Carlos Reding

Senior Bioinformatician,

University of Oxford

Carlos is a senior bioinformatician at the Nuffield Department of Medicine, University of Oxford (UK). His research interests include modelling of living systems, microbial regulatory networks, and development of quantitative methods, all aimed at studying microbial diversity and evolution.

After completing his PhD in Prof Beardmore’s laboratory in Exeter (UK), and postdocs in Lars Steinmetz’s laboratory in Stanford (USA) and Matthew Avison’s laboratory in Bristol (UK), Carlos joined the Modernising Medical Microbiology research group. The group is led by Profs Derrick Crook, Tim Peto and Sarah Walker, and Carlos will develop a novel pipeline to help bridge the gap between genomics and the diagnosis of bacterial infections in the clinic.

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Research

93% PERSPIRATION, 6% ELECTRICITY, 4% EVAPORATION, 2% BUTTERSCOTCH RIPPLE

AMR predictions from genomic datasets

Writing algorithms to screen through 2,000+ farm and human isolates and predict antibiotic resistance from their genomes—without requiring a reference genome.

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Exploiting the electrical properties of RNA/DNA

Development of milifluidic impedance biosensors to detect the presence of SARS-CoV-2 RNA molecules from human samples.

Regulation of multi-drug efflux pump AcrAB-TolC

The abundance of AcrAB-TolC protein seldom correlates with the number copies of acr operons in Escherichia coli. The regulation of this efflux pump is complex, so to understand this phenomenon I modelled its entire regulatory network.

Slides

Featured Research

Predicting the re‐distribution of antibiotic molecules caused by inter‐species interactions in microbial communities

Carlos Reding

November 5, 2022 ISME Commun., 2:110

Drug efficacy measured using pure cultures is not maintained in the presence of neighbouring microbes. Using simple physical laws, I pinpoint the mechanism for this change to demonstrate that drug efficacy can be predictably manupulated, and suggest why microbes began to co-operate and form communities.

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Image-based spectrophotometer: The Light-Modulator (LiMO®)

Robert Beardmore, Ivana Gudelj, Kai Longshaw, Carlos Reding

February 12, 2020 IPO

We dreamt of phenotyping microbes and running evolution experiments with antibiotics at much higher-throughput, using many more strains and conditions than before. The solution had to be cheap, small, portable and accurate. So, with ERC funding, we set about leveraging low-cost robotics, adapting some LED lighting technology and using our own algorithm-building expertise to create the kind of device we wished we could buy.

Patent Website

The unconstrained evolution of fast and efficient antibiotic-resistant bacterial genomes

Carlos Reding, Mark Hewlett, Sarah Duxbury, Fabio Gori, Ivana Gudelj, Robert Beardmore

January 30, 2017 Nat. Ecol. Evol., 0050

For decades it was hypothesised that the growth rate of populations and their size engage in a trade-off, but the data was always inconclusive. Using bacteria, we set off to underpin a physical mechanism for this trade-off, and then explain why it is not always found in the data.

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Research Outputs

Work that I have published, it’s on its way, or patented

Punyawee Dulyayangkul, Jordan E Sealey, Winnie WY Lee, Carlos Reding, Kate J. Heesom, Naphat Satapoomin, Philip B. Williams, Matthew B. Avison . Improving Nitrofurantoin Resistance Prediction in Escherichia coli from Whole Genome Sequence by Integrating NfsA/B Enzyme Assays. Antimicrob. Agents Chemother. 68(6):e00242-24, 2024.

Carlos Reding, Naphat Satapoomin, Matthew B. Avison . Hound: A novel tool for automated mapping of genotype to phenotype in bacterial genomes assembled de novo. Brief. Bioinform. 25(2), 1–10, 2024.

Oliver Mounsey, Laura Marchetti, Julián Parada, Laura V. Alarcón, Florencia Aliverti, Matthew B. Avison, Carlos S. Ayala, Cristina Ballesteros, Caroline M. Best, Judy Bettridge, Andrea Buchamer, Daniel Buldain, Alicia Carranza, Maite Cortiisgro, David Demeritt, María Paula Escobar, Lihuel Gortari Castillo, María Jaureguiberry, Mariana F. Lucas, L. Vanina Madoz, María José Marconi, Nicolás Moiso, Hernán D. Nievas, Marco A. Ramirez Montes De Oca, Carlos Reding, Kristen K. Reyher, Lucy Vass, Sara Williams, José Giraudo, R. Luzbel De La Sota, Nora Mestorino, Fabiana A. Moredo, Matías Pellegrino . 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. Appl. Env. Microbiol., 90(1):e01791-23, 2024.

Carlos Reding . Predicting the re‐distribution of antibiotic molecules caused by inter‐species interactions in microbial communities. ISME Commun., 2:110, 2022.

Carlos Reding . Plasmid carriage and the unorthodox use of Fisher's theorem in evolutionary biology. bioRxiv (undergoing peer-review), 2022.

Carlos Reding, Pablo Catalán, Gunther Jansen, Tobias Bergmiller, Emily Wood, Phillip Rosenstiel, Hinrich Schulenburg, Ivana Gudelj, Robert Beardmore . The Antibiotic Dosage of Fastest Resistance Evolution: Gene Amplifications Underpinning the Inverted-U. Mol. Biol. Evol., 38(9):3847–3863, 2021.

PDF Dataset Poster DOI

Robert Beardmore, Ivana Gudelj, Kai Longshaw, Carlos Reding . Image-based spectrophotometer: The Light-Modulator (LiMO®). IPO, 2020.

Robert Beardmore, Mark Hewlett, Rafael Peña Miller, Carlos Reding, Ivana Gudelj, Justin R. Meyer . Canonical host-pathogen tradeoffs subverted by mutations with dual benefits. bioRxiv, 2019.

Carlos Reding, Mark Hewlett, Tobias Bergmiller, Ivana Gudelj, Robert Beardmore . Fluorescence photography of patterns and waves of bacterial adaptation at high antibiotic doses. bioRxiv, 2019.

PDF Poster Slides DOI

Carlos Reding, Mark Hewlett, Sarah Duxbury, Fabio Gori, Ivana Gudelj, Robert Beardmore . The unconstrained evolution of fast and efficient antibiotic-resistant bacterial genomes. Nat. Ecol. Evol., 0050, 2017.

Ayari Fuentes Hernández, Jessica Plucain, Fabio Gori, Rafael Peña Miller, Carlos Reding, Gunther Jansen, Hinrich Schulenburg, Ivana Gudelj, Robert Beardmore . Using a Sequential Regimen to Eliminate Bacteria at Sublethal Antibiotic Dosages. PLoS Biol., 13(4), 2015.

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Rafael Peña Miller, Ayari Fuentes Hernández, Carlos Reding, Ivana Gudelj, Robert Beardmore . Testing the optimality properties of a dual antibiotic treatment in a two-locus, two-allele model. J. R. Soc. Interface 11: 20131035., 2014.

Antonio Jiménez, Diana Boomgard, Patricia Rivera, Carlos Reding, José Pérez Fígares . Regeneración retiniana asociada a hidrocefalia congénita debida a mutación en el gen que codifica alfa-SNAP. Rev. Neurol. 41 (Supl 2): 64., 2005.