New publication: detecting minor populations important for predicting fluoroquinolone resistance Philip Fowler, 5th April 20238th December 2023 When predicting if an infection is resistant or susceptible to a specific antibiotic, it is all too easy to think that the infection is homogeneous and, in fact, many bioinformatic variant callers encourage that point of view. Or, at best, you can subvert the format of, say, a variant call file (VCF) by using the functionality designed to report diploidy for reporting (up to) two mixed populations. (What plant geneticists do I have no idea). Reality is likely messier, especially in a slow-growing persistent infection like tuberculosis and there have been previous studies suggesting that minor populations that are resistant to an antibiotic can come to dominate and should lead to a prediction of resistant. In this free-to-read paper, Dr Alice Brankin shows how allowing just two or more reads that support one of the two most common resistance-conferring mutations to levofloxacin and moxifloxacin, leads to a significant improvement in the sensitivity of genetics-based resistance prediction with no significant drop in specificity. This is important because the fluoroquinolones are present in several different drug regimes used to treat tuberculosis and brings their performance into line with other antibiotics (such as rifampicin and isoniazid) for which we believe we have a similar level of understanding of the mechanisms of resistance. Share this: Click to share on X (Opens in new window) X Click to share on Bluesky (Opens in new window) Bluesky Click to email a link to a friend (Opens in new window) Email Click to share on LinkedIn (Opens in new window) LinkedIn Click to share on Mastodon (Opens in new window) Mastodon Related antimicrobial resistance clinical microbiology tuberculosis
I’m hiring! 26th June 20251st July 2025 Thanks to funding from the OxCoD4TB project, I am hiring a postdoctoral research associate. This… Share this: Click to share on X (Opens in new window) X Click to share on Bluesky (Opens in new window) Bluesky Click to email a link to a friend (Opens in new window) Email Click to share on LinkedIn (Opens in new window) LinkedIn Click to share on Mastodon (Opens in new window) Mastodon Read More
New publication: fast human read decontamination for SARS-CoV-2 16th May 202216th May 2022 ReadItAndKeep is a new human-read decontamination algorithm that works by mapping the reads in a… Share this: Click to share on X (Opens in new window) X Click to share on Bluesky (Opens in new window) Bluesky Click to email a link to a friend (Opens in new window) Email Click to share on LinkedIn (Opens in new window) LinkedIn Click to share on Mastodon (Opens in new window) Mastodon Read More
citizen science BashTheBug has won an NIHR Let’s Get Digital Award! 4th September 20175th August 2018 The National Institute for Health Research hold an annual competition, called Let’s Get Digital, to… Share this: Click to share on X (Opens in new window) X Click to share on Bluesky (Opens in new window) Bluesky Click to email a link to a friend (Opens in new window) Email Click to share on LinkedIn (Opens in new window) LinkedIn Click to share on Mastodon (Opens in new window) Mastodon Read More