Biology subjects

Kennedy, S. P.

Publications and source records attributed to Kennedy, S. P..

6 recordsLinked to original sources

bioRxiv2026

Competitive advantage of hypervirulent Group B Streptococcus for neonatal colonization revealed by metagenomic analysis of gut microbiota

Group B Streptococcus (GBS) is the leading cause of neonatal invasive infections. Late-onset infections (7-89 days after birth) are caused by GBS clonal complex 17 (CC17) in 50-80% of cases, likely resulting from bacterial translocation across the intestinal barrier. However, the factors influencing GBS colonization in neonates are incompletely understood. We used shotgun metagenomics on fecal samples from 100 neonates aged 21 days and identified taxonomic signatures of GBS colonization, including decreased Enterobacter hormaechei abundance in neonates colonized by non-CC17 GBS. Using in vitro assays with representative isolates, we demonstrate that GBS CC17 competes more effectively than GBS non-CC17 against E. hormaechei, with enhanced adherence to enterocytes mediated by the CC17-specific HvgA adhesin. Our findings highlight lineage-dependent interspecies interactions of GBS that likely influence its ability to colonize the neonatal gut. These interactions must be considered when developing microbiota-based strategies to mitigate neonatal colonization and infection by GBS.

microbiology↗

bioRxiv2023

Targeted Metagenomic Databases Provide Improved Analysis of Microbiota Samples

We introduce Moonbase, a flexible pipeline that can be used to build targeted, project-specific, databases in order to improve the accuracy of taxonomic detection and quantification in complex microbial communities. Moonbase was evaluated using synthetic metagenomic samples and compared against existing methods including MetaPhlAn3 and generalized Kraken2 databases. Our results indicate that Moonbase significantly improves species precision and quantification, outperforming marker genes and generalized databases. Construction of a phylogenetic tree from 16S data of genomes in Moonbase allows for the incorporation of UniFrac-type phylogenetic information into diversity calculations of samples. We demonstrate the resulting analysis has increased statistical power in distinguishing microbial communities. This study highlights the continual evolution of metagenomic tools with the goal of improving metagenomic analysis and highlights the potential of the Moonbase pipeline.

bioinformatics↗

bioRxiv2023

Identification of the active mechanism of aminoglycoside entry in V. cholerae through characterization of sRNA ctrR, regulating carbohydrate utilization and transport.

The possible active entry of aminoglycosides in bacterial cells has been debated since the development of this antibiotic family. Here we report the identification of their active transport mechanism in Vibrio species. We combined genome-wide transcriptional analysis and fitness screens to identify alterations driven by treatment of V. cholerae with sub-minimum inhibitory concentrations (sub-MIC) of the aminoglycoside tobramycin. RNA-seq data showed downregulation of the small non-coding RNA ncRNA586 during such treatment, while Tn-seq revealed that inactivation of this sRNA was associated with improved fitness in the presence of tobramycin. This sRNA is located near sugar transport genes and previous work on a homologous region in Vibrio tasmaniensis suggested that this sRNA stabilizes gene transcripts for carbohydrate transport and utilization, as well as phage receptors. The role for ncRNA586, hereafter named ctrR, in the transport of both carbohydrates and aminoglycosides, was further investigated. Flow cytometry on cells treated with a fluorescent aminoglycoside confirmed the role of ctrR and of carbohydrate transporters in differential aminoglycoside entry. Despite sequence diversity, ctrR showed functional conservation across the Vibrionales. This system in directly modulated by carbon sources, suggesting regulation by carbon catabolite repression, a widely conserved mechanism in Gram-negative bacteria, priming future research on aminoglycoside uptake by sugar transporters in other bacterial species.

microbiology↗

bioRxiv2023

Hospital and urban wastewaters shape the structure and active resistome of environmental biofilms

