New sequence type of an Enterobacter cloacae Complex strain with the potential to become a high-risk clone

KNECHT, CAMILA A.; ALLENDE, NATALIA GARCÍA; ÁLVAREZ, VERÓNICA E.; CORMICK, BÁRBARA PRACK MC; MASSÓ, MARIANA G.; CAMPOS, JOSEFINA; FOX, BARBARA; ALONSO, FERNANDO MARTÍN; DONIS, NICOLÁS; CANIGIA, LILIANA FERNÁNDEZ; QUIROGA, MARÍA PAULA; CENTRÓN, DANIELA

Journal of Global Antimicrobial Resistance

Journal of Global Antimicrobial Resistance

Año: 2022

2213-7165

Objectives: Enterobacter cloacae complex (ECC) has lately awakened interest due to its increasingresistance to carbapenems codified by several genes all over the globe. Even though there are somesequence types (ST) which represent high-risk clones, there is substantial clonal diversity in theECC. This work aimed to perform whole-genome sequencing (WGS), genomic analysis andphylogenetic studies of a KPC-producing multidrug-resistant (MDR) ECC isolate from Argentina.Methods: We analysed the genome of an MDR KPC-producing ECC strain isolated from a urinesample from a patient in a hospital in Argentina. The WGS was done by Illumina MiSeq-I. Thegenome was assembled with SPAdes 3.9.0, and annotated with PROKKA, RAST, and Blast.Plasmids were identified with PlasmidFinder. Antibiotic resistance genes were detected usingRESfinder, CARD, and Blastn. STs were identified with pubMLST.Results: The strain was identified as Enterobacter hormaechei which is an important emerginghuman pathogen. No ST could be assigned; 6 out of 7 alleles of multilocus sequence typing(MLST) were the same as for E. hormaechei ST66, which is a high-risk clone. We found multipleacquired antibiotic resistance genes including blaKPC-2 in an IncM1 plasmid, and a secretion system VI, which can favour the prevalence of ECC strains while competing with other bacteria.2Conclusions: Due to its MLST profile being so close to E. hormaechei ST66, the acquisition ofmultiple resistance genes, and the presence of the secretion systems, the potential of this strain forbecoming a new high-risk clone cannot be discarded.