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Veterinary Sciences
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Advanced Sequencing and Bioinformatics for Tracking MDR Bacteria in Veterinary...
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Advanced Sequencing and Bioinformatics for Tracking MDR Bacteria in Veterinary and One Health Interfaces

A special issue of Veterinary Sciences (ISSN 2306-7381). This special issue belongs to the section "Veterinary Microbiology, Parasitology and Immunology".

Deadline for manuscript submissions: closed (12 December 2025) | Viewed by 3063

Special Issue Editors

Prof. Dr. Ruichao Li

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Guest Editor
1. Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
2. Institute of Comparative Medicine, Yangzhou University, Yangzhou 225009, China
Interests: antimicrobial resistance; plasmids; transposons; microbial genomics; nanopore sequencing
Special Issues, Collections and Topics in MDPI journals
Dr. Muhammad Shoaib

E-Mail Website
Guest Editor
College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
Interests: AMR; AMR modulation; zoonosis; veterinary microbiology
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Edward Feil

E-Mail Website
Guest Editor
Department of Life Sciences, University of Bath, Bath BA2 7AY, UK
Interests: bacterial population genomics; evolutionary biology; molecular epidemiology; transmission; antibiotic resistance; one-health; wastewater microbiology; metagenomics; bioinformatics; human and animal bacterial pathogens; aquaculture

Special Issue Information

Dear Colleagues,

The growing threat of antimicrobial resistance (AMR), particularly multidrug-resistant (MDR) bacteria, poses a significant challenge to both animal and public health worldwide. In both veterinary and other One Health sectors, overuse of antibiotics accelerates the spread of resistance genes, making early detection and monitoring essential.

This Special Issue aims to highlight recent advances in sequencing technologies (e.g., DNBSEQ, Nanopore, PacBio) and bioinformatics tools that enable the accurate detection and characterization of MDR bacteria across diverse One Health settings, including livestock, companion animals, wildlife, and environmental reservoirs.

We welcome original research, reviews, and communications focusing on:

  • Application of metagenomics and whole-genome sequencing for MDR detection;
  • Bioinformatics pipelines for resistome analysis;
  • AMR epidemiology in veterinary medicine;
  • Insights into resistance gene evolution and transmission;
  • Integrated genomic surveillance strategies linking animal, human, and environmental health.

This collection aims to provide a focused platform for advancing cross-disciplinary dialogue and fostering innovative approaches to controlling antimicrobial resistance (AMR) in veterinary sciences and beyond.

Prof. Dr. Ruichao Li
Dr. Muhammad Shoaib
Prof. Dr. Edward Feil
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. Veterinary Sciences 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 2100 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)
  • multidrug-resistant (MDR) bacteria
  • whole-genome sequencing
  • One Health
  • surveillance
  • resistome
  • bioinformatics

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

Published Papers (2 papers)

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Research

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16 pages, 1283 KB  
Article
Antibiotic Resistance to Critically Important Antimicrobials and Virulence Genes in Enterococcus faecalis Strains Isolated from Eurasian Griffon Vultures (Gyps fulvus) and Their Association with Mobile Genetic Elements
by Ana Isabel Vela, Carlos Serna, María Ugarte-Ruiz, Aránzazu Buendia, Almudena Casamayor, Johan Manuel Calderón Bernal, Lucas Domínguez, María Dolores Cid and José Francisco Fernández-Garayzábal
Vet. Sci. 2025, 12(11), 1083; https://doi.org/10.3390/vetsci12111083 - 14 Nov 2025
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Abstract
The phenotypic resistance of 56 Enterococcus faecalis isolates from Eurasian griffon vultures was subjected to surveillance testing with the microdilution method using a standardized panel of antimicrobials. Isolates were also characterized by MLST. Additionally, the genome of 19 isolates with phenotypic resistance to [...] Read more.
The phenotypic resistance of 56 Enterococcus faecalis isolates from Eurasian griffon vultures was subjected to surveillance testing with the microdilution method using a standardized panel of antimicrobials. Isolates were also characterized by MLST. Additionally, the genome of 19 isolates with phenotypic resistance to linezolid, ciprofloxacin, chloramphenicol and/or high-level resistance to gentamicin were sequenced to determine their antimicrobial resistance (ARGs) and virulence-associated genes and to identify mobile genetic elements (MGEs). Most isolates (82.1%) exhibited non-wild-type phenotypes to six antimicrobial agents, and multidrug resistance (MDR) was detected in 34% of the isolates. Most MDR isolates (53%) belonged to ST16, ST116 and ST35. ARGs were localized on the chromosome as well as on various MGEs previously reported in human, food and livestock isolates, suggesting that vultures may acquire antibiotic-resistant bacteria (ARBs) and/or ARGs as a consequence of anthropogenic pollution. Overall, 22 virulence-associated genes encoding cell surface and secreted factors were identified, some of which were located on MGEs that also carried ARGs. The significant proportion of E. faecalis isolates recovered from vultures that exhibited MDR phenotypes and harbored MGEs carrying ARGs and virulence-associated genes is cause for concern, since vultures may act as spreaders of these genes to the environment, domestic animals and humans. Full article
(This article belongs to the Special Issue Advanced Sequencing and Bioinformatics for Tracking MDR Bacteria in Veterinary and One Health Interfaces)
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Review

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21 pages, 1429 KB  
Review
Nanopore Sequencing in Veterinary Pathogen Detection: A Review of Technologies and Applications
by Lei Xu, Leilei Zhao, Zeyu Tong, Kai Peng, Mianzhi Wang, Runsheng Li, Zhiqiang Wang and Ruichao Li
Vet. Sci. 2026, 13(3), 216; https://doi.org/10.3390/vetsci13030216 - 25 Feb 2026
Viewed by 1135
Abstract
Nanopore-based sequencing has emerged as a revolutionary tool for animal pathogen genomics, offering capabilities unattainable with Sanger and next-generation sequencing (NGS). Despite rapid technical progress, routine veterinary deployment still faces uncertainty in study design, sample preparation, and interpretation thresholds across diverse hosts and [...] Read more.
Nanopore-based sequencing has emerged as a revolutionary tool for animal pathogen genomics, offering capabilities unattainable with Sanger and next-generation sequencing (NGS). Despite rapid technical progress, routine veterinary deployment still faces uncertainty in study design, sample preparation, and interpretation thresholds across diverse hosts and sample matrices. Accordingly, this review consolidates recent evidence and provides workflow-oriented guidance for veterinary diagnostics and One Health surveillance. Its portability, ability to generate real-time long-read data, and minimal infrastructure requirements enable rapid, on-site sequencing for veterinary diagnostics and surveillance. This review examines the principles of nanopore sequencing and its advantages over conventional methods, surveying recent applications across viral, bacterial (including antimicrobial resistance, AMR), and parasitic pathogen detection in animals. In viral diagnostics, it facilitates rapid whole-genome sequencing and outbreak tracing in field settings. For bacterial pathogens, it enables near-complete genome assembly and identification of plasmid-borne AMR genes. Emerging studies also demonstrate its utility in parasitology, from high-resolution species identification to whole-genome assemblies. We compare these advancements with traditional diagnostics, highlighting strengths in speed and comprehensiveness while addressing current limitations in accuracy and host-DNA interference. As technology matures through improvements in chemistry and adaptive sampling, nanopore sequencing is poised to transform veterinary pathogen detection and bolster One Health surveillance of emerging zoonoses. Full article
(This article belongs to the Special Issue Advanced Sequencing and Bioinformatics for Tracking MDR Bacteria in Veterinary and One Health Interfaces)
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