Prospective One-Health investigation into low-abundant extended-spectrum β-lactamase producing Enterobacterales enables detection of potential dissemination events and persistence

Abstract

Background: Following a one-health approach, we sought to determine reservoirs of extended-spectrum β-lactamase (ESBL)-producing Enterobacterales (ESBL-PE), other than Escherichia coli or Klebsiella pneumoniae complex species (i.e., low-abundant species), and their associated ESBL genes and plasmid-replicon profiles.

Methods: From 06/2017-05/2019, ESBL-PE isolates were recovered from clinical samples routinely collected at the University Hospital Basel (Basel, Switzerland), as well as from wastewater and foodstuffs collected monthly at predefined locations throughout the city of Basel. Whole-genome sequencing was performed for characterization of ESBL-PE isolates.

Results: Among 1634 isolates recovered, 114 (7%) belonged to 17 low-abundant ESBL-PE species. Seven species originated from more than one compartment, mainly from clinical and wastewater samples (6/17). Sixteen different ESBL genes were identified, with bla_CTX-M-15 (27%), bla_FONA-6 (23%) and bla_SHV-12 (16%) being most frequent. The bla_CTX-M-1 gene was the only ESBL gene recovered from all three compartments. Putative plasmids constituted 60% of ESBL gene-containing contigs, while chromosomes comprised 40%. Foodstuff isolates showed the highest proportion (91%, 41/45) of ESBL genes located on chromosomes, whereas wastewater isolates had the highest proportion (95%, 37/39) of putative plasmids. Multi-replicon combinations were identified in 81% of the isolates. Epidemiological links were found among some clinical and wastewater isolates.

Conclusions: The dominance of bla_CTX-M-15 among low-abundant ESBL-PE species supports its species-independent transmission potential beyond the E. coli and K. pneumoniae complex, and bla_CTX-M-1 may be transmitted between strains recovered from different compartments. The substantial overlap between low-abundant ESBL-PE present in wastewater and clinical samples supports the utility of wastewater surveillance for antibiotic resistance monitoring.

Keywords: Antimicrobial resistance gene reservoirs; Clinical and environmental samples; ESBL; Foodstuffs; Incompatibility group genes; KESC group; Plasmid-replicons; Wastewater.