Biology subjects

Mather, A. E.

Publications and source records attributed to Mather, A. E..

11 recordsLinked to original sources

bioRxiv2026

Lessons from the equator: a window on the future of vibriosis in a warming Earth

Vibrios are important aquatic human pathogens, causing gastroenteritis, wound infections, and cholera. Vibriosis (non-cholera infection) has been increasing in temperate climates due to correlation between Vibrio abundance and water temperature. However, how warming oceans differentially influence various Vibrio species, and whether incidence is higher in tropical regions, remains understudied. We assembled the first comprehensive dataset of culture-confirmed vibriosis cases outside a temperate climate from equatorial Singapore. Comparison to cases from the detailed United States (US) CDC COVIS system revealed that vibriosis incidence is over two times higher in Singapore than the United States. Causative species also differ markedly, with Vibrio fluvialis and non-toxigenic Vibrio cholerae dominating in Singapore (>40%) but are much less prominent in the United States (<15%). Singapore cases have remained stable in the last decade, while US incidence is rising rapidly, especially for V. fluvialis and V. cholerae (13% and 17% per year). Differences in causative species in Singapore and the United States suggest ecological factors may shape infection dynamics, with some species benefitting more from warming oceans, raising their equatorial prominence. Incidence is stable in Singapore, likely due to slower warming of waters near the equator. In contrast, vibriosis in the United States will likely continue to increase steadily, with changing species composition, likely becoming tropicalized.

microbiology↗

bioRxiv2025

MetaPointFinder: Detection of Antimicrobial Resistance-Conferring Point Mutations (ARMs) from Metagenomic Reads

BackgroundMany clinically important antimicrobial resistance (AMR) phenotypes such as fluoroquinolones and rifamycins are driven by antimicrobial resistance-conferring mutations (ARMs) in conserved chromosomal loci (e.g., gyrA, parC, rpoB). Resistome profiling by metagenomics sequencing is often proposed as an ideal AMR surveillance tool as it is organism-agnostic, but currently, existing metagenomic AMR surveillance pipelines are only able to identify acquired AMR genes but not point mutations associated with AMR. This is a serious gap in metagenomics-based AMR surveillance, as the true extent of AMR may be underestimated. MethodsWe developed MetaPointFinder (v1), a read-based method that can process both long and short metagenomic reads. The tool identifies resistance-determining regions in reads using DIAMOND (translated protein) and KMA (nucleotide), and classifies known resistant versus wild-type variants by aligning the sequences using pwalign and assessing the observed mutations based on known resistance mutations in the AMRFinderPlus database. The tool outputs ARMs per read, per gene and per antibiotic class. ResultsIn proof-of-concept analyses, MetaPointFinder identified known AMR-associated mutations and quantified resistant/susceptible read counts and ratios from metagenomic samples with corroborating phenotypic resistance data when available. We benchmark our tool using simulated reads from DNA and from reverse-translated protein references with read lengths of 100-5000 bp and error rates between 0 and 30%, simulating both Illumina and Nanopore error rates. We show that MetaPointFinder outperforms any available method for detection of ARMs in metagenomics data. ConclusionMetaPointFinder complements gene-centric resistome profiling by capturing chromosomal mutation-based AMR directly from metagenomes. Impact StatementMany clinically important antimicrobial resistance (AMR) phenotypes such as fluoroquinolones and rifamycins are driven by antimicrobial resistance-conferring mutations (ARMs) in conserved chromosomal loci (e.g., gyrA, parC, rpoB). Resistome profiling by metagenomic sequencing is ideal for AMR surveillance, but existing pipelines detect only acquired genes and ignore point mutations. MetaPointFinder bridges this gap. The tool accurately identifies reads carrying resistance-determining regions using DIAMOND (protein) and KMA (DNA), aligns them, and classifies resistant versus wild-type variants using known mutations from the AMRFinderPlus database.

