Genomic surveillance of Salmonella spp. in the Philippines during 2013-2014
Abstract
BACKGROUND: Increasing antimicrobial resistance (AMR) in Salmonella has been observed in the Philippines. We aimed to characterise the population and AMR mechanisms of Salmonella with whole genome sequencing (WGS) and compare it with laboratory surveillance methods. METHODS: The serotype, multilocus sequence type, AMR genes and relatedness between isolates were determined from the genomes of 148 Salmonella Typhi (S. Typhi) and 65 non-typhoidal Salmonella (NTS) collected by the Antimicrobial Resistance Surveillance Program during 2013-2014. Genotypic serotypes and AMR prediction were compared with phenotypic data. RESULTS: AMR rates in S. Typhi were low, with sparse acquisition of mutations associated with reduced susceptibility to fluoroquinolones or extended-spectrum beta-lactamases (ESBL) genes. By contrast, 75% of NTS isolates were insusceptible to at least one antimicrobial, with more than half carrying mutations and/or genes linked to fluoroquinolone resistance. ESBL genes were detected in five genomes, which also carried other AMR determinants. The population of S. Typhi was dominated by likely endemic genotype 3.0, which caused a putative local outbreak. The main NTS clades were global epidemic S. Enteritidis ST11 and S. Typhimurium monophasic variant (I,4,[5],12: i: -) ST34. CONCLUSION: We provide the first genomic characterisation of Salmonella from the Philippines and evidence of WGS utility for ongoing surveillance.
Citation
Lagrada , M L , Argimón , S , Borlasa , J B , Abad , J P , Gayeta , J M , Masim , M L , Olorosa , A M , Cohen , V , Jeffrey , B , Abudahab , K , Sia , S B , Hufano , C M , Stelling , J , Holden , M T G , Aanensen , D M & Carlos , C C 2022 , ' Genomic surveillance of Salmonella spp. in the Philippines during 2013-2014 ' , Transactions of the Royal Society of Tropical Medicine and Hygiene , vol. 116 , no. 12 , trac080 , pp. 1202-1213 . https://doi.org/10.1101/2022.02.14.480363 , https://doi.org/10.1093/trstmh/trac080
Publication
Transactions of the Royal Society of Tropical Medicine and Hygiene
Status
Peer reviewed
ISSN
0035-9203Type
Journal article
Rights
© The Author(s) 2022. Published by Oxford University Press on behalf of Royal Society of Tropical Medicine and Hygiene. This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/ by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited.
Description
Funding: This work was supported by a Newton Fund award from the Medical Research Council (UK) MR/N019296/1 and the Philippine Council for Health Research and Development. This work was also partially supported by research grant U01CA207167 from the U.S. National Institutes of Health. SA and DMA were additionally supported by the National Institute for Health Research (UK) Global Health Research Unit on genomic Surveillance of AMR [16_136_111] and by the Centre for Genomic Pathogen Surveillance.Collections
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