Factors associated with plasmid antibiotic resistance gene carriage revealed using large-scale multivariable analysis

Plasmids are major vectors of bacterial antibiotic resistance, but understanding of factors associated with plasmid antibiotic resistance gene (ARG) carriage is limited. We curated > 14,000 publicly available plasmid genomes and associated metadata. Duplicate and replicate plasmids were excluded; where possible, sample metadata was validated externally (BacDive database). Using Generalised Additive Models (GAMs) we assessed the influence of 12 biotic/abiotic factors (e.g. plasmid genetic factors, isolation source, collection date) on ARG carriage, modelled as a binary outcome. Separate GAMs were built for 10 major ARG types. Multivariable analysis indicated that plasmid ARG carriage patterns across time (collection years), isolation sources (human/livestock) and host bacterial taxa were consistent with antibiotic selection pressure as a driver of plasmid-mediated antibiotic resistance. Only 0.42% livestock plasmids carried carbapenem resistance (compared with 12% human plasmids); conversely, tetracycline resistance was enriched in livestock vs human plasmids, reflecting known prescribing practices. Interpreting results using a timeline of ARG type acquisition (determined by literature review) yielded additional novel insights. More recently acquired ARG types (e.g. colistin and carbapenem) showed increases in plasmid carriage during the date range analysed (1994–2019), potentially reflecting recent onset of selection pressure; they also co-occurred less commonly with ARGs of other types, and virulence genes. Overall, this suggests that following acquisition, plasmid ARGs tend to accumulate under antibiotic selection pressure and co-associate with other adaptive genes (other ARG types, virulence genes), potentially re-enforcing plasmid ARG carriage through co-selection

Factors associated with plasmid antibiotic resistance gene carriage revealed using large-scale multivariable analysis

Plasmids are major vectors of bacterial antibiotic resistance, but understanding of factors associated with plasmid antibiotic resistance gene (ARG) carriage is limited. We curated > 14,000 publicly available plasmid genomes and associated metadata. Duplicate and replicate plasmids were excluded; where possible, sample metadata was validated externally (BacDive database). Using Generalised Additive Models (GAMs) we assessed the influence of 12 biotic/abiotic factors (e.g. plasmid genetic factors, isolation source, collection date) on ARG carriage, modelled as a binary outcome. Separate GAMs were built for 10 major ARG types. Multivariable analysis indicated that plasmid ARG carriage patterns across time (collection years), isolation sources (human/livestock) and host bacterial taxa were consistent with antibiotic selection pressure as a driver of plasmid-mediated antibiotic resistance. Only 0.42% livestock plasmids carried carbapenem resistance (compared with 12% human plasmids); conversely, tetracycline resistance was enriched in livestock vs human plasmids, reflecting known prescribing practices. Interpreting results using a timeline of ARG type acquisition (determined by literature review) yielded additional novel insights. More recently acquired ARG types (e.g. colistin and carbapenem) showed increases in plasmid carriage during the date range analysed (1994–2019), potentially reflecting recent onset of selection pressure; they also co-occurred less commonly with ARGs of other types, and virulence genes. Overall, this suggests that following acquisition, plasmid ARGs tend to accumulate under antibiotic selection pressure and co-associate with other adaptive genes (other ARG types, virulence genes), potentially re-enforcing plasmid ARG carriage through co-selection

Genomic Epidemiology of Complex, Multispecies, Plasmid-Borne bla KPC Carbapenemase in Enterobacterales in the United Kingdom from 2009 to 2014.

