Article
Biochemical Research Methods
Harleen K. Chaggar, Lauren K. Hudson, Ryan Kuster, Katie N. Garman, John R. Dunn, Thomas G. Denes
Summary: This paper presents ClustFinder, a command line tool designed to automate clustering of genomes based on genomic distance. This tool will aid researchers and public health professionals in the identification of epidemiological clusters. Here, we demonstrate the usage of ClustFinder with example datasets. ClustFinder is available at github.com/Denes-Lab/ClustFinder.
JOURNAL OF MICROBIOLOGICAL METHODS
(2023)
Review
Cell Biology
Frans Bianchi, Geert van den Bogaart
Summary: Intracellular pathogens such as Listeria monocytogenes, Salmonella enterica, Shigella spp., and Staphylococcus aureus use different strategies to survive and proliferate within host cells, with the strategy of vacuolar escape being particularly important for evading host-cell defenses and gaining access to nutrients. Understanding the molecular mechanisms of vacuolar membrane rupture by these pathogens could lead to the development of new therapeutic approaches to combat foodborne illnesses.
JOURNAL OF CELL SCIENCE
(2021)
Review
Infectious Diseases
Katarzyna Grudlewska-Buda, Justyna Bauza-Kaszewska, Natalia Wiktorczyk-Kapischke, Anna Budzynska, Eugenia Gospodarek-Komkowska, Krzysztof Skowron
Summary: Antibiotic resistance and multidrug resistance have been confirmed in major foodborne pathogens, including Campylobacter spp., Salmonella spp., Escherichia coli, and Listeria monocytogenes. Concerningly, new antibiotic-resistant food pathogens unrelated to food contamination or considered epidemiologically insignificant have also been reported. Thorough monitoring of strains isolated from food is necessary to understand the existing mechanisms of resistance.
Article
Environmental Sciences
Pallavi Gautam, Anand Kumar Pandey, Ankush Gupta, Suresh Kumar Dubey
Summary: Imidacloprid, a widely used insecticide, has toxic effects on non-targeted organisms. This study investigated the potential of Sphingobacterium sp. InxBP1 in degrading imidacloprid through genomic, proteomic, bioinformatic, and metabolomic analyses. The findings identified genes and enzymes involved in the oxidative degradation of imidacloprid, as well as their affinity and binding to the degradation intermediates. The metabolomic study validated the proposed degradation mechanism. These findings suggest that Sphingobacterium sp. InxBP1 can be utilized in developing in-situ remediation technologies for imidacloprid.
ENVIRONMENTAL POLLUTION
(2023)
Article
Food Science & Technology
Xinyu Liao, Yue Zhang, Qiyi Zhang, Jianwei Zhou, Tian Ding, Jinsong Feng
Summary: This review systematically summarizes the advances in microfluidic systems for detecting foodborne pathogens, with a focus on different substrates and enabled functions. It discusses the integration of IoT for real-time food safety inspection and future directions in microfluidic technology for detecting and monitoring foodborne pathogens.
TRENDS IN FOOD SCIENCE & TECHNOLOGY
(2023)
Review
Plant Sciences
Sydney Everhart, Nikita Gambhir, Remco Stam
Summary: This article provides a brief overview of topics relevant to the study of population genomics of filamentous plant pathogens, including different research question types, sampling strategies, sequencing strategies, data processing options, and population genomic data analysis tools. It highlights some of the hurdles along the population genomic workflow, offers cautionary warnings relative to assumptions and technical challenges, and presents future perspectives of the field.
Article
Microbiology
Aitor Atxaerandio-Landa, Ainhoa Arrieta-Gisasola, Lorena Laorden, Joseba Bikandi, Javier Garaizar, Irati Martinez-Malaxetxebarria, Ilargi Martinez-Ballesteros
Summary: The use of whole-genome sequencing (WGS) for bacterial characterisation has significantly increased in recent years. However, challenges in data analysis and management, as well as the lack of standardisation, hinder its routine use. This study presents a bioinformatics workflow for bacterial characterisation using WGS data, which includes genome annotation, species identification, serotype prediction, antimicrobial resistance prediction, virulence-related genes and plasmid replicon detection, phylogenetic clustering, and sequence typing.
Article
Food Science & Technology
Tong Zhao, Pingsheng Ji, Govindaraj Dev Kumar
Summary: The study demonstrated that the new bactericide comprising levulinic acid and sodium dodecyl sulfate effectively reduced the population of foodborne pathogens on tomato plants. Experiments showed significant decreases in Salmonella, STEC, and L.monocytogenes populations when compared with water and chlorine treatments.
