Submit to Genes Review for Genes Propose a Special Issue

Journal Menu

Journal Browser

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

Special Issue Editors
Special Issue Information
Keywords
Benefits of Publishing in a Special Issue
Published Papers

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

Deadline for manuscript submissions: closed (10 October 2025) | Viewed by 17648

Share This Special Issue

Special Issue Editors

Dr. Pedro Panzenhagen

E-Mail Website
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 250 words) can be sent to the Editorial Office for assessment.

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

Benefits of Publishing in a Special Issue

Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
Reprint: MDPI Books provides the opportunity to republish successful Special Issues in book format, both online and in print.

Further information on MDPI's Special Issue policies can be found here.

Published Papers (10 papers)

Download All Papers

Order results

Result details

Show export options Show export options

Select all

Export citation of selected articles as:

Editorial

Jump to: Research, Review

3 pages, 136 KB

Open AccessEditorial

Editorial for the Special Issue “Advances in Molecular Microbiology, Genetics, and Bioinformatics of Multiple-Drug-Resistant Bacteria in Public Health”

by Pedro Panzenhagen and Carlos Adam Conte-Junior

Genes 2026, 17(4), 366; https://doi.org/10.3390/genes17040366 - 24 Mar 2026

Viewed by 253

Abstract

Antimicrobial resistance (AMR) has emerged as one of the most significant global threats to public health, food safety, and environmental sustainability [...] Full article

(This article belongs to the Special Issue Advances in Molecular Microbiology, Genetics, and Bioinformatics of Multiple-Drug-Resistant Bacteria in Public Health)

Research

Jump to: Editorial, Review

14 pages, 856 KB

Open AccessArticle

Phenotypic and Whole-Genome Sequencing-Based Profiling of Antimicrobial Resistance and Virulence in Pseudomonas aeruginosa Isolated from Patients with Ventilator-Associated Pneumonia and Ventilator-Associated Tracheobronchitis in a Croatian Intensive Care Unit

by Marija Cavka, Marija Kvesic Ivankovic, Ana Maravic, Mia Dzelalija, Jelena Marinovic, Ivana Goic-Barisic, Marija Tonkic and Anita Novak

Genes 2026, 17(2), 130; https://doi.org/10.3390/genes17020130 - 26 Jan 2026

Cited by 1 | Viewed by 501

Abstract

Background/Objectives: Pseudomonas aeruginosa is one of the leading causes of ventilator-associated pneumonia (VAP) and ventilator-associated tracheobronchitis (VAT), with a worldwide spread of difficult-to-treat high-risk clones. This study aimed to investigate the virulence potential and to characterize phenotypic and genotypic antimicrobial resistance (AMR) in P. aeruginosa causing VAP/VAT in the Intensive Care Unit (ICU), University Hospital of Split, Croatia. Methods: The study included P. aeruginosa isolates obtained from ICU patients who met the criteria for VAP or VAT, between January 2023 and January 2024. Isolates were identified using MALDI-TOF MS and tested for antimicrobial susceptibility (AST). A subset of phenotypically multidrug-resistant (MDR) isolates was further analyzed using whole-genome sequencing (WGS) and multilocus sequence typing. Results: A high rate of resistance was detected to ceftazidime (23.4%), imipenem (39.6%), and meropenem (43.8%). WGS confirmed the presence of multiple AMR genes, including the bla_VIM-2 gene, whose genetic environment highlights a complex MDR locus integrating multiple AMR determinants and mobile genetic elements. All tested isolates possessed genes for class C (bla_PDC34, bla_PDC374 or bla_PDC16) and class D (bla_OXA-2, bla_OXA-10 or bla_OXA-50) β-lactamases, fosA, aph(3′)-IIb and crpP genes. Additionally, WGS analysis revealed the presence of numerous virulence genes including those for adherence (Type IV pili and Fap protein production), motility (such as flgF), biofilm formation (e.g., algE and mucE), quorum sensing (lasI, lasR, rhlI and rhlR), exotoxin (toxA and plcH) and exoenzyme activity (exoU, exoT, exoS, exoY, pcrV, hcp1 and lasA). The isolates belonged to four different sequence types: ST235, ST446, the high-risk ST253 and the widely distributed ST395. Phylogenomic comparison demonstrated that the isolates from this study do not originate from a single clonal source, but instead represent multiple globally distributed high-risk P. aeruginosa lineages introduced into the clinical setting. Conclusions: Due to the emergence of high-risk clones with broad AMR and strong virulence potential, ineffectiveness of standard empirical therapy may be anticipated, highlighting the urgent need for new therapeutic approaches (including those targeting major virulence factors). Full article

