Whole Genome Sequencing of Antimicrobial-Resistant Shigella sonnei Associated with Infection Acquired from International and Domestic Settings Reveals Gene Allelic Variants that Predict Global Lineages

Abstract

22Shigella spp. are a major cause of gastroenteritis worldwide, and S. sonnei is the most 23 common species isolated within the United States. Recently, advancements in technology have 24 made whole genome sequencing (WGS) readily available, and as such, laboratories are moving to 25 implement WGS in outbreak analysis, surveillance, and antimicrobial resistance (AMR) 26 monitoring of major foodborne pathogens. Accordingly, our study examined a collection of 22 27 antimicrobial resistant S. sonnei isolates from patients who either acquired the infections within 28 the United States or when travelling to international locations between 2009 to 2014. We applied 29 WGS to investigate both the relatedness of these isolates and the genetic determinants of AMR to 30 address the phenotypic differences seen in previous observations. We analyzed the phylogeny of 31 these strains and observed segmentation based on the previously described Global Lineages of S. 32 sonnei. Following these results, 17 gene sequences with lineage specific single nucleotide 33 polymorphisms (SNPs) were identified and developed into a lineage prediction test to determine 34 the Global Lineage of uncharacterized S. sonnei, which accurately predicted phylogenetic 35 segmentation and additionally showed specificity for S. sonnei genomes (97% accuracy, 38/39 36 genomes). Lastly, to determine differences between either the international or domestic isolates or 37 between the Global Lineages, the AMR determinants were identified. We found a variety of AMR 38 determinants within the genomes, and while the international and domestic S. sonnei carried 39 similar resistance determinants, differences between Global Lineages were observed. 40 United States and other developed countries, Shigella sonnei accounts for over 80% of all 45 shigellosis infections (4, 5). Research on S. sonnei has increased to investigate both the previously 46 under-described nature of this species and the shift in population within developed regions from 47 S. flexneri dominance to S. sonnei in recent history (6). Though many theories have been suggested 48 and the root cause of the shift from S. flexneri to S. sonnei still remains unknown, additional 49 research on S. sonnei is vital. 50 Characterization of S. sonnei has traditionally depended on pulsed-field gel electrophoresis 51 (PFGE) (7), but whole genome sequencing (WGS) has recently gained popularity due to its higher 52 resolution, increased availability, and lower costs. Accordingly, government and state laboratories 53 alike are updating characterization and surveillance techniques to utilize WGS. One area lacking 54 in observation is the phylogenomics of S. sonnei, specifically in the S. sonnei isolated within the 55 United States and how it relates to those found internationally. Holt et al. described a specific 56 clustering pattern within S. sonnei phylogeny known as the Global Lineage hypothesis, which 57showed that S. sonnei segment into 4 main clusters on a phylogenetic tree made using SNP variant 58 analysis ...