Review
Chemistry, Multidisciplinary
Lauren M. Castle, Daena A. Schuh, Erin E. Reynolds, Ariel L. Furst
Summary: Electrochemical sensors are well-suited for field-deployable monitoring of bacterial foodborne pathogens, offering quantitative and rapid detection without the need for expensive instrumentation. Innovative sensing strategies demonstrate high sensitivity and wide detection ranges, key for halting the spread of foodborne diseases.
Article
Food Science & Technology
Mayra Aguirre Garcia, Killian Hillion, Jean-Michel Cappelier, Michel Neunlist, Maxime M. Mahe, Nabila Haddad
Summary: Foodborne diseases cause significant morbidity and mortality globally. Understanding the interactions between bacteria and epithelial cells during infection is crucial for prevention and treatment. Traditional cell cultures have limitations, and the development of organoids has provided new insights into studying microbial infections and controlling foodborne hazards.
Article
Plant Sciences
Christina Straub, Elena Colombi, Honour C. McCann
Summary: Population genomics plays a crucial role in reshaping our understanding of pathogen biology and evolution, especially in the field of plant pathology. Through this discipline, we can address key issues such as pathogen origins, transmission pathways, host specificity, virulence, and adaptation to changing agricultural practices.
Article
Immunology
Hengwei Ge, Yizhe Wang, Xihong Zhao
Summary: Foodborne diseases caused by pathogens are a major health and safety issue, and the emergence of multi-drug resistant strains has made clinical treatment more difficult. Research on drug resistance mechanisms of foodborne pathogens has become an effective way to address multi-drug resistant strains. This paper systematically analyzes the drug resistance mechanisms of Salmonella, Listeria monocytogenes, and Escherichia coli, including reduced cell membrane permeability, efflux pump mechanism, target site mutation mechanism, and enzymatic hydrolysis. Additionally, potential new methods such as CRISPR and bacteriophages are discussed as means to solve drug resistance in foodborne pathogens.
MICROBIAL PATHOGENESIS
(2022)
Article
Food Science & Technology
Babak Pakbin, Zahra Amani, Zahra Rahimi, Somayeh Najafi, Behnaz Familsatarian, Alireza Khakpoor, Wolfram Manuel Brueck, Thomas B. Bruck
Summary: This study investigated the prevalences of antibiotic-resistance genes (ARGs) and foodborne bacterial pathogens in sweet samples from local markets in Iran. The results showed the presence of Staphylococcus aureus, Cronobacter sakazakii, Shigella spp., Campylobacter jejuni, and Campylobacter coli in the sweet samples. S. aureus was found to be the most prevalent bacterial pathogen. Additionally, a significant correlation was found between the presence of C. coli and Cr. sakazakii. The blaSHV resistance gene was detected in a high percentage of the sweet samples, while blaTEM was detected in only one sample.
Article
Microbiology
Zhongyou Li, Katja Koeppen, Victoria I. Holden, Samuel L. Neff, Liviu Cengher, Elora G. Demers, Dallas L. Mould, Bruce A. Stanton, Thomas H. Hampton
Summary: Researchers developed an algorithm called GAUGE, which automatically annotates GEO microbial data sets, increasing the percentage of analyzable data sets from 4% to 33%. The annotations provide valuable insights and facilitate the identification of consistent patterns of differential gene expression. Additionally, they created a web interface called GAPE for reanalyzing P. aeruginosa and E. coli transcriptomic data.
Article
Food Science & Technology
Raffaella Tavelli, Martijn Callens, Charlotte Grootaert, Mohamed F. Abdallah, Andreja Rajkovic
Summary: This article reviews the current state of research on the potential role of microplastics (MPs) in enhancing harmful bacterial traits and transporting them to humans. The findings highlight the need for further studies to determine the extent of their effect on human health.
