Biology subjects

Darby, E. M.

Publications and source records attributed to Darby, E. M..

4 recordsLinked to original sources

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

Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infants

Preterm infants (<37 weeks gestation) are often administered broad-spectrum antibiotics in hospitals due to their vulnerability to severe morbidity, including necrotising enterocolitis and sepsis. However, antibiotics can disrupt the development of early-life microbiota, potentially impairing gut immunity and colonisation resistance. Evidence shows that probiotics (e.g., certain Bifidobacterium strains) may help restore healthy gut microbiota. In this study, we examined the effects of probiotics and antibiotics on the preterm gut microbiome and resistome in two unique cohorts of 34 very-low-birth-weight, human-milk- fed preterm infants (moderate to very preterm), with one cohort receiving probiotics. Within each group, some infants were treated with antibiotics (benzylpenicillin and/or gentamicin) while others served as non-antibiotic treated controls. We performed shotgun metagenomic sequencing on 93 longitudinal faecal samples from 34 infants, generated >300 metagenome- assembled genomes, and obtained [~]90 isolate genomes through targeted culturomics, enabling analysis of the microbiome/resistome at species and strain levels. Additionally, we investigated in vitro horizontal gene transfer (HGT) capacity of preterm infant-derived multidrug-resistant (MDR) pathogen Enterococcus via neonatal gut models. Overall, probiotic supplementation significantly reduced antibiotic resistance gene prevalence, MDR pathogen load, and helped restore a typical early-life microbiota. However, the persistence of MDR pathogens like Enterococcus, with high HGT potential, highlights the need for ongoing surveillance in neonatal care. Our findings underscore the complex interactions between antibiotics, probiotics, and HGT in shaping the neonatal microbiome and support further research into probiotics for antimicrobial stewardship in preterm populations.

microbiology↗

bioRxiv2023

Differential development of antibiotic resistance and virulence between Acinetobacter species

The two species that account for most cases of Acinetobacter-associated bacteraemia in the UK are Acinetobacter lwoffii, often a commensal but also an emerging pathogen, and A. baumannii, a well-known antibiotic-resistant species. While these species both cause similar types of human infection and occupy the same niche, A. lwoffii (unlike A. baumannii) has thus far remained susceptible to antibiotics. Comparatively little is known about the biology of A. lwoffii and this is the largest study on it conducted to date, providing valuable insights into its behaviour and potential threat to human health. This study aimed to explain the antibiotic susceptibility, virulence, and fundamental biological differences between these two species. The relative susceptibility of A. lwoffii, was explained as it encoded fewer antibiotic resistance and efflux pump genes than A. baumannii (9 and 30 respectively). While both species had markers of horizontal gene transfer, A. lwoffii encoded more DNA defence systems and harboured a far more restricted range of plasmids. Furthermore, A. lwoffii displayed a reduced ability to select for antibiotic resistance mutations, form biofilm and infect both in vivo and in vitro models of infection. This study suggests that the emerging pathogen A. lwoffii has remained susceptible to antibiotics because mechanisms exist to make it highly selective about the DNA it acquires, and we hypothesise that the fact that it only harbours a single RND system restricts the ability to select for resistance mutations. This provides valuable insights into how development of resistance can be constrained in Gram negative bacteria. ImportanceAcinetobacter lwoffii is often a harmless commensal but is also an emerging pathogen and is the most common cause of Acinetobacter-derived blood stream infections in England and Wales. In contrast to the well-studied, and often highly drug resistant A. baumannii, A. lwoffii has remained susceptible to antibiotics. This study explains why this organism has not evolved resistance to antibiotics. These new insights are important to understand why and how some species develop antibiotic resistance, while others do not and could inform future novel treatment strategies.

microbiology↗

bioRxiv2022

RND pumps across the Acinetobacter genus; AdeIJK is the ancestral efflux system.

Acinetobacter are generally soil-dwelling organisms that can also cause serious human infections. A. baumannii is one of the most common causative agents of Acinetobacter infections and is extensively drug resistant. However, an additional 25 species within the genus have also been associated with infection. A. baumannii encodes 6 RND efflux pumps, the most clinically relevant class of efflux pumps for antibiotic export, however the distribution and types of RND efflux pumps across the genus is currently unknown. Sixty-three species making up the Acinetobacter genus were searched for RND systems within their genomes. We also developed a novel method using conserved RND residues to predict the total number of RND proteins including currently undescribed RND pump proteins. The total number of RND proteins differed both within a species and across the genus. Species associated with infection tended to encode more pumps. AdeIJK/AdeXYZ was found in all searched species of Acinetobacter, and through genomic, structural and phenotypic work we show that these genes are actually orthologues of the same system. This interpretation is further supported by structural analysis of the potential drug-binding determinants of the associated RND-transporters, which reveal their close similarity to each other, and distinctiveness from other RND-pumps in Acinetobacter, such as AdeB. Therefore, we conclude that AdeIJK is the fundamental RND system for species in the Acinetobacter genus. AdeIJK can export a broad range of antibiotics and provides crucial functions within the cell, for example lipid modulation of the cell membrane, therefore it is likely that all Acinetobacter require AdeIJK for survival and homeostasis. In contrast, additional RND systems, such as AdeABC and AdeFGH were only found in a subset of Acinetobacter, that are associated with infection. By understanding the roles and mechanisms of RND efflux systems in Acinetobacter, treatments for infections can avoid efflux-mediated resistance and improve patient outcomes. Impact statementEfflux pumps extrude antibiotics from within bacterial cells directly conferring antibiotic resistance and underpinning other mechanisms of resistance. By understanding the exact complement of efflux pumps and their roles across infection-causing organisms such as those within the Acinetobacter genus, it is possible to understand how cells become resistant to antibiotics and how this might be tackled. Efflux is an attractive target for inhibition to increase susceptibility to existing drugs and therefore, knowing which pumps are present in each species is important. Furthermore, we present a novel method using conserved RND residues to predict the total number of RND proteins including currently novel systems, within bacterial genomes. Data SummaryThis study made use of publicly available datasets downloaded from NCBIs GenBank. A full list of accession numbers can be found in supplementary text 3. Bioinformatics software used in this study was previously published and listed in the methods section. The BLASTp conserved residue files are in S1 text 1 and 2. The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.

microbiology↗