Journal of global antimicrobial resistance · 2026
Genomic analysis of an extensively drug-resistant Enterobacter cloacae NH77 from Thailand carrying an ∼82-kb chromosomal heavy-metal and antibiotic resistance island.
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Takarn Piyawan, Khongmee Aranya, Khamnoi Phadungkiat, Prommeenate Peerada, Phannachet Kulwadee
Аннотация
OBJECTIVE: This study aimed to characterize the mobile genetic context of an ∼ 82 kb chromosomal region showing co-localization of heavy-metal and an antibiotic resistance island in an extensively drug-resistant (XDR) Enterobacter cloacae NH77.
METHODS: Genomic DNA was sequenced using the Pacific Biosciences RS II platform. Long reads were de novo assembled with Canu v1.4 and annotated using Prokka v1.12b. The complete genome was analyzed to identify sequence type, antimicrobial resistance genes, integrons, insertion sequences, and plasmid type using MLST 2.0, ResFinder 4.7.2, Comprehensive Antibiotic Resistance Database (CARD) 4.0.1, INTEGRALL, and PlasmidFinder 2.1. Comparative analyses were performed using BLAST against Enterobacteriaceae genomes available in the NCBI GenBank database.
RESULTS: E. cloacae NH77 belonged to ST995 and was classified as XDR. The genome consisted of a 5 040 532 bp chromosome and a 41 179 bp IncN2 plasmid carrying blaNDM-1. A 49 286 bp chromosomal resistance gene island (RGI) contained two class 1 integrons (In191 and In705) associated with 15 antimicrobial resistance genes. BLAST analysis showed the high similarity of the ∼49 kb RGI to sequences found in the chromosomes of Enterobacter hormaechei and Enterobacter asburiae and Escherichia coli plasmid. The ∼49 kb RGI was located immediately downstream of a Tn7-sil-pco cluster, forming an ∼82 kb composite mobile resistance island. All sequences contained pcoSE located at the end of the ∼49 kb RGI.
CONCLUSIONS: This study describes an XDR-E. cloacae ST995 clinical isolate containing an ∼82 kb chromosomal resistance island comprising Tn7-sil-pco and a ∼49 kb RGI. The mobile genetic context suggests that pcoSE may function as a recombination target site for the ∼49 kb RGI.
METHODS: Genomic DNA was sequenced using the Pacific Biosciences RS II platform. Long reads were de novo assembled with Canu v1.4 and annotated using Prokka v1.12b. The complete genome was analyzed to identify sequence type, antimicrobial resistance genes, integrons, insertion sequences, and plasmid type using MLST 2.0, ResFinder 4.7.2, Comprehensive Antibiotic Resistance Database (CARD) 4.0.1, INTEGRALL, and PlasmidFinder 2.1. Comparative analyses were performed using BLAST against Enterobacteriaceae genomes available in the NCBI GenBank database.
RESULTS: E. cloacae NH77 belonged to ST995 and was classified as XDR. The genome consisted of a 5 040 532 bp chromosome and a 41 179 bp IncN2 plasmid carrying blaNDM-1. A 49 286 bp chromosomal resistance gene island (RGI) contained two class 1 integrons (In191 and In705) associated with 15 antimicrobial resistance genes. BLAST analysis showed the high similarity of the ∼49 kb RGI to sequences found in the chromosomes of Enterobacter hormaechei and Enterobacter asburiae and Escherichia coli plasmid. The ∼49 kb RGI was located immediately downstream of a Tn7-sil-pco cluster, forming an ∼82 kb composite mobile resistance island. All sequences contained pcoSE located at the end of the ∼49 kb RGI.
CONCLUSIONS: This study describes an XDR-E. cloacae ST995 clinical isolate containing an ∼82 kb chromosomal resistance island comprising Tn7-sil-pco and a ∼49 kb RGI. The mobile genetic context suggests that pcoSE may function as a recombination target site for the ∼49 kb RGI.