Carbapenem resistance in Enterobacterales is a public health threat. Klebsiella pneumoniae carbapenemase (encoded by alleles of the bla KPC family) is one of the most common transmissible carbapenem resistance mechanisms worldwide. The dissemination of bla KPC historically has been associated with distinct K. pneumoniae lineages (clonal group 258 [CG258]), a particular plasmid family (pKpQIL), and a composite transposon (Tn4401). In the United Kingdom, bla KPC has represented a large-scale, persistent management challenge for some hospitals, particularly in North West England. The dissemination of bla KPC has evolved to be polyclonal and polyspecies, but the genetic mechanisms underpinning this evolution have not been elucidated in detail; this study used short-read whole-genome sequencing of 604 bla KPC-positive isolates (Illumina) and long-read assembly (PacBio)/polishing (Illumina) of 21 isolates for characterization. We observed the dissemination of bla KPC (predominantly bla KPC-2; 573/604 [95%] isolates) across eight species and more than 100 known sequence types. Although there was some variation at the transposon level (mostly Tn4401a, 584/604 [97%] isolates; predominantly with ATTGA-ATTGA target site duplications, 465/604 [77%] isolates), bla KPC spread appears to have been supported by highly fluid, modular exchange of larger genetic segments among plasmid populations dominated by IncFIB (580/604 isolates), IncFII (545/604 isolates), and IncR (252/604 isolates) replicons. The subset of reconstructed plasmid sequences (21 isolates, 77 plasmids) also highlighted modular exchange among non-bla KPC and bla KPC plasmids and the common presence of multiple replicons within bla KPC plasmid structures (>60%). The substantial genomic plasticity observed has important implications for our understanding of the epidemiology of transmissible carbapenem resistance in Enterobacterales for the implementation of adequate surveillance approaches and for control

Complete_Enterobacteriaceae_plasmids

This dataset comprises sequences of 2097 complete Enterobacteriaceae plasmids, curated following initial retrieval from the NCBI nucleotide database on 26th August 2016. The 2097 nucleotide sequences are provided as a FASTA file ('nucleotideseq.fa'). Corresponding protein sequences (n=12,582), generated by translating each plasmid in all 6 frames, are also provided ('translatedproteinseq.fa'). In addition, there are two zipped Genbank files providing more information on accessions. One contains the 2097 curated accessions; the other contains 6952 accessions that were obtained initially, prior to curation.<div><br></div><div>The protein dataset ('translatedproteinseq.fa') is a useful resource for MOB typing plasmids (a method of plasmid classification based on detection of relaxase proteins). To conduct MOB typing, download the protein dataset, as well as scripts provided in a related Figshare code repository: https://figshare.com/s/3f8973dea1fe03c4f62f</div><div>Further instructions can be found on the Github page referenced in the Description section of the Figshare code repository.</div><div><br></div><div><div>For more details about the dataset provided here, see the associated journal article: "A curated dataset of complete Enterobacteriaceae plasmids compiled from the NCBI nucleotide database", Orlek <i>et al. </i>in press.</div></div

MOBtyping

MOB typing is a method of plasmid classification. It is based on the detection of 'relaxase' proteins, which are involved in plasmid mobility. Here, we provide code for detecting relaxases / assigning MOB types, using more powerful (iterative) PSI-BLAST searching. PSI-BLAST harnesses position-specific information about conservation of relaxase protein residues amongst plasmids in a database. A curated plasmid database is provided here: https://figshare.com/s/18de8bdcbba47dbaba41<div><div><br></div><div>For details on using the code, see the corresponding Github repository (referenced below).</div><div><br></div><div>This Figshare site is integrated with the Github repository, with auto-sync is configured. Therefore, code contained here will mirror the code within the latest Github release, although any subsequent commits will not be synced. Hence, whilst the code can be downloaded here, to ensure you have the latest version of the repository, you may wish to download directly from the Github repository.<br></div></div

