Article
Microbiology
Ellen C. Carbo, Anne Russcher, Margriet E. M. Kraakman, Caroline S. de Brouwer, Igor A. Sidorov, Mariet C. W. Feltkamp, Aloys C. M. Kroes, Eric C. J. Claas, Jutte J. C. de Vries
Summary: In this study, the mNGS approach was used for the identification and load monitoring of transplantation-related DNA viruses in immunocompromised patients. The results showed that the mNGS method performed comparably to qPCR in detection and viral load determination.
Review
Engineering, Environmental
Emily Garner, Benjamin C. Davis, Erin Milligan, Matthew Forrest Blair, Ishi Keenum, Ayella Maile-Moskowitz, Jin Pan, Mariah Gnegy, Krista Liguori, Suraj Gupta, Aaron J. Prussin, Linsey C. Marr, Lenwood S. Heath, Peter J. Vikesland, Liqing Zhang, Amy Pruden
Summary: The emergence of NGS technologies has revolutionized the water industry's ability to address complex microbiological challenges, although faced with barriers like cost and expertise. Research has focused on the applications of NGS in water, wastewater, and recycled water, highlighting key contributions and future directions for advancement.
Article
Genetics & Heredity
Moritz Kohls, Magdalena Kircher, Jessica Krepel, Pamela Liebig, Klaus Jung
Summary: Estimating the taxonomic composition of viral sequences using artificial neural networks and machine learning models proved to be more accurate than traditional mapping approaches. Training data sampled from the NCBI database with a focus on the biological order of viruses allowed for a higher prediction accuracy in classifying test reads to their viral order. The use of auxiliary test sets helped to estimate conditional class probabilities and correct the prior estimation of taxonomic distribution in the test set.
Article
Multidisciplinary Sciences
Zhenli Diao, Dongsheng Han, Rui Zhang, Jinming Li
Summary: This review summarizes the potential applications and challenges of metagenomic next-generation sequencing (mNGS) in the diagnosis of lower respiratory tract infections (LRIs), aiming to promote the integration of mNGS into the management of patients with respiratory tract infections in a clinical setting.
JOURNAL OF ADVANCED RESEARCH
(2022)
Article
Microbiology
German V. Roev, Nadezhda I. Borisova, Nadezhda V. Chistyakova, Matvey R. Agletdinov, Vasily G. Akimkin, Kamil Khafizov
Summary: Next-generation sequencing technologies have transformed virology by enabling complete viral genome sequencing, metagenomic studies, and identification of new viral pathogens. However, metagenomic sequencing faces challenges in data analysis and identifying novel viruses using traditional homology-based strategies. This study used advanced computational methods and experimental strategies to analyze bat feces from different Russian cities and identified a diverse range of viral pathogens.
Article
Oncology
Ariana Rostami, Scott Bratman, Kathy Han
Summary: Liquid biopsy approaches for detecting viral DNA play a crucial role in diagnosing virally-associated cancers. The CaptHPV method based on next-generation sequencing is discussed for its potential in detecting plasma HPV DNA in HPV-associated cancers and its potential clinical utility.
CLINICAL CANCER RESEARCH
(2021)
Review
Biochemistry & Molecular Biology
Pei Yee Tiew, Oliver W. Meldrum, Sanjay H. Chotirmall
Summary: Microbiomics has made significant advancements in the past decade due to the availability of next-generation sequencing (NGS) and multi-omic technologies. Integration of NGS and multi-omic datasets allows for comprehensive assessment of endophenotypes in chronic respiratory diseases like chronic obstructive pulmonary disease (COPD). Valuable insights have been gained into the role of microbial communities in COPD onset, progression, prognosis, and treatment response. Identifying specific microbes and metabolic signatures associated with COPD can lead to new therapeutic interventions and prognosis-related biomarkers. However, the analysis and interpretation of the large amount of data generated by these technologies remain challenging, and standardized methods are lacking.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Immunology
Ravina Kullar, Emanuele Chisari, James Snyder, Christopher Cooper, Javad Parvizi, Jason Sniffen
Summary: This article discusses the gaps in traditional culture and introduces the utility of next-generation sequencing (NGS) in diagnosing and treating peri-prosthetic joint infections. It highlights the clinical benefits of using NGS compared to culture alone and emphasizes the potential of NGS in improving the yield of identifying infective organisms in challenging cases.
CLINICAL INFECTIOUS DISEASES
(2023)
Article
Immunology
Denver T. Niles, Paula A. Revell, Daniel Ruderfer, Lucila Marquez, J. Chase McNeil, Debra L. Palazzi
Summary: Plasma metagenomic next-generation sequencing (mNGS) has the potential to detect multiple organisms with a single test. The study found that mNGS testing had the highest clinical impact in immunocompromised patients with well-defined deep-seated infections. Further research is needed to evaluate the full range of clinical scenarios for which mNGS testing is beneficial.
