Biology subjects

Reding, C.

Publications and source records attributed to Reding, C..

6 recordsLinked to original sources

bioRxiv2026

OxBreaker: species-agnostic pipeline for the analysis of outbreaks using nanopore sequencing

Real-time genomic surveillance may mitigate the spread of health-care-associated infections, but whole-genome sequencing costs and the need for specialised expertise constrain its wide implementation in public health. Here we present OxBreaker, an automated and species-agnostic pipeline optimised for the high-resolution analysis of bacterial and plasmid genomes sequenced via Oxford Nanopore Technologies (ONT). OxBreaker streamlines the transition from raw reads to phylogenetic inference through automated reference selection and high-accuracy variant calling. It is accessible via a graphical user interface (GUI) that can be easily installed locally and operated by non-specialists. Benchmarking against technical and biological replicates of high-priority pathogens demonstrates high accuracy, with false positive variant rates reduced to 0-4 single-nucleotide polymorphisms (SNPs) for common species. We further validated the pipeline by accurately characterising previously published clonal and plasmid-mediated outbreaks, reproducing established phylogenies with improved accessibility. By providing a stable, scalable, open-source offline-compatible solution that matches the resolution of short-read platforms while maintaining the speed of long-read technology, OxBreaker is designed to facilitate the adoption of local, real-time genomic surveillance for frontline infection prevention and control.

genomics↗

bioRxiv2024

Improving Nitrofurantoin Resistance Prediction in Escherichia coli from Whole Genome Sequence by Integrating NfsA/B Enzyme Assays

Nitrofurantoin resistance in Escherichia coli is primarily caused by mutations damaging two enzymes, NfsA and NfsB. Studies based on small isolate collections with defined nitrofurantoin MICs have found significant random genetic drift in nfsA and nfsB making it extremely difficult to predict nitrofurantoin resistance from whole genome sequence (WGS) where both genes are not obviously disrupted by nonsense or frameshift mutations or insertional inactivation. Here we report a WGS survey of 200 E. coli from community urine samples, of which 34 were nitrofurantoin resistant. We characterised individual non-synonymous mutations seen in nfsA and nfsB among this collection using complementation cloning and assays of NfsA/B enzyme activity in cell extracts. We definitively identified R203C, H11Y, W212R, A112E, A112T and A122T in NfsA and R121C, Q142H, F84S, P163H, W46R, K57E and V191G in NfsB as amino acid substitutions that reduce enzyme activity sufficiently to cause resistance. In contrast, E58D, I117T, K141E, L157F, A172S, G187D and A188V in NfsA and G66D, M75I, V93A and A174E in NfsB, are functionally silent in this context. We identified that 9/166 (5.4%) of nitrofurantoin susceptible isolates were "pre-resistant", defined as having loss of function mutations in nfsA or nfsB. Finally, using NfsA/B enzyme activity assay and proteomics we demonstrated that 9/34 (26.5%) of nitrofurantoin resistant isolates carried functionally wild-type nfsB or nfsB/nfsA. In these cases, enzyme activity was reduced through downregulated gene expression. Our biological understanding of nitrofurantoin resistance is greatly improved by this analysis, but is still insufficient to allow its reliable prediction from WGS data.

microbiology↗

bioRxiv2023

Harvesting and amplifying gene cassettes confers cross-resistance to critically important antibiotics

Amikacin and piperacillin/tazobactam are frequent antibiotic choices to treat bloodstream infection, which is commonly fatal and most often caused by bacteria from the family Enterobacterales. Here we show that two gene cassettes located side-by-side in and ancestral integron similar to In37 have been "harvested" by insertion sequence IS26 as a transposon that is already globally disseminated among the Enterobacterales. This transposon encodes the enzymes AAC(6)-Ib-cr and OXA-1, reported, respectively, as amikacin and piperacillin/tazobactam resistance mechanisms. However, by studying bloodstream infection isolates from 769 patients from, three hospitals serving a population of 1.5 million people in South West England, we show that increased enzyme production due to mutation in an IS26/In37-derived hybrid promoter or, more commonly, transposon copy number amplification is required to simultaneously remove these two key therapeutic options; in many cases leaving only the last-resort antibiotic, meropenem. These findings may help improve the accuracy of predicting piperacillin/tazobactam treatment failure, allowing stratification of patients to receive meropenem or piperacillin/tazobactam, which may improve outcome and slow the emergence of meropenem resistance.

microbiology↗

bioRxiv2023

Genomic epidemiology of third-generation cephalosporin-resistant Escherichia coli from Argentinian pig and dairy farms reveals animal-specific patterns of co-resistance and resistance mechanisms

