Biology subjects

Evans, B. A.

Publications and source records attributed to Evans, B. A..

10 recordsLinked to original sources

bioRxiv2026

The large conjugative plasmid pAB3 integrates into the chromosome of Acinetobacter baumannii ATCC 17978

ATCC 17978 is one of the most utilised lab strains of Acinetobacter baumannii. Current literature suggests ATCC 17978 can have either a sulfamethoxazole-resistant phenotype or have the type VI secretion system (T6SS) switched on depending on the presence/absence of the large conjugative plasmid pAB3, which encodes the antimicrobial resistance gene (ARG) sul2 and T6SS repressors tetR1/tetR2. Here, we show that pAB3 integrates into the ATCC 17978 chromosome, which enables a large inversion resulting in the chromosomal arrangement labelled GS2.24 by Socru. This integration has no transcriptional impact on nearby genes or tetR1/tetR2. We find several instances were a portion of integrated pAB3 containing tetR2 is lost but the rest of the sequence, including sul2, is maintained, suggesting pAB3 integration may serve to make further rearrangements more tractable, enabling a putative T6SS+ sulfamethoxazole-resistant phenotype.

microbiology↗

bioRxiv2026

Phylogeny informed international clone assignment with PhyloMLST

Multilocus sequence typing (MLST) remains the predominant method for typing bacterial strains. A common method for investigating particularly successful epidemic lineages within a species is to cluster isolates with similar MLST profiles into clonal complexes (CCs). Some CCs, such as international clones (ICs) in A. baumannii, are identified with specific sequence types (STs) and are of particular importance to human health. Although theoretically simple, there is a lack of convenient, user-friendly tools perform this analysis. Here we present PhyloMLST, a tool to cluster bacterial isolates into CCs and map them to ICs using the output from existing MLST tools and user-provided STs. As there is potential for aberrant IC assignment arising from excessively large CCs constructed with spurious links, PhyloMLST provides additional functionality to correct IC assignment with a user-provided phylogenetic tree. Although designed with A. baumannii in mind, PhyloMLST can be applied to any bacteria where construction and investigation of CCs based on MLST is performed. Impact statementMany bacterial pathogens are characterised by successful epidemic lineages that are responsible for a substantial number of infections, may be more virulent, and may carry an abundance of antimicrobial resistance genes. These epidemic lineages are comprised of a number of multilocus sequence typing (MLST) sequence types (STs), clustered into clonal complexes (CCs). To date, identifying which STs belong to which epidemic lineage has been challenging, with no simple analytical tools available. Here, we present PhyloMLST - a phylogenetically-aware method for assigning STs to epidemic lineages. The customisable nature of the tool will enable researchers to straightforwardly characterise any population of bacteria that they are working on using MLST data and user-defined definitions of epidemic lineages. Data summaryThe PhyloMLST source code and example data shown here is available at https://github.com/Mattn286/PhyloMLST.

microbiology↗

bioRxiv2026

Historical isolates provide insights into the evolution of Acinetobacter baumannii international clone 2 and its resistome

Acinetobacter baumannii remains a pervasive nosocomial pathogen, with international clone 2 (IC2) being the most successful lineage. IC2 is often discussed as a singular entity, and the genomic factors behind its success over other lineages are poorly characterised. This study aimed to track genomic changes occurring around the emergence of IC2 and further determine the within-clone population structure. A set of historical A. baumannii isolates from the 1970s to early 2000s were long-read sequenced and assembled into high-quality chromosomes. These were then used to supplement publicly available A. baumannii genomes, producing a dataset of 1,281 chromosomes derived from isolates collected across six continents. A recombination-free phylogeny was produced and combined with antimicrobial resistance gene (ARG) presence/absence data. Analysis showed that IC2 began to emerge as the dominant lineage around 2005, which coincides with the acquisition of oxa23 and AbGRI3. Further, IC2 can be split into at least four distinct groups. Groups 1, 2, and 3 represent incremental evolution of the A. baumannii chromosome over time, while group 4 represents a separate evolutionary path distinct from the main IC2 lineage, which has recently been isolated at higher frequency. Significance statementCharacterising the evolution and population structure of antimicrobial-resistant bacterial pathogens is of key importance both for epidemiological monitoring and developing approaches to combat infections and their spread. Here, we use a unique collection of historical isolates to show that the major international clone in the WHO priority pathogen Acinetobacter baumannii is comprised of different, independent groups with individual antimicrobial resistance gene compliments. This highlights new areas for research to understand the clinical impact of the different groups and the drivers underlying the evolution and spread of epidemic clones of antimicrobial-resistance bacterial pathogens.

