Article
Immunology
Suhua Xin, Hong Zhu, Chenglin Tao, Beibei Zhang, Lan Yao, Yaodong Zhang, Dosseh Jean Apotre Afayibo, Tao Li, Mingxing Tian, Jingjing Qi, Chan Ding, Shengqing Yu, Shaohui Wang
Summary: The TaqMan multiplex real-time PCR assay developed in this study proved to be highly specific and reliable for simultaneous detection and differentiation of S. Pullorum, S. Gallinarum, S. Enteritidis, and S. Typhimurium. The assay demonstrated analytical sensitivity down to three colony-forming units (CFUs) for the four Salmonella serovars and a detection limit of 500 CFU/g in artificially contaminated samples, improving to 10 CFU/g after pre-enrichment. When applied to clinical poultry samples, the multiplex real-time PCR assay yielded comparable results to traditional bacteriological examination, indicating its promising potential for clinical diagnostics and epidemiological studies of Salmonella in chicken farms and poultry products.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Food Science & Technology
Samir Mohammed Abd-Elghany, Takwa Mohammed Fathy, Amira Ibrahim Zakaria, Kalman Imre, Adriana Morar, Viorel Herman, Raul Pascalau, Laura Smuleac, Doru Morar, Mirela Imre, Khalid Ibrahim Sallam
Summary: This study investigated the presence of Salmonella spp. in buffalo meat in Egypt and studied the antimicrobial susceptibility of the isolated strains. The study found a high level of multidrug-resistant Salmonella contamination in Egyptian buffalo meat, highlighting the need for control measures to prevent Salmonella contamination.
Article
Public, Environmental & Occupational Health
Mysoon M. Al-Ansari, Moneerah M. Aljubali, Ali M. Somily, Ahmad M. Albarrag, Afshan Masood
Summary: The study revealed the presence of Salmonella in chicken meat sold in Riyadh, exhibiting resistance to multiple antibiotics and posing a potential risk of infection to consumers. The genotypic resistance pattern of Salmonella to antibiotics in both human and animal health was highlighted, urging the promotion of antibiotic-free poultry farming as an alternative option.
JOURNAL OF INFECTION AND PUBLIC HEALTH
(2021)
Article
Immunology
Emily M. Boerth, Joyce Gong, Becky Roffler, Claudette M. Thompson, Boni Song, Sasha F. Malley, Angelika Hirsch, Calman A. MacLennan, Fan Zhang, Richard Malley, Ying-Jie Lu
Summary: Bloodstream infections in low- and middle-income countries are primarily caused by invasive Salmonella disease. A preclinical development of a quadrivalent Salmonella vaccine targeting all four leading serotypes has shown promising results.
Article
Genetics & Heredity
Abdoulie Kanteh, Abdul Karim Sesay, Nabil-Fareed Alikhan, Usman Nurudeen Ikumapayi, Rasheed Salaudeen, Jarra Manneh, Yekini Olatunji, Andrew J. Page, Grant Mackenzie
Summary: Invasive non-typhoidal Salmonella (iNTS) disease remains a significant public health problem in sub-Saharan Africa due to clinical misdiagnosis, antimicrobial resistance, high case fatality, and lack of a vaccine. Genomic analysis of invasive Salmonella isolates revealed changes in incidence and proportion of atypical serovars, with potential acquisition of specific genetic virulence factors contributing to increased case fatality. Further investigations in Africa are needed to understand the distribution of iNTS serovars and virulence elements.
MICROBIAL GENOMICS
(2021)
Article
Food Science & Technology
Zhengwei Fang, Xiujuan Zhou, Xu Wang, Xianming Shi
Summary: A novel 3-plex droplet digital PCR (ddPCR) was developed for simultaneous identification and quantification of Salmonella and its two important serovars. The method showed high specificity and sensitivity, with a low detection limit for both genomic DNA and pure cultures. It was also demonstrated to be more sensitive than traditional cultivation method for the detection of Salmonella in food samples.
Article
Plant Sciences
Qingcong He, Dongwei Wang, Bei Tang, Jian Wang, Deyong Zhang, Yong Liu, Feixue Cheng
Summary: In this study, specific primers were designed for rapid identification and quantification of the plant-parasitic nematode Meloidogyne graminicola in soil. Both LAMP and real-time PCR showed higher sensitivity in detecting the nematode compared to conventional PCR. These methods have the potential to provide a useful platform for rapid species identification and quantification of economically important PPNs.
