Innuendo Whole Genome And Core Genome Mlst Schemas And Datasets For Salmonella Enterica

Rossi, Mirko; Silva, Mickael Santos Da; Ribeiro-Gonçalves, Bruno; Silva, Diogo N.; Machado, Miguel P.; Oleastro, Mónica; Borges, Vítor; Isidro, Joana; Viera, Luis; Halkilahti, Jani; Jaakkonen, Anniina; Palma, Federica Di; Salmenlinna, Saara; Hakkinen, Marjaana; Garaizar, Javier; Bikandi, Joseba; Hilbert, Friederike; Carriço, João André

doi:10.5281/zenodo.1323684

Cited by 6 publications

(7 citation statements)

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“…We use the following genomic collections: E-Coli and C-Elegans are, respectively, the full genomes of E. Coli (Sakai strain) and C. Elegans that were also used in the experimentation by Shibuya et al [40]; S-Enterica-100 is a pan-genome of 100 genomes of S. Enterica, collected by Rossi et al [36]; Human-Chr-13 is the 13-th human chromosome from the genome assembly GRCh38. Table 1 reports some basic statistics for the collections.…”

Section: Datasetsmentioning

confidence: 99%

On Weighted k-mer Dictionaries

Pibiri

2023

Preprint

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We consider the problem of representing a set of k-mers and their abundance counts, or weights, in compressed space so that assessing membership and retrieving the weight of a k-mer is efficient. The representation is called a weighted dictionary of k-mers and finds application in numerous tasks in Bioinformatics that usually count k-mers as a pre-processing step. In fact, k-mer counting tools produce very large outputs that may result in a severe bottleneck for subsequent processing. In this work we extend the recently introduced SSHash dictionary (Pibiri, Bioinformatics 2022) to also store compactly the weights of the k-mers. From a technical perspective, we exploit the order of the k-mers represented in SSHash to encode runs of weights, hence allowing much better compression than the empirical en-tropy of the weights. We study the problem of reducing the number of runs in the weights to improve compression even further and give an optimal algorithm for this problem. Lastly, we corroborate our findings with experiments on real-world datasets and comparison with competitive alternatives. Up to date, SSHash is the only k-mer dictionary that is exact, weighted, associative, fast, and small.

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Section: Datasetsmentioning

confidence: 99%

On Weighted k-mer Dictionaries

Pibiri

2023

Preprint

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“…We use the following genomic collections: E-Coli and C-Elegans are, respectively, the full genomes of E. Coli (Sakai strain) and C. Elegans that were also used in the experimentation by Shibuya et al [35]; S-Enterica-100 is a pan-genome of 100 genomes of S. Enterica, collected by Rossi et al [32]; Human-Chr-13 is the 13-th human chromosome from the genome assembly GRCh38. Table 1 reports some basic statistics for the collections.…”

Section: Datasetsmentioning

confidence: 99%

On Weighted K-Mer Dictionaries

Pibiri

2022

Preprint

View full text Add to dashboard Cite

We consider the problem of representing a set of k-mers and their abundance counts, or weights, in compressed space so that assessing membership and retrieving the weight of a k-mer is efficient. The representation is called a weighted dictionary of k-mers and finds application in numerous tasks in Bioinformatics that usually count k-mers as a pre-processing step. In fact, k-mer counting tools produce very large outputs that may result in a severe bottleneck for subsequent processing. In this work we extend the recently introduced SSHash dictionary (Pibiri, Bioinformatics 2022) to also store compactly the weights of the k-mers. From a technical perspective, we exploit the order of the k-mers represented in SSHash to encode runs of weights, hence allowing (several times) better compression than the empirical entropy of the weights. We also study the problem of reducing the number of runs in the weights to improve compression even further and illustrate a lower bound for this problem. We propose an efficient, greedy, algorithm to reduce the number of runs and show empirically that it performs well, i.e., very similarly to the lower bound. Lastly, we corroborate our findings with experiments on real-world datasets and comparison with competitive alternatives. Up to date, SSHash is the only k-mer dictionary that is exact, weighted, associative, fast, and small.

