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Volume 5, Issue 7

A global to local genomics analysis of ST1/RT027 identifies cryptic transmission events in a northern Arizona healthcare network Open Access

Abstract

is a ubiquitous, diarrhoeagenic pathogen often associated with healthcare-acquired infections that can cause a range of symptoms from mild, self-limiting disease to toxic megacolon and death. Since the early 2000s, a large proportion of cases have been attributed to the ribotype 027 (RT027) lineage, which is associated with sequence type 1 (ST1) in the multilocus sequence typing scheme. The spread of ST1 has been attributed, in part, to resistance to fluoroquinolones used to treat unrelated infections, which creates conditions ideal for colonization and proliferation. In this study, we analysed 27 isolates from a healthcare network in northern Arizona, USA, and 1352 publicly available ST1 genomes to place locally sampled isolates into a global context. Whole genome, single nucleotide polymorphism analysis demonstrated that at least six separate introductions of ST1 were observed in healthcare facilities in northern Arizona over an 18-month sampling period. A reconstruction of transmission networks identified potential nosocomial transmission of isolates, which were only identified via whole genome sequence analysis. Antibiotic resistance heterogeneity was observed among ST1 genomes, including variability in resistance profiles among locally sampled ST1 isolates. To investigate why ST1 genomes are so common globally and in northern Arizona, we compared all high-quality genomes and identified that ST1 genomes have gained and lost a number of genomic regions compared to all other genomes; analyses of other toxigenic sequence types demonstrate that this loss may be anomalous and could be related to niche specialization. These results suggest that a combination of antimicrobial resistance and gain and loss of specific genes may explain the prominent association of this sequence type with infection cases worldwide. The degree of genetic variability in ST1 suggests that classifying all ST1 genomes into a quinolone-resistant hypervirulent clone category may not be appropriate. Whole genome sequencing of clinical isolates provides a high-resolution surveillance strategy for monitoring persistence and transmission of and for assessing the performance of infection prevention and control strategies.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): antibiotic resistance , Clostridioides difficile , genomics and transmission
© 2019 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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2019-05-20
2024-04-16
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http://instance.metastore.ingenta.com/content/journal/mgen/10.1099/mgen.0.000271
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A global to local genomics analysis of Clostridioides difficile ST1/RT027 identifies cryptic transmission events in a northern Arizona healthcare network
M Gen 5, e000271 (2019); https://doi.org/10.1099/mgen.0.000271
/content/journal/mgen/10.1099/mgen.0.000271
/content/journal/mgen/10.1099/mgen.0.000271
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