PEDIATRIC INFECTIOUS DISEASE JOURNAL
(2022)
Article
Mathematics, Applied
Ashaq Hussain Bhat, Tu N. Nguyen, Korhan Cengiz, Puniethaa Prabhu
Summary: The HBEA clustering algorithm uses exact pairwise global alignment algorithm to improve cluster quality and extract cluster representatives. Experimental investigation showed that HBEA produces better operational taxonomic unit (OTU) clusters and computational complexity than other algorithms.
MATHEMATICAL METHODS IN THE APPLIED SCIENCES
(2021)
Review
Fisheries
Tina Kollannoor Johny, Rinu Madhu Puthusseri, Sarita Ganapathy Bhat
Summary: The fish gut is a complex ecosystem influenced by various factors, and the gut microbiota plays important roles in the physiological functions of the host. With technological advancements, the application of culture-independent techniques in studying fish gut microbiota is promising for a better understanding.
AQUACULTURE RESEARCH
(2021)
Article
Immunology
Rachel K. To, Nanda Ramchandar, Aamisha Gupta, Alice Pong, Christopher Cannavino, Jennifer Foley, Lauge Farnaes, Nicole G. Coufal
Summary: Pediatric infective endocarditis is associated with underlying heart disease, and accurate identification of pathogens is crucial for treatment. Plasma next-generation sequencing showed a high detection rate in this case series.
PEDIATRIC INFECTIOUS DISEASE JOURNAL
(2021)
Review
Biochemical Research Methods
Sergey Knyazev, Lauren Hughes, Pavel Skums, Alexander Zelikovsky
Summary: Advancements in next-generation sequencing have enabled detailed assessment of viral population complexity within hosts, extracting crucial epidemiological and biomedical information. However, the complex analysis of NGS data is required to handle the rapidly mutating viral populations.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Medicine, General & Internal
Junyan Qu, Zhiyong Zong
Summary: This case report presents a case of strongyloidiasis in a Chinese male patient diagnosed using metagenomic next-generation sequencing (mNGS). The study highlights the potential of mNGS in detecting uncommon infectious diseases and emphasizes the importance of raising awareness of strongyloidiasis in non-endemic areas.
FRONTIERS IN MEDICINE
(2022)
Article
Immunology
Mengjia Qian, Bijun Zhu, Yanxia Zhan, Lingyan Wang, Qi Shen, Miaomiao Zhang, Lei Yue, Duojiao Wu, Hao Chen, Xiangdong Wang, Yunfeng Cheng
Summary: The negative prediction accuracy rate of the original specimen is significant when the mNGS test is negative. However, other laboratory assays results and clinical presentations should always be carefully considered prior to drawing a diagnosis.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Agriculture, Dairy & Animal Science
J. Bokma, R. Boone, P. Deprez, B. Pardon
JOURNAL OF DAIRY SCIENCE
(2020)
Article
Agriculture, Dairy & Animal Science
B. Pardon, J. Callens, J. Maris, L. Allais, W. Van Praet, P. Deprez, S. Ribbens
JOURNAL OF DAIRY SCIENCE
(2020)
Article
Veterinary Sciences
Kirsten Proost, Bart Pardon, Elke Pollaris, Thijs Flahou, Lieven Vlaminck
JOURNAL OF VETERINARY INTERNAL MEDICINE
(2020)
Article
Veterinary Sciences
Kirsten Proost, Bart Pardon, Elke Pollaris, Thijs Flahou, Lieven Vlaminck
JOURNAL OF VETERINARY INTERNAL MEDICINE
(2020)
Article
Infectious Diseases
Jade Bokma, Linde Gille, Koen De Bleecker, Jozefien Callens, Freddy Haesebrouck, Bart Pardon, Filip Boyen
Article
Veterinary Sciences
H. Van Loo, O. Bogado Pascottini, S. Ribbens, J. Hooyberghs, B. Pardon, G. Opsomer
Summary: This study aimed to determine the prevalence of infectious agents associated with bovine abortion and perinatal mortality, and found that at least one potential causal agent was detected in 39% of cases. Neospora caninum was the most common pathogen, followed by Trueperella pyogenes, BVDv, Escherichia coli, and Aspergillus fumigatus. Winter was associated with lower positivity for Neospora caninum and BVDv compared to warmer seasons.
PREVENTIVE VETERINARY MEDICINE
(2021)
Article
Agriculture, Dairy & Animal Science
Victoria Rhodes, Eoin G. Ryan, Ciara J. Hayes, Catherine McAloon, Luke O'Grady, Seamus Hoey, John F. Mee, Bart Pardon, Bernadette Earley, Conor G. McAloon
Summary: The study investigated the effectiveness of using thoracic ultrasound scoring (TUS) and clinical respiratory scoring (CRS) to assess respiratory diseases in dairy calves, finding that TUS was associated with average daily gain (ADG) while CRS showed no association with ADG.
