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Microbial infections and disease research
Research Guide
What is Microbial infections and disease research?
Microbial infections and disease research is the scientific study of how microbes infect hosts, cause disease, and can be detected, typed, treated, and tracked using laboratory, genomic, and epidemiologic methods.
Microbial infections and disease research spans clinical microbiology workflows, pathogen taxonomy, antimicrobial mechanisms and resistance, and genomic epidemiology for outbreak investigation and surveillance. Core enabling methods include broad-range 16S rDNA PCR for bacterial phylogenetics (Weisburg et al., 1991) and high-throughput genome sequencing approaches that reduced time and cost for large-scale sequencing projects (Margulies et al., 2005). The provided corpus contains 106,370 works on this topic (5-year growth rate: N/A).
Research Sub-Topics
16S rRNA Sequencing for Microbial Identification
This sub-topic optimizes PCR-based 16S rRNA gene amplification for bacterial phylogeny and pathogen detection. Researchers develop databases and bioinformatics pipelines for clinical diagnostics.
Multilocus Sequence Typing of Pathogens
This sub-topic applies MLST schemes to track clonal lineages of bacterial pathogens. Researchers build public databases like PubMLST for epidemiology and outbreak tracing.
Bacterial Genome Sequencing Technologies
This sub-topic advances high-throughput sequencing platforms for microbial genomes. Researchers integrate short-read and long-read data for complete pathogen assemblies.
Antibiotic Resistance Mechanisms in Bacteria
This sub-topic elucidates molecular basis of resistance, focusing on efflux pumps and enzymatic inactivation. Researchers study tetracycline resistance epidemiology across pathogens.
Bacterial Population Genomics
This sub-topic uses whole-genome sequencing for evolutionary analysis of pathogen populations. Researchers develop tools like BIGSdb for core-genome MLST and recombination detection.
Why It Matters
This research directly supports real-world diagnosis, infection control, and treatment decisions by turning clinical specimens into actionable identifications, resistance interpretations, and transmission hypotheses. Standardized laboratory procedures compiled in the "Clinical Microbiology Procedures Handbook" (2016) operationalize routine culture, identification, and antimicrobial susceptibility testing across organism groups, enabling comparability and quality in clinical reporting. Therapeutic relevance is illustrated by Chopra and Roberts (2001) in "Tetracycline Antibiotics: Mode of Action, Applications, Molecular Biology, and Epidemiology of Bacterial Resistance", which synthesizes how a widely used antibiotic class acts and how resistance emerges and spreads across diverse microorganisms. Public-health impact is strengthened when genome data are made portable and comparable across sites: Maiden et al. (1998) in "Multilocus sequence typing: A portable approach to the identification of clones within populations of pathogenic microorganisms" defined MLST to enable inter-laboratory comparison of pathogen clones, and Jolley et al. (2018) in "Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications" described curated, open-access resources integrating sequence data with provenance and phenotype information for over 100 organisms. At the level of pathogen evolution and virulence, Zhou et al. (2011) in "PHAST: A Fast Phage Search Tool" provided a practical way to identify prophage sequences in bacterial genomes, supporting analyses where phage-encoded genes can contribute to strain differences relevant to disease.
Reading Guide
Where to Start
Start with Weisburg et al. (1991), "16S ribosomal DNA amplification for phylogenetic study", because it introduces a broadly applicable molecular method (wide-range bacterial PCR) that underpins many downstream identification and phylogenetic workflows in infection research.
Key Papers Explained
Methodologically, Weisburg et al. (1991) in "16S ribosomal DNA amplification for phylogenetic study" provides the conserved-marker approach to place bacteria on a phylogenetic tree, while Margulies et al. (2005) in "Genome sequencing in microfabricated high-density picolitre reactors" enables scaling from single loci to whole genomes. For epidemiology, Maiden et al. (1998) in "Multilocus sequence typing: A portable approach to the identification of clones within populations of pathogenic microorganisms" defines portable strain typing, and Larsen et al. (2012) in "Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria" connects that framework to total-genome sequence data. For shared infrastructure and data integration, Jolley et al. (2018) in "Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications" describes curated, open-access population-genomic databases that link sequence data to provenance and phenotype across over 100 organisms.
Paper Timeline
Most-cited paper highlighted in red. Papers ordered chronologically.
