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Abstract

Background

From 2019 to 2022, the French National Reference Centre for Antibiotic Resistance (NRC) received a total of 25 isolates of subsp. sequence type (ST)1740. All produced metallo-β-lactamase(s) and were from the Lyon area.

Aim

To understand these strains’ spread and evolution, more extended microbiological and molecular analyses were conducted.

Methods

Patients’ demographics and specimen type related to isolates were retrieved. All strains underwent short-read whole genome sequencing, and for 15, long-read sequencing to understand carbapenemase-gene acquisition. Clonal relationships were inferred from core-genome single nt polymorphisms (SNPs). Plasmids and the close genetic environment of each carbapenemase-encoding gene were analysed.

Results

Patients (10 female/15 male) were on average 56.6 years old. Seven isolates were recovered from infections and 18 through screening. With ≤ 27 SNPs difference between each other’s genome sequences, the 25 strains represented a clone dissemination. All possessed a chromosome-encoded gene inside a composite transposon flanked by two IS. While spreading, the clone independently acquired a -carrying plasmid of IncHI2 type (n = 12 isolates), or a -carrying plasmid of IncP-1 type (n = 1 isolate). Of the 12 isolates co-producing NDM-1 and VIM-4, seven harboured the colistin resistance gene ; the remaining five likely lost this gene through excision.

Conclusion

This long-term outbreak was caused by a chromosome-encoded NDM-1-producing ST1740 subsp. clone, which, during its dissemination, acquired plasmids encoding VIM-4 or IMP-13 metallo-β-lactamases. To our knowledge, IMP-13 has not prior been reported in Enterobacterales in France. Epidemiological and environmental investigations should be considered alongside microbiological and molecular ones.

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2024-03-14
2024-04-20
http://instance.metastore.ingenta.com/content/10.2807/1560-7917.ES.2024.29.11.2300521
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