Genetic and metabolic signatures of Salmonella enterica subsp. enterica associated with animal sources at the pangenomic scale

Nova, Meryl Vila; Durimel, Kévin; La, Kevin; Felten, Arnaud; Bessières, Philippe; Mistou, Michel‐Yves; Mariadassou, Mahendra; Radomski, Nicolas

doi:10.1186/s12864-019-6188-x

Cited by 30 publications

(30 citation statements)

References 138 publications

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“…Although the isolates exhibited different backgrounds, including sources, import origins, and sampling time points, they shared 3,625 genes overall. The number of core genes is higher than previous studies on Salmonella ( Jacobsen et al, 2011 ; Nova et al, 2019 ). Some of the genes with unknown functions may be associated with phage infection ( Dutilh et al, 2014 ).…”

Section: Discussioncontrasting

confidence: 71%

Genomic Characterization of Salmonella enterica Isolates From Retail Meat in Beijing, China

et al. 2021

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Salmonella enterica remains one of the leading causes of foodborne bacterial disease. Retail meat is a major source of human salmonellosis. However, comparative genomic analyses of S. enterica isolates from retail meat from different sources in China are lacking. A total of 341 S. enterica strains were isolated from retail meat in sixteen districts of Beijing, China, at three different time points (January 1st, May 1st, and October 1st) in 2017. Comparative genomics was performed to investigate the genetic diversity, virulence and antimicrobial resistance gene (ARG) profiles of these isolates. The most common serotype was S. Enteritidis (203/341, 59.5%), which dominated among isolates from three different time points during the year. Laboratory retesting confirmed the accuracy of the serotyping results predicted by the Salmonella In Silico Typing Resource (SISTR) (96.5%). The pangenome of the 341 S. enterica isolates contained 13,931 genes, and the core genome contained 3,635 genes. Higher Salmonella phage 118970 sal3 (219/341, 64.2%) and Gifsy-2 (206/341, 60.4%) prevalence contributed to the diversity of the accessory genes, especially those with unknown functions. IncFII(S), IncX1, and IncFIB(S) plasmid replicons were more common in these isolates and were major sources of horizontally acquired foreign genes. The virulence gene profile showed fewer virulence genes associated with type III secretion systems in certain isolates from chicken. A total of 88 different ARGs were found in the 341 isolates. Three beta-lactamases, namely, blaCTX–M–55 (n = 15), blaCTX–M–14 (n = 11), and blaCTX–M–65 (n = 11), were more prevalent in retail meats. The emergence of qnrE1 and blaCTX–M–123 indicated a potential increase in the prevalence of retail meats. After the prohibition of colistin in China, three and four isolates were positive for the colistin resistance genes mcr-1.1 and mcr-9, respectively. Thus, we explored the evolution and genomic features of S. enterica isolates from retail meats in Beijing, China. The diverse ARGs of these isolates compromise food security and are a clinical threat.

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Section: Discussioncontrasting

confidence: 71%

Genomic Characterization of Salmonella enterica Isolates From Retail Meat in Beijing, China

et al. 2021

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“…The genus Salmonella was detected in L2 and L5, being Salmonella enterica subsp. enterica serovars identified in both drawings (Vila Nova et al, 2019). In contrast, Escherichia was identified in L4-L6, with the species E. coli, which is a common inhabitant of the gut microbiota.…”

Section: Bacteriamentioning

confidence: 94%

The Microbiome of Leonardo da Vinci’s Drawings: A Bio-Archive of Their History

Piñar

Sclocchi²,

Pinzari³

et al. 2020

Front. Microbiol.