TRENDS IN FOOD SCIENCE & TECHNOLOGY
(2022)
Article
Microbiology
Kidon Sung, Dereje D. Gudeta, Miseon Park, Jungwhan Chon, Sungguk Kim, Mohamed S. Nawaz, Steven L. Foley, Saeed A. Khan
Summary: This study sequenced and annotated clinical MRSA isolates from hospitals in Pakistan to investigate genetic markers associated with antimicrobial resistance, virulence, and biofilm formation.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2022)
Article
Microbiology
Sung Guk Kim, Christine Summage-West, Dan A. Buzatu, Steven L. Foley
Summary: In this study, the draft genome sequence of Ralstonia pickettii strain NCTR106 isolated from milk carton paperboard in a commercial paper mill was reported. The genome sequence carries two beta-lactamase genes similar to those found in R. pickettii isolates collected from a hospital.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2022)
Article
Microbiology
Saeed A. Khan, Dereje D. Gudeta, Jungwhan Chon, Paula Snippes Vagnone, Mohamed S. Nawaz, Steven L. Foley, Kidon Sung
Summary: The draft genome sequences of nine hospital-associated methicillin-susceptible Staphylococcus aureus (HA-MSSA) strains from Minnesota were presented in this study. These strains harbored various virulence genes and exhibited diverse multilocus sequence typing and spa types.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2022)
Article
Microbiology
Saeed A. Khan, Dereje D. Gudeta, Nesreen Aljahdali, Jungwhan Chon, Paula Snippes Vagnone, Mohamed S. Nawaz, Steven L. Foley, Kidon Sung
Summary: In this study, the draft whole-genome sequences of 27 HA-MRSA strains isolated in Minnesota were presented to gain insight into their genomic makeup, antimicrobial resistance, biofilm formation, and virulence potentials.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2022)
Article
Biotechnology & Applied Microbiology
Sohyun Cho, Lari M. Hiott, Sandra L. House, Tiffanie A. Woodley, Elizabeth A. McMillan, Poonam Sharma, John B. Barrett, Eric S. Adams, Joshua M. Brandenburg, Kelley B. Hise, Jacob M. Bateman McDonald, Elizabeth A. Ottesen, Erin K. Lipp, Charlene R. Jackson, Jonathan G. Frye
Summary: Salmonella, traditionally considered a foodborne pathogen, has been found to potentially have an environmental source related to fresh produce and water. This study investigates the prevalence, diversity, and antimicrobial resistance of Salmonella in a mixed-use watershed in Georgia, USA. It reveals a high diversity of Salmonella strains in surface water, some of which are drug resistant and genetically similar to human isolates, supporting the role of environmental water as a significant reservoir and transmission route of this pathogen.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Microbiology
Sung Guk Kim, Miseon Park, Christine Summage-West, Seonggi Min, Steven L. Foley
Summary: Bacillus toyonensis, a member of the Bacillus cereus group, has been utilized as a probiotic in animal feeds and biological applications. In this study, we present the genome sequence of strain HA0190, which was isolated from a commercial hydroxyapatite nanoparticle product. The genome consists of a circular chromosome and two plasmids, pBT001 and pBT002.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2022)
Article
Engineering, Environmental
Julian Damashek, Jason R. Westrich, Jacob M. Bateman McDonald, Morgan E. Teachey, Charlene R. Jackson, Jonathan G. Frye, Erin K. Lipp, Krista A. Capps, Elizabeth A. Ottesen
Summary: Antibiotic resistance poses a global threat to human health. This study examined the presence of fecal marker genes and antibiotic resistant genes (ARGs) in stream water samples from the Upper Oconee watershed in Georgia, USA. The results showed widespread fecal contamination from humans, ruminants, and poultry, with a high percentage of samples testing positive for at least one of the six targeted ARGs. Non-point sources of fecal contamination, particularly aging wastewater infrastructure, were identified as critical disseminators of ARGs in the environment.
Article
Microbiology
Elizabeth A. McMillan, Margaret D. Weinroth, Jonathan G. Frye
Summary: S. Infantis has become a common serotype of Salmonella in the U.S., with most isolates carrying the pESI plasmid. Chromosomal differences were found between plasmid carriage groups, but no unique genes were identified. Isolates with the plasmid had more insertion sequences on average. This suggests that the proliferation of S. Infantis carrying the pESI plasmid is due to a single clonal strain that may have advantages in poultry or their environment.
Article
Biotechnology & Applied Microbiology
Elizabeth A. McMillan, Mark E. Berrang, Quentin D. Read, Surendra Rasamsetti, Amber K. Richards, Nikki W. Shariat, Jonathan G. Frye
Summary: Salmonella enterica is a common pathogen found in poultry food sources and is a major cause of foodborne illness in humans. The serovar Infantis, particularly those carrying the pESI plasmid, has emerged as a prevalent serovar in poultry meat samples and has caused recent human infections. A change in sampling method by the USDA-FSIS in 2016 to include neutralizing BPW (nBPW) as the rinsing agent raised concerns about the potential influence on the prevalence of ser. Infantis. However, experiments showed that the growth of ser. Infantis in nBPW was slightly slower initially but did not differ significantly from BPW after 6 hours. Furthermore, simulating regulatory sampling methods using nBPW did not affect the survival and growth of ser. Infantis in BPW. Therefore, the change in methodology is unlikely to have affected the emergence of ser. Infantis as a prevalent serovar in poultry meat products.
