Species-wide whole genome sequencing reveals historical global spread and recent local persistence in Shigella flexneri

Shigella flexneri is the most common cause of bacterial dysentery in low-income countries. Despite this, S. flexneri remains largely unexplored from a genomic standpoint and is still described using a vocabulary based on serotyping reactions developed over half-a-century ago. Here we combine whole genome sequencing with geographical and temporal data to examine the natural history of the species. Our analysis subdivides S. flexneri into seven phylogenetic groups (PGs); each containing two-or-more serotypes and characterised by distinct virulence gene complement and geographic range. Within the S. flexneri PGs we identify geographically restricted sub-lineages that appear to have persistently colonised regions for many decades to over 100 years. Although we found abundant evidence of antimicrobial resistance (AMR) determinant acquisition, our dataset shows no evidence of subsequent intercontinental spread of antimicrobial resistant strains. The pattern of colonisation and AMR gene acquisition suggest that S. flexneri has a distinct life-cycle involving local persistence.

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Evolutionary history of Tibetans inferred from whole-genome sequencing

PLoS Genetics ◽

10.1371/journal.pgen.1006675 ◽

2017 ◽

Vol 13 (4) ◽

pp. e1006675 ◽

Cited By ~ 37

Author(s):

Hao Hu ◽

Nayia Petousi ◽

Gustavo Glusman ◽

Yao Yu ◽

Ryan Bohlender ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Evolutionary History ◽

Whole Genome ◽

History Of

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Use of whole-genome sequencing for characterisation of a ST119 NDM-1-producing Acinetobacter pittii from a patient in Denmark with no history of recent travel

International Journal of Antimicrobial Agents ◽

10.1016/j.ijantimicag.2015.05.005 ◽

2015 ◽

Vol 46 (3) ◽

pp. 351-352 ◽

Cited By ~ 4

Author(s):

Anette M. Hammerum ◽

Frank Hansen ◽

Pia Littauer

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome ◽

Acinetobacter Pittii ◽

History Of

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Whole Genome Sequencing Characterization of Shiga Toxin–Producing Escherichia coli Isolated from Flour from Swiss Retail Markets

Journal of Food Protection ◽

10.4315/0362-028x.jfp-18-593 ◽

2019 ◽

Vol 82 (8) ◽

pp. 1398-1404 ◽

Cited By ~ 2

Author(s):

RENATE BOSS ◽

JOERG HUMMERJOHANN

Keyword(s):

Escherichia Coli ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Shiga Toxin ◽

Severe Disease ◽

Virulence Gene ◽

Whole Genome ◽

N 93 ◽

Human Infections

ABSTRACT Shiga toxin–producing Escherichia coli (STEC) strains are often found in food and cause human infections. Although STEC O157:H7 is most often responsible for human disease, various non-O157 subtypes have caused individual human infections or outbreaks. The importance of STEC serogroup typing is decreasing while detection of virulence gene patterns has become more relevant. Whole genome sequencing (WGS) reveals the entire spectrum of pathogen information, such as toxin variant, serotype, sequence type, and virulence factors. Flour has not been considered as a vector for STEC; however, this product has been associated with several STEC outbreaks in the last decade. Flour is a natural product, and milling does not include a germ-reducing step. Flour is rarely eaten raw, but the risks associated with the consumption of unbaked dough are probably underestimated. The aim of this study was to determine the prevalence of STEC in flour samples (n = 93) collected from Swiss markets and to fully characterize the isolates by PCR assay and WGS. The prevalence of STEC in these flour samples was 10.8% as indicated by PCR, and a total of 10 STEC strains were isolated (two flour samples were positive for two STEC subtypes). We found one stx2-positve STEC isolate belonging to the classic serogroups frequently associated with outbreaks that could potentially cause severe disease. However, we also found several other common or less common STEC subtypes with diverse virulence patterns. Our results reveal the benefits of WGS as a characterization tool and that flour is a potentially and probably underestimated source for STEC infections in humans.

