Intensive care unit sinks are persistently colonized with multidrug resistant bacteria and mobilizable, resistance-conferring plasmids

Abstract

Contamination of hospital sinks with microbial pathogens presents a serious potential threat to patients, but our understanding of sink colonization dynamics is largely based on infection outbreaks. Here, we investigate the colonization patterns of multidrug-resistant organisms (MDROs) in intensive care unit sinks and water from two hospitals in the USA and Pakistan collected over 27 months of prospective sampling. Using culture-based methods, we recovered 822 bacterial isolates representing 104 unique species and genomospecies. Genomic analyses revealed long-term colonization by Pseudomonas spp. and Serratia marcescens strains across multiple rooms. Nanopore sequencing uncovered examples of long-term persistence of resistance-conferring plasmids in unrelated hosts. These data indicate that antibiotic resistance (AR) in Pseudomonas spp. is maintained both by strain colonization and horizontal gene transfer (HGT), while HGT maintains AR within Acinetobacter spp. and Enterobacterales, independent of colonization. These results emphasize the importance of proactive, genomic-focused surveillance of built environments to mitigate MDRO spread. IMPORTANCE Hospital sinks are frequently linked to outbreaks of antibiotic-resistant bacteria. Here, we used whole-genome sequencing to track the long-term colonization patterns in intensive care unit (ICU) sinks and water from two hospitals in the USA and Pakistan collected over 27 months of prospective sampling. We analyzed 822 bacterial genomes, representing over 100 different species. We identified long-term contamination by opportunistic pathogens, as well as transient appearance of other common pathogens. We found that bacteria recovered from the ICU had more antibiotic resistance genes (ARGs) in their genomes compared to matched community spaces. We also found that many of these ARGs are harbored on mobilizable plasmids, which were found shared in the genomes of unrelated bacteria. Overall, this study provides an in-depth view of contamination patterns for common nosocomial pathogens and identifies specific targets for surveillance.

Identification of a novel CG307 sub-clade in third-generation-cephalosporin-resistant Klebsiella pneumoniae causing invasive infections in the USA

“…Interestingly, for both CG307 and CG29 strains, we observed highly genetically related bacteria causing infections over a several years’ time frame (), suggesting potential environmental sources as has been observed for Pseudomonas spp. [60] and vancomycin-resistant Enterococcus faecium [61]. The lack of clear epidemiological links between infected patients means that standard infection control approaches would be unlikely to detect such transmission events, emphasizing the potential complementary role that WGS could play in infection control efforts if real-time data were available [62].…”

Bacteria use a catabolic patchwork pathway of apparently recent origin for degradation of the synthetic buffer compound TRIS

“…For example, the antibiotic fosfomycin, which is produced and administered as a TRIS salt, was found at concentrations of 0.13 mM in the influent and 0.015 mM in the effluent of a wastewater treatment plant of a fosfomycin production plant [ 36 ], suggesting the presence of similar concentrations of its counterion TRIS. Second, sinks and water purification systems are hotspots for HGT [ 11 , 37 , 38 ], which additionally favors the evolution of novel catabolic pathways.…”

Practical Lessons on Antimicrobial Therapy for Critically Ill Patients

“…Antimicrobial stewardship activities and everyday hygiene audit practices or resistant microbe tracing programs were foregone in the face of the overwhelming COVID-19 spread. This is particularly concerning, as not only are patients often carrying multi-drug-resistant pathogens, but these pathogens can colonise the ICU environment [40].…”