Biology subjects

Felgate, H. M.

Publications and source records attributed to Felgate, H. M..

5 recordsLinked to original sources

bioRxiv2025

Staphylococcus haemolyticus Population Genomics Provides Insights into Pathogenicity and Commensalism

Staphylococcus haemolyticus is a common commensal bacterium but also an opportunistic pathogen, frequently implicated in bacteraemia and sepsis in preterm neonates and immunocompromised patients. Despite its clinical relevance, relatively little is known about the population structure of S. haemolyticus and how this relates to its ability to colonise humans or cause disease. In this study, we analysed commensal and clinical strains isolated from neonates and adults from 20 countries between 1957 - 2022. Whole genome sequencing of these isolates, combined with publicly available data, generated a comprehensive dataset of 986 genomes. This enabled us to characterise the species population structure and track the distribution of antimicrobial resistance (AMR) and virulence determinants. Our analysis revealed a highly diverse genome structure, with multiple phylogenetic groups showing distinct associations with commensalism or pathogenicity. We observed extensive variation in mobile genetic elements, prophages, and AMR genes, alongside increased carriage of plasmids and AMR genes over time. Furthermore, genes lined to metal homeostasis, detoxification, and oxidative stress tolerance were differently abundant between commensal and clinical isolates. This work provides the most detailed view to date of S. haemolyticus diversity, its evolutionary dynamics, and the genetic factors that may underpin the transition from commensal to pathogen.

genetics↗

bioRxiv2025

The metallophore staphylopine is essential for survival of Staphylococcus epidermidis in human synovial fluid

Due to extended life expectancies, prosthetic joint infections are an increasing burden on healthcare institutions worldwide. The most commonly isolated causative agents are staphylococci, though the mechanisms underpinning survival and proliferation in synovial fluid are still not fully understood. In this study, we aimed to identify genes important for survival in synovial fluid using a transposon mutant library and RNAseq. We produced a transposon mutant library, containing approximately 57,000 unique insertion mutants, in Staphylococcus epidermidis strain 846. This library was grown in Muller Hinton broth or processed human synovial fluid samples, and Transposon-directed Insertion Sequencing (TraDIS) was used to identify genes involved in survival in synovial fluid. This identified importance of the his, pur and cnt operons. These genes were also upregulated in both Staphylococcus epidermidis 846 and the model Staphylococcus epidermidis strain RP62A when exposed to human synovial fluid. All these key pathways contribute to production of the metallophore staphylopine. To confirm staphyopine production is essential for survival in synovial fluid, a defined transposon insertion in the gene encoding for staphylopine export (cntE) mutant was used. This demonstrated impaired survival in synovial fluid compared to the wild type. RT-qPCR also showed that cntE was more highly expressed after exposure to infected synovial fluid (where metals will be depleted) than non-infected fluid. In conclusion, TraDIS and RNASeq both identified the importance of staphylopine for survival in human synovial fluid. This suggests an opportunity for exploitation for therapeutic or diagnostic use. Author SummaryStaphylococcus epidermidis is a common cause of prosthetic joint infection, however accurate diagnosis remains difficult. In this work we explored the genetic basis of Staphylococcus epidermidis survival in human synovial fluid using a large transposon mutant library, and identified which genes were differentially expressed upon exposure to the fluid. We found crossover between the datasets, which pointed to the importance of the metal acquisition compound staphylopine. The expression levels of the gene required for staphylopine export were shown to be dependent on the infection status of the individual samples were obtained from. We also found the gene cluster to be conserved in a range of staphylococcal species isolated from cases of prosthetic joint infection. Our work provides a valuable resource in the from of a large transposon mutant library, and provides a greater understanding of the requirements for staphylococcal survival in human synovial fluid, providing potential biomarkers for future diagnostic development.

microbiology↗

bioRxiv2025

Staphylococcus haemolyticus is a reservoir of antibiotic resistance genes in the preterm infant gut