bioinformatics↗

bioRxiv2025

Megaplasmids associate with Escherichia coli and other Enterobacteriaceae

Humans and animals are ubiquitously colonized by Enterobacteriaceae, a bacterial family that contains both commensals and clinically significant pathogens. Here, we report Enterobacteriaceae megaplasmids of up to 1.58 Mbp in length in infant and adult guts, and other microbiomes. Of 19 complete plasmid genomes, one was reconstructed from an E. coli isolate; others were linked to species of Citrobacter and Enterobacter via analysis of genome modification patterns. The detection of related plasmids in different Enterobacteriaceae, conjugation machinery, and more diverse modified motifs in certain plasmids compared to hosts suggests that these elements are self-transmissible, with a broad host range. The plasmids encode multi-drug efflux systems and potential secreted effectors. Up to 208 tRNAs are encoded and include sequence variants that may counter tRNA-centric defense mechanisms. Overall, the vast megaplasmid coding capacity may broaden host range, increase competitiveness, control invasion by other elements, and counter programmed cell death.

microbiology↗

bioRxiv2025

Tissue destruction during food spoilage is associated with the formation of biofilms by Pseudomonas species

Members of the Pseudomonas genus are common spoilers of a range of meat, dairy and vegetable products. While we have a good understanding of the Pseudomonas species typically responsible for spoilage, we know very little about how these bacteria interact with food surfaces during spoilage. Here we assessed the spoilage capabilities of a large panel (n=124) of Pseudomonas species food-derived isolates on meat (chicken) and leafy greens (spinach). Most isolates (71/124) were capable of spoiling both foods, but some were only capable of spoiling only chicken (21/124) or spinach (23/124), or neither (9/124). Our data also demonstrated that the type of fresh food the strain was isolated from influenced spoilage capabilities: strains isolated from meat were likely to spoil both chicken and spinach, while those isolated from leafy greens were more likely to spoil only spinach. We used fluorescence microscopy to visualise how Pseudomonas spoilage species interacted with the meat or leaf tissue and observed significant tissue destruction associated with biofilm formation. For chicken, this was associated with the formation of dense biofilm pillars that penetrated deep into the tissue. For spinach we observed biofilms on the leaf in areas of tissue degradation. Finally, we explored the correlation between potentially relevant phenotypes (in vitro biofilm, motility and secreted enzyme production) and spoilage capabilities. There was no significant correlation between any of these phenotypes and spoilage, except for secreted protease activity and chicken spoilage. Overall, this study increases our understanding of processes involved in food spoilage by Pseudomonas species.

microbiology↗

bioRxiv2025

Environmental context as a key driver of Pseudomonas biocontrol activity against Salmonella.

Salmonella poses a significant threat to food security, with frequent outbreaks reported worldwide. A large percentage of these outbreaks are associated with fresh produce intended for raw consumption. Plant microbiomes harbour diverse microbial communities, including commensal microbes such as Pseudomonas that sometimes exhibit biocontrol activity against plant pathogens. However, little is known about whether Pseudomonas strains can effectively suppress foodborne pathogens and the mechanisms they employ. In this study, we identified and characterised food derived Pseudomonas isolates capable of inhibiting Salmonella growth in vitro and in planta. The identified isolates were active against a range of Salmonella serovars, and additionally E. coli isolates derived from food. We demonstrated that dynamics of the interaction between Pseudomonas and Salmonella are environment and application dependant. To uncover the mechanisms Pseudomonas employs to suppress Salmonella, we used transcriptomics coupled with pathway analysis in the two different settings. We showed that Pseudomonas metabolism undergoes significant environment-specific changes in the presence of Salmonella, implicating different pathways responsible for the control of the pathogen in the two different settings. Our results highlight the plasticity of Pseudomonas metabolism in response to Salmonella in two distinct environments and provide evidence that Pseudomonas biocontrol activity is multifactorial and environment dependent.