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Nanopore whole genome sequencing and partitioned phylogenetic analysis supports a new salmonid alphavirus genotype (SAV7)

Diseases of Aquatic Organisms ◽

10.3354/dao03546 ◽

2020 ◽

Vol 142 ◽

pp. 203-211

Author(s):

AJ Tighe ◽

MD Gallagher ◽

J Carlsson ◽

I Matejusova ◽

F Swords ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Rna Virus ◽

Whole Genome ◽

Pancreas Disease ◽

Codon Positions ◽

History Of ◽

Unique Strain ◽

Salmon Pancreas Disease Virus

Salmon pancreas disease virus, more commonly known as salmonid alphavirus (SAV), is a single-stranded positive sense RNA virus and the causative agent of pancreas disease and sleeping disease in salmonids. In this study, a unique strain of SAV previously isolated from ballan wrasse was subjected to whole genome sequencing using nanopore sequencing. In order to accurately examine the evolutionary history of this strain in comparison to other SAV strains, a partitioned phylogenetic analysis was performed to account for variation in the rate of evolution for both individual genes and codon positions. Partitioning the genome alignments almost doubled the observed branch lengths in the phylogenetic tree when compared to the more common approach of applying one model of substitution across the genome and significantly increased the statistical fit of the best-fitting models of nucleotide substitution. Based on the genomic data, a valid case can be made for the viral strain examined in this study to be considered a new SAV genotype. In addition, this study adds to a growing number of studies in which SAV has been found to infect non-salmonid fish, and as such we have suggested that the viral species name be amended to the more inclusive ‘piscine alphavirus’.

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Whole genome sequencing for the management of drug-resistant TB in low income high TB burden settings: Challenges and implications

Tuberculosis ◽

10.1016/j.tube.2017.09.005 ◽

2017 ◽

Vol 107 ◽

pp. 137-143 ◽

Cited By ~ 6

Author(s):

Sharana Mahomed ◽

Kogieleum Naidoo ◽

Navisha Dookie ◽

Nesri Padayatchi

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Low Income ◽

Whole Genome ◽

Drug Resistant

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Investigation of a possible outbreak of NDM-5-producing ST16 Klebsiella pneumoniae among patients in Denmark with no history of recent travel using whole-genome sequencing

Journal of Global Antimicrobial Resistance ◽

10.1016/j.jgar.2015.05.003 ◽

2015 ◽

Vol 3 (3) ◽

pp. 219-221 ◽

Cited By ~ 17

Author(s):

Anette M. Hammerum ◽

Frank Hansen ◽

Bente Olesen ◽

Carsten Struve ◽

Barbara J. Holzknecht ◽

...

Keyword(s):

Klebsiella Pneumoniae ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome ◽

History Of

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Requirement of Whole-Genome Sequencing and Background History of the National and International Genome Initiatives

Compendium of Plant Genomes - The Chickpea Genome ◽

10.1007/978-3-319-66117-9_9 ◽

2017 ◽

pp. 107-115

Author(s):

Mahendar Thudi ◽

Rajeev K. Varshney

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome ◽

History Of ◽

Background History

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Navigating Microbiological Food Safety in the Era of Whole-Genome Sequencing

Clinical Microbiology Reviews ◽

10.1128/cmr.00056-16 ◽

2016 ◽

Vol 29 (4) ◽

pp. 837-857 ◽

Cited By ~ 75

Author(s):

J. Ronholm ◽

Neda Nasheri ◽

Nicholas Petronella ◽

Franco Pagotto

Keyword(s):

Food Safety ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Antibiotic Resistance Gene ◽

Virulence Gene ◽

Complete Information ◽

Gene Profiling ◽

Whole Genome Sequence ◽

Whole Genome ◽

Molecular Subtyping

SUMMARYThe epidemiological investigation of a foodborne outbreak, including identification of related cases, source attribution, and development of intervention strategies, relies heavily on the ability to subtype the etiological agent at a high enough resolution to differentiate related from nonrelated cases. Historically, several different molecular subtyping methods have been used for this purpose; however, emerging techniques, such as single nucleotide polymorphism (SNP)-based techniques, that use whole-genome sequencing (WGS) offer a resolution that was previously not possible. With WGS, unlike traditional subtyping methods that lack complete information, data can be used to elucidate phylogenetic relationships and disease-causing lineages can be tracked and monitored over time. The subtyping resolution and evolutionary context provided by WGS data allow investigators to connect related illnesses that would be missed by traditional techniques. The added advantage of data generated by WGS is that these data can also be used for secondary analyses, such as virulence gene detection, antibiotic resistance gene profiling, synteny comparisons, mobile genetic element identification, and geographic attribution. In addition, several software packages are now available to generatein silicoresults for traditional molecular subtyping methods from the whole-genome sequence, allowing for efficient comparison with historical databases. Metagenomic approaches using next-generation sequencing have also been successful in the detection of nonculturable foodborne pathogens. This review addresses state-of-the-art techniques in microbial WGS and analysis and then discusses how this technology can be used to help support food safety investigations. Retrospective outbreak investigations using WGS are presented to provide organism-specific examples of the benefits, and challenges, associated with WGS in comparison to traditional molecular subtyping techniques.

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