Comparative Genomics of Human- and Wastewater-Derived CPE Isolates in The Netherlands Reveals Shared and Complementary Characteristics

TL;DR

This study compares antibiotic-resistant bacteria from human and wastewater sources in the Netherlands, finding genetic similarities that suggest wastewater surveillance can complement human monitoring.

Contribution

The study demonstrates that wastewater isolates of CPE share genetic characteristics with human isolates, validating wastewater as a surveillance tool.

Findings

25 clusters of genetically similar CPE isolates were identified from human and wastewater sources.

Plasmid analysis showed highly homologous carbapenemase-containing plasmids in human and wastewater isolates.

Six clusters contained spatiotemporally related isolates from both human and wastewater sources.

Abstract

Wastewater-based surveillance is gaining interest worldwide as a complementary tool informing human surveillance of pathogens, among which are antibiotic-resistant bacteria. The current study investigated whether CPE detected within the Dutch human CPE surveillance could be identified among isolates that were independently retrieved from Dutch wastewater. Whole genomes of 203 wastewater- and 1278 human-retrieved isolates were compared using whole-genome multilocus sequence typing (wgMLST), resistome, and plasmid analyses. Overall, 25 clusters (16 E. coli, 9 K. pneumoniae) with genetically highly related variants from both niches were detected. The maximum allelic difference between human- and wastewater-derived isolates in clusters was on average 0.51% (23/4503 alleles, E. coli) and 0.22% (11/4978 alleles K. pneumoniae). For seven clusters, in-depth plasmid analysis was performed, showing highly homologous (87–100%) carbapenemase-containing plasmids from human- and wastewater-retrieved isolates. Six clusters contained wastewater and human isolates that were spatiotemporally related. The sequence identity at chromosomal and plasmid level confirms the presence of human-associated CPE variants in wastewater. Ongoing comparisons between isolates from the national human CPE surveillance and wastewater surveillance will shed more light on the added value of wastewater-based surveillance for monitoring of CPE and other (emerging) antibiotic resistances.

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