(This article belongs to the Special Issue Advances in Molecular Microbiology, Genetics, and Bioinformatics of Multiple-Drug-Resistant Bacteria in Public Health)

► Show Figures

Figure 1

17 pages, 863 KB

Open AccessArticle

Genomic and Phenotypic Landscape of Antibiotic Resistance in Gut Lactic Acid Bacteria from Livestock Environments

by Anna Mikołajczuk-Szczyrba, Karolina Wnęk-Auguścik, Paulina Średnicka, Dziyana Shymialevich, Ewelina Jaroszewska, Adrian Wojtczak, Agnieszka Zapaśnik, Joanna Bucka-Kolendo, Hanna Cieślak and Justyna Nasiłowska

Genes 2025, 16(12), 1518; https://doi.org/10.3390/genes16121518 - 18 Dec 2025

Cited by 1 | Viewed by 829

Abstract

Background/Objectives: The widespread use of antibiotics in livestock has raised concerns about commensal gut bacteria, such as lactic acid bacteria (LAB), acting as reservoirs for antimicrobial resistance. This study aimed to characterize the antibiotic resistance profiles of LAB isolated from livestock feces by combining phenotypic susceptibility testing with whole-genome sequencing (WGS) to identify antibiotic resistance genes (ARGs) and their genomic context. Methods: Four LAB strains from farm animal fecal samples were subjected to antibiotic susceptibility testing for 9 antibiotics (ampicillin, gentamicin, kanamycin, clindamycin, chloramphenicol, erythromycin, streptomycin, tetracycline, and vancomycin) using MIC determinations. WGS was performed on each isolate to detect ARGs using curated databases and to determine the chromosomal or plasmid location of these genes. Results: All four isolates exhibited phenotypic resistance to at least one antibiotic class, most frequently to aminoglycosides. However, discrepancies between phenotype and genotype were noted: resistance to aminoglycosides was common despite the absence of known aminoglycoside-resistance genes, suggesting intrinsic, uptake-related mechanisms. In contrast, one strain carried the chromosomal lsa(D) gene but remained susceptible to clindamycin. WGS revealed that all strains harbored the chromosomal van(T) gene, while one isolate carried three additional plasmid-borne ARGs—erm(B), cat(A), and tet(W)—conferring resistance to macrolide–lincosamide–streptogramin antibiotics, chloramphenicol, and tetracycline. Another strain encoded van(Y), lsa(D), and arr on its chromosome. The detection of multiple plasmid-located ARGs in a single LAB isolate highlights their potential for horizontal gene transfer. Conclusions: This study provides a detailed phenotypic and genomic insight into antibiotic resistance in gut-derived LAB from livestock. The findings highlight that commensal LAB can harbor clinically relevant ARGs—sometimes on mobile genetic elements—without always expressing corresponding resistance phenotypes. Such LAB may serve as a hidden reservoir for antibiotic resistance, raising the risk of ARG dissemination through the food chain. These results underscore the importance of vigilant monitoring and genomic screening of LAB, especially those considered for use in foods or feed, to ensure they do not contribute to the spread of antimicrobial resistance. Full article

(This article belongs to the Special Issue Advances in Molecular Microbiology, Genetics, and Bioinformatics of Multiple-Drug-Resistant Bacteria in Public Health)

► Show Figures

Figure 1

26 pages, 6524 KB

Open AccessArticle

Preliminary Assessment of Arnica montana L. Extract: Antimicrobial Activity Against Acinetobacter baumannii and Biofilm-Related Gene Expression Profiling

by Sylwia Andrzejczuk, Magdalena Sozoniuk and Danuta Sugier

Genes 2025, 16(12), 1473; https://doi.org/10.3390/genes16121473 - 9 Dec 2025

Cited by 2 | Viewed by 687

Abstract

Background/Objectives: Arnica montana L. is widely recognized for its diverse biological activities, including antimicrobial effects. This study aimed to evaluate the antimicrobial and antibiofilm activity of A. montana L. extracts against Acinetobacter baumannii, a pathogen of urgent public health concern due to its increasing antibiotic resistance and capacity for biofilm formation. Methods: The antimicrobial activity of ethanolic (EtE) and aqueous (AqE) extracts of A. montana flowers was evaluated via the broth microdilution method. The minimal inhibitory concentration (MIC) and minimal bactericidal concentration (MBC), and the MBC/MIC ratio were used. The effects of EtE on A. baumannii biofilm formation were assessed via a crystal violet assay. Additionally, transcriptional profiling of biofilm-associated genes following exposure to sub-MIC levels of the extract was conducted via RT-qPCR. Results: The anti-Acinetobacter activity of EtE was demonstrated (MIC = 234.4 and 468.75 µg/mL for A. baumannii ATCC BAA-3252 and ATCC 19606, respectively). The EtE exhibited bactericidal activity against both strains, whereas the AqE showed no activity. Additionally, EtE inhibited biofilm formation and significantly downregulated the expression of key biofilm-associated genes, including those of the csu operon and ompA. Conclusions: Arnica montana EtE demonstrated antimicrobial and antibiofilm activities against A. baumannii and inhibited biofilm development by suppressing the transcription of genes involved in pilus assembly and surface adherence, highlighting their essential role in biofilm formation. Full article

