Hospital sink traps as a potential source of the emerging multidrug-resistant pathogen Cupriavidus pauculus: characterization and draft genome sequence of strain MF1

James Butler*, Sean D. Kelly, Katie J. Muddiman, Alexandros Besinis, Mathew Upton

*Corresponding author for this work

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Abstract

<jats:p> <jats:bold>Introduction.</jats:bold> <jats:italic> <jats:named-content content-type="species"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.8562" xlink:type="simple">Cupriavidus pauculus</jats:ext-link> </jats:named-content> </jats:italic> is historically found in soil and water but has more recently been reported to cause human infection and death. Hospital sink traps can serve as a niche for bacterial persistence and a platform for horizontal gene transfer, with evidence of dissemination of pathogens in hospital plumbing systems driving nosocomial infection.</jats:p> <jats:p> <jats:bold>Gap Statement.</jats:bold> This paper presents the first <jats:italic> <jats:named-content content-type="species"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.8562" xlink:type="simple">C. pauculus</jats:ext-link> </jats:named-content> </jats:italic> strain isolated from a hospital sink trap. There are only six genome assemblies available on NCBI for <jats:italic> <jats:named-content content-type="species"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.8562" xlink:type="simple">C. pauculus</jats:ext-link> </jats:named-content> </jats:italic>; two of these are PacBio/Illumina hybrids. This paper presents the first ONT/Illumina hybrid assembly, with five contigs. The other assemblies available consist of 37, 38, 111 and 227 contigs. This paper also presents data on biofilm formation and lethal dose in <jats:italic>Galleria mellonella</jats:italic>; there is little published information describing these aspects of virulence.</jats:p> <jats:p> <jats:bold>Aim.</jats:bold> The aims were to identify the isolate found in a hospital sink trap, characterize its genome, and assess whether it could pose a risk to human health.</jats:p> <jats:p> <jats:bold>Methodology.</jats:bold> The genome was sequenced, and a hybrid assembly of short and long reads produced. Antimicrobial susceptibility was determined by the broth microdilution method. Virulence was assessed by measuring <jats:italic>in vitro</jats:italic> biofilm formation compared to <jats:italic> <jats:named-content content-type="species"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.2553" xlink:type="simple">Pseudomonas aeruginosa</jats:ext-link> </jats:named-content> </jats:italic> and <jats:italic>in vivo</jats:italic> lethality in <jats:italic>Galleria mellonella</jats:italic> larvae.</jats:p> <jats:p> <jats:bold>Results.</jats:bold> The isolate was confirmed to be a strain of <jats:italic> <jats:named-content content-type="species"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.8562" xlink:type="simple">C. pauculus</jats:ext-link> </jats:named-content> </jats:italic>, with a 6.8 Mb genome consisting of 6468 coding sequences and an overall G+C content of 63.9 mol%. The genome was found to contain 12 antibiotic resistance genes, 8 virulence factor genes and 33 metal resistance genes. The isolate can be categorized as resistant to meropenem, amoxicillin, amikacin, gentamicin and colistin, but susceptible to cefotaxime, cefepime, imipenem and ciprofloxacin. Clear biofilm formation was seen in all conditions over 72 h and exceeded that of <jats:italic> <jats:named-content content-type="species"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.2553" xlink:type="simple">P. aeruginosa</jats:ext-link> </jats:named-content> </jats:italic> when measured at 37 °C in R2A broth. Lethality in <jats:italic>G. mellonella</jats:italic> larvae over 48 h was relatively low.</jats:p> <jats:p> <jats:bold>Conclusion.</jats:bold> The appearance of a multidrug-resistant strain of <jats:italic> <jats:named-content content-type="species"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.8562" xlink:type="simple">C. pauculus</jats:ext-link> </jats:named-content> </jats:italic> in a known pathogen reservoir within a clinical setting should be considered concerning. Further work should be completed to compare biofilm formation and <jats:italic>in vivo</jats:italic> virulence between clinical and environmental strains, to determine how easily environmental strains may establish human infection. Infection control teams and clinicians should be aware of the emerging nature of this pathogen and further work is needed to minimize the impact of contaminated hospital plumbing systems on patient outcomes.</jats:p>
Original languageEnglish
Number of pages0
JournalJournal of Medical Microbiology
Volume71
Issue number2
Early online date3 Feb 2022
DOIs
Publication statusPublished - 3 Feb 2022

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