Advanced Directions
Advanced work often combines population genomics with functional annotation of mobile genetic elements; Zhou et al. (2011) in "PHAST: A Fast Phage Search Tool" is a practical entry point for integrating prophage detection into genome interpretation. For clinically anchored studies, pairing standardized workflows from the "Clinical Microbiology Procedures Handbook" (2016) with genomic typing and database deposition practices described in Jolley et al. (2018) supports reproducible, multi-site analyses.
Papers at a Glance
| # | Paper | Year | Venue | Citations | Open Access |
|---|---|---|---|---|---|
| 1 | 16S ribosomal DNA amplification for phylogenetic study | 1991 | Journal of Bacteriology | 11.6K | ✓ |
| 2 | Genome sequencing in microfabricated high-density picolitre re... | 2005 | Nature | 7.6K | ✓ |
| 3 | Tetracycline Antibiotics: Mode of Action, Applications, Molecu... | 2001 | Microbiology and Molec... | 4.3K | ✓ |
| 4 | Multilocus sequence typing: A portable approach to the identif... | 1998 | Proceedings of the Nat... | 3.8K | ✕ |
| 5 | Open-access bacterial population genomics: BIGSdb software, th... | 2018 | Wellcome Open Research | 3.1K | ✓ |
| 6 | The Minimal Gene Complement of <i>Mycoplasma genitalium</i> | 1995 | Science | 2.5K | ✕ |
| 7 | Bergey's Manual of Determinative Bacteriology | 1975 | American Journal of Tr... | 2.5K | ✕ |
| 8 | Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria | 2012 | Journal of Clinical Mi... | 2.2K | ✓ |
| 9 | Clinical Microbiology Procedures Handbook | 2016 | ASM Press eBooks | 2.2K | ✕ |
| 10 | PHAST: A Fast Phage Search Tool | 2011 | Nucleic Acids Research | 2.0K | ✓ |
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Code & Tools
The **Viral Lens** is a bioinformatic pipeline deal with short-read sequencing data generated from the bait-capture protocols for enrichment design...
MicrobioLink is a computational pipeline designed to predict host-microbe protein-protein interactions and analyze their downstream effects on host...
**nf-core/pathogensurveillance**is a population genomics pipeline for pathogen identification, variant detection, and biosurveillance.
The Ersilia Model Hub is the main project of the Ersilia Open Source Initiative . The aim is to provide a platform for a user-friendly deployment o...
MAGMA (**M**aximum**A**ccessible**G**enome for**M**tb**A**nalysis) is a pipeline for comprehensive genomic analyses of Mycobacterium tuberculosis w...
Recent Preprints
Infectious Microbes & Diseases
- Standardized Sample Acquisition for Microbiome Profiling in Large-scale Experiments (S-SAMPLE): An initiative - Fluoroquinolone-Resistant _Escherichia coli_: Mechanisms of Resistance, Environme...
Frontiers in Microbiology | Infectious Agents and Disease
- [Editorial\ \ Published on 05 Jan 2026\ \ **Editorial: Antimicrobial surfaces and airborne pathogens: the new frontiers in hospital safety** \ \ in Infectious Agents and Disease\ \ - Smagul Karaz...
Large-scale testing of antimicrobial lethality at single-cell resolution predicts mycobacterial infection outcomes
Even in the absence of antibiotic resistance, treatment outcomes for bacterial infections, including urinary tract, respiratory and bloodstream infections, are often poor 8 , 9 , 10 , 11 . This cha...
Bacterial pathogenesis articles from across Nature Portfolio
Definition Bacterial pathogenesis is the process by which bacteria infect and cause disease in a host. Not all bacteria are pathogens and have the ability for pathogenesis (also known as virulence)...
Infectious diseases articles within Nature
### Albumin orchestrates a natural host defence mechanism against mucormycosis Albumin selectively inhibits Mucorales growth through the release of bound free fatty acids. - Antonis Piko...
Latest Developments
Recent developments in microbial infections and disease research include the creation of a new test that accurately determines which antibiotics truly kill bacteria, potentially improving treatment efficacy for tuberculosis and lung infections (published January 12, 2026) (ScienceDaily). Additionally, there are emerging strategies for combating bacterial infections, with a major conference scheduled for May 2026, focusing on beyond antibiotics approaches (Keystone Symposia). Other notable advances involve understanding antimicrobial resistance, including rising incidences of drug-resistant infections in Europe and the genetic mechanisms behind resistance and virulence, such as colistin resistance plasmids that enhance bacterial pathogenicity (CIDRAP, Nature Communications).
