Population structure of human Group B Streptococcus in Brazil: vaccine targets, sequence types, and antimicrobial resistance markers

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Abstract Background Group B Streptococcus (GBS) is a major cause of neonatal and maternal disease and can also cause infections in non-pregnant adults. Currently available prophylactic approaches do not prevent all forms of GBS disease, while increasing antimicrobial resistance poses additional challenges to treatment and prevention. Maternal vaccines targeting six capsular types (GBS6) or the Alpha-like protein family (GBS-AlpN) are in advanced development, but their potential coverage depends on the distribution of these antigens across GBS populations. Still, genomic data from Latin America, including Brazil, remain limited. Methods We characterized the population structure, antimicrobial resistance determinants, and vaccine-associated targets of 394 GBS isolates from maternal (mGBS, n = 349), neonatal (nGBS, n = 6), and non-pregnant adults (aGBS, n = 39) in Brazil (1978–2024). Whole-genome sequencing was performed using Illumina platforms, and genomes were analyzed with the GBS typing pipeline v1.0.10 for serotype, sequence type, antimicrobial resistance (AMR)-associated genes, and surface protein genes, with additional clonal complex and core-genome phylogenetic analyses. Results Serotype Ia was predominant overall (44.4%) and among mGBS and aGBS isolates, whereas serotype III predominated among nGBS isolates, although only six neonatal isolates were available. Eleven clonal complexes (CCs) were identified, with CC23 (40.6%), CC19 (17.3%), CC24 (11.9%), CC1 (8.9%), and CC17 (6.3%) accounting for most isolates. Alpha-like protein genes (with rib being the most frequent, 50.3%), pilus islands, and serine-rich repeat protein genes were widely distributed. Phylogenetic analysis revealed major clustering of CC23/CC24 and CC10/CC130/CC569, while CC17 and CC103 formed more distinct clades. CC-specific analyses further identified sub-lineage structure associated with ST, serotype, Alp genes, pilus islands, and AMR determinants. Genome-based predicted coverage was high for both GBS6 and GBS-AlpN across host groups, ranging from 94.9% to 100%. Tetracycline-associated genes were the most frequently detected AMR determinants, particularly tetM (77.4%), whereas MLS B - and aminoglycoside-associated genes were less frequent. One mGBS isolate carrying amino acid substitutions in PBP2X, PBP1A, and PBP2B was phenotypically non-susceptible to penicillin (MIC of 0.75 µg/mL). Eight isolates carried substitutions in gyrA and/or parC genes; among the six isolates available for phenotypic testing, four were phenotypically resistant to levofloxacin, whereas two isolates carrying S79F in parC alone were susceptible. Conclusion This study provides a genome-based characterization of human GBS isolates in Brazil across a 47-year period, revealing the diversity in population structure, vaccine-associated targets, and AMR determinants. The high genome-based predicted coverage of GBS6 and GBS-AlpN supports continued evaluation of these vaccine strategies in the Brazilian setting, while the detection of AMR-associated determinants highlights the importance of genomic surveillance combined with phenotypic antimicrobial susceptibility testing.

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