Evidence map›Paper›PMID 38888768›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2024

Methods for Genomic Epidemiology of Bacterial Pathogens: Example Salmonella.

Haley Sanderson, Aaron P White

Abstract read
PubMed Publisher
In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2024. 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

2 authors.

Haley SandersonVaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada.
Aaron P WhiteVaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada. aaron.white@usask.ca.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Genomics has revolutionized how we characterize and monitor infectious diseases for public health. The surveillance and characterization of Salmonella has improved drastically within the past decade. In this chapter, we discuss the prerequisites for good bacterial genomics studies and make note of advantages and disadvantages of this research approach. We discuss methods for outbreak detection and the evolutionary and epidemiological characterization of Salmonella spp. We provide an outline for determining the sequence type and serotype of isolates, building a core genome phylogenetic tree, and detecting antimicrobial resistance genes, virulence factors, and mobile genetic elements. These methods can be used to study other pathogenic bacterial species.

Indexed as

Genome, BacterialGenomicsMolecular EpidemiologyPhylogenySalmonellaSalmonella InfectionsDisease OutbreaksDrug Resistance, BacterialHumansInterspersed Repetitive SequencesVirulence FactorsVirulence FactorsBioinformaticsGenomic epidemiologyMicrobial ecologyOutbreak detectionPhylogeneticsReference microbiologySalmonella

Identifiers

PMID38888768

What OpenQuestion holds

Textmetadata
Read underepoch 390

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.