JOURNAL OF DAIRY SCIENCE
(2021)
Article
Veterinary Sciences
Stan Jourquin, Jade Bokma, Lieze De Cremer, Katharina van Leenen, Nick Vereecke, Bart Pardon
Summary: This study evaluated the treatment efficacy for respiratory disease by assessing lung reaeration through thoracic ultrasound examination and compared the effectiveness of florfenicol and oxytetracycline. The results showed that florfenicol resulted in a faster cure and reduction in antimicrobial usage compared to oxytetracycline.
JOURNAL OF VETERINARY INTERNAL MEDICINE
(2022)
Article
Veterinary Sciences
T. Lowie, J. Callens, J. Maris, S. Ribbens, B. Pardon
Summary: Respiratory tract infections in cattle operations remain a significant problem, leading to economic losses, compromised animal welfare, and overuse of antimicrobials globally. A study was conducted to develop decision trees for pathogen identification in outbreaks of bovine respiratory disease based on environmental factors, utilizing PCR for pathogen detection and data from 201 outbreaks between 2016 and 2019. The developed trees showed promise but lacked sensitivity and specificity to be a reliable tool for practice, although they can still provide some informative guidance for decision making in outbreaks.
PREVENTIVE VETERINARY MEDICINE
(2021)
Article
Agriculture, Dairy & Animal Science
T. Lowie, K. Van Leenan, S. Jourquin, M. L. Pas, J. Bokma, B. Pardon
Summary: This study aimed to identify clinical signs associated with ultrasound-confirmed pneumonia and found that cough was the most correlated symptom with lung consolidation in all production types. Fever was also a significant factor in beef and veal calves. Postweaning, clinical signs were not significantly associated with pneumonia, except for cough in dairy calves. Spontaneous or induced cough as a single clinical sign performed the best.
JOURNAL OF DAIRY SCIENCE
(2022)
Article
Agriculture, Dairy & Animal Science
Jill Derix, Richard Ducatelle, Bart Pardon, Evi Croes, Niels Groot Nibbelink, Linda Van Deurzen-Duineveld, Filip Van Immerseel, Evy Goossens
Summary: Necro-hemorrhagic enteritis in calves, caused by Clos-tridium perfringens type A, is a fatal disease affecting calves in intensive rearing systems. Lack of development of active immunity against alpha toxin is the main trigger. This study investigates the effect of milk replacer components on alpha toxin production and the effect of lactose on antibody production.
JOURNAL OF DAIRY SCIENCE
(2023)
Article
Veterinary Sciences
Jade Bokma, Sabrina Stuyvaert, Bart Pardon
Summary: The study compares the diagnostic test accuracy of three commercially available M. bovis antibody ELISAs and explores optimal cutoff values for screening purposes. ID-screen showed the highest diagnostic accuracy, while adjusting cutoff values could increase the sensitivity of Bio-X tests, making them also applicable as screening tools.
Article
Agriculture, Dairy & Animal Science
Stan Jourquin, Thomas Lowie, Florian Debruyne, Laurens Chantillon, Nick Vereecke, Filip Boyen, Randy Boone, Jade Bokma, Bart Pardon
Summary: This prospective cohort study aims to investigate the dynamics of lung consolidation in male dairy calves and its association with antimicrobial therapy, respiratory diagnostics, average daily gain (ADG), and cold carcass weight (CCW). The study found a high incidence of lung consolidation upon arrival and a significant association with chronic pneumonia and reduced performance.
JOURNAL OF DAIRY SCIENCE
(2023)
Article
Veterinary Sciences
Mathilde L. L. Pas, Jade Bokma, Thomas Lowie, Filip Boyen, Bart Pardon
Summary: This study aimed to identify factors associated with mortality in critically ill calves and describe bacteria obtained from blood cultures of calves with sepsis and their antimicrobial resistance. The results showed that sepsis, abnormal behavior, and hypothermia were significantly associated with higher mortality risk. Escherichia coli was the most frequently isolated bacteria, with a high percentage of multidrug resistance. The study highlights the importance of appropriate antimicrobial use in treating critically ill calves.
JOURNAL OF VETERINARY INTERNAL MEDICINE
(2023)
Article
Veterinary Sciences
Justine Clinquart, Katharina van Leenen, Jade Bokma, Bart Pardon
Summary: This study distinguishes different cytological profiles in nonbronchoscopic bronchoalveolar lavage (nBAL) from grouped housed calves and characterizes these profiles on individual and herd levels. The study provides a first step in the development of cytological guidelines for the assessment of airway health and inflammation in calves through nBAL fluid cytology.
JOURNAL OF VETERINARY INTERNAL MEDICINE
(2023)