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“…ECDC encourages countries to interview those cases for possible exposure to chocolate products described in this ROA. Any new information on human cases linked to this event should be reported in [5],12:i:-is the third most common serovar (or rather variant of Typhimurium) among human Salmonella infections in the EU/EEA [8]. Between 2016 and 2020, it accounted for 8.9% of reported salmonellosis cases.…”

Section: Options For Responsementioning

confidence: 99%

“…Between 2016 and 2020, 14 EU countries (Austria, Belgium, Denmark, Estonia, France, Greece, Ireland, Italy, Luxembourg, the Netherlands, Portugal, Slovenia, Spain and Sweden) reported antimicrobial susceptibility results for monophasic S. Typhimurium 1,4, [5],12:i:-on the antimicrobial classes mentioned above to TESSy. Of 7 157 tested isolates, only 37 (0.5%) were resistant to ampicillin, sulfonamides, tetracycline, gentamicin (streptomycin and kanamycin data not collected), chloramphenicol and trimethoprim while being susceptible to ciprofloxacin and cefotaxime/ceftazidime, with the highest number of cases in 2018 (Figure A2).…”

Section: Options For Responsementioning

confidence: 99%

“…(https://github.com/B-UMMI/chewBBACA) using the schema as described by Rossi et al 2018 [5] for Salmonella enterica made available by chewie Nomenclature Server [6] at https://chewbbaca.online/species/4. Isolates with more than 1% of missing loci (32 over a total of 3 225 loci) were excluded from the analysis.…”

Section: European Whole Genome Sequencing Analysis Of Human and Non-h...mentioning

confidence: 99%

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Multi‐country outbreak of monophasic Salmonella Typhimurium sequence type 34 linked to chocolate products – first update – 18 May 2022

2022

EFS3

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On 17 February 2022, the United Kingdom (UK) reported a cluster of cases with monophasic Salmonella Typhimurium sequence type 34 infection. As of 18 May 2022, 324 cases had been reported in 12 EU/EEA countries and the UK, including two distinct strains. Most cases are below ten years of age and 41% of all cases have been hospitalised. The two strains are multidrug‐resistant and some tested isolates also carry resistance to disinfectants that are based on quaternary ammonium compounds and hydrogen peroxide, but remain susceptible to azithromycin, ciprofloxacin, meropenem, and third generation cephalosporins. Epidemiological investigations suggested specific chocolate products of Brand A, produced by Company A in Processing Plant B in Belgium, as likely vehicles of infection. Two strains of monophasic Salmonella Typhimurium matching the outbreak strains were identified in the anhydrous milk fat (AMF) buttermilk line at Plant B between December 2021 and January 2022. The AMF buttermilk was provided by an Italian supplier where Salmonella was not detected. This supplier delivered the AMF buttermilk to other plants of Company A where, based on the available evidence, Salmonella was not detected. On 8 April 2022, based on official controls, the food safety authority in Belgium decided to withdraw the authorisation for production of the Plant B due to lack of transparency and insufficient guarantees for safe production. Company A globally recalled all products of Brand A produced at Plant B. Public warnings were issued by the competent national authorities in different countries. This outbreak has evolved rapidly, with children most at risk for severe infection. The closure of Plant B and the global recall of all their products have reduced the risk of exposure. However, eight cases cannot be explained by consumption of chocolate products such as those manufactured at Plant B, suggesting that there may also be other sources of infection.

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Innuendo Whole Genome And Core Genome Mlst Schemas And Datasets For Salmonella Enterica

Cited by 6 publications

References 0 publications

On Weighted k-mer Dictionaries

On Weighted k-mer Dictionaries

On Weighted K-Mer Dictionaries

Multi‐country outbreak of monophasic Salmonella Typhimurium sequence type 34 linked to chocolate products – first update – 18 May 2022

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