(This article belongs to the Special Issue Advances in Molecular Microbiology, Genetics, and Bioinformatics of Multiple-Drug-Resistant Bacteria in Public Health)

► Show Figures

Graphical abstract

15 pages, 290 KB

Open AccessArticle

Antibiotic Resistance Profiles and Genetic Determinants of Listeria innocua Isolated from Food Sources in Poland

by Anna Zawiasa and Agnieszka Olejnik-Schmidt

Genes 2025, 16(12), 1455; https://doi.org/10.3390/genes16121455 - 5 Dec 2025

Cited by 1 | Viewed by 602

Abstract

Background: Antimicrobial resistance (AMR) is a growing public health concern affecting both medicine and food safety. While Listeria monocytogenes is the primary pathogen of concern, Listeria innocua—commonly found in food and food-processing environments—may serve as a reservoir for resistance genes and a useful indicator of species for surveillance. This study aimed to assess the phenotypic antibiotic susceptibility and detect resistance-associated genes in L. innocua isolates from meat products and processing environments in Poland. Methods: A total of 51 L. innocua isolates were analyzed, originating from raw and processed meat products as well as meat-processing environments. Antimicrobial susceptibility was determined using the disc diffusion method against 18 antibiotics representing multiple classes. Phenotypic resistance was interpreted following CLSI guidelines (CLSI, 2020). Isolates exhibiting resistance or intermediate resistance were further screened for resistance-associated genes using PCR. Results: All isolates were fully susceptible to ampicillin, benzylpenicillin, chloramphenicol, gentamicin, rifampin, trimethoprim-sulfamethoxazole, and vancomycin. High susceptibility was observed for ciprofloxacin, erythromycin, meropenem, trimethoprim, and nitrofurantoin, with only sporadic intermediate responses. Moderate resistance levels were noted for streptomycin (10%) and tetracycline (12%). The lowest susceptibility was recorded for clindamycin and linezolid, with most isolates exhibiting intermediate or resistant phenotypes. Universal resistance to cefotaxime and oxacillin was found. Eighteen distinct resistance patterns were identified. PCR confirmed the presence of several resistance-associated genes, including mecA, lnuA, lnuB, cfr, optrA, and poxtA, consistent with observed phenotypes. Conclusions: This study provides the first detailed characterization of AMR in L. innocua from Polish meat and processing environments. The findings highlight its heterogeneous resistance profiles and potential role as a reservoir of clinically relevant resistance genes. Incorporating L. innocua into surveillance programs may strengthen early detection of emerging resistance and enhance food safety monitoring. Full article

(This article belongs to the Special Issue Advances in Molecular Microbiology, Genetics, and Bioinformatics of Multiple-Drug-Resistant Bacteria in Public Health)

19 pages, 5117 KB

Open AccessArticle

Comparative Genomics and Functional Profiling Reveal Lineage-Specific Metabolic Adaptations in Globally Emerging Fluoroquinolone-Resistant Salmonella Kentucky ST198

by Juned Ahmed, Rachel C. Soltys, Smriti Shringi, Jean Guard, Bradd J. Haley and Devendra H. Shah