Control measures are being introduced globally to reduce the prevalence of antibiotic resistant (ABR) bacteria on farms. However, little is known about the current prevalence and molecular ecology of ABR in key opportunistic human pathogens such as Escherichia coli on South American farms. Working with 30 dairy cattle farms and 40 pig farms across two provinces in central-eastern Argentina, we report a comprehensive genomic analysis of third-generation cephalosporin resistance (3GC-R) in E. coli. 3GC-R isolates were recovered from 34.8% (cattle) and 47.8% (pigs) of samples from faecally contaminated sites. Phylogenetic analysis revealed substantial diversity suggestive of long-term horizontal transmission of 3GC-R mechanisms. Despite this, mechanisms such as CTX-M-15 and CTX-M-2 were detected more often in dairy farms, while CTX-M-8 and CMY-2, and co-carriage of amoxicillin/clavulanate resistance and florfenicol resistance were more commonly detected in pig farms. This suggests different selective pressures of antibiotic use in these two animal types, particularly the balance of fourth-versus third-generation cephalosporin use, and of amoxicillin/clavulanate and florfenicol use. We identified the {beta}-lactamase gene blaROB in 3GC-R E. coli, which has previously only been reported in the family Pasteurellaceae, including farmed animal pathogens. blaROB was found alongside a novel florfenicol resistance gene - ydhC - also mobilised from a pig pathogen as part of a new plasmid-mediated composite transposon, which is already widely disseminated. These data set a baseline from which to measure the effects of interventions aimed at reducing on-farm ABR and provide an opportunity to investigate zoonotic transmission of resistant bacteria in this region. ImportanceLittle is known about the ecology of critically important antibiotic resistance among opportunistic human pathogens (e.g. Escherichia coli) on South American farms. By studying 70 farms in central-eastern Argentina, we identified that third-generation cephalosporin resistance (3GC-R) in E. coli was mediated by mechanisms seen more often in certain species (pigs or dairy cattle) and that 3GC-R pig E. coli were more likely to be co-resistant to florfenicol and amoxicillin/clavulanate. This suggests that on-farm antibiotic usage is key to selecting the types of E. coli present on these farms. 3GC-R E. coli were highly phylogenetically variable and we identified the de novo mobilisation of the resistance gene blaROB, alongside a novel florfenicol resistance gene, from pig pathogens into E. coli on a mobile genetic element that was widespread in the study region. Overall, this shows the importance of surveying poorly studied regions for critically important antibiotic resistance which might impact human health.

microbiology↗

bioRxiv2020

Theory of (antimicrobial) relativity: When competitors determine a species' drug sensitivity.

Microbes associate in nature forming complex communities, but they are often studied in purified form. Here I show that neighbouring species enforce the re-distribution of carbon and antimicrobial molecules, predictably changing drug efficacy with respect to standard laboratory assays. A simple mathematical model, validated experimentally using pairwise competition assays, suggests that differences in drug sensitivity between the competing species causes the re-distribution of drug molecules without affecting carbon uptake. The re-distribution of drug is even when species have similar drug sensitivity, reducing drug efficacy. But when their sensitivities differ the re-distribution is uneven: The most sensitive species accumulates more drug molecules, increasing efficacy against it. Drug efficacy tests relying on samples with multiple species are considered unreliable and unpredictable, but study demonstrates that efficacy in these cases can be qualitatively predicted. It also suggests that living in communities can be beneficial even when all species compete for a single carbon source, as the relationship between cell density and drug required to inhibit their growth may be more complex than previously thought.

microbiology↗

bioRxiv2020

Clinical Antibiotic Resistance Patterns Across 70 Countries

We sought global patterns of antibiotic resistant pathogenic bacteria within the AMR Research Initiative database, Atlas. This consists of 6.5M clinical minimal inhibitory concentrations (MICs) observed in 70 countries in 633k patients between 2004 and 2017. Stratifying MICs according to pathogens (P), antibiotics (A) and countries (C), we found that the frequency of resistance was higher in Atlas than other publicly available databases. We determined global MIC distributions and, after showing they are coherent between years, we predicted MIC changes for 43 pathogens and 827 pathogen-antibiotic (PAs) pairings that exhibit significant resistance dynamics, including MIC increases and even decreases. However, many MIC distributions are multi-modal and some PA pairs exhibit sudden changes in MIC. We therefore analysed Atlas after replacing the clinical classification of pathogens into susceptible, intermediate and resistant with an information-optimal, cluster-based classifier to determine subpopulations with differential resistance that we denote S and R. Accordingly, S and R clusters for different PA pairs exhibit signatures of stabilising, directional and disruptive selection because their respective MICs can have different dynamics. Finally, we discuss clinical applications of a (R, dR/dt) phase plane whereby the MIC of R is regressed against change in MIC (dR/dt), a methodology we use to detect PA pairs at risk of developing clinical resistance.

microbiology↗