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Advances in Molecular Microbiology, Genetics, and Bioinformatics of Multiple-Drug-Resistant Bacteria...
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Advances in Molecular Microbiology, Genetics, and Bioinformatics of Multiple-Drug-Resistant Bacteria in Public Health

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Microbial Genetics and Genomics".

Deadline for manuscript submissions: 10 October 2025 | Viewed by 2692

Special Issue Editors

Dr. Pedro Panzenhagen

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Guest Editor
Laboratory of Advanced Analyzes in Biochemistry and Molecular Biology, Department of Biochemistry, Chemistry Institute, Federal University of Rio de Janeiro, Av. Athos da Silveira Ramos, nº 149, Bloco A-Sala 534 A, Centro de Tecnologia, Cidade Universitária, Rio de Janeiro 21941-909, Brazil
Interests: molecular microbiology; antimicrobial resistance; bacterial pathogens; WGS; genomic epidemiology; bioinformatics; pathogen virulence factors; multidrug-resistant bacteria; genetic analysis of bacteria
Special Issues, Collections and Topics in MDPI journals
Dr. Dália Dos Prazeres Rodrigues

E-Mail Website
Guest Editor
Laboratory of Enterobacteria, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Avenida Brasil, 4365 Pav. Rocha Lima, Manguinhos, Rio de Janeiro 21040-900, Brazil
Interests: antimicrobial resistance; enteropathogens; bacterial pathogenicity; foodborne diseases; molecular epidemiology; zoonoses
Prof. Dr. Carlos Adam Conte Júnior

E-Mail Website
Guest Editor
Center for Food Analysis (NAL-LADETEC), Department of Biochemistry, Chemistry Institute, Federal University of Rio de Janeiro, Av. Horácio Macedo, Polo de Química, bloco C, 1281-Cidade Universitária, Rio de Janeiro 21941-598, RJ, Brazil
Interests: animal science; molecular biology; biochemistry; molecular techniques; food science; food microbiology; animal-based food; bovine tuberculosis; antimicrobial resistance; analytical method development
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

We are pleased to announce this Special Issue of the journal Genes entitled “Advances in Molecular Microbiology, Genetics, and Bioinformatics of Multiple-Drug-Resistant Bacteria in Public Health”. This Special Issue highlights the latest breakthroughs across these disciplines, focusing on cutting-edge research that applies molecular microbiology, genetics, and bioinformatics to study pathogenic bacteria. The “One Health” concept, which integrates advanced technologies for pathogen research and monitoring, has gained unprecedented significance in response to the escalating global crisis of antimicrobial resistance (AMR). This crisis has dramatically reshaped scientific priorities, driving innovation in developing new therapies to mitigate the threats posed by multi-drug-resistant bacteria to both human and animal health. Advances in molecular microbiology are crucial for elucidating cellular and molecular mechanisms, while breakthroughs in bacterial genetics provide essential insights into genomic characteristics and evolutionary processes. This knowledge underpins the development of improved diagnostics, treatments, and therapies. Tools such as genome sequencing, CRISPR, and other genetic technologies, combined with bioinformatics, enable comprehensive data analysis, facilitating precise pathogen tracking, characterization, and the monitoring of drug-resistant bacteria. The synergy between molecular microbiology, genetics, and bioinformatics is essential for the epidemiological studies of high-impact resistant bacteria. These fields enhance disease surveillance, prevention, and control strategies, ultimately strengthening public health responses worldwide. In this particular Special Issue, we invite submissions that explore the intersection of molecular microbiology, genetics, and bioinformatics in the context of multi-drug-resistant bacteria relevant to public health. We encourage contributions that provide new insights, address current challenges, or present innovative approaches in these fields.

Dr. Pedro Panzenhagen
Dr. Dália Dos Prazeres Rodrigues
Prof. Dr. Carlos Adam Conte Júnior
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. Genes 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 2600 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.

Keywords

  • One Health
  • pathogen genomics
  • whole genome sequencing (WGS)
  • proteomics
  • CRISPR technology
  • infectious disease outbreaks
  • antimicrobial resistance
  • genomic epidemiology
  • public health surveillance
  • bioinformatics in pathogen research

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Published Papers (3 papers)