Among coagulase-negative staphylococci, Staphylococcus haemolyticus is a primary cause of bloodstream infections in preterm infants, with gut colonisation being recognised as a risk factor for subsequent infection. Through a re-analysis of a 16S rRNA gene sequencing dataset (n=497 preterm infants), we found that S. haemolyticus was abundant and prevalent in the gut in the first month of life. To better understand the diversity of S. haemolyticus among preterm infants, we generated genome sequences of S. haemolyticus strains (n=140), which were isolated from 44 stool samples of 22 preterm infants from four different hospitals in the United Kingdom. Core genome phylogenetic analyses, incorporating 126 publicly available S. haemolyticus genome sequences, showed that 85/140 (60.1%) of the isolates, from three different hospitals, formed a clonal group with 79/85 (92.9%) strains being assigned to Multi-Locus Sequence Type (ST) 49. Antibiotic resistance genes were highly prevalent in the genome sequences. Using logistic regression, we found a strong association between the presence of the gene mecA and phenotypic resistance to oxacillin (odds ratio [OR]: 158.00, p<0.0001), and the aacA-aphD gene and phenotypic resistance to gentamicin aacA-aphD (OR: 162.00, p<0.001). None of the strains from the preterm infant cohort had a complete Staphylococcal Cassette Chromosome mec (SCCmec) element. The aacA-aphD gene was associated with the transposon Tn4001. Using hybrid genome assemblies, we found it to be present on the chromosome (54.5% of strains) or on diverse plasmids (27.3%). Four strains (18.2%) had Tn4001 copies on both plasmid and chromosome. Our data suggest the existence of a distinct sub-population of S. haemolyticus that has adapted to colonise the gut of preterm infants. Prevalent resistance to antibiotics is of clinical concern and the diversity of genetic contexts of mecA and Tn4001 suggests widespread horizontal gene transfer and recombination in this species.

microbiology↗

bioRxiv2024

Sticking together: Independent evolution of biofilm formation in different species of staphylococci has occurred multiple times via different pathways

Various species of staphylococci cause a wide range of infections, including implant-associated infections which are often difficult to treat due to the presence of biofilms. Whilst some proteins involved in biofilm formation are known, the differences in biofilm production between staphylococcal species remains understudied. Currently biofilm formation by Staphylococcus aureus is better understood than for other members of the genus as more research effort has focused on this species. We assembled a panel of 385 non-aureus Staphylococcus isolates of 19 species from prosthetic joint infection as well as other clinical sources and reference strains. We assessed the biofilm forming ability of all strains using a high-throughput crystal violet assay. This identified distinct biofilm formation categories and we then compared the prevalence of Pfam domains and identified those which distinguished the categories as well as using machine learning to identify amino acid 20-mers linked to biofilm formation. This identified some domains within proteins already positively linked to biofilm formation but we also identified important domains not previously linked to biofilm formation. RT-qPCR confirmed the expression of selected genes predicted to encode important domains within biofilms in Staphylococcus epidermidis. The prevalence and distribution of biofilm associated domains showed a link to phylogeny, suggesting different Staphylococcus species have independently evolved different mechanisms of biofilm production. This work has identified different routes to biofilm formation in diverse species of Staphylococcus as well as suggesting independent evolution of biofilm has occurred multiple times across the genus. Understanding the mechanisms of biofilm formation in any given species is likely to require detailed study of relevant strains and the ability to generalise across the genus may be limited.

microbiology↗

bioRxiv2022

Characterisation of neonatal Staphylococcus capitis NRCS-A isolates compared with non NRCS-A Staphylococcus capitis from neonates and adults.

Staphylococcus capitis is a frequent cause of Late-Onset Sepsis (LOS) in neonates admitted to Neonatal Intensive Care Units (NICU). The NRCS-A clone of S. capitis has been isolated from NICUs globally although the reasons for the global success of this clone are not understood. We analysed a collection of S. capitis colonising babies admitted to two NICUs, one in the UK and one in Germany as well as corresponding pathological clinical isolates. Genome analysis identified 3 groups; non-NRCS-A isolates, NRCS-A isolates, and a group of proto NRCS-A - isolates closely related to NRCS-A but not associated with neonatal infection. All bloodstream isolates belonged to the NRCS-A group and were indistinguishable from strains carried on the skin or in the gut. NRCS-A isolates showed increased tolerance to chlorhexidine and antibiotics relative to the other S. capitis as well as enhanced ability to grow at higher pH values. Analysis of 138 pangenomes of the clades identified characteristic nsr and tarJ genes in the NRCS-A and proto groups with a CRISPR-cas system only seen in NRCS-A isolates which also showed enrichment of genes for metal acquisition and transport. We found evidence for transmission of S. capitis NRCS-A within NICU, with related isolates shared between babies and multiple acquisitions by some babies. Our data show NRCS-A strains commonly colonise uninfected babies in NICU representing a potential reservoir for potential infection. This work provides more evidence that adaptation to survive in the gut and on skin facilitates spread of NRCS-A, and that metal acquisition and tolerance may be important to the biology of NRCS-A. Understanding how NRCS-A survives in NICUs can help develop infection control procedures against this clone.

genomics↗