Genomic Analysis Reveals New Integrative Conjugal Elements and Transposons in GBS Conferring Antimicrobial Resistance

Abstract

Streptococcus agalactiae or group B streptococcus (GBS) is a leading cause of neonatal sepsis and increasingly found as an invasive pathogen in older patient populations. Beta-lactam antibiotics remain the most effective therapeutic with resistance rarely reported, while the majority of GBS isolates carry the tetracycline resistance gene tet(M) in fixed genomic positions amongst five predominant clonal clades. In the UK, GBS resistance to clindamycin and erythromycin has increased from 3% in 1991 to 11.9% (clindamycin) and 20.2% (erythromycin), as reported in this study. Here, a systematic investigation of antimicrobial resistance genomic content sought to fully characterise the associated mobile genetic elements within phenotypically resistant GBS isolates from 193 invasive and non-invasive infections of UK adult patients collected during 2014 and 2015. Resistance to erythromycin and clindamycin was mediated by erm(A) (16/193, 8.2%), erm(B) (16/193, 8.2%), mef(A)/msr(D) (10/193, 5.1%), lsa(C) (3/193, 1.5%), lnu(C) (1/193, 0.5%), and erm(T) (1/193, 0.5%) genes. The integrative conjugative elements (ICEs) carrying these genes were occasionally found in combination with high gentamicin resistance mediating genes aac(6′)-aph(2″), aminoglycoside resistance genes (ant(6-Ia), aph(3′-III), and/or aad(E)), alternative tetracycline resistance genes (tet(O) and tet(S)), and/or chloramphenicol resistance gene cat(Q), mediating resistance to multiple classes of antibiotics. This study provides evidence of the retention of previously reported ICESag37 (n = 4), ICESag236 (n = 2), and ICESpy009 (n = 3), as well as the definition of sixteen novel ICEs and three novel transposons within the GBS lineage, with no evidence of horizontal transfer.

Genomic insights into the diversity, virulence, and antimicrobial resistance of group B Streptococcus clinical isolates from Saudi Arabia

“…The few isolates showing the L phenotype coherently harbored the lsa(C) gene and belonged exclusively to CC19 expressing serotype III-1. On the other hand, the high rate of resistance to tetracycline was largely mediated by tet(M) and to a lesser extent by tet(O) , which was largely in agreement with previously published studies ( Bergal et al., 2015 ; Jin et al., 2022 ; Rodgus et al., 2022 ; Khan et al., 2023 ). Sequence analysis linked gentamicin resistance with the presence of the gene encoding the bifunctional aminoglycoside-modifying enzyme AAC(6’)-APH(2’), and also identified other genes associated with resistance to kanamycin and streptomycin (i.e., ant(6)-Ia , aph(3’)-III , and aadE ) in a small proportion of isolates (16.85%, n = 15/89), mainly belonging to CC17 and CC12.…”

“…Of particular concern was the high proportion of isolates with reduced susceptibility to macrolides and lincosamides, which are the antibiotics of choice for the treatment of GBS infections in patients with penicillin allergies. Here also, the molecular mechanisms of resistance to these antibiotics were consistent with those previously described for this species ( Bergal et al., 2015 ; Jin et al., 2022 ; Rodgus et al., 2022 ; Khan et al., 2023 ). Phylogenetic analysis showed that resistance to macrolides and lincosamides was not necessarily linked to the expansion of certain CCs but was distributed across all detected CCs.…”

“…Sequence analysis linked gentamicin resistance with the presence of the gene encoding the bifunctional aminoglycoside-modifying enzyme AAC(6’)-APH(2’), and also identified other genes associated with resistance to kanamycin and streptomycin (i.e., ant(6)-Ia , aph(3’)-III , and aadE ) in a small proportion of isolates (16.85%, n = 15/89), mainly belonging to CC17 and CC12. The coexistence of erm(B) , tet(O) with aminoglycoside resistance genes ant(6)-Ia , aph(3’)-III , and aadE in sequenced isolates was linked to the acquisition of the integrative conjugative element ICESag37, which was recently described in the species ( Khan et al., 2023 ). Interestingly, multidrug resistance in a handful of isolates exhibiting resistance to macrolides, tetracycline, ciprofloxacin, and gentamicin was predominantly linked to ST19.…”

“…This might explain the high rate of resistance to these antibiotics in the species that is likely to impact their use for the prevention and treatment of GBS infections. Isolates showing the cMLS B phenotype were distributed across all major CCs and carried the methyltransferase-encoding gene erm(B) , while the isolates exhibiting the iMLS B phenotype belonged to CC1 and CC19 and carried the erm(A) gene ( Lopes et al., 2018 ; Martins et al., 2022 ; Rodgus et al., 2022 ; Khan et al., 2023 ). The few isolates showing the L phenotype coherently harbored the lsa(C) gene and belonged exclusively to CC19 expressing serotype III-1.…”

Microbiological monitoring of antibiotic resistance of strains of Streptococcus agalactiae among pregnant women

“…The high level of resistance to gentamicin is due to the production of bifunctional APH (2')-ACC(6) enzymes, which determine the reduction of synergism between all aminoglycosides (except streptomycin and arbekacin) and beta-lactams and glycopeptides, regardless of MIC levels (Guo et al, 2018;Dobrut et al, 2022). GBS resistance to tetracycline is most often caused by two mediated genes, tet(M) and tet(O), which are transmitted mainly by transposons (Ali et al, 2020;Khan et al, 2023). The resistance of GBS to fluoroquinolones is due to the presence of mutations in the gyrA and parC genes, therefore, in the bacteriological laboratory, the phenotypic definition of resistance to this group of antibacterial drugs is determined by sensitivity to norfloxacin as a screening test.…”