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

Abstract

Introduction. Cupriavidus pauculus 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. Gap Statement. This paper presents the first C. pauculus strain isolated from a hospital sink trap. There are only six genome assemblies available on NCBI for C. pauculus ; 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 Galleria mellonella; there is little published information describing these aspects of virulence. Aim. 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. Methodology. 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 in vitro biofilm formation compared to Pseudomonas aeruginosa and in vivo lethality in Galleria mellonella larvae. Results. The isolate was confirmed to be a strain of C. pauculus , 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 P. aeruginosa when measured at 37 °C in R2A broth. Lethality in G. mellonella larvae over 48 h was relatively low. Conclusion. The appearance of a multidrug-resistant strain of C. pauculus in a known pathogen reservoir within a clinical setting should be considered concerning. Further work should be completed to compare biofilm formation and in vivo 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.

A fatal case of cupriavidus pauculus causing septicemia after duodenal perforation: Case report from university teaching hospital

“…12 The MALDI-TOF MS, nanopore, 16S rRNA and next generation sequencing (NGS) technologies allows rapid and accurate detection of bacterial pathogens. 13 The isolate identified in the present case was multidrug resistant and showed resistance to various group of antibiotics including imipenem, amikacin, gentamicin, and tobramycin which appears to be in concordance with previous studies. The optimal therapeutic regimen for treating infections caused by C. pauculus remains unclear because of the limited data.…”

Characterization of heavy metal-resistant rhizobia and non-rhizobia isolated from root nodules of Trifolium sp. in a lead and zinc mining area

“…Our results showed that, Cupriavidus paucula had three heavy metals genes nccA, pbrA, and czcD. Butler et al (2022), also demonstrated that Cupriavidus paucula had many heavy metals resistance genes as cnrR, cnrY, czcA-D, czcI, czcN, and nikR that code for resistance to nickel, cobalt, cadmium and zinc.…”

The Urinary Metabolome of Newborns with Perinatal Complications

“…Moreover, 2,5-Furandicarboxylic acid is a microbial metabolite, a product of the oxidation of hydroxymethylfurfural (HMF) by the enzyme furfural/HMF oxidoreductase, which is found in the Gram-negative environmental bacterium Cupriavidus basilensis (family Burkholderiaceae). Dissemination of these environmental pathogens in hospital plumbing systems has been reported, driving nosocomial infection [ 65 ], and clinical isolates have been collected and sequenced. Moreover, 2,5-Furandicarboxylic acid increases with the level of fructose consumed [ 66 ].…”