Sources
Frequently Asked Questions
What is the difference between identifying a microbe and typing a strain in microbial infections and disease research?
Identification determines what organism is present, while typing distinguishes closely related strains to support epidemiology and transmission analysis. Maiden et al. (1998) in "Multilocus sequence typing: A portable approach to the identification of clones within populations of pathogenic microorganisms" framed MLST specifically to make clone identification portable and comparable among laboratories.
How does 16S rDNA PCR support research on bacterial infections?
Weisburg et al. (1991) in "16S ribosomal DNA amplification for phylogenetic study" described oligonucleotide primers and methods that initiate PCR amplification across a phylogenetically wide range of bacteria. This enables phylogenetic placement and taxonomic assessment from a conserved genetic marker when studying bacterial infections.
How did high-throughput sequencing become practical for large-scale microbial disease studies?
Margulies et al. (2005) in "Genome sequencing in microfabricated high-density picolitre reactors" described a scalable, highly parallel sequencing system with raw throughput greater than capillary electrophoresis approaches. This type of throughput increase supports pathogen genome sequencing at scales needed for population studies and surveillance.
Which approaches make strain typing more efficient when whole genomes are available?
Larsen et al. (2012) in "Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria" addressed how MLST can be performed using whole-genome sequence data rather than traditional, more time-consuming laboratory workflows. This links the established MLST framework to genome-scale data produced in modern microbiology.
How do researchers study antibiotic use and resistance in common antibacterial classes?
Chopra and Roberts (2001) in "Tetracycline Antibiotics: Mode of Action, Applications, Molecular Biology, and Epidemiology of Bacterial Resistance" reviewed tetracyclines as inexpensive, widely used antibiotics with activity across multiple microorganism groups and summarized resistance biology and epidemiology. This provides a reference point for connecting mechanism to observed resistance patterns in infection research.
Which resources support standardized clinical microbiology methods and bacterial classification?
The "Clinical Microbiology Procedures Handbook" (2016) compiles procedures spanning bacteriology, mycology, parasitology, virology, and antimicrobial susceptibility testing for clinical and infection-control use. "Bergey's Manual of Determinative Bacteriology" (1975) provides structured descriptions and characterization criteria for groups of bacteria used in classification and identification.
Open Research Questions
- ? Which prophage features identified with "PHAST: A Fast Phage Search Tool" (2011) best explain clinically relevant strain-to-strain differences within the same bacterial species?
- ? How can MLST frameworks from "Multilocus sequence typing: A portable approach to the identification of clones within populations of pathogenic microorganisms" (1998) be most effectively integrated with whole-genome workflows described in "Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria" (2012) without losing inter-laboratory portability?
- ? Which standardized laboratory workflows from the "Clinical Microbiology Procedures Handbook" (2016) most strongly influence downstream comparability of population-genomic datasets curated via "Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications" (2018)?
- ? How should broad-range 16S approaches from "16S ribosomal DNA amplification for phylogenetic study" (1991) be combined with genome sequencing approaches from "Genome sequencing in microfabricated high-density picolitre reactors" (2005) to resolve cases where taxonomy and within-species transmission questions must both be answered from limited clinical material?
Recent Trends
The provided topic-scale data indicate a large literature base (106,370 works; 5-year growth rate: N/A), and the most-cited methodological papers reflect a shift from marker-based identification to genome-enabled epidemiology.
Weisburg et al. in "16S ribosomal DNA amplification for phylogenetic study" represents broad-range PCR for phylogenetics, while Margulies et al. (2005) in "Genome sequencing in microfabricated high-density picolitre reactors" represents the move toward scalable, parallel sequencing for large projects.
1991Epidemiologic portability and open data infrastructure are emphasized by Maiden et al. in "Multilocus sequence typing: A portable approach to the identification of clones within populations of pathogenic microorganisms" and Jolley et al. (2018) in "Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications", with Larsen et al. (2012) in "Multilocus Sequence Typing of Total-Genome-Sequenced Bacteria" explicitly bridging MLST into whole-genome contexts.
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