bla</i><sub>TEM-1,</sub><i>strA-strB, sul2</i> and <i>tet</i>(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.
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | antimicrobial resistance, multidrug resistance, non-typhoidal Salmonella enterica, whole genome sequencing, public health surveillance, One Health |
| Divisions: | Faculty of Health and Life Sciences Faculty of Health and Life Sciences > Institute of Infection, Veterinary and Ecological Sciences |
| Depositing User: | Symplectic Admin |
| Date Deposited: | 15 Sep 2023 10:57 |
| Last Modified: | 11 Oct 2023 17:00 |
| DOI: | 10.3389/fmicb.2018.00592 |
| Related URLs: | |
| URI: | https://livrepository.liverpool.ac.uk/id/eprint/3172786 |
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