Genomic analysis of virulence, antimicrobial resistance, and capsular polysaccharide locus of group B Streptococcus isolated from Indonesia

Abstract

Background

Group B Streptococcus (GBS) is one of most common pathogen infecting neonates. This study aims to analyze the genomic characteristics of GBS, including antibiotic resistance genes, virulence genes, and the capsular polysaccharide (CPS) locus, in isolates from Indonesia.

Methods

Genomic DNA was extracted from 18 archived GBS isolated from colonized pregnant women in Jakarta, Indonesia in 2015–2020, and library preparation was performed using the TruSeq DNA Nano® kit. Genome sequencing was conducted using Illumina platform. Raw sequencing data were analyzed through de novo assembly using the ASA³P pipeline and annotation was performed on the Microscope server. Circular genome visualization was generated with the Blast Ring Image Generator (BRIG). Serotyping was conducted using the GBS typer pipeline.

Result

Among the eighteen isolates, we identified seven serotype II isolates, three serotype Ia isolates, three serotype IV isolates, two serotype VI isolates, one serotype Ib isolate, one serotype III isolate, and one non-typeable (NT) isolate. The NT isolate, M167, clustered with serotype II but lacked specific genes such as cpsG, cpsH, and cpsI. Sequence type (ST) identified ST1 as the most prevalent ST (n = 10), followed by ST196 (n = 3), ST23 (n = 2), ST24 (n = 1), and ST17 (n = 1). ST1 (serotype II) were grouped into CC1, ST23 to CC23, ST24 to CC452, ST196 (serotype IV) to CC459, and ST17 (serotype III) to CC17. A total of 15 isolates carried the tetM gene, while three isolates carried the ermB gene. Most virulence genes were shared among all isolates. However, the fbsB virulence gene was only present in serotype Ia and serotype III, which are known to exhibit higher levels of virulence.

Conclusion

Serotype II was the most frequently identified and resistance to tetracycline and macrolides was the most detected among GBS isolates. Genomic data from Indonesian GBS isolates provide insights into virulence and antibiotic resistance genes.