High-throughput sequencing technologies in the detection of livestock pathogens, diagnosis, and zoonotic surveillance

Suminda, Godagama Gamaarachchige Dinesh; Bhandari, Srishti; Won, Yoonkyung; Goutam, Umesh; Pulicherla, K. K.; Son, Young‐Ok; Ghosh, Mrinmoy

doi:10.1016/j.csbj.2022.09.028

Cited by 21 publications

(2 citation statements)

References 148 publications

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“…The global MRSA pandemic underscores the need for diagnostic tests that are rapid, accurate, cost-effective, and deployable at the point of care, which would aid in both infection control and patient management. Conventional bacterial culture, RT-PCR, mass spectrometry, and metagenomic next-generation sequencing (mNGS) are current techniques for S. aureus and MRSA detections, which all have long turnaround times, require well-trained personnel, and rely on expensive equipment ( 33 – 35 ). These drawbacks are accentuated in limited-resource settings and at the point of care.…”

Section: Discussionmentioning

confidence: 99%

Cas12a/Guide RNA-Based Platforms for Rapidly and Accurately Identifying Staphylococcus aureus and Methicillin-Resistant S. aureus

et al. 2023

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Section: Discussionmentioning

confidence: 99%

Cas12a/Guide RNA-Based Platforms for Rapidly and Accurately Identifying Staphylococcus aureus and Methicillin-Resistant S. aureus

et al. 2023

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“…of samples, funding, and computational infrastructure available. When monitoring food safety in terms of screening food for pathogens, a large number of samples may be involved especially at the scale of food industries [ 214 , 215 ]. The rapid analysis timelines offered by HTS compared to culture-based methods promotes the application of metagenomics in food quality control enabling quick and informed decisions on product recall.…”

Section: Applications Of Metagenomics In the Fermented Food Industrymentioning

confidence: 99%

The Application of Metagenomics to Study Microbial Communities and Develop Desirable Traits in Fermented Foods

Srinivas

O’Sullivan

Cotter

et al. 2022

Foods

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The microbial communities present within fermented foods are diverse and dynamic, producing a variety of metabolites responsible for the fermentation processes, imparting characteristic organoleptic qualities and health-promoting traits, and maintaining microbiological safety of fermented foods. In this context, it is crucial to study these microbial communities to characterise fermented foods and the production processes involved. High Throughput Sequencing (HTS)-based methods such as metagenomics enable microbial community studies through amplicon and shotgun sequencing approaches. As the field constantly develops, sequencing technologies are becoming more accessible, affordable and accurate with a further shift from short read to long read sequencing being observed. Metagenomics is enjoying wide-spread application in fermented food studies and in recent years is also being employed in concert with synthetic biology techniques to help tackle problems with the large amounts of waste generated in the food sector. This review presents an introduction to current sequencing technologies and the benefits of their application in fermented foods.

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Emerging strategies and therapeutic innovations for combating drug resistance in Staphylococcus aureus strains: A comprehensive review

Gopikrishnan,

Haryini,

2024

J Basic Microbiol

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In recent years, antibiotic therapy has encountered significant challenges due to the rapid emergence of multidrug resistance among bacteria responsible for life‐threatening illnesses, creating uncertainty about the future management of infectious diseases. The escalation of antimicrobial resistance in the post‐COVID era compared to the pre‐COVID era has raised global concern. The prevalence of nosocomial‐related infections, especially outbreaks of drug‐resistant strains of Staphylococcus aureus, have been reported worldwide, with India being a notable hotspot for such occurrences. Various virulence factors and mutations characterize nosocomial infections involving S. aureus. The lack of proper alternative treatments leading to increased drug resistance emphasizes the need to investigate and examine recent research to combat future pandemics. In the current genomics era, the application of advanced technologies such as next‐generation sequencing (NGS), machine learning (ML), and quantum computing (QC) for genomic analysis and resistance prediction has significantly increased the pace of diagnosing drug‐resistant pathogens and insights into genetic intricacies. Despite prompt diagnosis, the elimination of drug‐resistant infections remains unattainable in the absence of effective alternative therapies. Researchers are exploring various alternative therapeutic approaches, including phage therapy, antimicrobial peptides, photodynamic therapy, vaccines, host‐directed therapies, and more. The proposed review mainly focuses on the resistance journey of S. aureus over the past decade, detailing its resistance mechanisms, prevalence in the subcontinent, innovations in rapid diagnosis of the drug‐resistant strains, including the applicants of NGS and ML application along with QC, it helps to design alternative novel therapeutics approaches against S. aureus infection.

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High-throughput sequencing technologies in the detection of livestock pathogens, diagnosis, and zoonotic surveillance

Cited by 21 publications

References 148 publications

Cas12a/Guide RNA-Based Platforms for Rapidly and Accurately Identifying Staphylococcus aureus and Methicillin-Resistant S. aureus

Cas12a/Guide RNA-Based Platforms for Rapidly and Accurately Identifying Staphylococcus aureus and Methicillin-Resistant S. aureus

The Application of Metagenomics to Study Microbial Communities and Develop Desirable Traits in Fermented Foods

Emerging strategies and therapeutic innovations for combating drug resistance in Staphylococcus aureus strains: A comprehensive review

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