Genomic and Evolutionary Analysis of <i>Salmonella enterica</i> Serovar Kentucky Sequence Type 198 Isolated From Livestock In East Africa

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Abstract

Since its emergence in the beginning of the 90’s, multidrug-resistant (MDR) Salmonella enterica subsp . enterica serovar Kentucky has become a significant public health problem, especially in East Africa. This study aimed to investigate the antimicrobial resistance profile and the genotypic relatedness of Salmonella Kentucky isolated from animal sources in Ethiopia and Kenya (n=19). We also investigated population evolutionary dynamics through phylogenetic and pangenome analyses with additional publicly available Salmonella Kentucky ST198 genomes (n=229). All the 19 sequenced Salmonella Kentucky isolates were identified as ST198. Among these isolates, the predominant genotypic antimicrobial resistance profile observed in ten (59.7%) isolates included the aac(3)-Id, aadA7, strA- strB, bla _TEM-1B, sul1, and tet(A) genes, which mediated resistance to gentamicin, streptomycin/spectinomycin, streptomycin, ampicillin, sulfamethoxazole and tetracycline, respectively; and gyrA and parC mutations associated to ciprofloxacin resistance. Four isolates harbored plasmid types Incl1 and/or Col8282; two of them carried both plasmids. Salmonella Pathogenicity islands (SPI-1 to SPI-5) were highly conserved in the 19 sequenced Salmonella Kentucky isolates. Moreover, at least one Pathogenicity Island (SPI 1–4, SPI 9 or C63PI) was identified among the 229 public Salmonella Kentucky genomes. The phylogenetic analysis revealed that almost all Salmonella Kentucky ST198 isolates (17/19) stemmed from a single strain that has accumulated ciprofloxacin resistance-mediating mutations. A total of 8,104 different genes were identified in a heterogenic and still open Salmonella Kentucky ST198 pangenome. Considering the virulence factors and antimicrobial resistance genes detected in Salmonella Kentucky, the implications of this pathogen to public health and the epidemiological drivers for its dissemination must be investigated.

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Most cited references 61

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Trimmomatic: a flexible trimmer for Illumina sequence data

Anthony M. Bolger, Marc Lohse, Bjoern Usadel (2014)

Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.

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RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

Alexandros Stamatakis (2014)

Motivation: Phylogenies are increasingly used in all fields of medical and biological research. Moreover, because of the next-generation sequencing revolution, datasets used for conducting phylogenetic analyses grow at an unprecedented pace. RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood. Since the last RAxML paper in 2006, it has been continuously maintained and extended to accommodate the increasingly growing input datasets and to serve the needs of the user community. Results: I present some of the most notable new features and extensions of RAxML, such as a substantial extension of substitution models and supported data types, the introduction of SSE3, AVX and AVX2 vector intrinsics, techniques for reducing the memory requirements of the code and a plethora of operations for conducting post-analyses on sets of trees. In addition, an up-to-date 50-page user manual covering all new RAxML options is available. Availability and implementation: The code is available under GNU GPL at https://github.com/stamatak/standard-RAxML. Contact: alexandros.stamatakis@h-its.org Supplementary information: Supplementary data are available at Bioinformatics online.

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SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.

Anton Bankevich, Sergey Nurk, Dmitry Antipov … (2012)

The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

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Author and article information

Contributors

Mauro de Mesquita Sousa Saraiva: URI : https://loop.frontiersin.org/people/1465068

Valdinete Pereira Benevides: URI : https://loop.frontiersin.org/people/1591348

Núbia Michelle Vieira da Silva: URI : https://loop.frontiersin.org/people/1602434

Alessandro de Mello Varani: URI : https://loop.frontiersin.org/people/359804

Oliveiro Caetano de Freitas Neto: URI : https://loop.frontiersin.org/people/133195

Ângelo Berchieri Jr: URI : https://loop.frontiersin.org/people/786956

Enrique Jesús Delgado-Suárez: URI : https://loop.frontiersin.org/people/1315661

Alan Douglas de Lima Rocha: URI : https://loop.frontiersin.org/people/1563902

Celso José Bruno de Oliveira: URI : https://loop.frontiersin.org/people/862316

Journal

Journal ID (nlm-ta): Front Cell Infect Microbiol

Journal ID (iso-abbrev): Front Cell Infect Microbiol

Journal ID (publisher-id): Front. Cell. Infect. Microbiol.

Title: Frontiers in Cellular and Infection Microbiology

Publisher: Frontiers Media S.A.

ISSN (Electronic): 2235-2988

Publication date (Electronic): 20 June 2022

Publication date Collection: 2022

Volume: 12

Electronic Location Identifier: 772829

Affiliations

[1] ¹ Department of Pathology, Theriogenology, and One Health, Sao Paulo State University (FCAV-Unesp) , Jaboticabal, Brazil

[2] ² Department of Preventive Veterinary Medicine, College of Veterinary Medicine, The Ohio State University , Columbus, OH, United States

[3] ³ Department of Animal Science, Center for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB) , Areia, Brazil

[4] ⁴ Department of Technology, Sao Paulo State University (FCAV-Unesp) , Jaboticabal, Brazil

[5] ⁵ Department of Preventive Veterinary Medicine, Veterinary School, Federal University of Minas Gerais (UFMG) , Belo Horizonte, Brazil

[6] ⁶ Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México (UNAM) , Mexico City, Mexico

[7] ⁷ Aklilu Lemma Institute of Pathobiology, Addis Ababa University , Addis Ababa, Ethiopia

[8] ⁸ Centre for Microbiology Research, Kenya Medical Research Institute , Nairobi, Kenya

[9] ⁹ Global One Health Initiative (GOHi), The Ohio State University , Columbus, OH, United States

Author notes

Edited by: Ana Cristina Gales, UNIFESP, Brazil

Reviewed by: Thomas Jové, INSERM U1092 Anti-Infectieux: supports moléculaires des résistances et innovations thérapeutiques, France; Abdennaceur Hassen, Centre de Recherches et des Technologies des Eaux, Tunisia; Geovana Brenner Michael, Independent Researcher, Augsburg, Germany

*Correspondence: Celso José Bruno de Oliveira, celso.oliveira@ 123456academico.ufpb.br

This article was submitted to Clinical Microbiology, a section of the journal Frontiers in Cellular and Infection Microbiology

Article

DOI: 10.3389/fcimb.2022.772829

PMC ID: 9251186

PubMed ID: 35795189

SO-VID: 20708ed7-e5db-401a-8b1c-bdf300cc1141

License:

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

History

Date received : 08 September 2021

Date accepted : 20 April 2022

Page count

Figures: 4, Tables: 2, Equations: 0, References: 67, Pages: 12, Words: 5419

Funding

Funded by: Coordenação de Aperfeiçoamento de Pessoal de Nível Superior , doi 10.13039/501100002322;

Award ID: Finance Code 001, 88881.131934/2016-01, 88881.311776/2018-01

Funded by: Financiadora de Estudos e Projetos , doi 10.13039/501100004809;

Funded by: Conselho Nacional de Desenvolvimento Científico e Tecnológico , doi 10.13039/501100003593;

Funded by: Fundação de Amparo à Pesquisa do Estado de São Paulo , doi 10.13039/501100001807;

Genomic and Evolutionary Analysis of Salmonella enterica Serovar Kentucky Sequence Type 198 Isolated From Livestock In East Africa

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Abstract

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Point-Of-Care Testing for AMR

Most cited references 61

Trimmomatic: a flexible trimmer for Illumina sequence data

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.

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