Genomic epidemiology of carbapenemase-producing Enterobacter cloacae complex in Argentina: a retrospective analysis (2016–2022)

Abstract

ABSTRACT Enterobacter spp., after Klebsiella pneumoniae, is among the most common hospital-acquired enterobacteria associated with antimicrobial resistance (AMR) worldwide, yet it remains underexplored. We determined the taxonomic and epidemiological distribution of 131 representative carbapenemase-producing Enterobacter spp. recovered from infections across Argentina between 2016 and 2022. The sample included one isolate per patient from 17 jurisdictions and 68 hospitals. Outbreak-related and surveillance isolates were excluded. Sequencing was performed using Illumina, and bioinformatic analyses were used to determine species (average nucleotide identity [ANI] ≥94%) and subspecies (ANI ≥98%) using BactInspector/fastANI. Sequence types (STs) were assigned by multilocus sequence typing (MLST) via PubMLST, and resistance genes were identified using AMRfinderPlus/Resfinder. Samples were obtained from (n; %) urine (43; 33%), blood (41; 31%), and other sites (47; 36%). Seven species were identified, with Enterobacter hormaechei (EH) predominating ( 120; 92%) and comprising five subspecies. E. hormaechei subsp. steigerwaltii was the most abundant (60; 45%), followed by E. hormaechei subsp. xiangfangensis (29; 22%). Enterobacter cloacae subsp. cloacae was underrepresented (3; 2.3%). KPC-2 was the predominant carbapenemase, followed by NDM-1 and OXA-163. A total of 58 STs were identified, 38 represented by a single isolate. EH included 50 STs, with the most abundant being ST88 (12; 9%), ST78 (12; 9%), and ST66 (8; 6%). No clear associations were observed between species/subspecies, clones, and carbapenemase types. Overall, the population structure of carbapenemase-producing Enterobacter spp. in Argentina is complex and diverse, characterized by multiple species, subspecies, clonal diversity, and varied carbapenemase types and combinations. Notably, 50% of the isolates belonged to E. hormaechei subsp. steigerwaltii, suggesting a major role of this subspecies in the dissemination of AMR. IMPORTANCE Carbapenemase-producing Enterobacter spp. rank as the most common Enterobacterales associated with carbapenemase production. Despite their clinical relevance, the taxonomy and population structure of this group remain poorly characterized. This study provides a comprehensive genomic overview of clinical carbapenemase-producing Enterobacter spp. circulating in Argentina, revealing a highly diverse population composed of species, subspecies, and clonal types, harboring mainly KPC-2, followed by NDM-1 and combinations. We identified international clones within E. hormaechei, such as ST88 and ST78, which may play important roles in the dissemination of antimicrobial resistance. Notably, 50% of the isolates belonged to E. hormaechei subsp. steigerwaltii, suggesting a major role of this subspecies in the dissemination of antimicrobial resistance (AMR). By improving our understanding of this complex bacterial group, this work supports the strengthening of antimicrobial resistance surveillance networks and the development of targeted strategies for infection control and antibiotic stewardship in healthcare settings. Carbapenemase-producing Enterobacter spp. rank as the most common Enterobacterales associated with carbapenemase production. Despite their clinical relevance, the taxonomy and population structure of this group remain poorly characterized. This study provides a comprehensive genomic overview of clinical carbapenemase-producing Enterobacter spp. circulating in Argentina, revealing a highly diverse population composed of species, subspecies, and clonal types, harboring mainly KPC-2, followed by NDM-1 and combinations. We identified international clones within E. hormaechei, such as ST88 and ST78, which may play important roles in the dissemination of antimicrobial resistance. Notably, 50% of the isolates belonged to E. hormaechei subsp. steigerwaltii, suggesting a major role of this subspecies in the dissemination of antimicrobial resistance (AMR). By improving our understanding of this complex bacterial group, this work supports the strengthening of antimicrobial resistance surveillance networks and the development of targeted strategies for infection control and antibiotic stewardship in healthcare settings.