Article
Microbiology
Seung Hun Lee, Sangmi Lee, Sang Hun Park, Ok Kyung Koo
Summary: In this study, a Listeria monocytogenes strain responsible for a foodborne outbreak in South Korea was characterized. The strain exhibited specific characteristics in antibiotic resistance and virulence genes. These findings will contribute to assessing the characteristics of CC224 strains in South Korea that have the potential to cause listeriosis outbreaks.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Food Science & Technology
Catherine D. Carrillo, Burton W. Blais
Summary: Whole-genome sequencing technologies are increasingly used in food microbiology laboratories to develop more effective detection methods, reduce testing development costs, and support food safety regulatory and industry goals.
FRONTIERS IN SUSTAINABLE FOOD SYSTEMS
(2021)
Article
Multidisciplinary Sciences
Lingzi Xiaoli, Jill V. Hagey, Daniel J. Park, Christopher A. Gulvik, Erin L. Young, Nabil-Fareed Alikhan, Adrian Lawsin, Norman Hassell, Kristen Knipe, Kelly F. Oakeson, Adam C. Retchless, Migun Shakya, Chien-Chi Lo, Patrick Chain, Andrew J. Page, Benjamin J. Metcalf, Michelle Su, Jessica Rowell, Eshaw Vidyaprakash, Clinton R. Paden, Andrew D. Huang, Dawn Roellig, Ketan Patel, Kathryn Winglee, Michael R. Weigand, Lee S. Katz
Summary: This study provides benchmark datasets for public health laboratories to build sequencing and bioinformatics capacity, benchmark workflows and pipelines, and calibrate quality control thresholds. These datasets contribute to accurate and timely outbreak investigation and surveillance, and facilitate the development of new pipelines.
Article
Food Science & Technology
Qian Zhou, Yu-jing Zhong, Zhu-zhou Shan, Xue-xue Pan, Jing-yu Huang, Jing-shu Xiang, De-zhu Zhang, Wei-wei Li, Jun Li, Ying Liu, Shi-jun Li, Li Zhou
Summary: This study investigated the molecular epidemiology and pathogenesis of Salmonella Senftenberg isolates associated with a foodborne disease outbreak in Guizhou Province. The results showed that these isolates carried various drug resistance and virulence genes and were related to previous infection outbreaks in Tianjin and Jilin, suggesting that the outbreak may have been caused by imported contamination.
FOODBORNE PATHOGENS AND DISEASE
(2023)
Article
Microbiology
Mariana Meneguzzi, Caroline Pissetti, Raquel Rebelatto, Julian Trachsel, Suzana Satomi Kuchiishi, Adrienny Trindade Reis, Roberto Mauricio Carvalho Guedes, Joice Aparecida Leao, Caroline Reichen, Jalusa Deon Kich
Summary: Clinical salmonellosis has been increasing significantly in Brazil, with a majority of strains demonstrating high rates of multi-drug resistance. The identification of a major Choleraesuis clonal group in several Brazilian states suggests closely related strains. This highlights the endemic nature of salmonellosis in key pig-producing regions in Brazil.
Article
Infectious Diseases
Andrey L. Rakitin, Yulia K. Yushina, Elena V. Zaiko, Dagmara S. Bataeva, Oksana A. Kuznetsova, Anastasia A. Semenova, Svetlana A. Ermolaeva, Aleksey V. Beletskiy, Tat'yana V. Kolganova, Andrey V. Mardanov, Sergei O. Shapovalov, Timofey E. Tkachik
Summary: This study investigated the occurrence of antimicrobial resistance among Salmonella strains isolated from food products. Multiple serovars of Salmonella with resistance to commonly used antibiotics were identified. Genomic analysis revealed the presence of antibiotic resistance genes within integrons in plasmids or chromosomal islands. Pathogenicity islands were also found in the genomes of the sequenced strains. The emergence of multidrug-resistant Salmonella strains highlights the need for further research on transmission pathways and monitoring of these microorganisms' distribution.
