Genomic surveillance of Salmonella spp. in the Philippines during 2013-2014
| Autor: | Marietta L Lagrada, Silvia Argimón, Janice B Borlasa, Jaywardeen P Abad, June M Gayeta, Melissa L Masim, Agnettah M Olorosa, Victoria Cohen, Benjamin Jeffrey, Khalil Abudahab, Sonia B Sia, Charmian M Hufano, John Stelling, Matthew T G Holden, David M Aanensen, Celia C Carlos |
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| Přispěvatelé: | University of St Andrews. School of Medicine, University of St Andrews. Biomedical Sciences Research Complex, University of St Andrews. St Andrews Bioinformatics Unit, University of St Andrews. Infection and Global Health Division |
| Jazyk: | angličtina |
| Rok vydání: | 2022 |
| Předmět: |
Antimicrobial drug resistance
MCC Philippines Public Health Environmental and Occupational Health General Medicine Microbial Sensitivity Tests Genomics QR Microbiology 3rd-DAS Salmonella typhi AC Anti-Bacterial Agents QR Infectious Diseases Epidemiology/surveillance SDG 3 - Good Health and Well-being Salmonella Whole genome sequencing Drug Resistance Bacterial Humans Parasitology Typhoid Fever Typhoid fever Fluoroquinolones |
| Popis: | Increasing antimicrobial resistance (AMR) in Salmonella has been observed in the Philippines. This study aims to utilize whole genome sequencing (WGS) to characterize the population and AMR mechanisms of Salmonella captured by the Philippine Antimicrobial Resistance Surveillance Program (ARSP) and contrast to traditional laboratory methods.We sequenced the whole genomes of 148 Salmonella Typhi (S. Typhi) and 65 non-typhoidal Salmonella (NTS) collected in the Philippines in 2013–2014. From the genome sequences, we determined the serotype, multilocus sequence type, presence of determinants of antimicrobial resistance and relatedness between isolates. We also compared the genotypic predictions of serotype and AMR to the phenotypic data.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. In contrast, three quarters of NTS isolates were insusceptible to at least one antimicrobial, with more than half carrying mutations and/or genes linked to resistance to fluoroquinolones. ESBL genes were detected in five genomes that also carried other AMR determinants. The population of S. Typhi was dominated by the likely endemic genotype 3.0, which also caused of a putative local outbreak susceptible to antibiotics. The main NTS clades were global epidemic S. Enteritidis ST11 and the monophasic variant of S. Typhimurium (I 4,[5],12:i:-) ST34, which had frequently been serotyped as S. Typhimurium in the laboratory.This was the first time that Salmonella isolated from the Philippines were characterized by WGS and we provide evidence of its utility for ongoing surveillance at the ARSP. |
| Databáze: | OpenAIRE |
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