Abstract
Shigella species are a major cause of gastroenteritis worldwide, and Shigella sonnei is the most common species isolated within the United States. Previous surveillance work in Pennsylvania documented increased antimicrobial resistance (AMR) in S. sonnei associated with reported illnesses. The present study examined a subset of these isolates by whole genome sequencing (WGS) to determine the relationship between domestic and international isolates, to identify genes that may be useful for identifying specific Global Lineages of S. sonnei and to test the accuracy of WGS for predicting AMR phenotype. A collection of 22 antimicrobial-resistant isolates from patients infected within the United States or while travelling internationally between 2009 and 2014 was chosen for WGS. Phylogenetic analysis revealed both international and domestic isolates were one of two previously defined Global Lineages of S. sonnei, designated Lineage II and Lineage III. Twelve of 17 alleles tested distinguish these two lineages. Lastly, genome analysis was used to identify AMR determinants. Genotypic analysis was concordant with phenotypic resistance for six of eight antibiotic classes. For aminoglycosides and trimethoprim, resistance genes were identified in two and three phenotypically sensitive isolates, respectively. This article contains data hosted by Microreact.
Highlights
Shigella species are agents of bacillary gastrointestinal illness responsible for an estimated 80–165 million cases worldwide [1, 2]
SNP calling was performed after whole genome sequencing (WGS) of the 22 isolates obtained from the Pennsylvania Department of Health, and a maximum-likelihood tree was generated to visualize the relatedness of these S. sonnei
The four isolates from Pennsylvania mentioned above (SS-32, SS-37, SS-38 and SS-40) clustered with strains in Lineage II, and the other 18 isolates clustered with Lineage III
Summary
Shigella species are agents of bacillary gastrointestinal illness responsible for an estimated 80–165 million cases worldwide [1, 2]. Shigella is the fourth most common cause of bacterial foodborne illnesses in the USA [3]. Lineages I and IV were primarily found in Europe, while isolates of Lineage III appear to be the most widespread [8]. These studies, did not include any S. sonnei from the USA. A recent study in California concluded that Lineage III isolates were responsible for outbreaks occurring between 2014 and 2015 in the San
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