Article
Microbiology
Gaspard Grouteau, Cedric Mignonat, Bruno Marchou, Guillaume Martin-Blondel, Olivier Glass, Claire Roubaud-Baudron, Pauline Lansalot-Matras, Simon Alik, Laurent Balardy, Thomas De Nadai, Lucie Benejat, Quentin Jehanne, Alain Le Coustumier, Philippe Lehours
Summary: In June 2021, a cluster of seven cases of Campylobacter fetus infections occurred in a rehabilitation center and caused significant morbidity in elderly patients, including five with bacteremia and two with osteoarticular medical device infections. Whole genome sequencing confirmed that the different strains of Campylobacter fetus had a common source, indicating a foodborne outbreak likely caused by the consumption of unpasteurized dairy products, such as raw milk cheese from a farm-to-fork strategy.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Microbiology
Alexandra Chiaverini, Fabrizia Guidi, Marina Torresi, Vicdalia Aniela Acciari, Gabriella Centorotola, Alessandra Cornacchia, Patrizia Centorame, Cristina Marfoglia, Giuliana Blasi, Marco Di Domenico, Giacomo Migliorati, Sophie Roussel, Francesco Pomilio, Yann Sevellec
Summary: The study investigated a severe outbreak of Listeria monocytogenes ST7 strain in Central Italy, linked to a meat food-producing plant contaminated by the outbreak strain, which reemerged in the same region causing another listeriosis case. The epidemic and reemergent strains were genetically closer to a ST7 clone with different PFGE profiles, and were associated with the pork production chain. The persistence and reemergence of the outbreak were likely due to both the presence of truly persistent clones and the repeated introduction of new ones, along with the contribution of prophage genes promoting their survival. Despite no significant genomic differences between the outbreak and reemergent strains, transcriptional factor and phage genes associated with the phage LP-114 helped differentiate the related clones detected during the outbreak.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Food Science & Technology
Yu Hsuan Tseng, Joana Barbosa, Teresa Bento de Carvalho, Paula Teixeira
Summary: Due to the increasing demand for a healthy diet and convenience, the market for fresh fruit, especially melons, is growing. However, the safety of cut fruit, specifically melons, remains a concern. This pilot study in Portugal demonstrated the risk of foodborne pathogen transmission through the cutting process and the potential bacterial growth when melon slices are stored at abusive temperatures. The study highlights the need for education campaigns to raise awareness among sellers and consumers.
Article
Food Science & Technology
Lijun Hu, Eric W. Brown, Guodong Zhang
Summary: The study analyzed antimicrobial resistance, stress resistance, and virulence factors of 192 isolates through whole genome sequencing. The findings revealed the potential risks posed to public health by these isolates.
FRONTIERS IN SUSTAINABLE FOOD SYSTEMS
(2023)
Article
Food Science & Technology
Erin Jenkins, Ifueko Gardenhire, Brooke M. Whitney, Krystalyn B. Martin, Colin Schwensohn, Laura Gieraltowski, Molly M. Leeper, Vivien McCurdy, Monica McClure, Allison Wellman, Arthur Pightling, Michelle Smith, Angela Swinford, Lisa Hainstock, Alvin J. Crosby, Michael C. Bazaco, Stelios Viazis
Summary: In 2020, there was an outbreak of Salmonella Newport infections in the United States linked to melons from southwest Indiana, resulting in 80 ill persons and 18 hospitalizations reported across 15 states. The investigation was unable to determine whether the vehicle for the infections was cantaloupe alone or both cantaloupe and watermelons. This outbreak highlights the need for further efforts to identify the source and extent of environmental contamination in the melon growing region and promote farm practices to reduce pathogen contamination of melons.