Genes 2025, 16(9), 1051; https://doi.org/10.3390/genes16091051 - 8 Sep 2025

Cited by 1 | Viewed by 1170

Abstract

Background: Salmonella Kentucky comprises two major lineages, ST152 and fluoroquinolone-resistant (Flu^R) ST198, which have diverged genotypically and phenotypically along distinct evolutionary and epidemiological trajectories. ST198 is linked to global human disease, while ST152 is primarily animal-associated in the U.S. We hypothesized that lineage-specific metabolic adaptations contribute to their differing host associations and pathogenicity. Methods: We performed comparative metabolic profiling of ST198 (n = 3) and ST152 (n = 4) strains across 948 substrates and environmental conditions. Growth assays tested the ability of these lineages and other non-typhoidal Salmonella (NTS) serovars (n = 5) to utilize myo-inositol and lactulose as sole carbon sources. Comparative genomic analyses of 294 ST198, 173 ST152, and 1300 other NTS serovars identified nutrient utilization genes. Results: ST198 exhibited significantly higher respiratory activity and broader metabolic versatility across carbon, nitrogen/sulfur sources, and stress conditions. The canonical iol gene cluster for myo-inositol catabolism was conserved in ST198 but absent in ST152, which nonetheless showed weak growth on myo-inositol, suggesting an alternative metabolic pathway for myo-inositol may exist. We also report for the first time that, despite lineage-specific differences in metabolic efficiency, multiple NTS serovars, including S. Kentucky, can metabolize lactulose, a synthetic disaccharide traditionally associated with beneficial gut microbes. These results suggest the potential existence of a novel lactulose metabolic pathway in NTS. Conclusions: These findings highlight ST198’s metabolic adaptability and reveal novel metabolic capacities in NTS. A mechanistic understanding of nutrient utilization pathways, particularly of myo-inositol and lactulose, will provide novel insights into the mechanisms underlying nutrient metabolism that likely modulate the ecological success and pathogenic potential of NTS in human and animal hosts. Full article

(This article belongs to the Special Issue Advances in Molecular Microbiology, Genetics, and Bioinformatics of Multiple-Drug-Resistant Bacteria in Public Health)

► Show Figures

Figure 1

20 pages, 3015 KB

Open AccessArticle

Integrated Whole-Genome Sequencing and In Silico Characterization of Salmonella Cerro and Schwarzengrund from Brazil

by Nathaly Barros Nunes, Vinicius Silva Castro, Adelino da Cunha-Neto, Fernanda Tavares Carvalho, Ricardo César Tavares Carvalho and Eduardo Eustáquio de Souza Figueiredo

Genes 2025, 16(8), 880; https://doi.org/10.3390/genes16080880 - 26 Jul 2025

Cited by 1 | Viewed by 1551

Abstract

Background: Salmonella is a bacterium that causes foodborne infections. This study characterized two strains isolated from cheese and beef in Brazil using whole-genome sequencing (WGS). Objectives: We evaluated their antimicrobial resistance profiles, virulence factors, plasmid content, serotypes and phylogenetic relationships. Methods: DNA was extracted and sequenced on the NovaSeq 6000 platform; the pangenome was assembled using the Roary tool; and the phylogenetic tree was constructed via IQ-TREE. Results and Discussion: For contextualization and comparison, 3493 Salmonella genomes of Brazilian origin from NCBI were analyzed. In our isolates, both strains carried the aac(6′)-Iaa_1 gene, while only Schwarzengrund harbored the qnrB19_1 gene and the Col440I_1 plasmid. Cerro presented the islands SPI-1, SPI-2, SPI-3, SPI-4, SPI-5 and SPI-9, while Schwarzengrund also possessed SPI-13 and SPI-14. Upon comparison with other Brazilian genomes, we observed that Cerro and Schwarzengrund represented only 0.40% and 2.03% of the national database, respectively. Furthermore, they revealed that Schwarzengrund presented higher levels of antimicrobial resistance, a finding supported by the higher frequency of plasmids in this serovar. Furthermore, national data corroborated our findings that SPI-13 and SPI-14 were absent in Cerro. A virulence analysis revealed distinct profiles: the cdtB and pltABC genes were present in the Schwarzengrund isolates, while the sseK and tldE1 family genes were exclusive to Cerro. The results indicated that the sequenced strains have pathogenic potential but exhibit low levels of antimicrobial resistance compared to national data. The greater diversity of SPIs in Schwarzengrund explains their prevalence and higher virulence potential. Conclusions: Finally, the serovars exhibit distinct virulence profiles, which results in different clinical outcomes. Full article

(This article belongs to the Special Issue Advances in Molecular Microbiology, Genetics, and Bioinformatics of Multiple-Drug-Resistant Bacteria in Public Health)

► Show Figures

Figure 1

20 pages, 3104 KB

Open AccessArticle

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

Cited by 5 | Viewed by 2773

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, 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)

► Show Figures

Figure 1

19 pages, 3783 KB

Open AccessArticle

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

Cited by 2 | Viewed by 1850

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 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)

► Show Figures

Figure 1

Review

Jump to: Editorial, Research

21 pages, 1811 KB

Open AccessReview

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 - 24 May 2025

Cited by 24 | Viewed by 5832

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 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)

► Show Figures

Journal Menu

Journal Browser

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

Share This Special Issue

Special Issue Editors

Special Issue Information

Keywords

Benefits of Publishing in a Special Issue

Published Papers (10 papers)

Editorial

Research

Review

Further Information

Guidelines

MDPI Initiatives

Follow MDPI