ReviewInfection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases2018
Microbial sequence typing in the genomic era.
Review in Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers, 1 of them a synthesis that pooled it.
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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.
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.
Who cites it
29 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The Application of High-Throughput Technologies for the Study of Microbiome and Cancer.Frontiers in genetics · 2021Pooled it
- Molecular typing ofApplied and environmental microbiology · 2026Article
- Evaluating the performance of Fourier transform infrared spectroscopy for typing and outbreak investigation of methicillin-resistant and -susceptibleMicrobiology spectrum · 2026Article
- Typing ofMicroorganisms · 2025Article
- A New Multilocus Sequence Typing Scheme for Lactobacillus delbrueckii subsp. bulgaricus Based on Whole-Genome Sequencing Data.Current microbiology · 2025Article
- Genomic diversity and tracing ofMicrobial genomics · 2025Article
- Molecular epidemiological and antimicrobial-resistant mechanisms analysis of prolongedJAC-antimicrobial resistance · 2024Article
- Laboratory Methods for Culture and Identification.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Contamination of Plant Foods withMicroorganisms · 2023Article
- Genotyping-driven diversity assessment of biocontrol potent Bacillus spp. strain collection as a potential method for the development of strain-specific biomarkers.Archives of microbiology · 2023Article
- Rapid and Routine Molecular Typing Using Multiplex Polymerase Chain Reaction and MinION Sequencer.Frontiers in microbiology · 2022Article
- Genetic analysis of plasmid-encodedJAC-antimicrobial resistance · 2021Article
- Antimicrobial Resistance and Genomic Characterization of Six New Sequence Types in Multidrug-ResistantAntibiotics (Basel, Switzerland) · 2021Article
- Whole-genome sequencing and ad hoc shared genome analysis of Staphylococcus aureus isolates from a New Zealand primary school.Scientific reports · 2021Article
- Amplicon-Based Next Generation Sequencing for Rapid Identification ofPathogens (Basel, Switzerland) · 2021Article
- Article
- One is not enough: On the effects of reference genome for the mapping and subsequent analyses of short-reads.PLoS computational biology · 2021Article
- Characterization of genetic diversity and population structure within Staphylococcus chromogenes by multilocus sequence typing.PloS one · 2021Article
- Antibiotic resistance: Time of synthesis in a post-genomic age.Computational and structural biotechnology journal · 2021Review
- The phylogenomics of CRISPR-Cas system and revelation of its features in Salmonella.Scientific reports · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Next-generation sequencing (NGS), also known as high-throughput sequencing, is changing the field of microbial genomics research. NGS allows for a more comprehensive analysis of the diversity, structure and composition of microbial genes and genomes compared to the traditional automated Sanger capillary sequencing at a lower cost. NGS strategies have expanded the versatility of standard and widely used typing approaches based on nucleotide variation in several hundred DNA sequences and a few gene fragments (MLST, MLVA, rMLST and cgMLST). NGS can now accommodate variation in thousands or millions of sequences from selected amplicons to full genomes (WGS, NGMLST and HiMLST). To extract signals from high-dimensional NGS data and make valid statistical inferences, novel analytic and statistical techniques are needed. In this review, we describe standard and new approaches for microbial sequence typing at gene and genome levels and guidelines for subsequent analysis, including methods and computational frameworks. We also present several applications of these approaches to some disciplines, namely genotyping, phylogenetics and molecular epidemiology.
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Registered trials
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.