Rapid Increase of CTX-M-Producing Shigella sonnei Isolates in Switzerland: Spread of Common Plasmids and International Clones

Campos-Madueno, Edgar I.; Bernasconi, Odette J.; Moser, Aline I.; Keller, Peter M.; Luzzaro, Francesco; Maffioli, Carola; Bodmer, Thomas; Kronenberg, Andreas; Endimiani, Andrea (2020). Rapid Increase of CTX-M-Producing Shigella sonnei Isolates in Switzerland: Spread of Common Plasmids and International Clones. Antimicrobial agents and chemotherapy, 64(10) American Society for Microbiology 10.1128/AAC.01057-20

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The Swiss Centre for Antibiotic Resistance (ANRESIS) has recently noted an increase of extended-spectrum cephalosporin-resistant (ESC-R) S. sonnei isolates nationwide (3.8% in 2016 vs. 37.5% in 2019). To understand this phenomenon, we analyzed 25 representative isolates (of which 14 ESC-R) collected in Switzerland during 2016-2019. Whole-genome sequencing was achieved using both Illumina and Nanopore platforms. Both ESC-R and susceptible isolates belonged to ST152. The ESC-R isolates carried blaCTX-M-3 in IncI1-pST57 (n=5), blaCTX-M-15 in IncFII (F2:A-:B-) (n=5), blaCTX-M-15 in IncI1-pST16, and blaCTX-M-27, blaCTX-M-55, or blaCTX-M-134 in other IncFII plasmids (n=1 each). Plasmids having the same bla and Inc group exhibited high genetic identity to each other, but also to plasmids previously reported in other Enterobacterales. Core-genome analysis showed that there were 4 main clusters, each of which included strains that differed by <58 SNVs, both blaCTX-M-positive and blaCTX-M-negative isolates. Moreover, most isolates belonging to the same cluster shared an identical cgST. For instance, cluster-1 included 4 isolates of cgST113036, of which only 3 harbored the IncI1-pST57 blaCTX-M-3-positive plasmid. The 25 S. sonnei isolates were also subjected to phylogenetic comparison with deposited international strains. As a result, matching isolates (same cgST and differing by <8 SNVs) have been reported in the UK, USA, France, and the Netherlands. Overall, our results suggest that some common S. sonnei clusters can spread between continents and can be imported into other nations after international trips. Such clusters include, in part, isolates that do not possess blaESBL-harboring plasmids, indicating their tendency to acquire them from other Enterobacterales.

Item Type:

Journal Article (Original Article)

Division/Institute:

04 Faculty of Medicine > Service Sector > Institute for Infectious Diseases > Research
04 Faculty of Medicine > Service Sector > Institute for Infectious Diseases
04 Faculty of Medicine > Service Sector > Institute for Infectious Diseases > Clinical Microbiology
04 Faculty of Medicine > Service Sector > Institute for Infectious Diseases > General Bacteriology
04 Faculty of Medicine > Service Sector > Institute for Infectious Diseases > Mycobacteriology

UniBE Contributor:

Campos-Madueno, Edgar Igor; Bernasconi, Odette Joëlle; Moser, Aline; Keller, Peter Michael; Kronenberg, Andreas Oskar and Endimiani, Andrea

Subjects:

500 Science > 570 Life sciences; biology
600 Technology > 610 Medicine & health

ISSN:

0066-4804

Publisher:

American Society for Microbiology

Funders:

[4] Swiss National Science Foundation

Projects:

[1124] Whole Genome and Plasmid Sequencing for MDR Enterobacteriaceae Simultaneously Isolated from Multiple Human and Non-Human Settings: Deciphering Impact, Risks, and Dynamics for Resistance Transmission and Spread

Language:

English

Submitter:

Andrea Endimiani

Date Deposited:

28 Jul 2020 11:41

Last Modified:

01 Feb 2021 02:30

Publisher DOI:

10.1128/AAC.01057-20

BORIS DOI:

10.7892/boris.145419

URI:

https://boris.unibe.ch/id/eprint/145419

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