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Seven emblematic Leonardo da Vinci’s drawings were investigated through third generation sequencing technology (Nanopore). In addition, SEM analyses were carried out to acquire photographic documentation and to infer the nature of the micro-objects removed from the surface of the drawings. The Nanopore generated microbiomes can be used as a “bio-archive” of the drawings, offering a kind of fingerprint for current and future biological comparisons. This information might help to create a biological catalog of the drawings (cataloging), a microbiome-fingerprint for each single analyzed drawing, as a reference dataset for future studies (monitoring) and last but not least a bio-archive of the history of each single object (added value). Results showed a relatively high contamination with human DNA and a surprising dominance of bacteria over fungi. However, it was possible to identify typical bacteria of the human microbiome, which are mere contaminants introduced by handling of the drawings as well as other microorganisms that seem to have been introduced through vectors, such as insects and their droppings, visible through the SEM analyses. All drawings showed very specific bio-archives, but a core microbiome of bacteria and fungi that are repeatedly found in this type of material as true degraders were identified, such as members of the phyla Proteobacteria, Actinobacteria, and Firmicutes among bacteria, and fungi belonging to the classes Sordariomycetes and Eurotiomycetes. In addition, some similarities were observed that could be influenced by their geographical location (Rome or Turin), indicating the influence of this factor and denoting the importance of environmental and storage conditions on the specific microbiomes.

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“…Twenty-two strains were excluded by the study because of the low genome quality values (data not shown). Genome assemblies were generated using an inhouse workflow called ARTwork (Vila Nova et al, 2019; https://github.com/afelten-Anses/ARtWORK). The raw reads were normalized to 100× with Bbnorm using the Salmonella Typhimurium_LT2_AE006468 reference genome.…”

Section: Sequencing and Assemblymentioning

confidence: 99%

The Spatiotemporal Dynamics and Microevolution Events That Favored the Success of the Highly Clonal Multidrug-Resistant Monophasic Salmonella Typhimurium Circulating in Europe

et al. 2021

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The European epidemic monophasic variant of Salmonella enterica serovar Typhimurium (S. 1,4,[5],12:i:-) characterized by the multi locus sequence type ST34 and the antimicrobial resistance ASSuT profile has become one of the most common serovars in Europe (EU) and the United States (US). In this study, we reconstructed the time-scaled phylogeny and evolution of this Salmonella in Europe. The epidemic S. 1,4,[5],12:i:- ST34 emerged in the 1980s by an acquisition of the Salmonella Genomic Island (SGI)-4 at the 3′ end of the phenylalanine phe tRNA locus conferring resistance to copper and arsenic toxicity. Subsequent integration of the Tn21 transposon into the fljAB locus gave resistance to mercury toxicity and several classes of antibiotics used in food-producing animals (ASSuT profile). The second step of the evolution occurred in the 1990s, with the integration of mTmV and mTmV-like prophages carrying the perC and/or sopE genes involved in the ability to reduce nitrates in intestinal contents and facilitate the disruption of the junctions of the host intestinal epithelial cells. Heavy metals are largely used as food supplements or pesticide for cultivation of seeds intended for animal feed so the expansion of the epidemic S. 1,4,[5],12:i:- ST34 was strongly related to the multiple-heavy metal resistance acquired by transposons, integrative and conjugative elements and facilitated by the escape until 2011 from the regulatory actions applied in the control of S. Typhimurium in Europe. The genomic plasticity of the epidemic S. 1,4,[5],12:i:- was demonstrated in our study by the analysis of the plasmidome. We were able to identify plasmids harboring genes mediating resistance to phenicols, colistin, and fluoroquinolone and also describe for the first time in six of the analyzed genomes the presence of two plasmids (pERR1744967-1 and pERR2174855-2) previously described only in strains of enterotoxigenic Escherichia coli and E. fergusonii.

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Genetic and metabolic signatures of Salmonella enterica subsp. enterica associated with animal sources at the pangenomic scale

Cited by 30 publications

References 138 publications

Genomic Characterization of Salmonella enterica Isolates From Retail Meat in Beijing, China

Genomic Characterization of Salmonella enterica Isolates From Retail Meat in Beijing, China

The Microbiome of Leonardo da Vinci’s Drawings: A Bio-Archive of Their History

The Spatiotemporal Dynamics and Microevolution Events That Favored the Success of the Highly Clonal Multidrug-Resistant Monophasic Salmonella Typhimurium Circulating in Europe

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