Dear Colleagues,

This Special Issue is a continuation of our 2022 Special Issue "New Insights into Epidemiology, Detection and Characterization of Bacterial Pathogens".

Bacterial infections are a major cause of morbidity and mortality worldwide, posing considerable health, social, and economic burdens. Therefore, rapid detection and accurate identification of the causative agents play a crucial role to optimize treatment and control measures. The need for rapid and precise methods for detection and characterization is of peculiar importance in the case of highly virulent bacteria associated with severe life-threatening diseases and of multidrug-resistant agents associated with difficult to treat infections. For most cases, the gold standard for the laboratory diagnosis of bacterial infections has been based on usually time consuming phenotypic approaches that include the isolation of the etiologic agent by using growth-supporting media, identification by a variety of techniques and antimicrobial susceptibility testing.  Additionally, typing methods with high discriminatory power are needed to trace pathogens at the strain level, in order to understand the source and dissemination of bacterial strains, allowing the study of bacterial population dynamics and epidemiological surveillance of bacterial infections. The introduction and increasing improvements and applications of molecular techniques, in conjunction with advances in technologies associated with bioinformatics an artificial intelligence to handle large scale data analysis, resulted in the development of a multitude of tools that have revolutionized the diagnosis and epidemiology of infectious diseases.

In this Special Issue, we aim to address the most recent advances on the use of molecular methods based on genomic and proteomic approaches, mass spectrometry, digital microbiology, machine learning and bioinformatics applied to the detection, characterization and epidemiology of bacteria and bacterial infections.

We welcome the submission of Original Research Articles, Rewiews mainly focused on, but not limited to, the following topics:

• Genomics and proteomics applied to the detection and characterization of bacterial agents
• Whole-Genome Sequencing and MALDI-TOF MS as bacterial species Identification tools
• MALDI-TOF Mass Spectrometry for detection of bacterial agents in clinical specimens
• Bacterial molecules as diagnostic markers
• Detection of bacterial markers by immunological, genomic and proteomic approaches
• PCR-based techniques for detection and characterization of bacterial agents
• Genome typing and epidemiology of bacterial pathogens
• Bioinformatics analysis of microbial sequence data
• Prediction of antimicrobial resistance in bacterial isolates by analysis of whole genome sequences, machine learning or MALDI-TOF MS
• New tools to evaluate epidemiology, population structure and evolution of bacterial pathogens
• Application and impact of Machine Learning in Bacteriology

Prof. Dr. Lúcia Martins Teixeira
Dr. Cheryl Andam
Dr. Stephanie S. R. Souza
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2200 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

• bacterial pathogens
• bacterial infections
• molecular detection
• molecular identification
• molecular epidemiology
• strain typing
• genomics and proteomics
• whole-genome sequencing
• MALDI-TOF MS
• antimicrobial resistance
• bacterial evolution
• bioinformatics analysis
• machine learning