microbiology↗

bioRxiv2024

Lapidary: Identifying and reporting amino acid sequences in metagenomes using sequence reads and Diamond

Genome and metagenome comparisons rely on identifying genetic elements that differ or are in common between samples. These genetic elements can be identified by assembling sequenced reads and identifying the genetic element in the assembly, or by aligning nucleotide sequences in the reads to the nucleotide sequences of a reference genetic element. The first relies on the complete assembly of the genetic element of interest, and the second relies on a reference sequence represented in nucleotides. This is particularly challenging with metagenome data, where the genetic elements, including genes, are often fragmented because sequences are shared between different species in the metagenomic data, resulting in contig breaks in or around genetic elements. This presents a difficulty when identifying genetic elements through the first approach. A common approach with metagenomes is to map reads against reference nucleotide sequences and extract the depth and coverage from those reference sequences. However, currently no software exists to identity and report genetic elements using DNA-protein alignments in metagenomes. We have developed the software Lapidary to identify the identity, coverage, depth, and most likely sequence of amino acid sequences from both genome and metagenome read files. We tested the effectiveness of the method against simulated, genomic and metagenomic read datasets. Lapidary is more sensitive than assembly methods for metagenomic data that often have fragmented assemblies but is less sensitive when assemblies are more complete, as is the case with genomic data.

bioinformatics↗

bioRxiv2023

Scalable neighbour search and alignment with uvaia

Despite millions of SARS-CoV-2 genomes being sequenced and shared globally, manipulating such data sets is still challenging, especially selecting sequences for focused phylogenetic analysis. We present a novel method, uvaia, which is based on partial and exact sequence similarity for quickly extracting database sequences similar to query sequences of interest. Many SARS-CoV-2 phylogenetic analyses rely on very low numbers of ambiguous sites as a measure of quality since ambiguous sites do not contribute to single nucleotide polymorphism (SNP) differences, which uvaia alleviates by using measures of sequence similarity that consider partially ambiguous sites. Such fine-grained definition of similarity allows not only for better phylogenetic analyses, but also for improved classification and biogeographical inferences. Uvaia works natively with compressed files, can use multiple cores and efficiently utilises memory, being able to analyse large data sets on a standard desktop.

bioinformatics↗

bioRxiv2020

CoronaHiT: large scale multiplexing of SARS-CoV-2 genomes using Nanopore sequencing

The COVID-19 pandemic has spread to almost every country in the world since it started in China in late 2019. Controlling the pandemic requires a multifaceted approach including whole genome sequencing to support public health interventions at local and national levels. One of the most widely used methods for sequencing is the ARTIC protocol, a tiling PCR approach followed by Oxford Nanopore sequencing (ONT) of up to 96 samples at a time. There is a need, however, for a flexible, platform agnostic, method that can provide multiple throughput options depending on changing requirements as the pandemic peaks and troughs. Here we present CoronaHiT, a method capable of multiplexing up to 96 small genomes on a single MinION flowcell or >384 genomes on Illumina NextSeq, using transposase mediated addition of adapters and PCR based addition of barcodes to ARTIC PCR products. We demonstrate the method by sequencing 95 and 59 SARS-CoV-2 genomes for routine and rapid outbreak response runs, respectively, on Nanopore and Illumina platforms and compare to the standard ARTIC LoCost nanopore method. Of the 154 samples sequenced using the three approaches, genomes with [≥] 90% coverage (GISAID criteria) were generated for 64.3% of samples for ARTIC LoCost, 71.4% for CoronaHiT-ONT, and 76.6% for CoronaHiT-Illumina and have almost identical clustering on a maximum likelihood tree. In conclusion, we demonstrate that CoronaHiT can multiplex up to 96 SARS-CoV-2 genomes per MinION flowcell and that Illumina sequencing can be performed on the same libraries, which will allow significantly higher throughput. CoronaHiT provides increased coverage for higher Ct samples, thereby increasing the number of high quality genomes that pass the GISAID QC threshold. This protocol will aid the rapid expansion of SARS-CoV-2 genome sequencing globally, to help control the pandemic.

