Streptococcus agalactiae Strains with Chromosomal Deletions Evade Detection with Molecular Methods

Abstract

Surveillance of circulating microbial populations is critical for monitoring the performance of a molecular diagnostic test. In this study, we characterized 31 isolates of Streptococcus agalactiae (group B Streptococcus [GBS]) from several geographic locations in the United States and Ireland that contain deletions in or adjacent to the region of the chromosome that encodes the hemolysin gene cfb, the region targeted by the Xpert GBS and GBS LB assays. PCR-negative, culturepositive isolates were recognized during verification studies of the Xpert GBS assay in 12 laboratories between 2012 and 2018. Whole-genome sequencing of 15 GBS isolates from 11 laboratories revealed four unique deletions of chromosomal DNA ranging from 181 bp to 49 kb. Prospective surveillance studies demonstrated that the prevalence of GBS isolates containing deletions in the convenience sample was Ͻ1% in three geographic locations but 7% in a fourth location. Among the 15 isolates with chromosomal deletions, multiple pulsed-field gel electrophoresis types were identified, one of which appears to be broadly dispersed across the United States.

Comparative study of Revogene GBS LB assay and GeneXpert GBS LB assay for the detection of group B Streptococcus in prenatal screening samples

“…A major advantage of the Revogene was higher sensitivity, though based on repeat testing, there were more false positive results. It is noteworthy to highlight the single discrepant sample that resulted in GBS-negative GeneXpert results compared to GBS-positive Revogene and culture results (Table 1) [14].…”

“…The cfb gene was believed to be present in almost all GBS isolates, yet recent findings have described cases of cfb-negative isolates that were missed by the GeneXpert system [15,16]. The isolate that was recovered by culture from the discordant specimen was sent to Cepheid for further analysis, which revealed a rare deletion across the primer/probe region adjacent to the cfb gene [14].…”

Comparative study of Revogene GBS LB Assay and GeneXpert GBS LB Assay for the detection of Group B Streptococcus in prenatal screening samples.

“…A major advantage of the Revogene was higher sensitivity, though based on repeat testing, there were more false positive results. It is noteworthy to highlight the single discrepant sample that resulted in GBSnegative GeneXpert results compared to GBS-positive Revogene and culture results (Table 1) (16).…”

“…The cfb gene was believed to be present in almost all GBS isolates, yet recent findings have described cases of cfb-negative isolates that were missed by the GeneXpert system (14,15). The isolate that was recovered by culture from the discordant specimen was sent to Cepheid for further analysis, which revealed a rare deletion across the primer/probe region adjacent to the cfb gene (16).…”

Visual multiple cross displacement amplification for the rapid identification of S. agalactiae immediately from vaginal and rectal swabs

“…Currently, the gold standard used for the detection and identification of S. agalactiae was the enrichment culture, followed by biochemical analyses (Verani et al 2010 ; Tickler et al 2019 ). As the enrichment culture usually takes 48–72 h for obtaining the final result, which is a too long time for those women at delivery (Venkatesh et al 2010 ; Connell et al 2007 ; Kim et al 2015 ).…”