Evidence map›Paper›PMID 42867800›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2027

Genomic Tracing of Transmission Dynamics in Invasive Non-typhoidal Salmonella Outbreaks.

Hao Wang, Chenghao Jia, Haiyang Zhou, Min Yue

Abstract read
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In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2027. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

4 authors.

Hao Wang *School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.ORCID http://orcid.org/0000-0001-6985-4643
Chenghao Jia *School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China.ORCID http://orcid.org/0000-0003-4406-9213
Haiyang Zhou *Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou, China.ORCID http://orcid.org/0009-0002-9864-8288
Min YueSchool of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China. myue@ucas.ac.cn.ORCID http://orcid.org/0000-0002-6787-0794

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Whole-genome sequencing (WGS) provides high-resolution evidence for investigating bacterial transmission during outbreaks of invasive non-typhoidal Salmonella (iNTS). Here we describe a reproducible workflow for genomic tracing of transmission dynamics using short-read sequencing data. The protocol includes read quality assessment, genome assembly, reference-based single nucleotide polymorphism (SNP) calling, core-genome alignment, pairwise SNP distance analysis, phylogenetic reconstruction, and characterization of mobile genetic elements (MGEs) and antimicrobial resistance (AMR) determinants. Putative transmission links are defined using a rationally selected SNP threshold and are further interpreted together with isolate source metadata. This workflow enables the identification of transmission clusters, the classification of likely transmission patterns, and the comparative analysis of accessory genomic content across sources. The protocol is suitable for outbreak investigation, surveillance studies, and comparative genomic analysis of iNTS populations.

Indexed as

Disease OutbreaksGenome, BacterialGenomicsSalmonellaSalmonella InfectionsDrug Resistance, BacterialHumansInterspersed Repetitive SequencesPhylogenyPolymorphism, Single NucleotideWhole Genome SequencingAntimicrobial resistanceiNTSInvasive non-typhoidal SalmonellaMobile genetic elementsOutbreak genomicsPhylogenySNP analysisSource attributionTransmission tracingWhole-genome sequencing

Identifiers

PMID42867800

What OpenQuestion holds

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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.