microbiology↗

bioRxiv2025

Plasticity in a bacterial global regulatory switch that drives a shift in antibiotic resistance and virulence

Antibiotic resistance and expression of virulence factors can impact the outcome of infection by Pseudomonas aeruginosa. Pathogenesis is often modelled using the P. aeruginosa PAO1 reference strain but laboratory lineages vary in the sequence and activity of MexT, a global regulator impacting virulence, biofilm formation and ciprofloxacin resistance. We defined the impact of active versus inactive MexT in PAO1 and observed global transcriptomic changes affecting the expression of 900 genes. Phenotyping revealed altered metabolism, antibiotic resistance and virulence - resulting in striking variation across a single model organism. We propose that antibiotic-resistance, introduced during work with the original PAO1 strain, has caused plasticity in mexT that accounts for variation across lineages. To test this, we introduced antibiotic resistance into clinical P. aeruginosa isolates and observed downstream mutations in mexT when selective pressure was removed, supporting the proposed evolutionary pathway. Overall, we have demonstrated the transcriptomic basis of MexT as a phenotypic switch in PAO1 and implicated antibiotic resistance as a cause of downstream changes in mexT in P. aeruginosa. Furthermore, MexS/MexT-regulated efflux is implicated in the antibiotic stress response and virulence, helping identify the mechanisms for rapid phenotypic switching through mexT and confirming that PAO1 is a very different organism compared to most isolates. Improved understanding of the regulatory changes linked to antibiotic resistance is particularly relevant to P. aeruginosa where cycles of antibiotic treatment are common.

microbiology↗

bioRxiv2023

Emergence of Acinetobacter baumannii International Clone 10 predominantly found in the Middle East

Acinetobacter baumannii is a globally distributed human pathogen. Infections caused by carbapenem-resistant isolates of A. baumannii (CRAB) are of great concern, as treatment options are very limited. Despite having among the highest rates reported worldwide, there exists limited genomic data from CRAB strains isolated in the Middle East. Here we report epidemiological, phenotypic, and genome sequencing data (short reads and long reads) on a set of 60 A. baumannii isolates belonging to Sequence Type ST158 (Pasteur MLST scheme). They represent a novel international clone (IC), designated IC10, with limited geographic spread beyond the Middle East. Specific antibiotic-resistance genes associated with this clone were identified and data on the plasmid content associated with this lineage are presented.

microbiology↗

bioRxiv2023

The anticancer chemotherapy drug 5-Fluorouracil has positive interaction with antibiotics and can select for antibiotic resistance in Staphylococcus aureus

Antibiotic resistance is a major global issue in healthcare and understanding the drivers of resistance is key in developing effective strategies to counter it. Many non-antibiotic drugs, such as cancer chemotherapy drugs, can have antimicrobial properties but their effects on bacteria in the context of infection and drug resistance have only recently begun to be explored. Here we investigate the antimicrobial properties of the cancer drug 5-fluorouracil (5-FU) on the common human commensal and pathogen Staphylococcus aureus. 5-FU can be metabolized by S. aureus and ultimately results in the inhibition of ThyA, involved in the folate synthesis and thymine synthesis pathways. Bacterial growth was inhibited by 5-FU, and the drug had additive or synergistic interactions with the antibiotics trimethoprim and sulfamethoxazole. The addition of thymidine overcame the inhibitory effects of 5-FU. Strains of S. aureus evolved in the presence of 5-FU developed mutations in the thymidine kinase gene tdk, likely inhibiting the thymine salvage pathway. In mixtures of clinical trimethoprim-resistant S. aureus strains and sensitive strains, the presence of 5-FU conferred a large fitness advantage to the resistant strains and selected for them over the sensitive strains. Together these data show that 5-FU has antimicrobial effects against S. aureus with these effects targeting the same pathway as existing antibiotics, and that the use of 5-FU in patients may be selecting for antibiotic-resistant bacteria.

microbiology↗

bioRxiv2023

Spatial reorganization of Escherichia coli chromosome contextualizes triclosan stress-related genetic, epigenetic and transcriptome changes

