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Microorganisms
Special Issues
Advances in Microbial Genomics in the AMR Field
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Advances in Microbial Genomics in the AMR Field

A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Antimicrobial Agents and Resistance".

Deadline for manuscript submissions: 31 October 2026 | Viewed by 2079

Special Issue Editors

Prof. Dr. Rosalba Troncoso-Rojas

E-Mail Website
Guest Editor
Coordinación de Tecnología en Alimentos de Origen Vegetal, Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Carretera Gustavo Enrique Astiazarán Rosas, No. 46, Col. La Victoria, Hermosillo C.P. 83304, Sonora, Mexico
Interests: RNA-seq; fungal defense response; antifungal activity compounds
Special Issues, Collections and Topics in MDPI journals
Dr. María Elena Báez-Flores

E-Mail Website
Guest Editor Assistant
Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Sinaloa, Calle de las Américas y Josefa Ortiz de Domínguez, Culiacán C.P. 80013, Sinaloa, Mexico
Interests: microbial genomics; antimicrobial resistance; molecular microbiology

Special Issue Information

Dear Colleagues,

The global dissemination of antimicrobial resistance (AMR) is among the most serious challenges to public health, food production, and ecological integrity. In recent years, the integration of microbial genomics and high-throughput sequencing has transformed our ability to detect, monitor, and predict resistance patterns across ecosystems. Genomic sciences are rapidly enhancing our understanding of microbial resistance mechanisms, the evolution of AMR in pathogens, and the emergence of novel resistance pathways under selective pressure. Additionally, advances in bioinformatics, artificial intelligence, and functional genomics are providing new opportunities for targeted intervention and therapeutic innovation. Phage therapy, CRISPR-based tools, and genome-informed surveillance strategies represent promising alternatives to conventional antibiotics. At the same time, international collaborative platforms and databases are enabling real-time global monitoring and data sharing, representing key elements for effective AMR control under a One Health approach. Despite these advances, gaps remain in translating genomic data into actionable insights, especially in low-resource settings, where AMR surveillance is often limited.

This Special Issue of Microorganisms aims to gather original research and review articles that present recent advances in the genomics of antimicrobial resistance (AMR), including novel approaches for its study, monitoring, and control. We welcome contributions that explore new technologies, analytical methods, and applications of microbial genomic data across clinical, agricultural, and environmental contexts.

The scope of this Special Issue includes, but is not limited to, innovations in AMR surveillance, the application of CRISPR technologies and phages in AMR control, AI-based genomic analysis, the development of global platforms and databases for AMR research, and international collaborative strategies aligned with the One Health framework.

Prof. Dr. Rosalba Troncoso-Rojas
Guest Editor

Dr. María Elena Báez-Flores
Guest Editor Assistant

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. 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 2700 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

  • antimicrobial resistance (AMR)
  • microbial genomics
  • AMR genomic surveillance
  • CRISPR-Cas systems and AMR
  • phage therapy in AMR
  • One Health framework and AMR
  • artificial intelligence in AMR
  • AMR monitoring tools
  • machine learning in AMR
  • bioinformatics for AMR study

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Published Papers (3 papers)