Field Trip: Sonic Acts of Noticing x Landscape Lab

In connection with Baltic Centre for Contemporary Art’s group exhibition Hinterlands (22 October 2022-30 April 2023), Foundation Press invited people to contribute their ideas to this collective book. Through an open call, we asked for written instructions proposing ways of making art in the landscape. To take part we are asking for the following: 1. Write a simple instruction (no more than 60 words) guiding someone to make something in the landscape. 2. Follow your own prompt to create an example. The exhibition Hinterlands is rooted in the landscape of the North East of England, whilst many of the instructions in this book suggest we get out into nature, we hope the instructions are flexible enough to be transposed to different places and situations – wherever you might find yourself. Ultimately instructions are stepping stones for you to shape your own process and ideas. This book celebrates brief moments of creative play – the unpredictable coming together of people in a place trying something out. It contains 35 instructions proposing ways that you could make something ‘in the landscape’. Whether these prompts sow the seeds for further making or perhaps simply produce an out-of-the- ordinary moment, we hope you enjoy the trip. FOUNDATION PRESS Contributors: Alison Diamond, Alison Lloyd, Anne Vibeke Mou, Backgroundcamel, Beth J Ross, Caroline Locke, Chloe Henson, Christina Kolaiti, Christine Mackey, David Eckersley, Deane Hodgson, Eileen White, E McKenna, Emily Birkett, Emily Jardine, Erika Cann, Fiona Jesson, Foundation Press, Froso Papadimitriou, Hannah Gawne/Walter and Edith, Jane Pitt, Janina Sabaliauskaite, Jenny Purrett, Karis Richardson & Molly Traynor, Kath Bell, Kathryn Frund, Laura Harrington, Lena Wurz, Marcia Ley, Matthias Neumann, Natasha Armstrong, Noah Petit Navarro, Sarah Legow, Soft Radicle, Sonic Acts of Noticin

Sonic acts of noticing: Future architecture rooms

Sonic Acts of Noticing Sonic Acts of Noticing deploys listening as critical spatial practice that can alter subjectivities and remake space in ways that emphasise care, ecological relations and emancipatory learning. We prototype an interactive audio-textual environment, where sound compositions comprised of field recordings from three sites in Sheffield, UK, collide with textual artefacts that are temporally coded to the audio. Provocations, quotations, and critical and journalistic writing, augment, subvert, amplify and dissonate listening, in relation to your navigation of the site and spaces of the street, opening new possibilities and configurations. Authors: Julia Udall, Alex De Little, Jon Orlek, Joe Gilmore and Richard Cook We share with you some of the high street sites where we are working, in Sheffield, interspersed wth some sneak peeks of our website as a tool to encourage careful listening. Cast: Julia Udall, Alex De Little, Jon Orlek Video Production: Jules Lister. Direction: Jon Orlek. Audio: Alex DeLittle. Annimation: Joe Gilmore and Richard Cook. Script Julia Udall and Jon Orlek. All videos and images for illustrative purposes only. Location: Sheffield, UK Our team is composed of two architectural designers and educators, a sound artist, and two web design-researchers. We come together to explore the potential of foregrounding the sonic in the creation of emancipatory spaces. We operate at the intersection of practice, teaching and research; the material, the sonic and the virtual, in order to find modes and sites of intervention that will support collective learning and transformative change. https://sonicactsofnoticing.org/

Sonic Acts of Noticing

This publication is a unique inclusive attempt to bring together institutions and independent practitioners in architecture and culture with a hybrid format. You will be wandering through fifteen practices which unfold the landscapes of care in different directions. These ideas are collated by the editor of this publication, research collective Nomaos, with support from architecture research practice dpr-barcelona. Thirteen of the contributors and the editor are among the 27 selected ideas of Future Architecture Platform in 2021, with two guest contributors to add more complexity and criticality into the discourse. Throughout the book you may notice that landscapes of care do not limit themselves to physical spaces. Although in some cases taken to be forests or rivers, it is in fact the crucial plurality of spaces, activities and relationships that characterises landscapes of care. Forests, bodies, and cities are only a small number of territories, but they represent the varied types of landscapes through which care can flow. We might therefore think of ‘landscapes of care’ as the practice linking different territories and bodies, and the landscape established by their interdependence. The previous six publications showcasing ideas of Future Architecture Creative Exchange centered around a monolithic, one-word theme. It is fitting that for this final instalment the theme consists of two words and where they overlap. A landscape that we can use to visualise this overlap might be the ecotone

Chromosomal_SNPs-InDels

Variant Call Format files for chromosome encoded SNPs/InDels identified for each isolate from this study