Molecular Epidemiology of Invasive Group B Streptococcus in South Africa, 2019-2020

Abstract

Background: Group B Streptococcus (GBS) is a leading cause of neonatal meningitis and sepsis and an important cause of disease in adults. Capsular polysaccharide and protein-based GBS vaccines are currently under development.

Methods: Through national laboratory-based surveillance, invasive GBS isolates were collected from patients of all ages between 2019 and 2020. Phenotypic serotyping and antimicrobial susceptibility testing were conducted, followed by whole-genome sequencing for analysis of population structure and surface protein and resistance genes.

Results: In total, 1748 invasive GBS cases were reported. Of these, 661 isolates underwent characterization, with 658 yielding both phenotypic and genotypic results. Isolates (n = 658) belonged to 5 clonal complexes (CC1, CC8/10, CC17, CC19, and CC23) and 6 serotypes were detected: III (42.8%), Ia (27.9%), V (11.9%), II (8.4%), Ib (6.7%), and IV (2.3%). Phenotypically, only 1 isolate exhibited reduced penicillin susceptibility (minimum inhibitory concentration 0.25 µg/mL). Phenotypic resistance to erythromycin, clindamycin, and tetracycline was observed in 16.1%, 3.8%, and 91.5% of isolates, respectively. ermTR (34.9%) and mefA/E (30.1%) genes were most common among erythromycin-resistant isolates, while ermB predominated in clindamycin-resistant isolates (32.0%). tetM accounted for 95.8% of tetracycline resistance. All isolates carried at least 1 of the 3 pilus gene clusters, 1 of the 4 homologous alpha/Rib family determinants, and 98% harbored 1 of the serine-rich repeat protein genes. hvgA was found exclusively in CC17 isolates.

Conclusions: In our setting, β-lactam antibiotics remain appropriate for GBS treatment and polysaccharide and protein-based vaccines under development are expected to provide good coverage.

Keywords: Streptococcus agalactiae; antibiotic resistance; molecular characterization; population structure; vaccine targets.

Graphical Abstract

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Figure 1.

Distribution of invasive group B Streptococcus serotypes by age group in South Africa, 2019–2020 (n = 656). Abbreviations: EOD, early-onset disease; LOD, late-onset disease.

Figure 2.

A core SNP-based maximum likelihood phylogeny of 435 invasive GBS isolates collected from South African patients of all age groups from 2019 to 2020. Branch highlights in the tree represent CCs and the inner thin strip correspond to STs. The subsequent strips (from inner to outer strip) indicate age, province, serotype (Ia–V), PI determinants, alpha protein family determinants, SRR protein determinants, and the hypervirulent GBS adhesion (hvgA) protein. Noncolored branches represent singletons STs that to do not fall within a specific CC. The tree only included isolates that produced high-quality sequences with ≤ 150 contigs and N50 ≥ 30 000. Asterisks represent STs that could not be confidently assigned due to insufficient quality during base calling on 1 of the 7 housekeeping genes; however, the overall genome quality was good. Abbreviations: CC, clonal complex; EC, Eastern Cape; EOD, early-onset disease; FS, Free State; GA, Gauteng; GBS, group B Streptococcus; KZ, KwaZulu-Natal; LOD, late-onset disease; LP, Limpopo; MP, Mpumalanga; NC, Northern Cape; neg, negative; NW, North West; PI, pilus island; pos, positive; SNP, single-nucleotide polymorphism; SRR, serine-rich repeat; ST, sequence type; WC, Western Cape.