Article
Microbiology
Daniel F. M. Monte, Matthew A. Nethery, Hanna Berman, Shivaramu Keelara, Nilton Lincopan, Paula J. Fedorka-Cray, Rodolphe Barrangou, Mariza Landgraf
Summary: This study characterized the resistome, phylogenetic structure, and CRISPR array composition of Salmonella enterica serovar Heidelberg strains isolated from the poultry production chain in Brazil. The results showed that these strains have a broad host range and are multidrug-resistant, with a widespread distribution of antibiotic-resistant strains from farm to market. The study also highlights the potential role of S. Heidelberg as a key pathogen disseminated from farm to fork and emphasizes the importance of CRISPR-based genotyping for salmonellae.
FRONTIERS IN MICROBIOLOGY
(2022)
Review
Biotechnology & Applied Microbiology
Luping Xu, Xingjian Bai, Arun K. Bhunia
Summary: Foodborne disease outbreaks remain a concern. Testing products promptly is crucial for protecting consumers. Various approaches have been explored to incorporate antibodies, oligonucleotides, phages, and mammalian cells as signal transducers on biosensor platforms. High specificity and low detection limits are the ultimate goal. Advancements in sensors using mammalian cells and bacteriophages show promise in pathogen detection.
JOURNAL OF FOOD PROTECTION
(2021)
Article
Chemistry, Multidisciplinary
Claudia S. Marques, Susana Sousa, Antonio Castro, Vania Ferreira, Paula Teixeira, Jose M. Correia da Costa
Summary: The monitoring of microbial quality in the industrial environment has focused mainly on bacteria, while protozoa have been routinely ignored. Recent studies have shown that fresh produce may serve as an important source of transmission for Toxoplasma gondii, highlighting the need to include protozoa in microbial criteria for foodstuffs and improve their inactivation and removal procedures.
APPLIED SCIENCES-BASEL
(2022)
Article
Microbiology
Kranti Konganti, Elizabeth Reed, Mark Mammel, Tunc Kayikcioglu, Rachel Binet, Karen Jarvis, Christina M. M. Ferreira, Rebecca L. L. Bell, Jie Zheng, Amanda M. M. Windsor, Andrea Ottesen, Christopher J. J. Grim, Padmini Ramachandran
Summary: Most current Salmonella subtyping analyses rely on whole genome sequencing (WGS), which focuses on the high-resolution analysis of single genomes or multiple single genomes from the isolated colonies on microbiological agar plates. In this study, bioinformatics innovations were introduced for a metagenomic outbreak response workflow that accurately identifies multiple Salmonella serovars at the same time. bettercallsal outperformed k-mer, Seqsero2, and Kallisto in identifying multiple serovars from enrichment cultures using shotgun metagenomic sequencing.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Public, Environmental & Occupational Health
R. Paul McClung, Mateusz Karwowski, Caroline Castillo, Jevon McFadden, Sarah Collier, Jim Collins, Marty Soehnlen, Stephen Dietrich, Eija Trees, Grete Wilt, Christina Harrington, Ashley Miller, Elizabeth Adam, Hannah Reses, Jennifer Cope, Katie Fullerton, Vincent Hill, Jonathan Yoder
AMERICAN JOURNAL OF PUBLIC HEALTH
(2020)
Article
Multidisciplinary Sciences
Ruth E. Timme, Patricia C. Lafon, Maria Balkey, Jennifer K. Adams, Darlene Wagner, Heather Carleton, Errol Strain, Maria Hoffmann, Ashley Sabol, Hugh Rand, Rebecca Lindsey, Deborah Sheehan, Joseph D. Baugher, Eija Trees
Article
Genetics & Heredity
Nikki W. Shariat, Ruth E. Timme, Abigail T. Walters
Summary: Salmonella enterica subspecies arizonae displays unique evolutionary patterns revealed through whole-genome sequencing data and core genome phylogenetic analysis, including polyphyly, high conservation of antigens, presence of prophages and plasmids, and specific pathogenic islands. These characteristics make subspecies arizonae a distinct lineage within the highly diverse species of Salmonella.