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Research

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20 pages, 3104 KiB  
Article
Worldwide Population Dynamics of Salmonella Saintpaul: Outbreaks, Epidemiology, and Genome Structure
by Pedro Panzenhagen, Devendra H. Shah, Dalia dos Prazeres Rodrigues and Carlos Adam Conte Junior
Genes 2025, 16(3), 254; https://doi.org/10.3390/genes16030254 - 22 Feb 2025
Viewed by 1305
Abstract
Background/Objectives: Salmonella Saintpaul (SSa) is increasingly linked to foodborne outbreaks in Brazil and globally. Despite its rising public health significance, its epidemiology, genomic diversity, and pathogenic potential remain underexplored. This study addresses these gaps through a comprehensive global analysis of SSa population dynamics, [...] Read more.
Background/Objectives: Salmonella Saintpaul (SSa) is increasingly linked to foodborne outbreaks in Brazil and globally. Despite its rising public health significance, its epidemiology, genomic diversity, and pathogenic potential remain underexplored. This study addresses these gaps through a comprehensive global analysis of SSa population dynamics, outbreak patterns, and genetic structures, along with an in-depth phenotypic and genomic characterization of strain PP_BR059, isolated from a hospitalized patient in Ceará, Brazil. Methods: We analyzed 1,953 publicly available SSa genomes using core-genome multi-locus sequence typing (cgMLST), antimicrobial resistance (AMR) profiling, pan-genome analysis, and phylogenetic inference. A genome-wide association study (GWAS) identified genetic determinants of virulence and AMR. The invasiveness and intracellular survival of PP_BR059 were assessed using in vitro macrophage infection assays, while whole-genome sequencing (WGS) provided genetic insights. Results: Phylogenetic analysis identified 49 sequence types (STs), with ST-50 (787 genomes) and ST-27 (634 genomes) being most prevalent. ST-50 included all clinical strains from South America, including PP_BR059. AMR analysis showed 60% of SSa genomes were pan-susceptible, while ST-27 had the highest proportion of AMR strains. GWAS revealed distinct evolutionary lineages within ST-50 and ST-27. PP_BR059 exhibited lower macrophage invasion (3.82%) but significantly higher intracellular survival at 2 h (68.72%) and 20 h (25.68%) post-infection. WGS confirmed a pan-susceptible AMR profile and plasmid absence. Conclusions: This study highlights SSa’s global dissemination, evolutionary trends, and pathogenic variability, emphasizing the need for molecular surveillance to inform public health interventions. Full article
(This article belongs to the Special Issue Advances in Molecular Microbiology, Genetics, and Bioinformatics of Multiple-Drug-Resistant Bacteria in Public Health)
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19 pages, 3783 KiB  
Article
Whole Genome Sequencing and Comparative Genomics Analysis of Goat-Derived Klebsiella oxytoca
by Yu Zhang, Zhenxing Zhang, Ziying Wang, Yimei Chen, Lianjie Liao, Li Du, Hongyan Gao, Qiaoling Chen, Churiga Man, Si Chen and Fengyang Wang
Genes 2025, 16(1), 13; https://doi.org/10.3390/genes16010013 - 26 Dec 2024
Viewed by 830
Abstract
Background: This research aims to enhance the genomic database of Klebsiella oxytoca by identifying virulence genes through the whole genome sequencing and comparative analysis of a goat-derived K. oxytoca (KOHN1) strain, while clarifying the relationship between its genetic evolution and virulence, ultimately providing [...] Read more.
Background: This research aims to enhance the genomic database of Klebsiella oxytoca by identifying virulence genes through the whole genome sequencing and comparative analysis of a goat-derived K. oxytoca (KOHN1) strain, while clarifying the relationship between its genetic evolution and virulence, ultimately providing a theoretical foundation for clinical prevention and diagnosis. Methods: Third-generation Oxford Nanopore Technologies (ONT) sequencing and second-generation Illumina sequencing were used to sequence the strain and analyze the database annotations. Screening for 10 virulence genes was conducted using PCR. Comparative genomic analyses of the strain KOHN1 with four human-derived K. oxytoca model strains were performed using collinearity analysis, taxonomy classification through ANI analysis, and gene function family analysis. Results: The genome size of the KOHN1 strain was 5,817,806 bp, and the GC content was 55.14%. It contained 5227 predicted coding genes, including 25 rRNA genes, 85 tRNA genes, and 53 sRNA genes. A total of 14 type VI secretion system effector proteins and 146 virulence factor-related genes were annotated. Additionally, eight virulence genes—fimA, fimH, entB, mrkD, clpV, rmpA, vgrG, and hcp—were detected through PCR identification. The strain has 448 drug resistance genes, mainly against β-lactams and fosfomycins. Comparative genomic analysis indicated that its closest relation is the human isolate ASM338647. Conclusions: In this study, the whole genome sequence of a goat-derived K. oxytoca (KOHN1) strain was obtained, revealing its evolutionary relationship with domestic and foreign isolates and providing a reference for future studies on the mechanisms of antimicrobial resistance and the pathogenicity of K. oxytoca. Full article
(This article belongs to the Special Issue Advances in Molecular Microbiology, Genetics, and Bioinformatics of Multiple-Drug-Resistant Bacteria in Public Health)
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Review

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21 pages, 1146 KiB  
Review
Impact of Heavy Metal and Resistance Genes on Antimicrobial Resistance: Ecological and Public Health Implications
by Carlos G. Sánchez-Corona, Luis Uriel Gonzalez-Avila, Cecilia Hernández-Cortez, Jorge Rojas-Vargas, Graciela Castro-Escarpulli and Hugo G. Castelán-Sánchez
Genes 2025, 16(6), 625; https://doi.org/10.3390/genes16060625 (registering DOI) - 24 May 2025
Abstract
Heavy metals (HMs) are widespread pollutants that can exert selection pressure on microbial populations due to their toxicity and persistence, leading to the evolution of heavy metal resistance genes (HMRGs). These genes are part of the resistome, and their spread often occurs via [...] Read more.
Heavy metals (HMs) are widespread pollutants that can exert selection pressure on microbial populations due to their toxicity and persistence, leading to the evolution of heavy metal resistance genes (HMRGs). These genes are part of the resistome, and their spread often occurs via mobile genetic elements that allow co-selection with antibiotic and biocide resistance genes. Such processes have an impact on microbial biodiversity, biogeochemical cycling and public health in agriculture, industry and urban areas. The selection pressure exerted by HM promotes the spread of multidrug-resistant strains and thus increases ecological and health risks. This review discusses the interaction between HMRGs and genetic determinants such as virulence genes that influence biofilm formation, cellular homeostasis and oxidative stress. It also discusses the dual role of HMRGs in promoting ecological functions such as bioremediation while potentially limiting them by reducing microbial diversity. Understanding such interactions contributes significantly to targeting different systems to overcome the challenges associated with antimicrobial resistance (AMR). Full article
(This article belongs to the Special Issue Advances in Molecular Microbiology, Genetics, and Bioinformatics of Multiple-Drug-Resistant Bacteria in Public Health)
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