Changes in the spatial organization of bacterial chromosomes under stress conditions and its biological implications remain poorly understood. We mapped the structural landscape of wild-type and {Delta}dcm E. coli chromosomes under triclosan stress using Hi-C to identify triclosan-induced chromosomal interaction domains (CIDs). Two CIDs were common to the wild-type and {Delta}dcm E. coli, including a CID with a common boundary at fabI gene, which encodes the triclosan target. All mutations and structural variants under triclosan stress were observed within or in close proximity to triclosan-induced CIDs. Absence of Dcm methylation impacts both short- and long-range interactions in triclosan stress. Single-base resolution methylome maps reveal hypermethylation of adenines (in wild-type and {Delta}dcm) and cytosines (in wild-type) in the two common triclosan-induced CIDs. Furthermore, global gene expression profiling identified enrichment of highly expressed genes within the two common CIDs. Our findings suggest that stress-induced CIDs in E. coli are hotspots for genetic variations and are associated with enhanced transcriptional activity and hypermethylation of Dam/Dcm motifs.

microbiology↗

bioRxiv2020

Diversity of carbapenem-resistant Acinetobacter baumannii and bacteriophage-mediated spread of the Oxa23 carbapenemase

Carbapenem-resistant A. baumannii are prevalent in low- and middle-income countries such as Egypt, but little is known about the molecular epidemiology and mechanisms of resistance in these settings. Here we characterise carbapenem-resistant A. baumannii from Alexandria, Egypt, and place it in a regional context. 54 carbapenem-resistant isolates from Alexandria Main University Hospital, Egypt, collected between 2010 and 2015 were genome sequenced using Illumina technology. Genomes were de novo assembled and annotated. Genomes for 36 isolates from the Middle East region were downloaded from GenBank. Core gene compliment was determined using Roary, and analyses of recombination were performed in Gubbins. MLST sequence type and antibiotic resistance genes were identified. The majority of Egyptian isolates belonged to one of 3 major clades, corresponding to Pasteur MLST clonal complex (CCPAS) 1, CCPAS2 and sequence type (STPAS) 158. Strains belonging to STPAS158 have been reported almost exclusively from North Africa, the Middle East and Pakistan, and may represent a region-specific lineage. All isolates carried an oxa23 gene, six carried blaNDM-1, and one carried blaNDM-2. The oxa23 gene was located on a variety of different mobile elements, with Tn2006 predominant in CCPAS2 strains, and Tn2008 predominant in other lineages. Of particular concern, in 8 of the 11 CCPAS1 strains, the carbapenemase gene was located in a temperate bacteriophage phiOXA, previously identified only once before in a CCPAS1 clone from the US military. The carbapenem-resistant A. baumannii population in Alexandria Main University hospital is very diverse, and indicates an endemic circulating population, including a region-specific lineage. The major mechanism for oxa23 dissemination in CCPAS1 isolates appears to be a bacteriophage, presenting new concerns about the ability of these carbapenemases to spread throughout the bacterial population. Data SummaryThe whole genome shotgun sequences of the isolates from this study have been deposited at DDBJ/ENA/GenBank under the BioProject accession number PRJNA659545. The individual genome accession numbers for each isolate are as follows: A1a, JACSUC000000000; A2, JACSUB000000000; A4, JACSVQ000000000; A5, JACSUA000000000; A6, JACSTZ000000000; A7-T, JACSVP000000000; A8-T, JACSVO000000000; A8a, JACSTY000000000; A9, JACSTX000000000; A10, JACSTW000000000; A10a, JACSTV000000000; A11a, JACSTU000000000; A13a, JACSTT000000000; A14a, JACSTS000000000; A15, JACSTR000000000; A16, JACSTQ000000000; A18, JACSTP000000000; A21, JACSVN000000000; A22, JACSTO000000000; A27, JACSTN000000000; A30, JACSTM000000000; A31, JACSTL000000000; A34, JACSTK000000000; A35, JACSTJ000000000; A36, JACSTI000000000; A39, JACSTH000000000; A40, JACSTG000000000; A41, JACSTF000000000; A42, JACSTE000000000; A43, JACSTD000000000; A44, JACSTC000000000; A45, JACSTB000000000; A46, JACSTA000000000; A64, JACSSZ000000000; A68, JACSSY000000000; A69, JACSSX000000000; A70, JACSSW000000000; A71, JACSVM000000000; A72, JACSSV000000000; A73, JACSSU000000000; A74, JACSST000000000; A75, JACSSS000000000; A78, JACSSR000000000; A82, JACSSQ000000000; A83, JACSVL000000000; A84, JACSSP000000000; A85, JACSSO000000000; A86, JACSVK000000000; A87, JACSSN000000000; A88, JACSSM000000000; A89, JACSSL000000000; A92, JACSSK000000000; A5910, JACSSJ000000000; A6135, JACSVJ000000000.

