Genomic and phenotypic characterisation of invasive neonatal and colonising group B Streptococcus isolates from Slovenia, 2001-2018

Abstract

Background: Group B Streptococcus (GBS) is the leading cause of invasive neonatal disease in the industrialized world. We aimed to genomically and phenotypically characterise invasive GBS isolates in Slovenia from 2001 to 2018 and contemporary colonising GBS isolates from screening cultures in 2018.

Methods: GBS isolates from 101 patients (invasive isolates) and 70 pregnant women (colonising isolates) were analysed. Basic clinical characteristics of the patients were collected from medical records. Antimicrobial susceptibility and phenotypic capsular serotype were determined. Whole-genome sequencing was performed to assign multilocus sequence types (STs), clonal complexes (CCs), pathogenicity/virulence factors, including capsular genotypes, and genome-based phylogeny.

Results: Among invasive neonatal disease patients, 42.6% (n = 43) were females, 41.5% (n = 39/94) were from preterm deliveries (< 37 weeks gestation), and 41.6% (n = 42) had early-onset disease (EOD). All isolates were susceptible to benzylpenicillin with low minimum inhibitory concentrations (MICs; ≤0.125 mg/L). Overall, 7 serotypes were identified (Ia, Ib, II-V and VIII); serotype III being the most prevalent (59.6%). Twenty-eight MLST STs were detected that clustered into 6 CCs. CC-17 was the most common CC overall (53.2%), as well as among invasive (67.3%) and non-invasive (32.9%) isolates (p < 0.001). CC-17 was more common among patients with late-onset disease (LOD) (81.4%) compared to EOD (47.6%) (p < 0.001). The prevalence of other CCs was 12.9% (CC-23), 11.1% (CC-12), 10.5% (CC-1), 8.2% (CC-19), and 1.8% (CC-498). Of all isolates, 2.3% were singletons.

Conclusions: A high prevalence of hypervirulent CC-17 isolates, with low genomic diversity and characteristic profile of pathogenicity/virulence factors, was detected among invasive neonatal and colonising GBS isolates from pregnant women in Slovenia. This is the first genomic characterisation of GBS isolates in Slovenia and provides valuable microbiological and genomic baseline data regarding the invasive and colonising GBS population nationally. Continuous genomic surveillance of GBS infections is crucial to analyse the impact of IND prevention strategies on the population structure of GBS locally, nationally, and internationally.

Keywords: Capsular type; GBS; Group B Streptococcus; Hypervirulent CC-17; Molecular epidemiology; Neonatal infection; Pathogenicity/virulence factors; Slovenia.

Fig. 1

Single nucleotide polymorphism (SNP)-based maximum-likelihood phylogenomic tree with bootstrap values for the major branches including metadata: consisting of isolate group (invasive/colonising), disease type (early-onset/late-onset), serotype, MLST sequence type, MLST clonal complex, and surface/pathogenicity/virulence factors genotype (pili, alpha-like protein family, hvgA, srr, scpB, lmb, fbsA, fbsB and bibA). Colour of the bar depicts the genotype or lack of any named genotype or MLST sequence type or clonal complex (white bars). Pili, ALP, srr and hvgA genotypes were named in accordance with Metcalf et al. [22]. Alleles of scpB, lmb, fbsA and fbsB were arbitrarily assigned consecutive numbers

Fig. 2

Single nucleotide polymorphism (SNP)-based maximum-likelihood phylogenomic tree after regions of recombination have been excluded using Gubbins [26]. Group (invasive/non-invasive) and MLST clonal complex are described for each isolate and white bars depict isolates that do not belong to any of the five named major MLST clonal complexes. Genomic regions with high frequency of recombination are mapped to the reference genome of Streptococcus agalactiae NEM316 (annotated in blue on top). Each row represents an isolate and the columns relate to bases in the reference genome. The red columns are recombinations shared by multiple isolates and occuring in the internal branches. The blue columns are recombinations in the terminal branch and represented by unique isolates