Article
Public, Environmental & Occupational Health
Indukumari M. Sarath, Noyal Mariya Joseph, Imola Jamir
Summary: This study aimed to evaluate the usefulness of quantitative real-time polymerase chain reaction (PCR) in the clinical diagnosis of leprosy. The results showed that the sensitivity of quantitative real-time PCR for leprosy was 93.1%, and the specificity was 100%. Therefore, the use of real-time PCR as a diagnostic tool for leprosy is strongly recommended.
AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE
(2023)
Article
Food Science & Technology
Chenxi Huang, Binti Youssouf Mahboubat, Yifeng Ding, Qile Yang, Jia Wang, Min Zhou, Xiaohong Wang
Summary: The study developed a rapid and accurate detection method for Salmonella using the lytic Siphovirus phage LPST10, which showed a detection limit of <30 CFU/mL in different food matrices. The method involves magnetic separation and real-time PCR detection, allowing for quick and efficient detection of Salmonella in complex food samples.
LWT-FOOD SCIENCE AND TECHNOLOGY
(2021)
Article
Engineering, Biomedical
Johnson V. John, Alec McCarthy, Yajuan Su, Daniel N. Ackerman, S. M. Shatil Shahriar, Mark A. Carlson, St. Patrick Reid, Joshua L. Santarpia, Wuqiang Zhu, Jingwei Xie
Summary: This study presents a novel nanofiber capsule that can be used for minimally invasive collection of biological samples, facilitating early diagnosis and screening of various diseases.
ACTA BIOMATERIALIA
(2022)
Article
Microbiology
Qinghua Ye, Yuting Shang, Moutong Chen, Rui Pang, Fan Li, Xinran Xiang, Chufang Wang, Baoqing Zhou, Shuhong Zhang, Jumei Zhang, Xiaojuan Yang, Liang Xue, Yu Ding, Qingping Wu
Summary: The accurate and rapid classification of Salmonella serovars is crucial for the identification of isolates involved in disease in humans and animals. This study successfully identified specific genes for Albany and Hadar serovars in Salmonella C2 serogroups and designed PCR primers with high specificity. The sensitivity and detection limits of the specific PCR method in food samples were also determined, highlighting the potential for rapid and sensitive detection of these specific serovars.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemical Research Methods
K. Mohanapriya, Himani Agri, Subbaiyan Anbazhagan, Damini Khawaskar, Varsha Jayakumar, Michael V. Lalrinzuala, K. M. Himani, I Sophia, Asok K. Mariappan, Pallab Abhishek, Viswas Konasagara Nagaleekar, Dharmendra K. Sinha, Pallab Chaudhuri, Vinod K. Chaturvedi, Bhoj R. Singh, Prasad Thomas
Summary: Salmonella species are a group of Gram-negative bacteria with numerous serovars, some of which are associated with diseases in livestock and humans. Molecular methods, such as PCR, have been applied to predict the serovars by detecting specific genetic elements. In this study, two multiplex PCR assays were developed to detect important Salmonella serovars associated with poultry in India. The assays showed high specificity and applicability for routine diagnosis.
JOURNAL OF MICROBIOLOGICAL METHODS
(2023)
Article
Biochemistry & Molecular Biology
Surangi H. H. Thilakarathna, Taryn Stokowski, Linda Chui
Summary: The vPCR protocol using PMAxx (TM) as the intercalating agent was optimized for selective amplification of live bacterial DNA. The study examined different methods of PMAxx (TM) addition, a wash step post-treatment, and a tube change before DNA extraction. The optimized protocol successfully eliminated false positives and minimized false negatives. With further improvements, vPCR has great potential as a culture-independent diagnostic tool.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Soumya Ranjan Mahapatra, Jyotirmayee Dey, Gajraj Singh Kushwaha, Puspasree Puhan, Nirmal Kumar Mohakud, Santosh Kumar Panda, S. Lata, Namrata Misra, Mrutyunjay Suar
Summary: Developing a multi-epitope subunit vaccine peptide targeting multi-drug resistance proteins in Salmonella is a promising strategy to increase vaccine success. The designed vaccine construct showed high immunogenicity and strong binding affinity to HLA alleles. This immunoinformatic approach could potentially stimulate immune responses in typhoidal Salmonella serovars.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2022)
Article
Multidisciplinary Sciences
Walid Hossain, Mohabbat Hossain, Khalid Arafath, Subarna Sayed Ety, Mahade Hasan Shetu, Mazbahul Kabir, Farjana Akther Noor, Kalissar Mannoor
Summary: The study aimed to reduce the run time of multiplex RT-PCR for detecting SARS CoV-2 N1 and N2 sequences and human RNase P (RP) sequence. By optimizing the Fast PCR protocol and comparing it with conventional PCR, the researchers found that Fast PCR significantly shortened the run time while yielding comparable results to conventional PCR.