BackgroundDemonstration of the transfer, dynamics, and regulation of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in a complex environmental matrix is yet experimentally challenging, with many essential open questions such as how and where transfer and dissemination of ARGs happens in nature. The extent and conditions of MGEs transfer that carry ARGs is still largely unexplored in natural environments and microbial communities. Biofilms are structures that include high density multi-species bacterial communities embedded in self-produced extracellular polymeric substances (EPS) constituting a matrix that facilitates gene transfer and where bacteria exhibit high tolerance to stress and to antibiotics. In this study we implemented a sampling and analysis approach that allows phenotypic and genomic analyses of in situ and reconstituted in vitro hospital and urban wastewater (WW) biofilms. To assess the potential of hospital and urban WW biofilms to efficiently disseminate ARGs in the WW system, we explored the EPS within the biofilm matrix and assessed the expression of the resistome (ARGs) and mobilome (MGEs) by metatranscriptomics. ResultsWe first showed that a) the composition of EPS differs depending on their growth environment (in situ and in vitro) and their sampling origin (hospital vs urban WW) and that b) a low amount of ciprofloxacin impacted the composition of the EPS. Next, the metatranscriptomic approach showed that a) expression of ARGs and MGEs increase upon adding a low amount of ciprofloxacin for biofilms from hospital WW but not for those from urban WW and b) that expression of specific plasmids that carry individual or multiple ARGs varies depending on the WW origins of the biofilms. When the same plasmids were expressed in both, urban and hospital WW biofilms, they carried and expressed different ARGs. ConclusionWe show that hospital and urban wastewaters shape the structure and active resistome of environmental biofilms, and we confirmed that hospital WW is an important hot spot for the dissemination and selection of AMR. The different responses to antibiotic pressure in hospital vs urban biofilms, coupled with differences in biofilm structure helps delineate distinct characteristics of hospital and urban WW biofilms highlighting the relationships between the resistome and its expression in environmental biofilms and their surrounding ecosystems.

microbiology↗

bioRxiv2019

Classification of hospital and urban wastewater resistome and microbiota over time and their relationship to the eco-exposome.

Wastewaters (WW) are important sources for the dissemination of antimicrobial resistance (AMR) into the environment. Hospital WW (HWW) contain higher loads of micro-pollutants and AMR markers than urban WW (UWW). Little is known about the long-term dynamics of H and U WW and the impact of their joined treatment on the general burden of AMR. Here, we characterized the resistome, microbiota and eco-exposome signature of 126 H and U WW samples treated separately for three years, and then mixed, over one year. Multi-variate analysis and machine learning revealed a robust signature for each WW with no significant variation over time before mixing, and once mixed, both WW closely resembled U signatures. We demonstrated a significant impact of pharmaceuticals and surfactants on the resistome and microbiota of H and U WW. Our results present considerable targets for AMR related risk assessment of WW.

microbiology↗

bioRxiv2017

Prediction of the intestinal resistome by a novel 3D-based method

The intestinal microbiota is considered to be a major reservoir of antibiotic resistance determinants (ARDs) that could potentially be transferred to bacterial pathogens. Yet, this question remains hypothetical because of the difficulty to identify ARDs from intestinal bacteria. Here, we developed and validated a new annotation method (called pairwise comparative modelling, PCM) based on homology modelling in order to characterize the Human resistome. We were able to predict 6,095 ARDs in a 3.9 million protein catalogue from the Human intestinal microbiota. We found that predicted ARDs (pdARDs) were distantly related to known ARDs (mean amino-acid identity 29.8%). Among 3,651 pdARDs that were identified in metagenomic species, 3,489 (95.6%) were assumed to be located on the bacterial chromosome. Furthermore, genes associated with mobility were found in the neighbourhood of only 7.9% (482/6,095) of pdARDs. According to the composition of their resistome, we were able to cluster subjects from the MetaHIT cohort (n=663) into 6 \"resistotypes\". Eventually, we found that the relative abundance of pdARDs was positively associated with gene richness, but not when subjects were exposed to antibiotics. Altogether, our results support that most ARDs in the intestinal microbiota should be considered as intrinsic genes of commensal microbiota with a low risk of transfer to bacterial pathogens.

microbiology↗