Molecular epidemiological data on Group A Streptococcus (GAS) infection in Africa is scarce. We characterized the emm-types and emm-clusters of 433 stored clinical GAS isolates from The Gambia collected between 2004 and 2018. To reduce the potential for strain mistyping, we used a newly published primer for emm-typing. There was considerable strain diversity, highlighting the need for vaccine development offering broad strain protection.

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a positive-sense single stranded RNA virus with high human transmissibility. This study generated Whole Genome data to determine the origin and pattern of transmission of SARS-CoV-2 from the first six cases tested in The Gambia. Total RNA from SARS-CoV-2 was extracted from inactivated nasopharyngeal-oropharyngeal swabs of six cases and converted to cDNA following the ARTIC COVID-19 sequencing protocol. Libraries were constructed with the NEBNext ultra II DNA library prep kit for Illumina and Oxford Nanopore Ligation sequencing kit and sequenced on Illumina MiSeq and Nanopore GridION, respectively. Sequencing reads were mapped to the Wuhan reference genome and compared to eleven other SARS-CoV-2 strains of Asian, European and American origins. A phylogenetic tree was constructed with the consensus genomes for local and non-African strains. Three of the Gambian strains had a European origin (UK and Spain), two strains were of Asian origin (Japan). In The Gambia, Nanopore and Illumina sequencers were successfully used to identify the sources of SARS-CoV-2 infection in COVID-19 cases.

Lancefield group C/G streptococci (GCS/GGS) are increasingly recognized as significant human pathogens that cause a disease spectrum similar to Streptococcus pyogenes . Despite their high clinical burden in the UK, their genomic diversity remains poorly understood. We performed whole-genome sequencing on a prospective collection of 109 consecutive GCS/GGS isolates from any infection types in Sheffield, UK, over 5 months in 2020. Streptococcus dysgalactiae subsp. equisimilis (SDSE) accounted for 104 isolates, while 5 were identified as Streptococcus canis . The SDSE population was highly diverse, comprising 15 genomic clusters and 38 unique emm -ST combinations. We identified the presence of the ST20/stG62647 international lineage (24% of isolates), a cluster globally associated with severe invasive disease. Antimicrobial resistance genes were prevalent (49%), predominantly linked to mobile genetic elements carrying tetracycline and macrolide resistance. Furthermore, a variation in the penicillin-binding protein PBP2X (P601L) was linked to reduced penicillin sensitivity (minimum inhibitory concentration 0.03 mg l ⁻¹ ). There were few or no genetic changes in isolates obtained from the same patient, even when they were collected 8–10 weeks apart, indicating long-term persistence within a host. The unexpected detection of S. canis in human infections and the high diversity of SDSE, persistence and virulence-associated regions underscore the need for enhanced national genomic surveillance to track emerging virulent and antibiotic-resistant SDSE lineages.

Lancefield group C/G streptococci (GCS/GGS) are increasingly recognised as significant human pathogens that cause a disease spectrum similar to Streptococcus pyogenes . Despite their high clinical burden in the UK, their genomic diversity remains poorly understood. We performed whole-genome sequencing (WGS) on a prospective collection of 109 consecutive GCS/GGS isolates from all infection types in Sheffield, UK, over five months in 2020. Streptococcus dysgalactiae subsp. equisimilis (SDSE) accounted for 104 isolates, while five were identified as Streptococcus canis . The SDSE population was highly diverse, comprising 15 genomic clusters and 38 unique emm -ST combinations. We identified the presence of the ST20/stG62647 international lineage (24% of isolates), a cluster globally associated with severe invasive disease. Antimicrobial resistance genes were prevalent (49%), predominantly linked to mobile genetic elements carrying tetracycline and macrolide resistance. Furthermore, a variation in the penicillin-binding protein PBP2X (P601L) was linked to reduced penicillin sensitivity (MIC 0.03 mg/L). There were few or no genetic changes in isolates obtained from the same patient, even when they were collected 8-10 weeks apart, indicating long-term persistence within a host. The unexpected detection of S. canis in human infections and the high diversity of SDSE, persistence and virulence-associated regions underscore the need for enhanced national genomic surveillance to track emerging virulent and antibiotic-resistant SDSE lineages. Impact statement: Lancefield group C and G streptococci, most often the species Streptococcus dysgalactiae subsp. equisimilis (SDSE), are an increasingly significant human pathogen, often mirroring the severity of infections caused by Lancefield group A Streptococcus ( S. pyogenes ). Despite its clinical importance, we know little about the population of SDSE circulating in the UK. This study provides the first comprehensive genomic analysis of SDSE isolates from a single UK region, identifying a highly diverse population comprising 15 distinct genomic clusters but with evidence of long-term persistence within a single host. Notably, we confirm the presence of the international stG 62647/ST20 lineage in the UK, which is globally associated with severe invasive disease. Our findings also reveal a high prevalence of antimicrobial resistance genes (∼49%), primarily linked to mobile genetic elements, and the presence of a specific variation in the penicillin-binding protein PBP2X that reduces penicillin sensitivity. Additionally, the unexpected detection of S. canis in human infections rather than animals highlights a need for monitoring. By defining the UK’s SDSE population structure and its resistance landscape, this research underscores the critical need for enhanced national genomic surveillance to track emerging high-virulence and antibiotic-resistant lineages Data summary: Sequence files for isolates from Sheffield used for this study have been uploaded to the sequence read archive with project accession number PRJNA1333937 and accession numbers provided in Supplementary Dataset 1. The completed genome for SDE096 been deposited on GenBank with the accession number JBSXMJ000000000.