Article
Microbiology
Ben Vezina, Louise M. Judd, Fiona K. McDougall, Wayne S. J. Boardman, Michelle L. Power, Jane Hawkey, Sylvain Brisse, Jonathan M. Monk, Kathryn E. Holt, Kelly L. Wyres
Summary: The study identified the dynamics of Klebsiella pneumoniae strain transmission clusters within grey-headed flying fox colonies, including both intra- and inter-colony transmission, and highlighted gene flow between human clinical and flying fox isolates. Additionally, inter-species horizontal plasmid transmission was observed. The metabolic models generated showed no distinction in metabolic capabilities, instead being consistent with population structure and lineage.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Jane Hawkey, Ben Vezina, Jonathan M. Monk, Louise M. Judd, Taylor Harshegyi, Sebastian Lopez-Fernandez, Carla Rodrigues, Sylvain Brisse, Kathryn E. Holt, Kelly L. Wyres
Summary: KpSC is a group of Klebsiella bacteria that can cause opportunistic healthcare-associated infections in humans. Researchers generated strain-specific genome-scale metabolic models (GEMs) for 37 isolates, representing all seven taxa. These models revealed strain-specific differences within and between species.
Article
Infectious Diseases
Uduak A. Okomo, Saffiatou Darboe, Saikou Y. Bah, Abigail Ayorinde, Sheikh Jarju, Abdul Karim Sesay, Ngange Kebbeh, Abdou Gai, Tida Dibbasey, Mary Grey-Johnson, Kirsty Le Doare, Kathryn E. Holt, Joy E. Lawn, Beate Kampmann
Summary: In this study, we found a low prevalence of vertical transmission of maternal genital tract colonization in maternal-newborn pairs for early-onset neonatal sepsis in the West African context.
CLINICAL MICROBIOLOGY AND INFECTION
(2023)
Article
Genetics & Heredity
Mailis Maes, Fahad Khokhar, Sam A. J. Wilkinson, Andrew D. Smith, Ganna Kovalenko, Gordon Dougan, Joshua Quick, Nicholas J. Loman, Stephen Baker, Martin D. Curran, Jordan P. Skittrall, Charlotte J. Houldcroft
Summary: Human adenovirus F41 causes acute gastroenteritis in children and is associated with an increase in paediatric hepatitis. The genetic diversity of adenovirus F41 in UK children is not well understood, and the impact of the COVID-19 pandemic on viral diversity in the UK is unclear. In this study, we used a new method to sequence F41 genomes from clinical samples and found two F41 lineages in paediatric patients in the East of England. Our findings suggest that the circulating F41 lineages existed before the COVID-19 pandemic.
MICROBIAL GENOMICS
(2023)
Article
Microbiology
Margaret M. C. Lam, Jonathan Koong, Kathryn E. Holt, Ruth M. Hall, Mehrad Hamidian
Summary: Plasmids in Acinetobacter species, which contribute to the spread of antibiotic resistance genes, were classified into 3 groups based on Rep protein domains, with 80 distinct types identified using nucleotide clustering. The study established a typing system that will aid in tracking plasmids and resistance genes, as well as identifying plasmids in other Acinetobacter species.
MICROBIOLOGY SPECTRUM
(2023)
Letter
Infectious Diseases
Margaret M. C. Lam, Kathryn E. Holt, Kelly L. Wyres
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
(2023)
Article
Infectious Diseases
Sophie L. Higham, Stephen Baker, Katie E. Flight, Aishwarya Krishna, Paul Kellam, Stephen T. Reece, John S. Tregoning
Summary: This study aimed to develop a clinically relevant model of A. baumannii respiratory tract infection and test the impact of different immunization routes on the protective immunity provided by an OMV vaccine. Results showed that intramuscular and subcutaneous immunizations did not provide effective protection, while intranasal immunization significantly reduced airway and systemic infection.
