Use of whole genome sequencing in surveillance for antimicrobial-resistant  Shigella sonnei  infections acquired from domestic and international sources

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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.

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Microreact: visualizing and sharing data for genomic epidemiology and phylogeography

Silvia Argimón, Khalil Abudahab, Richard J. E. Goater … (2016)

Visualization is frequently used to aid our interpretation of complex datasets. Within microbial genomics, visualizing the relationships between multiple genomes as a tree provides a framework onto which associated data (geographical, temporal, phenotypic and epidemiological) are added to generate hypotheses and to explore the dynamics of the system under investigation. Selected static images are then used within publications to highlight the key findings to a wider audience. However, these images are a very inadequate way of exploring and interpreting the richness of the data. There is, therefore, a need for flexible, interactive software that presents the population genomic outputs and associated data in a user-friendly manner for a wide range of end users, from trained bioinformaticians to front-line epidemiologists and health workers. Here, we present Microreact, a web application for the easy visualization of datasets consisting of any combination of trees, geographical, temporal and associated metadata. Data files can be uploaded to Microreact directly via the web browser or by linking to their location (e.g. from Google Drive/Dropbox or via API), and an integrated visualization via trees, maps, timelines and tables provides interactive querying of the data. The visualization can be shared as a permanent web link among collaborators, or embedded within publications to enable readers to explore and download the data. Microreact can act as an end point for any tool or bioinformatic pipeline that ultimately generates a tree, and provides a simple, yet powerful, visualization method that will aid research and discovery and the open sharing of datasets.

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Global burden of Shigella infections: implications for vaccine development and implementation of control strategies.

K L Kotloff, J. Winickoff, B. Ivanoff … (1999)

Few studies provide data on the global morbidity and mortality caused by infection with Shigella spp.; such estimates are needed, however, to plan strategies of prevention and treatment. Here we report the results of a review of the literature published between 1966 and 1997 on Shigella infection. The data obtained permit calculation of the number of cases of Shigella infection and the associated mortality occurring worldwide each year, by age, and (as a proxy for disease severity) by clinical category, i.e. mild cases remaining at home, moderate cases requiring outpatient care, and severe cases demanding hospitalization. A sensitivity analysis was performed to estimate the high and low range of morbid and fatal cases in each category. Finally, the frequency distribution of Shigella infection, by serogroup and serotype and by region of the world, was determined. The annual number of Shigella episodes throughout the world was estimated to be 164.7 million, of which 163.2 million were in developing countries (with 1.1 million deaths) and 1.5 million in industrialized countries. A total of 69% of all episodes and 61% of all deaths attributable to shigellosis involved children under 5 years of age. The median percentages of isolates of S. flexneri, S. sonnei, S. boydii, and S. dysenteriae were, respectively, 60%, 15%, 6%, and 6% (30% of S. dysenteriae cases were type 1) in developing countries; and 16%, 77%, 2%, and 1% in industrialized countries. In developing countries, the predominant serotype of S. flexneri is 2a, followed by 1b, 3a, 4a, and 6. In industrialized countries, most isolates are S. flexneri 2a or other unspecified type 2 strains. Shigellosis, which continues to have an important global impact, cannot be adequately controlled with the existing prevention and treatment measures. Innovative strategies, including development of vaccines against the most common serotypes, could provide substantial benefits.

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Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe

Kathryn E. Holt, Stephen Baker, François-Xavier Weill … (2012)

Shigella are human-adapted Escherichia coli that have gained the ability to invade the human gut mucosa and cause dysentery 1,2 , spreading efficiently via low-dose fecal-oral transmission 3,4 . Historically, S. sonnei has been predominantly responsible for dysentery in developed countries, but is now emerging as a problem in the developing world, apparently replacing the more diverse S. flexneri in areas undergoing economic development and improvements in water quality 4-6 . Classical approaches have shown S. sonnei is genetically conserved and clonal 7 . We report here whole-genome sequencing of 132 globally-distributed isolates. Our phylogenetic analysis shows that the current S. sonnei population descends from a common ancestor that existed less than 500 years ago and has diversified into several distinct lineages with unique characteristics. Our analysis suggests the majority of this diversification occurred in Europe, followed by more recent establishment of local pathogen populations in other continents predominantly due to the pandemic spread of a single, rapidly-evolving, multidrug resistant lineage.

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Author and article information

Journal

Journal ID (nlm-ta): Microb Genom

Journal ID (iso-abbrev): Microb Genom

Journal ID (hwp): mgen

Journal ID (publisher-id): mgen

Title: Microbial Genomics

Publisher: Microbiology Society

ISSN (Electronic): 2057-5858

Publication date Collection: May 2019

Publication date (Electronic): 17 May 2019

Publication date PMC-release: 17 May 2019

Volume: 5

Issue: 5

Electronic Location Identifier: e000270

Affiliations

[1 ]departmentDepartment of Food Science , The Pennsylvania State University , University Park, Pennsylvania, USA

[2 ]Pennsylvania Department of Health , Harrisburg, Pennsylvania, USA

[3 ]departmentHuck Institutes of the Life Sciences , The Pennsylvania State University , University Park, Pennsylvania, USA

[4 ]departmentE. coli Reference Center , The Pennsylvania State University , University Park, Pennsylvania, USA

Author notes

*Correspondence: Edward G. Dudley, egd100@ 123456psu.edu

Author information

Edward G. Dudley https://orcid.org/0000-0003-1298-1603

Article

Publisher ID: 000270

DOI: 10.1099/mgen.0.000270

PMC ID: 6562246

PubMed ID: 31099740

SO-VID: c6422ba1-988b-4718-8261-fc7343829334

License:

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.