Genomic characterization of multidrug-resistant <i>Salmonella</i> serovar Kentucky ST198 isolated in poultry flocks in Spain (2011–2017)

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Abstract

Salmonella Kentucky is commonly found in poultry and rarely associated with human disease. However, a multidrug-resistant (MDR) S. Kentucky clone [sequence type (ST)198] has been increasingly reported globally in humans and animals. Our aim here was to assess if the recently reported increase of S. Kentucky in poultry in Spain was associated with the ST198 clone and to characterize this MDR clone and its distribution in Spain. Sixty-six isolates retrieved from turkey, laying hen and broiler in 2011–2017 were subjected to whole-genome sequencing to assess their sequence type, genetic relatedness, and presence of antimicrobial resistance genes (ARGs), plasmid replicons and virulence factors. Thirteen strains were further analysed using long-read sequencing technologies to characterize the genetic background associated with ARGs. All isolates belonged to the ST198 clone and were grouped in three clades associated with the presence of a specific point mutation in the gyrA gene, their geographical origin and isolation year. All strains carried between one and 16 ARGs whose presence correlated with the resistance phenotype to between two and eight antimicrobials. The ARGs were located in the Salmonella genomic island (SGI-1) and in some cases ( bla _SHV-12 , catA1 , cmlA1, dfrA and multiple aminoglycoside-resistance genes) in IncHI2/ IncI1 plasmids, some of which were consistently detected in different years/farms in certain regions, suggesting they could persist over time. Our results indicate that the MDR S. Kentucky ST198 is present in all investigated poultry hosts in Spain, and that certain strains also carry additional plasmid-mediated ARGs, thus increasing its potential public health significance.

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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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The Sequence Alignment/Map format and SAMtools

Heng Li, Bob Handsaker, Alec Wysoker … (2009)

Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: rd@sanger.ac.uk

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Fast and accurate short read alignment with Burrows–Wheeler transform

Heng Li, Richard Durbin (2009)

Motivation: The enormous amount of short reads generated by the new DNA sequencing technologies call for the development of fast and accurate read alignment programs. A first generation of hash table-based methods has been developed, including MAQ, which is accurate, feature rich and fast enough to align short reads from a single individual. However, MAQ does not support gapped alignment for single-end reads, which makes it unsuitable for alignment of longer reads where indels may occur frequently. The speed of MAQ is also a concern when the alignment is scaled up to the resequencing of hundreds of individuals. Results: We implemented Burrows-Wheeler Alignment tool (BWA), a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. BWA supports both base space reads, e.g. from Illumina sequencing machines, and color space reads from AB SOLiD machines. Evaluations on both simulated and real data suggest that BWA is ∼10–20× faster than MAQ, while achieving similar accuracy. In addition, BWA outputs alignment in the new standard SAM (Sequence Alignment/Map) format. Variant calling and other downstream analyses after the alignment can be achieved with the open source SAMtools software package. Availability: http://maq.sourceforge.net Contact: rd@sanger.ac.uk

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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: 2022

Publication date (Electronic): 8 March 2022

Publication date PMC-release: 8 March 2022

Volume: 8

Issue: 3

Electronic Location Identifier: 000773

Affiliations

[ ¹ ] departmentVISAVET Health Surveillance Centre , Complutense University of Madrid , 28040 Madrid, Spain

[ ² ] departmentDepartment of Animal Health , Faculty of Veterinary Medicine, Complutense University of Madrid , 28040 Madrid, Spain

[ ³ ] departmentTRAGSATEC , Tecnologías y Servicios Agrarios S.A , 28037 Madrid, Spain

[ ⁴ ] departmentMolecular Basis of Adaptation , Department of Animal Health, Faculty of Veterinary, Complutense University of Madrid , 28040 Madrid, Spain

[ ⁵ ] departmentKoret School of Veterinary Medicine , The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem , 76100 Rehovot, Israel

[ ⁶ ] departmentDepartment of Veterinary Population Medicine , College of Veterinary Medicine, University of Minnesota , Saint Paul, MN 55455, USA

[ ⁷ ] departmentBioinformatics and Computational Biology Program , University of Minnesota , Rochester, MN 55455, 55455 Minnesota, USA

[ ⁸ ] departmentMolecular Biology and Microbiology Laboratory , Instituto Tecnológico Agrario de Castilla y León (ITACyL), Junta de Castilla y León , 47009 Valladolid, Spain

[ ⁹ ] departmentSubdirección General de Sanidad e Higiene Animal y Trazabilidad , Dirección General de la Producción Agraria, Ministerio de Agricultura, Pesca y Alimentación , 28010 Madrid, Spain

[ ¹⁰ ] departmentLaboratorio Central de Veterinaria , Ministerio de Agricultura, Pesca y Alimentación , 28110 Madrid, Spain