Coinfections in COVID-19

Introduce yourself

Let everyone know who you are, what you do and why you are interested in research in co-infections and secondary infections in COVID-19

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I’m Mike Cox, a microbial ecologist at University of Birmingham, UK. I mostly work on the respiratory microbiome in chronic and acute respiratory diseases using a range of techniques including 16S sequencing, metagenomics and culture of primary samples from patients.

With Nick Loman we’ve set up the forum to help create a research community around secondary infections which are often important in acute respiratory infections such as COVID-19, but there are few details emerging on the topic at the moment.

@mikeyj on twitter!

Hi all, I’m a microbiologist at the University of Warwick, UK. My group has a research focus on bacterial biofilm infections, including lung infections. We’ve been having conversations about the possible roles of lung microbiome / pathogens in COVID-19 - we being me, my technician Esther and PhD student Niamh, who will hopefully join this platform soon.

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Hi Everyone,

I’m Justine Rudkin, a postdoc in Daniel Wilson’s group in Oxford. I just wanted to see if you were aware of a new resource that has been made available to Biobank users- our group has created a dynamic linkage system which updates daily with covid-19 test results for Biobank participants. We originally set this up linkage system between the Public Health England reporting systems (SGSS) and Biobank to study bacterial infections in the Biobank cohort, but have now linked covid-19 test results too. We have a pre-print about the system- maybe it would be useful to you?

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Hi all,
I am Jose Bengoechea, microbiologists at Queen’s University Belfast. My team is working on host-pathogen interactions with a major focus on Gram negative pathogens. We have in place a co-infection model of human airway epithelium.

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Hi everyone,
I’m Ícaro Castro, a PhD student of Bioinfomatics program at University of São Paulo (USP), Brazil. I’m currently working with a meta transcriptomics approach to evaluate the microbiome-host interactions in infectious diseases. I’m interested to include COVID-19 in my research project to evaluate how the interaction of lung microbiome and host immunological system can impact the clinical outcome of patients.

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Hi everyone,

I am a human cell biologist at the University of Warwick working with bacteriophages both as antibacterials via testing in vitro model systems of phage therapy, but also as tools to detect bacterial infection/diagnostics. My lab has different human cell lines that mimic diseases caused by pathogens as well as phages targeting well-known pathogens that affect the respiratory system, such as E.coli K1, Staph.aureus, Acinetobacter baumannii etc.

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Hi All, thanks for stopping by! Feel free to create new topics on things of particular interest to you.

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@JustineRudkin this looks really cool. Any plans to make summaries of the organisms found available? Which ones are being detected and from which tests maybe?

Hi everyone!
I’m Victor Passarelli, an ID resident doctor at the Federal University of São Paulo, Brazil. My view is more from what we’re seeing on the daily practice in the hospital, but I’m an enthusiast on the topic and hopefully starting a post graduation on it soon.

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Hi everyone, I’m Vicky Enne, a microbiologist currently based at UCL. My main research interests are amr, rapid diagnostics & pneumonia. We’re currently running a study on secondary infections in covid patients in icu - more details in projects

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Hi all. My name is Lisa Lamberte, a postdoc working with Prof. Willem van Schaik at the University of Birmingham, UK. I am currently working on a project looking at the spread of antimicrobial resistance in the preterm infant gut microbiome. My interest in this forum lies in looking at secondary bacterial infections in infants and children, as well as the impact of COVID-19 on antimicrobial resistance.

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Hi everyone, my name is Ronan McCarthy, a microbiologist based in Brunel University London. My group works on understanding antibiotic resistance and biofilm formation in Gram negative pathogens including Pseudomonas aeruginosa and Acinetobacter baumannii. I am interested in exploring the role of biofilm formation and AMR in the bacterial pathogens that are being isolated from COVID-19 patients.

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Hello everyone

I am a PhD student at the veterinary virology lab of Ghent University (under lead of Hans Nauwynck; http://www.vetvirology.ugent.be/). We are currently working together with the Ghent University hospital in performing WGS of COVID-19 samples using ONT sequencing.

My personal scientific background is quite diverse:

  1. Immunological due to my 2 years of work on Trypanosoma brucei infections, focusing on its impact on splenic B cells in a murine trypanosomiasis model;

  2. Virology, focusing on viral diagnostics as my supervisor (Sebastiaan Theuns) has major expertise in long-read sequencing (ONT) based porcine diagnostics in both respiratory (e.g. PRRSV typing) and enteric (e.g. RVA) infections. Furthermore, our metagenomics approach allows the identification/characterization of viral disease complexes. This all in combination with in vitro growth of viruses in diverse cell lines.

  3. Bacterial diagnostics and AMR detection as my major contribution over the last months, focusing on M. bovis infection in cattle.

For the COVID-19 part we started a BOF-funded WGS and metagenomics project (in colaboration with the laboratory of Bruno Verhasselt and Linos Vandekerckhove both at the Ghent University Hospital). We are focusing on country-wide WGS and characterization of both viral and bacterial metagenomes and their potential roles in COVID-19 disease.

Any questions? Just shoot!

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Thanks for starting this group.
I am at Vedanta Biosciences. We are developing drugs based on defined bacterial consortia for uses including prevention of infections. These consist of standardized mixes of gut commensals. One of our focus areas is in preventing intestinal infections following antibiotic use. We too are interested in learning about superinfections that follow antibiotic use in COVID-19 patients.

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Hello all,

I’m Evelien Adriaenssens, a (relatively) new Group Leader at the Quadram Institute Biosciences in Norwich. My lab is specialised in bacteriophages and viromics, but mainly focused on the human gut. I’m just putting my name out there because I’m interested in the coinfections from both a viromics and phage therapy perspective, but I’m not doing any active COVID19 research at the moment.

Willing to help where necessary. We have a small collection of Klebsiella phages in the lab, which might be useful later on.

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Hi Eveline! Relatively new group leaders are my favourite sort :wink:

Great to have you here Bernat, always nice when industry are interested in a problem too!

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Hi everyone! I’m Olga Francino, researcher at the Vet School (Universitat Autonoma de Barcelona) and founding partner of Vetgenomics (microbiome and genetic diagnostics of pathogens, most of them zoonotic) and recently Nano1Health (infection control, AMR, genomics epidemiology, and personalized diagnostics from a One-Health approach).
Using Nanopore for the assembly of bacterial genomes and metagenomic data, AMR, and clinical metagenomics for infectious diseases in animal health. Now working in new collaborations for SARS-CoV-2 metagenomics identification, plus microbiome profile and secondary infections for COVID-19 outcome.

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Hi Everyone
I am Ellie Jameson, an environmental microbiologist working on bacteriophages at the University of Warwick. My group focuses on Klebsiella phages and I have sent these for use in compassionate phage therapy. I am interested in knowing what is causing secondary infections to understand if we could use phage therapy to improve patient outcomes and reduce time in ICU.

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Hi everyone
I am Tatiana Pinto, Associate Professor of Microbiology in Universidade Federal do Rio de Janeiro, Brazil. Our group focuses on surveillance of pneumococcus colonization (serotypes, AMR) in children and adults and surveillance of group B Streptococcus (GBS) and Candida in pregnant women. We don’t have expertise in Virology but we would like to explore and know more about Strep colonization/infection in COVID-19.

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