MICROBIAL GENOMICS
(2021)
Correction
Biotechnology & Applied Microbiology
John J. Miller, Bart C. Weimer, Ruth Timme, Catharina H. M. Ludeke, James B. Pettengill, D. J. Darwin Bandoy, Allison M. Weis, James Kaufman, B. Carol Huang, Justin Payne, Errol Strain, Jessica L. Jones
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Biochemical Research Methods
Alexandre Souvorov, Richa Agarwala
Summary: SAUTE and SAUTE_PROT are assemblers proposed to assist with the assembly of repeat regions and to report multiple well supported variants when target sequences are provided. These assemblers utilize de Bruijn graphs on reads, with targets ranging from RNA-seq to genomic reads.
BMC BIOINFORMATICS
(2021)
Article
Biology
Emma J. Griffiths, Ruth E. Timme, Catarina Ines Mendes, Andrew J. Page, Nabil-Fareed Alikhan, Dan Fornika, Finlay Maguire, Josefina Campos, Daniel Park, Idowu B. Olawoye, Paul E. Oluniyi, Dominique Anderson, Alan Christoffels, Anders Goncalves da Silva, Rhiannon Cameron, Damion Dooley, Lee S. Katz, Allison Black, Ilene Karsch-Mizrachi, Tanya Barrett, Anjanette Johnston, Thomas R. Connor, Samuel M. Nicholls, Adam A. Witney, Gregory H. Tyson, Simon H. Tausch, Amogelang R. Raphenya, Brian Alcock, David M. Aanensen, Emma Hodcroft, William W. L. Hsiao, Ana Tereza R. Vasconcelos, Duncan R. MacCannell
Summary: PHA4GE is a global coalition working to improve openness, interoperability, and consistency in public health microbial bioinformatics. They have developed a SARS-CoV-2 contextual data specification package to support data collection and harmonization in public biorepositories.
Article
Biotechnology & Applied Microbiology
Eric L. Stevens, Heather A. Carleton, Jennifer Beal, Glenn E. Tillman, Rebecca L. Lindsey, A. C. Lauer, Arthur Pightling, Karen G. Jarvis, Andrea Ottesen, Padmini Ramachandran, Leslie Hintz, Lee S. Katz, Jason P. Folster, Jean M. Whichard, Eija Trees, Ruth E. Timme, Patrick McDermott, Beverly Wolpert, Michael Bazaco, Shaohua Zhao, Sabina Lindley, Beau B. Bruce, Patricia M. Griffin, Eric Brown, Marc Allard, Sandra Tallent, Kari Irvin, Maria Hoffmann, Matt Wise, Robert Tauxe, Peter Gerner-Smidt, Mustafa Simmons, Bonnie Kissler, Stephanie Defibaugh-Chavez, William Klimke, Richa Agarwala, James Lindsay, Kimberly Cook, Suelee Robbe Austerman, David Goldman, Sherri McGARRY, Kis Robertson Hale, Uday Dessai, Steven M. Musser, Chris Braden
Summary: This report provides an overview of the use of whole genome sequencing (WGS) technology for detecting and characterizing foodborne pathogens and identifying their sources. It highlights the collaborative efforts among federal agencies in food safety and describes the methods used in genetic analysis networks. The report emphasizes the application of WGS in pathogen characterization and source attribution, as well as the impact of culture-independent diagnostic tests on food safety analysis.
JOURNAL OF FOOD PROTECTION
(2022)
Article
Food Science & Technology
Angela Poates, Jenny Truong, Rebecca Lindsey, Taylor Griswold, Amanda J. Williams-Newkirk, Heather Carleton, Eija Trees
Summary: This study aims to optimize and validate the Illumina DNA Prep kit for sequencing enteric pathogens and compare its performance against the Nextera XT kit. The Prep libraries outperformed the XT libraries, especially in Escherichia sequences, and showed better accuracy in predicting O group and detecting related genes.
