Molecular characteristics of global β-lactamase-producing Enterobacter cloacae by genomic analysis

Abstract

Objective To analyze the characteristics of global β-lactamase-producing Enterobacter cloacae including the distribution of β-lactamase, sequence types (STs) as well as plasmid replicons. Methods All the genomes of the E. cloacae were downloaded from GenBank. The distribution of β-lactamase encoding genes were investigated by genome annotation after the genome quality was checked. The STs of these strains were analyzed by multi-locus sequence typing (MLST). The distribution of plasmid replicons was further explored by submitting these genomes to the genome epidemiology center. The isolation information of these strains was extracted by Per program from GenBank. Results A total of 272 out of 276 strains were found to carry β-lactamase encoding genes. Among them, 23 varieties of β-lactamase were identified, blaCMH (n = 130, 47.8%) and blaACT (n = 126, 46.3%) were the most predominant ones, 9 genotypes of carbapenem-hydrolyzing β-lactamase (CHβLs) were identified with blaVIM (n = 29, 10.7%) and blaKPC (n = 24, 8.9%) being the most dominant ones. In addition, 115 distinct STs for the 272 ß-lactamase-carrying E. cloacae and 48 different STs for 106 CHβLs-producing E. cloacae were detected. ST873 (n = 27, 9.9%) was the most common ST. Furthermore, 25 different plasmid replicons were identified, IncHI2 (n = 65, 23.9%), IncHI2A (n = 64, 23.5%) and IncFII (n = 62, 22.8%) were the most common ones. Notably, the distribution of plasmid replicons IncHI2 and IncHI2A among CHβLs-producing strains were significantly higher than theat among non-CHβLs-producing strains (p < 0.05). Conclusion Almost all the E. cloacae contained β-lactamase encoding gene. Among the global E. cloacae, blaCMH and blaACT were main blaAmpC genes. BlaTEM and blaCTX-M were the predominant ESBLs. BlaKPC, blaVIM and blaNDM were the major CHβLs. Additionally, diversely distinct STs and different replicons were identified.

Genomic, Epigenomic, and Transcriptional Characterisation of Carbapenem and Colistin Resistance Mechanisms inKlebsiella pneumoniaeandEnterobacterspecies

“…The Enterobacter species, G5, and G8 harboured bla CMH , which is the most common β-lactamase gene within the Enterobacter genus. Additionally, bla ACT which is also commonly found in this genus 30 , was present within A5 and G3. The Enterobacter species also harboured three other resistance genes: fosA , conferring resistance to Fosfomycin 31 , oqxAB , conferring resistance to quinolones, tigecycline, nitrofurantoin, several detergents, and disinfects 32 .…”

Draft genome sequence of Enterobacter cloacae ST473 harbouring blaCMH-3 isolated from a human patient diagnosed with recurrent bacteriuria in Nigeria

“…cloacae harbouring bla CMH-3 has been reported despite the detection of this bla AmpC variant in several publicly available E. cloacae genomes [2]. Here we report the draft genome sequence of an E.…”

“…Isolates from Enterobacter species are reported to present intrinsic resistance to ampicillin, amoxicillin-clavulanic acid, first- and second-generation cephalosporins due to the chromosomal encoded AmpC beta-lactamase [1]. Furthermore extended-spectrum beta-lactamases (ESBL) have also been reported in Enterobacter species [1, 2]. Analysis of 272 E.…”

“…cloacae genome assemblies belonging to a variety of STs showed that almost all of them encode a β-lactamase gene with bla CMH and bla ACT being the main bla AmpC genes [2]. Among the bla CMH genes found in this 272-genome dataset, bla CMH-6 ( n =41), bla CMH-4 ( n =26), bla CMH-5 ( n =21), bla CMH-3 ( n =21) and bla CMH-1 ( n =16) were the most prevalent [2]. bla CMH-1 has been identified as plasmid-mediated β-lactamase gene in E.…”

“…despite the detection of this blaAmpC variant in several publicly available E. cloacae genomes [2]. Here we report the draft genome sequence of an E. cloacae isolate collected in March 2021 at the Laboratory unit of Alex Ekwueme Federal Teaching Hospital Abakaliki, Ebonyi State, Nigeria from the urine sample of an adult male outpatient with recurrent urinary tract infection (UTI).…”