Biology subjects

Lopes, B. S.

Publications and source records attributed to Lopes, B. S..

3 recordsLinked to original sources

bioRxiv2025

Adaptive trade-offs between niche-driven defence system selection and horizontal gene transfer suggests clinical success in Acinetobacter spp.

2.IntroductionBacteria face relentless selective pressure from both antibiotics and bacteriophages, driving the evolution of diverse defence systems and shaping horizontal gene transfer (HGT) dynamics. Gap StatementThe relationship between bacterial defence system repertoires and horizontal gene transfer in clinically relevant Acinetobacter species remains poorly understood, limiting our ability to predict resistance evolution and design targeted phage therapies. AimTo characterize defence arsenal across Acinetobacter species and investigate their associations with different HGT markers MethodologyWe performed a comparative genomic analysis of 132 genomes from 18 Acinetobacter species, focusing on the interplay between defence architectures and HGT markers. ResultsOur result reveals pronounced differences in defence system repertoires between lineages: while most Acinetobacter spp. harbour a multilayered arsenal, the clinically dominant A. baumannii international clone 2 (IC2) exhibits a depleted but specialised defence landscape, notably enriched in the phosphorothioation-based SspBCDE system and nearly devoid of restriction-modification systems. Strikingly, many defence systems display mutual exclusivity, and defence system is tightly linked to the presence of mobile elements, antibiotics, and heavy metal resistance. Plasmid-borne defence systems, especially BREX, are prevalent, highlighting the role of mobile elements in distributing both immunity and resistance traits. These patterns suggest that successful clinical lineages finely balance immune defences and genetic plasticity, facilitating rapid adaptation under antimicrobial selection and phage threats. ConclusionThese findings provide insights into evolutionary trade-offs underpinning multidrug resistance and have implications for designing targeted phage therapies against recalcitrant Acinetobacter infections. 3. Data summaryAll bioinformatics analysis workflows, custom scripts, and R code are publicly available at https://github.com/vikos77/Acinetobacter-defence-systems. The repository includes bash scripts for genome downloading and tool execution (scripts 1-10), R scripts for statistical analysis and visualization (scripts 1-9), and conda environment files for reproducible software installation. Complete analysis protocols are documented in the repository README and individual script headers. All software versions and parameters are specified in the code documentation. 4. Impact StatementThis study reveals how defence system composition in Acinetobacter species is shaped by ecological niche and linked to horizontal gene transfer, antibiotic resistance, and mobile genetic elements. Notably, the clinically dominant A. baumannii IC2 lineage exhibits a streamlined defence repertoire favouring genetic plasticity, facilitating rapid adaptation under antibiotic and phage pressure. These findings enhance our understanding of resistance evolution and support the rational design of phage-based therapies targeting multidrug-resistant pathogens.

bioinformatics↗

bioRxiv2020

Dissemination of carbapenem-resistance and plasmids encoding carbapenemases in Gram-negative bacteria isolated from India

Carbapenem resistance in Gram-negative bacteria is an ongoing public-health problem of global dimensions leaving very few treatment options for severely infected patients. This study focuses on the dissemination of plasmid-borne carbapenemase genes in Gram-negative bacteria in Tamil Nadu, India. A total of 151 non-repetitive isolates belonging to 11 genera were collected from a diagnostic center in Tamil Nadu. E. coli (n=57) isolates were classified as, Enteropathogenic (n=12), Enteroaggregative (n=9), Enterohemorrhagic (n=8), Enterotoxigenic (n=3), Enteroinvasive (n=1) and unclassified E. coli (n=24). Of the 45 Klebsiella species, 14 were K1 whereas 11 were K2 serotype and in 20 Klebsiella serotype could not be determined. Other isolates (n=49) consisted of P. aeruginosa, S. typhi, E. cloacae, A. baumannii, S. marcescens, A. xylosoxidans, P. mirabilis and E. meningoseptica. Of the 151 isolates, 71% (n=107) and 68% (n=103) were found to be resistant to meropenem and imipenem respectively. The most prevalent beta-lactamase gene was blaNDM-1 (21%, 12/57) followed by blaOXA-181 (16%, 9/57), blaGES-9 (n=8), blaOXA-23 (n=7), blaIMP-1 (n=3), blaGES-1 (n=11) and blaOXA-51 (n=9). The unusual presence of blaOXA-23 was seen in E. coli (n=4), and blaOXA-23 and blaOXA-51 (IncA/C) in K. pneumoniae (n=3). Plasmid incompatibility (inc/rep) typing results showed that the plasmids carrying resistance genes (n=11) belonged to IncX, IncA/C, IncFIA-FIB and IncFIIA groups. E. coli and K. pneumoniae were able to transfer plasmid-borne carbapenemase via conjugation. This study highlights the prevalence of carbapenem resistance and the acquisition of plasmid-borne carbapenemase genes in Gram-negative bacteria highlighting the role of plasmid transfer in disseminating resistance.

microbiology↗

bioRxiv2019

Domestication of Campylobacter jejuni NCTC 11168

Reference and type strains of well-known bacteria have been a cornerstone of microbiology research for decades. The sharing of well-characterised isolates among laboratories has parallelised research efforts and enhanced the reproducibility of experiments, leading to a wealth of knowledge about trait variation in different species and the underlying genetics. Campylobacter jejuni strain NCTC 11168, deposited at the National Collection of Type Cultures in 1977, has been adopted widely as a reference strain by researchers worldwide and was the first Campylobacter for which the complete genome was published (in 2000). In this study, we collected 23 C. jejuni NCTC 11168 reference isolates from laboratories across the UK and compared variation in simple laboratory phenotypes with genetic variation in sequenced genomes. Putatively identical isolates identified previously to have aberrant phenotypes varied by up to 281 SNPs (in 15 genes) compared to the most recent reference strain. Isolates also display considerable phenotype variation in motility, morphology, growth at 37{degrees}C, invasion of chicken and human cell lines and susceptibility to ampicillin. This study provides evidence of ongoing evolutionary change among C. jejuni isolates as they are cultured in different laboratories and highlights the need for careful consideration of genetic variation within laboratory reference strains.\n\nImpact statementIn this paper, we comment on the changing role of laboratory reference strains. While the model organism allows basic comparison within and among laboratories, it is important to remember the effect even small differences in isolate genomes can have on the validity and reproducibility of experimental work. We quantify differences in 23 reference Campylobacter genomes and compare them with observable differences in common laboratory phenotypes.\n\nData summaryShort read data are archived on the NCBI SRA associated with BioProject accession PRJNA517467 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA517467).\n\nAll assembled genomes are also available on FigShare (doi: 10.6084/m9.figshare.7849268). Phylogeny visualised on microreact: https://microreact.org/project/NCTC11168.\n\nRepositoriesShort read data are archived on the NCBI SRA repository, associated with BioProject accession PRJNA517467 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA517467; Table S1).\n\nThe authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.

microbiology↗