Surveillance and Detection of Antimicrobial Resistance: Tools and Trends

A special issue of Antibiotics (ISSN 2079-6382).

Deadline for manuscript submissions: 31 March 2026 | Viewed by 1401

Special Issue Editor


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Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan
Interests: clinical pathology; molecular diagnosis; genome; epidemiology
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Special Issue Information

Dear Colleagues,

Antimicrobial resistance (AMR) represents one of the most formidable challenges facing global health today, threatening to reverse decades of medical advancement and compromise fundamental healthcare interventions. Robust surveillance systems and rapid, precise detection methodologies are essential in monitoring the emergence and dissemination of resistant pathogens, guiding evidence-based clinical practice, and informing strategic public health interventions.

This Special Issue will present cutting-edge advances and emerging trends in AMR surveillance and detection across diverse environments, encompassing healthcare facilities, community settings, agricultural systems, and environmental reservoirs. We welcome contributions that explore innovative diagnostic technologies, laboratory-based and point-of-care detection platforms, genomic and proteomic surveillance approaches, and transformative digital health solutions including artificial intelligence and big data analytics.

Manuscripts exploring the translation of surveillance data into actionable public health strategies, as well as studies examining implementation challenges and global real-world applications of AMR detection systems, are particularly encouraged. Through this comprehensive platform, we aim to accelerate scientific progress in AMR control and promote interdisciplinary collaboration among researchers, clinicians, and public health practitioners worldwide.

Prof. Dr. Hung-Sheng Shang
Guest Editor

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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. Antibiotics is an international peer-reviewed open access monthly journal published by MDPI.

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Keywords

  • antimicrobial resistance
  • surveillance systems
  • pathogen detection
  • rapid diagnostics
  • genomic surveillance
  • artificial intelligence
  • point-of-care testing
  • public health strategy
  • molecular epidemiology
  • big data analytics

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Published Papers (1 paper)

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Research

12 pages, 1253 KB  
Article
Rapid Nanopore Sequencing of Positive Blood Cultures Using Automated Benzyl-Alcohol Extraction Improves Time-Critical Sepsis Management
by Chi-Sheng Tai, Hsing-Yi Chung, Tai-Han Lin, Chih-Kai Chang, Cherng-Lih Perng, Po-Shiuan Hsieh, Hung-Sheng Shang and Ming-Jr Jian
Antibiotics 2025, 14(10), 1001; https://doi.org/10.3390/antibiotics14101001 - 9 Oct 2025
Viewed by 1068
Abstract
Background/Objective: Timely identification of bloodstream pathogens is critical for sepsis management; however, PCR inhibitors such as sodium polyanetholesulfonate (SPS) in blood culture broth compromise nucleic acid recovery and long read sequencing. We assessed whether coupling a benzyl alcohol SPS-removal step to the [...] Read more.
Background/Objective: Timely identification of bloodstream pathogens is critical for sepsis management; however, PCR inhibitors such as sodium polyanetholesulfonate (SPS) in blood culture broth compromise nucleic acid recovery and long read sequencing. We assessed whether coupling a benzyl alcohol SPS-removal step to the fully automated LabTurbo AIO extractor improves Oxford Nanopore-based pathogen detection. Methods: Thirteen positive blood culture broths were pre-treated with benzyl alcohol and divided: half volumes were purified on the LabTurbo AIO; paired aliquots underwent manual QIAamp extraction. DNA purity was evaluated by NanoDrop and Qubit. Barcoded libraries were sequenced on MinION R9.4.1 flow cells for 6 h. Results: Automated eluates showed a median A260/A280 of 1.92 and A260/A230 of 1.96, versus 1.80 and 1.48 for manual extracts. The automated workflow generated 1.69 × 106 total reads compared with 3.9 × 105 reads for manual extraction. The median N50 read length increased from 5.9 kb to 8.7 kb, and the median proportion of reads classified to species increased from 62% to 84%. The hands-on time was <5 min and the sample-to-answer turnaround was <8 h, compared with >9 h and 90 min for the manual protocol, respectively. Conclusions: Benzyl alcohol SPS removal integrated into the LabTurbo AIO extractor yielded purer, longer, and higher read counts, enhancing nanopore sequencing depth and accuracy while compressing diagnostic turnaround to a single working day. This represents a practical advance for rapid blood culture pathogen identification in critical care settings. Full article
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