Phylogenomic Investigation of Increasing Fluoroquinolone Resistance among Belgian Cases of Shigellosis between 2013 and 2018 Indicates Both Travel-Related Imports and Domestic Circulation

Bogaerts, Bert; Winand, Raf; Braekel, Julien Van; Mattheus, Wesley; Keersmaecker, Sigrid C. J. De; Roosens, Nancy; Marchal, Kathleen; Vanneste, Kevin; Ceyssens, Pieter‐Jan

doi:10.3390/microorganisms9040767

Cited by 4 publications

(3 citation statements)

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“…Ciprofloxacin resistance is not only limited to the mobile qnrS gene. In Belgium in similar years as for this study, chromosomal mutations in the Shigella gyrA and parC have been reported to contribute to rising ciprofloxacin resistance [ 44 ]. In the ESBL-positive Shigella isolates of this study, 51/100 had a point mutation in gyrA and/or parC , with gyrA p.S83L and p.D87G and parC p.S80I being the most common mutations (Table S9).…”

Section: Resultsmentioning

confidence: 99%

“…sonnei and S. flexneri was caused by a combination of domestic circulation and international travel [44]. In contrast to bla CTX-M genes, ciprofloxacin resistance is mostly linked to chromosomal point mutations and only in a few cases by the mobile qnr gene.…”

Section: Introductionmentioning

confidence: 99%

“…Based on phenotypic and in-house genotyping assays [ 43 ], it was not previously possible to elucidate the location and genetic context of the corresponding ESBL genes in these isolates. A previous genomic-based study in Belgium demonstrated that an increase in ciprofloxacin resistance in S. sonnei and S. flexneri was caused by a combination of domestic circulation and international travel [ 44 ]. In contrast to bla CTX-M genes, ciprofloxacin resistance is mostly linked to chromosomal point mutations and only in a few cases by the mobile qnr gene.…”

Section: Introductionmentioning

confidence: 99%

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Using a combination of short- and long-read sequencing to investigate the diversity in plasmid- and chromosomally encoded extended-spectrum beta-lactamases (ESBLs) in clinical Shigella and Salmonella isolates in Belgium

et al. 2023

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For antimicrobial resistance (AMR) surveillance, it is important not only to detect AMR genes, but also to determine their plasmidic or chromosomal location, as this will impact their spread differently. Whole-genome sequencing (WGS) is increasingly used for AMR surveillance. However, determining the genetic context of AMR genes using only short-read sequencing is complicated. The combination with long-read sequencing offers a potential solution, as it allows hybrid assemblies. Nevertheless, its use in surveillance has so far been limited. This study aimed to demonstrate its added value for AMR surveillance based on a case study of extended-spectrum beta-lactamases (ESBLs). ESBL genes have been reported to occur also on plasmids. To gain insight into the diversity and genetic context of ESBL genes detected in clinical isolates received by the Belgian National Reference Center between 2013 and 2018, 100 ESBL-producing Shigella and 31 ESBL-producing Salmonella were sequenced with MiSeq and a representative selection of 20 Shigella and six Salmonella isolates additionally with MinION technology, allowing hybrid assembly. The bla CTX-M-15 gene was found to be responsible for a rapid rise in the ESBL Shigella phenotype from 2017. This gene was mostly detected on multi-resistance-carrying IncFII plasmids. Based on clustering, these plasmids were determined to be distinct from the circulating plasmids before 2017. They were spread to different Shigella species and within Shigella sonnei between multiple genotypes. Another similar IncFII plasmid was detected after 2017 containing bla CTX-M-27 for which only clonal expansion occurred. Matches of up to 99 % to plasmids of various bacterial hosts from all over the world were found, but global alignments indicated that direct or recent ESBL-plasmid transfers did not occur. It is most likely that travellers introduced these in Belgium and subsequently spread them domestically. However, a clear link to a specific country could not be made. Moreover, integration of bla CTX-M in the chromosome of two Shigella isolates was determined for the first time, and shown to be related to ISEcp1. In contrast, in Salmonella , ESBL genes were only found on plasmids, of which bla CTX-M-55 and IncHI2 were the most prevalent, respectively. No matching ESBL plasmids or cassettes were detected between clinical Shigella and Salmonella isolates. The hybrid assembly data allowed us to check the accuracy of plasmid prediction tools. MOB-suite showed the highest accuracy. However, these tools cannot replace the accuracy of long-read and hybrid assemblies. This study illustrates the added value of hybrid assemblies for AMR surveillance and shows that a strategy where even just representative isolates of a collection used for hybrid assemblies could improve international AMR surveillance as it allows plasmid tracking.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%