Genomic epidemiology and longitudinal sampling of ward wastewater environments and patients reveals complexity of the transmission dynamics of bla_KPC-carbapenemase-producing Enterobacterales in a hospital setting

Abstract

BackgroundHealthcare-associated wastewater reservoirs and asymptomatic gastrointestinal patient colonisation by carbapenemase-producing Enterobacterales (CPE) can be important in nosocomial CPE dissemination and infection. We characterised these niches and within-niche diversity in a blaKPC-associated CPE (KPC-E) endemic healthcare setting, to better understand transmission potential.MethodsWe systematically sampled wastewater sites and patients across three units (six wards) over 6-12 months in 2016 in a KPC-E endemic hospital. We used Illumina sequencing to characterise up to five isolates per sample. Recombination-adjusted phylogenies were used to define genetically related strains; assembly and mapping-based typing approaches were used to characterise antimicrobial resistance gene and insertion sequence profiles, and Tn4401 types/target site sequences. The wider accessory genome was evaluated in a subset of the largest clusters, and those crossing niches.FindingsWastewater site KPC-E-positivity was substantial (101/349 sites [28.9%] positive, 319/4,488 [7.1%] sampling events positive); 183/4,425 (4.1%) of patients were CPE culture-positive over the same timeframe. 13 species and 109 KPC-E strains were observed across niches, and 24% of wastewater and 26% of patient KPC-E-positive samples harboured ≥1 strain. Most diversity was explained by the individual niche, suggesting highly localised factors are important in selection and spread. Tn4401+target site sequence (TSS) diversity was greater in wastewater sites (p<0.001), suggesting these might favour Tn4401-associated transposition/evolution and dissemination. Shower/bath and sluice/mop-associated sites were more likely to be KPC-E-positive (Adjusted Odds Ratio [95% CI]: 2.69 [1.44-5.01], p=0.0019 and 2.60 [1.04-6.52], p=0.0410, respectively). Different strains had different transmission and blaKPC dissemination dynamics.InterpretationThere may be substantial KPC-E colonisation of wastewater sites and patients in KPC-E-endemic healthcare settings. Niche-specific factors, and different strains with different transmission dynamics influence carbapenemase gene dissemination. New transmission models incorporating complex, multi-level dynamics are needed to better quantify CPE dissemination to inform interventions and reduce transmission.FundingThis study was supported by the National Institute for Health Research, UK.RESEARCH IN CONTEXTEvidence before this studyWe searched PubMed to identify previous studies using whole genome sequencing (WGS) to characterise in-hospital dissemination and persistence of carbapenemase-producing Enterobacterales (CPEs) or the presence of CPEs in hospital wastewater reservoirs. In our search (01/Jan/1996-30/Sep/2021) we used the terms ((((CPE) OR (KPC)) AND (healthcare-associated OR nosocomial OR hospital-associated)) AND (genom*) AND ((environment OR patient))). We had no restrictions on language. We found sixty-six studies, but these were limited by: (i) evaluating single species or lineages only (n=34), (ii) including patients or environmental outbreaks only, and not both (n=23), (iii) sampling only small numbers (n<50) of patients or environmental sites (n=26), or (iv) performing no evaluation of within-niche diversity (n=64). 13 studies were not relevant (e.g. investigating non-hospital locations, ex vivo or in vivo evolution), two studies did not use WGS, and one study was not primary research.Added value of this studyWe provide a comprehensive assessment of healthcare-associated CPE dissemination and persistence in hospital wastewater reservoirs through systematic sampling of a large number of environmental sites (n=349 sites, n=4,488 samples) and patients (n=4,425) over 6-12 months in a single hospital. For all CPE-positive environmental samples (n=319) and a subset of CPE-positive patient samples (n=97/399 [24.3%] samples from 76/183 [41.5%] CPE-positive patients), we sampled up to five CPE isolates per sample to capture within-niche diversity, and used short-read Illumina WGS (n=1,732 isolates successfully sequenced) to characterise within-niche diversity, changes in colonisation over time, and genetic overlap between patient and environmental niches.Implications of all the available evidenceThrough a detailed and resource-intensive study we captured the dynamics of seeding and dissemination of important carbapenemase genes amongst patients and environmental reservoirs within a hospital. We found differential colonisation and dissemination dynamics for different species and lineages within and between niches. Improved approaches incorporating variable within-niche diversity, accessory distances and horizontal gene transfer in transmission evaluations are required to better understand CPE dissemination and persistence, in order to direct interventions limiting transmission.

Genomic dissection of endemic carbapenem resistance: metallo-beta-lactamase gene dissemination through clonal, plasmid and integron transfer pathways

“…This propagator pair was able to act as a reservoir of blaIMP-4, likely through occupying an environmental niche as we noted during sampling of ICU sinks. The colonisation of hospital plumbing by CPOs has been well documented 9,[28][29][30][31] , including blaIMP-4harbouring S. marcescens in an Australian setting that was unable to be eradicated 32 . This environmental colonisation enabled not only clonal spread of blaIMP-4 harbouring S. marcescens but also drove diversification through inter-strain transfer of blaIMP-4 IncC plasmids and inter-plasmid transfer of the blaIMP-4 class I integron.…”