Genomic surveillance of methicillin-resistant Staphylococcus aureus in the Philippines, 2013-2014.

Melissa Masim,Sonia Sia,David Aanensen,Khalil Abudahab,Benjamin Jeffrey,Silvia Argimon,John Stelling,Holly Espiritu,Marietta Lagrada,Victoria Cohen,Celia Carlos,June Gayeta,Matthew Holden,Charmian Hufano,Mariane Magbanua,Agnettah Olorosa

doi:10.5365/wpsar.2020.11.1.004

Abstract

Methicillin-resistant Staphylococcus aureus (MRSA) remains one of the leading causes of both nosocomial and community infections worldwide. In the Philippines, MRSA rates have remained above 50% since 2010, but resistance to other antibiotics, including vancomycin, is low. The MRSA burden can be partially attributed to pathogen-specific characteristics of the circulating clones, but little was known about the S. aureus clones circulating in the Philippines.We sequenced the whole genomes of 116 S. aureus isolates collected in 2013–2014 within the Antimicrobial Resistance Surveillance Program. The multilocus sequence type, spa type, SCCmec type, presence of antimicrobial resistance (AMR) determinants and virulence genes and relatedness between the isolates were all derived from the sequence data. The concordance between phenotypic and genotypic resistance was also determined.The MRSA population in the Philippines comprised a limited number of genetic clones, including several international epidemic clones, such as CC30-spa-t019-SCCmec-IV-PVL+, CC5-SCCmec-typeIV and ST239-spa-t030-SCCmec-typeIII. The CC30 genomes were related to the South-West Pacific clone but formed a distinct, diverse lineage, with evidence of global dissemination. We showed independent acquisition of resistance to sulfamethoxazole/trimethoprim in various locations and genetic clones but mostly in paediatric patients with invasive infections. The concordance between phenotypic and genotypic resistance was 99.68% overall for eight antibiotics in seven classes.We have made the first comprehensive genomic survey of S. aureus in the Philippines, which bridges the gap in genomic data from the Western Pacific Region and will constitute the genetic background for contextualizing prospective surveillance.

Highlights

The Methicillin-resistant Staphylococcus aureus (MRSA) population in the Philippines comprised a limited number of genetic clones, including several international epidemic clones, such as CC30-spa-t019-staphylococcal cassette chromosome mec (SCCmec)-IV-Panton-Valentine leukocidin (PVL)+, CC5-SCCmec-typeIV and ST239-spa-t030-SCCmectypeIII
Of the 118 MRSA isolates submitted for WGS, 116 were confirmed as S. aureus in silico, while two isolates were identified as Staphylococcus argenteus and were not included in the downstream analyses
The largest clade represented by CC30-spa-t019-SCCmec-IV was characterized by broad geographical distribution across the 17 sentinel sites in this data set (Table 4), as it was found in both community- and health-care-associated isolates obtained from at least 11 different specimen types

Summary

Introduction

The MRSA population in the Philippines comprised a limited number of genetic clones, including several international epidemic clones, such as CC30-spa-t019-SCCmec-IV-PVL+, CC5-SCCmec-typeIV and ST239-spa-t030-SCCmectypeIII. Data on a total of 6211 S. aureus isolates were collected by the Antimicrobial Resistance Surveillance Program (ARSP) of the Philippines Department of Health during the period January 2013 to December 2014.

Results

Conclusion