Genomic analysis of Enterococcus faecium strain RAOG174 associated with acute chorioamnionitis carried antibiotic resistance gene: is it time for precise microbiological identification for appropriate antibiotic use?

Abstract

Background Preterm labor syndrome is associated with high perinatal morbidity and mortality, and intra-amniotic infection is a cause of preterm labor. The standard identification of causative microorganisms is based on the use of biochemical phenotypes, together with broth dilution-based antibiotic susceptibility from organisms grown in culture. However, such methods could not provide an accurate epidemiological aspect and a genetic basis of antimicrobial resistance leading to an inappropriate antibiotic administration. Hybrid genome assembly is a combination of short- and long-read sequencing, which provides better genomic resolution and completeness for genotypic identification and characterization. Herein, we performed a hybrid whole genome assembly sequencing of a pathogen associated with acute histologic chorioamnionitis in women presenting with PPROM. Results We identified Enterococcus faecium, namely E. faecium strain RAOG174, with several antibiotic resistance genes, including vancomycin and aminoglycoside. Virulence-associated genes and potential bacteriophage were also identified in this genome. Conclusion We report herein the first study demonstrating the use of hybrid genome assembly and genomic analysis to identify E. faecium ST17 as a pathogen associated with acute histologic chorioamnionitis. The analysis provided several antibiotic resistance-associated genes/mutations and mobile genetic elements. The occurrence of E. faecium ST17 raised the awareness of the colonization of clinically relevant E. faecium and the carrying of antibiotic resistance. This finding has brought the advantages of genomic approach in the identification of the bacterial species and antibiotic resistance gene for E. faecium for appropriate antibiotic use to improve maternal and neonatal care.

Genomic characterization of vancomycin-resistant Enterococcus faecium clonal complex 17 isolated from urine in tertiary hospitals in Northeastern Thailand

“…Similarly, the VREfm isolates in the current study were resistant to ampicillin and quinolone, indicating a human-origin lineage. VREfm belonging to ST17 and ST80 have been reported worldwide, including in Germany (Neumann et al, 2020), France (Sassi et al, 2019), Australia (Lee et al, 2020), Libya (Ahmed et al, 2020), and Thailand, having been isolated from placental tissue, urine, blood, and rectal swabs (Wongnak et al, 2021;Pongchaikul et al, 2023). In Asia, ST17 and ST80 have been reported in China (Sun et al, 2019), India (Bakthavatchalam et al, 2022), and Taiwan (Kuo et al, 2018), whereas an outbreak of VREfm ST761 has been reported in France (Kamus et al, 2022), while ST117 has been identified in Denmark (Pinholt et al, 2019), Greece (Papagiannitsis et al, 2017), and Germany (Xanthopoulou et al, 2020).…”