Genomic Surveillance of Salmonella spp. in the Philippines, 2013-2014

Abstract

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 SalmonellaTyphi (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.

Genomic analysis of Salmonella enterica from Metropolitan Manila abattoirs and markets reveals insights into circulating virulence and antimicrobial resistance genotypes

“…Salmonella studies with confirmed serovar identification are limited to clinical samples from the Philippine Department of Health − Antimicrobial Resistance Surveillance Program (DOH-ARSP) of the RITM. In a surveillance study covering blood and stool samples obtained from 17 sentinel sites all over the country from 2013 to 2014, in silico genotyping using WGS revealed that the most dominant serovars were S. Typhi as well as S. Enteritidis and ST34 (I 4, [5],12: i: -) for the non-typhoidal types (Lagrada et al, 2022).…”