Initial characterisation of Helcococcus ekapensis isolated from the nasopharynx of infants in Western Cape, South Africa

Background The nasopharynx serves as a major reservoir for both commensal and pathogenic bacteria, with growing evidence linking its microbial composition to respiratory health and disease susceptibility. Here, we present the isolation and initial characterisation of a potentially novel Helcococcus taxon, provisionally named Helcococcus ekapensis . Isolates were cultured from archived nasopharyngeal samples collected as part of the Drakenstein Child Health study based in South Africa. Although Helcococcus species have previously been identified in the human respiratory tract, the genus remains poorly characterised within the human nasopharynx. Results We describe the isolation and culturing of three H. ekapensis isolates , SA-HE-C1 , SA-HE-207 , and SA-HE-338 , and report its colony and cellular morphology. Our prevalence screening demonstrates that H. ekapensis colonisation of the infant nasopharynx increases with age over the first two years of life. Further, we report three draft genomes of these isolates, sharing close to 99% average nucleotide identity. Genomic analyses revealed limited metabolic capacity, including incomplete amino acid biosynthesis pathways. In addition, several putative genes were identified, including ABC-type transporters and bacteriocin-like genes. Conclusion Altogether, this work provides an initial phenotypic and genomic characterisation of a potentially novel Helcococcus taxon isolated from the human nasopharynx and highlights its potential relevance within the developing infant nasopharyngeal microbiome. These findings provide a foundation for future studies to investigate its role within the nasopharynx and warrants formal taxonomic description.