JOURNAL OF INFECTION
(2023)
Article
Multidisciplinary Sciences
Elina Khatri, Kedar Baral, Amit Arjyal, Rajesh Kumar Yadav, Sushila Baral
Summary: A cross-sectional study was conducted among adolescents from nine schools in a Sub-metropolitan city of Nepal to determine the prevalence and risk factors of overweight. The study found that overweight has become a concerning issue among urban adolescents due to their unhealthy lifestyle habits. It is therefore important to emphasize the importance of healthy food habits and physical activity for adolescents to maintain a healthy weight.
Article
Microbiology
Sydney L. L. Miles, Vincenzo Torraca, Zoe A. A. Dyson, Ana Teresa Lopez-Jimenez, Ebenezer Foster-Nyarko, Damian Lobato-Marquez, Claire Jenkins, Kathryn E. E. Holt, Serge Mostowy
Summary: By analyzing the genetic sequences of ST99 E. coli, we found that there are two subsets of strains, one with a virulence plasmid pINV and one without. The results of zebrafish infection experiments show that the virulence of ST99 E. coli is temperature-dependent. Furthermore, it was discovered that ST99 strains may have been virulent before the acquisition of pINV, indicating the importance of pINV in the dissemination of ST99 E. coli.
Article
Biochemical Research Methods
Ryan R. R. Wick, Louise M. M. Judd, Kathryn E. E. Holt
Summary: A perfect bacterial genome assembly requires improved long-read sequencing, assemblers, and polishers. By combining Oxford Nanopore Technologies long reads and Illumina short reads, we suggest using Trycycler long-read assembly, Medaka long-read polishing, Polypolish short-read polishing, and additional short-read polishing tools and manual curation. We also discuss potential challenges and provide an online tutorial for reference.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Genetics & Heredity
Ebenezer Foster-Nyarko, Hugh Cottingham, Ryan R. Wick, Louise M. Judd, Margaret M. C. Lam, Kelly L. Wyres, Thomas D. Stanton, Kara K. Tsang, Sophia David, David M. Aanensen, Sylvain Brisse, Kathryn E. Holt
Summary: Oxford Nanopore Technologies (ONT) sequencing has potential for genomic epidemiology and public health investigations of bacterial pathogens, but low base-call accuracy limits its reliability for critical tasks. In this study, we tested the accuracy of ONT-only assemblies for genotyping and cluster detection. We found that the SUP basecalling method performed the best, accurately identifying capsule type, multi-locus sequence type, and acquired antimicrobial resistance genes. However, cluster detection was challenging with ONT data.
MICROBIAL GENOMICS
(2023)
Article
Genetics & Heredity
Marit A. K. Hetland, Jane Hawkey, Eva Bernhoff, Ragna-Johanne Bakksjo, Hakon Kaspersen, Siren I. Rettedal, Arnfinn Sundsfjord, Kathryn E. Holt, Iren H. Lohr
Summary: Klebsiella pneumoniae ST17 is a globally disseminated clone that causes multidrug-resistant hospital infections. An outbreak of MDR ST17 occurred at a neonatal intensive care unit in Norway, with long-term colonization observed in the children even after discharge. The within-host evolution of ST17 during colonization showed stability with minimal genetic changes and persistent carriage of a specific plasmid. ST17 has diverse lineages with various AMR genes and virulence loci, but many strains do not acquire AMR. The non-human sources and human colonization may play a crucial role in severe infections.
MICROBIAL GENOMICS
(2023)
Article
Immunology
Vincenzo Torraca, Dominik Brokatzky, Sydney L. Miles, Charlotte E. Chong, P. Malaka De Silva, Stephen Baker, Claire Jenkins, Kathryn E. Holt, Kate S. Baker, Serge Mostowy
Summary: Shigella, including specific serotypes, can establish persistent infection in the zebrafish model. The O-antigen plays a crucial role in this process, and the serotype-associated effects observed in humans are also observed in zebrafish.
JOURNAL OF INFECTIOUS DISEASES
(2023)
Article
Biology
Matthew Silcocks, Sarah J. Dunstan
Summary: The Two Layer hypothesis suggests that East Asian population history was shaped by hunter-gatherer groups who migrated via a southern route and were assimilated by agriculturalist migrants from the north. By analyzing the phylogeographic signatures of Mycobacterium tuberculosis (Mtb) and the human Y-chromosome, researchers found that the Y-chromosome lineages associated with the hunter-gatherer groups in East Asia have characteristics consistent with a southern entry route, while the Y-chromosome lineages linked to agriculture development in modern-day China have characteristics incompatible with a southern entry route. This model opens up new research hypotheses for host-pathogen coevolution in East Asia.
COMMUNICATIONS BIOLOGY
(2023)