FOODBORNE PATHOGENS AND DISEASE
(2022)
Article
Microbiology
Jingzhang Feng, Devin Daeschel, Damion Dooley, Emma Griffiths, Marc Allard, Ruth Timme, Yi Chen, Abigail B. B. Snyder
Summary: The regular analysis of whole-genome sequence data is crucial for detecting outbreaks of infectious diseases, but the metadata in existing databases are often incomplete and of poor quality. We generated large-scale, open-source DNA sequence databases by collecting microbial pathogens from built environments. To analyze these data for public health surveillance, the complex metadata associated with the swab site locations need to be digitized. Through content analysis, we identified 5 informational facets described by 338 unique terms and developed a schema that has been integrated into a publicly available pathogen metadata standard.
Article
Microbiology
Brandon Kocurek, Padmini Ramachandran, Christopher J. Grim, Paul Morin, Laura Howard, Andrea Ottesen, Ruth Timme, Susan R. Leonard, Hugh Rand, Errol Strain, Daniel Tadesse, James B. Pettengill, David W. Lacher, Mark Mammel, Karen G. Jarvis, Luxin Wang
Summary: This study investigated the microbial diversity in food production environments and demonstrated the successful assembly of L. monocytogenes genomes using shotgun quasimetagenomic sequencing. Additionally, the study showed that pathogen detection can still be achieved with low genome coverage in a metagenome sequencing data set.
MICROBIOLOGY SPECTRUM
(2023)
Article
Microbiology
Matthew A. Crawford, Christine Lascols, Sara Lomonaco, Ruth E. Timme, Debra J. Fisher, Kevin Anderson, David R. Hodge, Stephen A. Morse, Segaran P. Pillai, Shashi K. Sharma, Erum Khan, Marc W. Allard, Molly A. Hughes
Summary: This study presents draft genomes of 45 Enterobacterales clinical isolates collected in Pakistan between 1998 and 2016, including drug-resistant strains. The emergence and spread of antimicrobial resistance among pathogenic bacteria pose continuous threats to health and economy.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Biotechnology & Applied Microbiology
John J. Miller, Bart C. Weimer, Ruth Timme, Catharina H. M. Luedeke, James B. Pettengill, D. J. Darwin Bandoy, Allison M. Weis, James Kaufman, B. Carol Huang, Justin Payne, Errol Strain, Jessica L. Jones
Summary: Through genome sequencing of 132 North American Vibrio parahaemolyticus isolates, this study revealed the population structure of this species along the Gulf and Atlantic Coasts, with some sequence types shared between the Gulf Coast and the coastal waters of Washington State. The identification of functional gene categories enriched in isolates from clinical sources provides insight into the potential pathogenicity of Vibrio parahaemolyticus and its adaptability in different environments.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2021)
Review
Public, Environmental & Occupational Health
Ruth E. Timme, William J. Wolfgang, Maria Balkey, Sai Laxmi Gubbala Venkata, Robyn Randolph, Marc Allard, Errol Strain
ONE HEALTH OUTLOOK
(2020)
Article
Microbiology
Narjol Gonzalez-Escalona, George John Kastanis, Ruth Timme, Dwayne Roberson, Maria Balkey, Sandra M. Tallent
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2020)
Article
Public, Environmental & Occupational Health
M. Laughlin, L. Bottichio, J. Weiss, J. Higa, E. McDonald, R. Sowadsky, D. Fejes, A. Saupe, G. Provo, S. Seelman, J. Concepcion-Acevedo, L. Gieraltowski, J. Narang, M. Needham, A. Barnes, A. Maroufi, H. Buonomo, C. Neiss, L. Negado, J. Healy, F. Ni, K. Trinh, L. McCullough, C. Rigdon, J. Ayers, E. Reed, S. Viazis, A. Crosby, A. Tesfai, S. Lance, L. Whitlock, E. Trees, D. Wagner, A. Sabot, I Williams
EPIDEMIOLOGY AND INFECTION
(2019)