Multilocus sequence type analysis of coagulase-negative staphylococci from the neonatal intensive care unit of a teaching hospital in Ghana.

Abstract

Introduction: coagulase-negative staphylococci (CoNS) have emerged as significant pathogens in neonatal intensive care units (NICUs), especially as a leading cause of neonatal sepsis. In low-income countries, efforts to prevent sepsis-related mortality are hampered by a lack of comprehensive molecular data on bacterial isolates responsible for these infections. This study aims to address this gap by generating whole-genome sequencing data, identifying novel multilocus sequence (MLS) types, and investigating antibiotic resistance genes in Staphylococcus epidermidis and Staphylococcus haemolyticus from the NICU of Ho Teaching Hospital in Ghana.

Methods: a total of 123 CoNS isolates were tested for minimum inhibitory concentrations (MIC) of 13 antibiotics using VITEK2, and 16 isolates (7 S. epidermidis and 9 S. haemolyticus) were selected for further genomic analysis. Genomic DNA was extracted and sequenced using an Illumina NovaSeq 6000 platform. Draft genome sequences were assembled using MEGAHIT and annotated with Prokka. MLS types were identified using the Center for Genomic Epidemiology´s MLST tool, and antibiotic resistance genes were detected via the Comprehensive Antibiotic Resistance Database (CARD) and BlastArg-annot Nt tools.

Results: draft genome sequences were established for 7 S. epidermidis and 9 S. haemolyticus isolates and deposited in public databases. Five novel MLST types were discovered: ST89, ST90, and ST91 for S. haemolyticus, and ST993 and ST994 for S. epidermidis. These novel strains exhibited multidrug resistance, with multiple antimicrobial resistance genes identified in their genomes. Three of the newly identified MLST types were isolated from the blood of neonates, while two others were found on the nasal mucosa of clinical staff and a baby cot.

Conclusion: our findings highlight the presence of multidrug-resistant and novel CoNS MLST types in the NICU, suggesting an urgent need for a nationwide database on CoNS MLST types circulating in Ghana. Such data would be critical for developing informed public health policies and strategies to manage neonatal sepsis in the Region.