genomics↗

bioRxiv2019

Phylogenomic analysis of Clostridium perfringens identifies isogenic strains in gastroenteritis outbreaks, and novel virulence-related features

Clostridium perfringens is a major enteric pathogen known to cause gastroenteritis in human adults. Although major outbreak cases are frequently reported, limited Whole Genome Sequencing (WGS) based studies have been performed to understand the genomic epidemiology and virulence gene content of C. perfringens-associated outbreak strains. We performed both genomic and phylogenetic analysis on 109 C. perfringens strains (human and food) isolated from disease cases in England and Wales between 2011-2017. Initial findings highlighted the enhanced discriminatory power of WGS in profiling outbreak C. perfringens strains, when compared to the current Public Health England referencing laboratory technique of Fluorescent Amplified Fragment Length Polymorphism (fAFLP). Further analysis identified that isogenic C. perfringens strains were associated with nine distinct care home-associated outbreaks over the course of a 5-year interval, indicating a potential common source linked to these outbreaks or transmission over time and space. As expected the enterotoxin CPE gene was encoded in all but 4 isolates (96.4%; 105/109), with virulence plasmids encoding cpe (particularly pCPF5603- and pCPF4969-family plasmids) extensively distributed (82.6%;90/109). Genes encoding accessory virulence factors, such as beta-2 toxin, were commonly detected (46.7%; 50/109), and genes encoding phage proteins were also frequently identified, with additional analysis indicating their contribution to increased virulence determinants within the genomes of gastroenteritis-associated C. perfringens. Overall this large-scale genomic study of gastroenteritis-associated C. perfringens suggested that 3 major sub-types underlie these outbreaks: strains carrying (1) pCPF5603 plasmid, (2) pCPF4969 plasmid, and (3) strains carrying cpe on transposable element Tn5565(usually integrated into chromosome). Our findings indicate that further studies will be required to fully probe this enteric pathogen, particularly in relation to developing intervention and prevention strategies to reduce food poisoning disease burden in vulnerable patients, such as the elderly.

microbiology↗

bioRxiv2019

Genetic variation associated with infection and the environment in the accidental pathogen Burkholderia pseudomallei

The environmental bacterium Burkholderia pseudomallei causes melioidosis, an endemic disease in tropical and sub-tropical countries. This bacterium occupies broad ecological niches ranging from soil, contaminated water, single-cell microbes and plants to human infection. Here, we performed genome-wide association studies for genetic determinants of environmental and human adaptation using a combined dataset of 1,011 whole genome sequences of B. pseudomallei from Northeast Thailand (discovery cohort, number of clinical isolates = 325, environmental isolates =428) and Australia (validation cohort, number of clinical isolates = 185, environmental isolates = 73), representing two major global disease hotspots. With these data, we (i) identified 47 genes from 26 distinct loci associated with clinical or environmental isolates from Thailand and replicated 13 loci in an independent Australian cohort; (ii) outlined the selective pressures on the genetic loci (dN/dS) and the frequency at which they had been gained or lost throughout their evolutionary history, reflecting the bacterial adaptability to a wide range of ecological niches; and (iii) highlighted loci implicated in human disease.

microbiology↗

bioRxiv2017

ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads

Antimicrobial resistance (AMR) is one of the major threats to human and animal health worldwide, yet few high-throughput tools exist to analyse and predict the resistance of a bacterial isolate from sequencing data. Here we present a new tool, ARIBA, that identifies AMR-associated genes and single nucleotide polymorphisms directly from short reads, and generates detailed and customisable output. The accuracy and advantages of ARIBA over other tools are demonstrated on three datasets from Gram-positive and Gram-negative bacteria, with ARIBA outperforming existing methods. ARIBA is available at https://github.com/sanger-pathogens/ariba.

bioinformatics↗