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Research

14 pages, 1765 KB  
Article
Genomic Characteristics of a Multidrug-Resistant Extraintestinal Pathogenic Escherichia coli RZ-13 Isolates from Diarrheic Calves with High Mortality in China
by Di-Di Zhu, Liang Zhang, Shao-Hua Yang, Chuan-Hui Ge, Jia-Qi Chen, Teng-Fei Ma and Hong-Jun Yang
Microorganisms 2026, 14(3), 521; https://doi.org/10.3390/microorganisms14030521 - 24 Feb 2026
Viewed by 348
Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC) poses escalating threats to human and veterinary health amid rising antimicrobial resistance. We isolated a highly virulent ExPEC strain RZ-13 (ST345, O134:H21) from diarrheic calves at a large beef cattle farm in Rizhao City, and conducted whole genome [...] Read more.
Extraintestinal pathogenic Escherichia coli (ExPEC) poses escalating threats to human and veterinary health amid rising antimicrobial resistance. We isolated a highly virulent ExPEC strain RZ-13 (ST345, O134:H21) from diarrheic calves at a large beef cattle farm in Rizhao City, and conducted whole genome sequencing, conjugation experiments, and antimicrobial susceptibility testing to elucidate its genomic architecture and resistance mechanisms. The RZ-13 genome comprises one chromosome and four plasmids. The chromosome harbors virulence factors for adhesion, invasion, biofilm formation, and iron acquisition. Notably, plasmids pRZ13-1 (265,777 bp, IncHI2-IncHI2A) and pRZ13-3 (74,304 bp, IncFII) carry the majority of resistance genes. Plasmid pRZ13-1 carries 25 resistance genes, including blaCTX-M-55, floR, qnrS1, sul3, and tet(A), as well as a complete tellurite resistance gene cluster, terABCDEFZY1. Its multidrug resistance (MDR) region features an IS26-mediated tandem amplification and an approximately 29 kb inverted structure. Comparative analysis indicated that the MDR region carried by this plasmid is highly prevalent in both animal-derived and human-derived isolates. Plasmid pRZ13-3 harbors an IS91-mediated mobile region that integrates both antimicrobial resistance and stress adaptation genes, which have been repeatedly identified in plasmids from diverse sources, including animals and humans. Conjugation experiments confirmed both pRZ13-1 and pRZ13-3 plasmids are self-transmissible and confer multidrug-resistant phenotypes to recipient strains, with pRZ13-3 exhibiting an exceptionally high transfer frequency of 8.9 × 10−2, substantially exceeding that of previously reported IncFII plasmids. These findings demonstrate that pRZ13-1 and pRZ13-3 serve as critical vehicles for resistance dissemination through complex mobile genetic element structures and efficient horizontal transfer, highlighting the urgent need for surveillance of livestock-reservoir ExPEC to mitigate public health risks. Full article
(This article belongs to the Special Issue Advances in Microbial Genomics in the AMR Field)
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17 pages, 5577 KB  
Article
Tracking Global Transmission Dynamics of the Plasmid-Mediated mcr Gene: A Genomic Epidemiological Analysis
by Jinzhao Long, Xin Wang, Mengyue Liu, Jie Wu, Haiyan Yang, Shuaiyin Chen and Guangcai Duan
Microorganisms 2026, 14(1), 28; https://doi.org/10.3390/microorganisms14010028 - 22 Dec 2025
Viewed by 728
Abstract
The emergence and spread of mobile colistin resistance (mcr) genes pose a significant challenge in controlling multidrug-resistant Gram-negative pathogens. Understanding the epidemiology of mcr-carrying plasmids is essential for mitigating their dissemination across humans, animals, and the environment. To characterize their [...] Read more.
The emergence and spread of mobile colistin resistance (mcr) genes pose a significant challenge in controlling multidrug-resistant Gram-negative pathogens. Understanding the epidemiology of mcr-carrying plasmids is essential for mitigating their dissemination across humans, animals, and the environment. To characterize their spatiotemporal dynamics on a global scale, we analyzed an extensive collection of 5,549 mcr-carrying plasmids spanning 1995 to the present. We found that cross-genera transmission patterns of mcr-carrying plasmids varied across four distinct periods. Initially, IncHI2/HI2A plasmids provided a survival advantage across genera and regions, followed by IncI2, and ultimately by IncX4. Moreover, the three plasmid lineages (i.e., IncX4, IncI2, and IncHI2/HI2A) have reached a stable distribution across diverse bacterial hosts and geographic regions through horizontal gene transfer and clonal expansion. By integrating sequence similarity clustering of plasmids and mcr-related genetic environments, we identified 79 cross-genus, 43 intra-E. coli, and 10 intra-S. enterica transmission units. Molecular dating analysis traced the origin of IncX4 plasmids to 1990 in animal hosts, with phylogenetic evidence indicating potential cross-host, -genus, and -region exchange. Notably, IncP1 plasmids emerged as important vectors of mcr-1 and mcr-3 spread, particularly in Southeast Asia, warranting enhanced surveillance. These findings provide critical insights into the global transmission networks of plasmid-mediated mcr genes and underscore the urgent need for coordinated interventions. Full article
(This article belongs to the Special Issue Advances in Microbial Genomics in the AMR Field)
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14 pages, 2424 KB  
Article
Genomic Insights into Antimicrobial Resistance and Virulence of Monophasic Salmonella enterica I 4,[5],12:i:- Isolates from Clinical and Environmental Sources in Jeollanam-do, Korea
by Eunbyeul Go, Bo Ra Kang, Hye Young Na, Hyung Woo Lim, Hye Lin Yang, Mi Young Shin, Yang Joon An, Sook Park and Ki-Bok Yoon
Microorganisms 2025, 13(12), 2729; https://doi.org/10.3390/microorganisms13122729 - 29 Nov 2025
Viewed by 606
Abstract
This study investigated the molecular epidemiology, virulence, antimicrobial resistance, and mobile genetic elements (MGEs) of Salmonella enterica serovar I 4,[5],12:i:- isolates collected in Jeollanam-do, South Korea, between 2021 and 2023. A total of 135 isolates were tested for antimicrobial susceptibility and 14 virulence-associated [...] Read more.
This study investigated the molecular epidemiology, virulence, antimicrobial resistance, and mobile genetic elements (MGEs) of Salmonella enterica serovar I 4,[5],12:i:- isolates collected in Jeollanam-do, South Korea, between 2021 and 2023. A total of 135 isolates were tested for antimicrobial susceptibility and 14 virulence-associated genes were screened by PCR. Pulsed-field gel electrophoresis (PFGE) assessed clonal relatedness, and whole-genome sequencing (WGS) enabled multilocus sequence typing (MLST), core genome MLST (cgMLST), SNP phylogeny, resistance gene detection, and MGE analysis. Nine virulence profiles (VP1–VP9) were identified. VP1 (74.1%) was strongly associated with multidrug resistance (MDR), while VP2 (14.8%), which carried plasmid-encoded spv genes, remained largely susceptible. Overall, 83.7% of isolates were resistant to at least one antimicrobial, and 65.2% were MDR, with ampicillin and tetracycline consistently forming the backbone of MDR phenotypes. PFGE revealed high genetic diversity, with 72 pulsotypes, yet certain clones (e.g., SMOX01.006, SMOX01.012) were widely distributed and corresponded to VP2 isolates. WGS confirmed two dominant sequence types, ST34 (n = 24) and ST19 (n = 20), with SNP phylogeny showing VP1 isolates mainly clustered with ST34 and VP2 with ST19. Genotype–phenotype concordance showed strong agreement for most antimicrobials, except cefoxitin, ciprofloxacin, amikacin, and trimethoprim/sulfamethoxazole. MGE analysis revealed that tet(B) was consistently associated with ISVsa5, while ISEc59 was linked to multiple resistance genes, though only aac(3)-IV was phenotypically expressed. These findings demonstrate that MDR and virulence gene composition were closely associated with clonal clustering and that MGEs may contribute to resistance gene expression. This study provides a basis for understanding the dissemination of resistant and virulent Salmonella in the region and underscores the need for continuous genomic surveillance. Full article
(This article belongs to the Special Issue Advances in Microbial Genomics in the AMR Field)
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