microbiology↗

bioRxiv2020

Variability in carbapenemase activity of intrinsic OxaAb (OXA-51-like) beta-lactamase enzymes in Acinetobacter baumannii

ObjectivesThis study aimed to measure the variability in carbapenem susceptibility conferred by different OxaAb variants, characterise the molecular evolution of oxaAb and elucidate the contribution of OxaAb and other possible carbapenem resistance factors in the clinical isolates using WGS and LC-MS/MS. MethodsDisc susceptibility and MIC broth microdilution tests were performed on ten clinical A. baumannii isolates and interpreted according to CLSI guidelines. Imipenem and meropenem MICs were evaluated for all oxaAb variants cloned into susceptible A. baumannii CIP70.10 and increased adeABC efflux pump gene expression BM4547 backgrounds, with and without their natural promoters. Molecular evolution analysis of the oxaAb variants was performed using FastTree and SplitsTree4. Resistance determinants were studied in the clinical isolates using WGS and LC-MS/MS analysis. ResultsOxaAb(82), OxaAb(83), OxaAb(107), and OxaAb(110) carrying I129L and L167V substitutions increased carbapenem MICs when transferred into susceptible A. baumannii backgrounds without an upstream IS element. Carbapenem resistance was conferred with the addition of their natural upstream ISAba1 promoter. LC-MS/MS analysis on the original clinical isolates showed no differences in expression levels of proteins commonly associated with carbapenem resistance. ConclusionsISAba1-driven overexpression of OxaAb variants with substitutions I129L and L167V confers carbapenem resistance with no need for additional resistance mechanisms.

microbiology↗

bioRxiv2019

Microevolution in the major outer membrane protein OmpA of Acinetobacter baumannii

Acinetobacter baumannii is nowadays a relevant nosocomial pathogen characterized by multidrug resistance (MDR) and concomitant difficulties to treat infections. OmpA is the most abundant A. baumannii outer membrane (OM) protein, and is involved in virulence, host cell recognition, biofilm formation, regulation of OM stability, permeability, and antibiotic resistance. OmpA members are two-domain proteins with an N-terminal eight-stranded {beta}-barrel domain with four external loops (ELs) interacting with the environment, and a C-terminal periplasmic domain binding non-covalently to the peptidoglycan. Here, we combined data from genome sequencing, phylogenetic, and multilocus sequence analyses from 242 strains of the Acinetobacter calcoaceticus/Acinetobacter baumannii complex (ACB), 222 from A. baumannii, to explore ompA microevolutionary divergence. Five major ompA variant groups were identified (V1 to V5) comprising 50 different alleles coding for 29 different proteins. Polymorphisms were concentrated in 5 regions corresponding to the four ELs and the C-terminal end, and provided evidence for different intra-genic recombination events. ompA variants were not randomly distributed across the A. baumannii phylogeny, with the most frequent V1a1 allele almost exclusive to clonal complex 1 (CC1) strains and the second most frequent V2a1 allele found in the majority of CC2 strains. Evidence was found for assortative exchanges of ompA alleles not only between different A. baumannii clonal lineages, but also different ACB species. Within A. baumannii ompA non-synonymous substitutions were concentrated in the ELs regions, but were more abundant in the transmembrane regions between different Acinetobacter species. The overall results have implications for A. baumannii evolution, epidemiology, virulence, and vaccine design.\n\nImportanceAcinetobacter baumannii is an increasing MDR threat in nosocomial settings associated with prolonged hospitalization and concomitantly increased healthcare costs. The main A. baumannii OM protein, OmpA, is a multifaceted two-domain protein implicated in host cell recognition and adhesion, cytotoxicity, biofilm formation, and as a slow porin for antibiotics and small hydrophilic nutrients. A. baumannii OmpA has been proposed as a potential target for anti-virulence drugs and as a vaccine candidate. Given the many interactions of this protein with environmental factors including host defenses, it is certainly subjected to many selective pressures. Here, we analyzed the microevolution of this OM protein in the A. baumannii population to obtain clues on the extent to which selection in the clinical setting has shaped this protein. The results provide relevant information on the main causes driving evolution of this protein, with potential implications in A. baumannii epidemiology, virulence, and vaccine design.

microbiology↗