JOURNAL OF FOOD PROTECTION
(2023)
Article
Astronomy & Astrophysics
Stefan J. Green, Tamas Torok, Jonathan E. Allen, Emiley Eloe-Fadrosh, Scott A. Jackson, Sunny C. Jiang, Stuart S. Levine, Shawn Levy, Lynn M. Schriml, W. Kelley Thomas, Jason M. Wood, Scott W. Tighe
Summary: Molecular biology methods and technologies have advanced significantly, and NASA conducted a technology workshop to assess the feasibility of incorporating these methods into planetary protection. The workshop focused on modernizing and supplementing current assays and recommended metagenomics approaches as a revolutionary advance. Implementing metagenomics as an additional workflow will dramatically improve technology advancement for planetary protection.
Article
Nutrition & Dietetics
Riley L. L. Hughes, Cara L. L. Frankenfeld, Daryl M. M. Gohl, Curtis Huttenhower, Scott A. A. Jackson, Doris Vandeputte, Emily Vogtmann, Sarah S. S. Comstock, Mary E. E. Kable
Summary: The microbial cells in the human body play a vital role in regulating and maintaining human health. Understanding the specific associations between the human microbiome and health outcomes can help develop targeted recommendations and treatments to prevent and treat diseases. However, the potential of these recommendations and treatments to improve human health has not been fully realized. Technological advancements have provided tools and methods for collecting and analyzing microbiome samples, but differences in methodology can lead to variability in results and hinder the detection and validation of associations. Therefore, a satellite session was hosted to review available methods, best practices, and tools to improve the comparability of microbiome research and enhance the understanding of the associations between the human microbiome and health.
Article
Infectious Diseases
Sohyun Cho, Lari M. Hiott, Quentin D. Read, Julian Damashek, Jason Westrich, Martinique Edwards, Roland F. Seim, Donna A. Glinski, Jacob M. Bateman McDonald, Elizabeth A. Ottesen, Erin K. Lipp, William Matthew Henderson, Charlene R. Jackson, Jonathan G. Frye
Summary: The aquatic environment is recognized as a source of antibiotic resistance (AR). A comprehensive survey was conducted to evaluate AR in a mixed-use watershed and wastewater treatment plants (WWTPs). The survey found antibiotic-resistant bacteria (ARB), antibiotic resistance genes (ARGs), and antibiotic residues in surface water. The analysis also showed that WWTPs did not completely remove AR contaminants from the water.
Article
Microbiology
Sung Guk Kim, Christine V. Summage-West, Mariela Reyna, Danielle Sopovski, Lillie M. Sims, Steven L. Foley
Summary: The study reports the identification of Shigella flexneri strain P099, a 4.8-Mbp complete genome isolated from the gum of a rhesus monkey with gingivitis.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Review
Biotechnology & Applied Microbiology
Sohyun Cho, Charlene R. Jackson, Jonathan G. Frye
Summary: Surface water is a favorable environment for the accumulation and spread of antibiotic resistant bacteria, including ESBL-producing Enterobacteriaceae. The prevalence of ESBL-producing Enterobacteriaceae, particularly E. coli and K. pneumoniae, in aquatic environments worldwide poses a growing threat to public health. This review aims to explore the contamination of ESBL-producing Enterobacteriaceae in freshwater environments and understand their sources and transmission routes, as well as the factors driving their presence.
JOURNAL OF APPLIED MICROBIOLOGY
(2023)
Article
Veterinary Sciences
William B. Crosby, Brandi B. Karisch, Lari M. Hiott, Lee J. Pinnell, Alexandra Pittman, Jonathan G. Frye, Charlene R. Jackson, John Dustin Loy, William B. Epperson, John Blanton, Sarah F. Capik, Paul S. Morley, Amelia R. Woolums
Summary: This study aimed to evaluate the impact of tulathromycin metaphylaxis on antimicrobial resistance in MH isolated from stocker calves, and found that metaphylaxis increased the risk of isolation of multidrug resistant MH. However, the antimicrobial resistance genes identified in the isolated MH were primarily associated with integrative conjugative elements (ICE).
FRONTIERS IN VETERINARY SCIENCE
(2023)