Article
Microbiology
Lauren K. K. Hudson, William E. E. Andershock, Xiaorong Qian, Paula L. L. Gibbs, Kelly Orejuela, Katie N. N. Garman, John R. R. Dunn, Thomas G. G. Denes
Summary: This study evaluated the clinical and epidemiological significance of Salmonella enterica subsp. enterica serovar Newport. The results showed that Newport serovar is the second most prevalent clinically isolated Salmonella serovar in the United States and can contaminate various food products. The study also identified 18 potential epidemiological clusters and highlighted the importance of this research for public health surveillance and the Salmonella research community.
MICROBIOLOGY SPECTRUM
(2023)
Article
Immunology
Shamima Nasrin, Fabien J. Fuche, Khandra T. Sears, Jennifer A. Jones, Myron M. Levine, Raphael Simon, Sharon M. Tennant
Summary: Non-typhoidal Salmonella is a major cause of gastroenteritis, but research on vaccines is limited. Researchers developed a live attenuated O:8 vaccine with good tolerability and immune response against COPS, showing protection in a mouse model.
Article
Biotechnology & Applied Microbiology
Seth Commichaux, Hugh Rand, Kiran Javkar, Erin K. Molloy, James B. Pettengill, Arthur Pightling, Maria Hoffmann, Mihai Pop, Victor Jayeola, Steven Foley, Yan Luo
Summary: The Salmonella enterica serovar Newport red onion outbreak in 2020 was the largest in over a decade. The epidemiological investigation identified two farms as potential sources, but SNP analysis showed no link between farm and clinical isolates. However, analysis of plasmids in the clinical isolates provided evidence for a connection to the farms, highlighting the potential of this method for source tracking investigations.
Article
Multidisciplinary Sciences
Eby M. Sim, Qinning Wang, Peter Howard, Rady Kim, Ling Lim, Kirsty Hope, Vitali Sintchenko, Ruslan Kalendar
Summary: This study analyzed sequential isolates of Salmonella enterica serovar Typhi from a single host with persistent asymptomatic infection, revealing distinct genetic patterns and providing more information through sequencing the host's bile fluid. These findings are important for understanding the within-host dynamics of S. Typhi in cases of persistent infection and informing epidemiological investigations of transmission events associated with chronic carriers.
Article
Microbiology
Silvia Garcia-Soto, Herbert Tomaso, Joerg Linde, Ulrich Methner
Summary: The study investigated 74 S. Dublin strains collected from 10 federal states in Germany, and found important virulence determinants in all strains, but multidrug resistance in German S. Dublin organisms is uncommon. By analyzing cgSNPs, the study revealed the spreading patterns of S. Dublin in Germany and indicated both persistence and spread within and between federal states over short and longer time periods.
MICROBIOLOGY SPECTRUM
(2021)
Article
Microbiology
Stephy Mol Robinson, Vyshakh Rajachandran, Suchismita Majumdar, Satabdi Saha, Sneha Das, Sujay Chattopadhyay
Summary: Detecting adaptive mutations leading to gene inactivation or loss of function is crucial for understanding the evolution of bacterial virulence and antibiotic resistance. Truncation mutations, which trim the length of encoded proteins, can contribute to gene inactivation. This study analyzed the accumulation of truncation mutations in two serovars of Salmonella, finding distinct sets of core truncated genes in each serovar. These truncation mutations were acquired by different subsets of isolates and were also targeted by convergent amino acid mutations in different serovars, suggesting adaptation. Further research is needed to investigate the impact of adaptive truncation mutations on bacterial virulence evolution.
MICROBIOLOGY SPECTRUM
(2022)
Review
Microbiology
Wan Ratmaazila Wan Wan Makhtar, Izwan Bharudin, Nurul Hidayah Samsulrizal, Nik Yusnoraini Yusof
Summary: The advancement in whole-genome sequencing technology in recent years has revolutionized the study of infectious diseases, providing new insights into various fields related to infectious diseases. By examining the genomes of Salmonella enterica serovar Typhi, researchers have enhanced their understanding of genetic evolution and pathogenic mechanisms, potentially advancing the development of typhoid vaccines and medications.
Article
Microbiology
Silvia Garcia-Soto, Joerg Linde, Ulrich Methner
Summary: Cattle-adapted serovar Salmonella Dublin is the most important serovar causing enteritis and systemic diseases in cattle in the German state of Schleswig-Holstein. Whole-genome sequencing was used to analyze the genetic traits of 78 S. Dublin strains collected over six years, revealing transmission routes between herds and persistence at single farms. The spreading of manure on pastures and grassland may be a possible risk factor for the repeated occurrence of S. Dublin in certain districts of Schleswig-Holstein. Farm-specific analysis and whole-genome sequencing of outbreak strains are necessary for effective control of S. Dublin.
Article
Microbiology
Maria G. Winter, Elizabeth R. Hughes, Matthew K. Muramatsu, Angel G. Jimenez, Rachael B. Chanin, Luisella Spiga, Caroline C. Gillis, Michael McClelland, Helene Andrews-Polymenis, Sebastian E. Winter
Summary: Salmonella utilizes formate as an electron donor to support respiration, and formate oxidation predominantly occurs in the mucus layer of the gut. The bacteria in the mucus layer have higher transcription levels of formate dehydrogenases and pyruvate-formate lyase compared to those in the lumen. Our findings enhance understanding of microbial metabolism in different gut microenvironments and may have implications for other enteric pathogens.
Article
Microbiology
Yu Han, Yu Li, Zhiwei Zeng, Wenjing Li, Saixiang Feng, Weisheng Cao
Summary: This study explores the resistance mechanism and activity of the antimicrobial peptide MccY against Salmonella strains. The deletion of Ton system genes resulted in resistance to MccY and mutants showed increased susceptibility to MccY under a low-iron condition. MccY may decrease the virulence of S. Typhimurium by altering multiple physiological properties.
MICROBIOLOGY SPECTRUM
(2022)
Article
Immunology
Sophie Octavia, Ka Lip Chew, Raymond T. P. Lin, Jeanette W. P. Teo
Summary: Global travel has led to the occasional introduction of multidrug-resistant Salmonella Typhi into industrialized countries. Azithromycin-resistant Salmonella Typhi has been detected in Singapore, with 2 isolates likely being locally acquired. Ongoing vigilance and surveillance are necessary to minimize the public health risk posed by this serious pathogen.
EMERGING INFECTIOUS DISEASES
(2021)
Article
Gastroenterology & Hepatology
Meiying Yan, Yongming Zhou, Yang Cao, Zhenpeng Li, Xin Lu, Bo Pang, Shukun Wang, Biao Kan
Summary: This study discovered a new serovar of Salmonella (S. enterica subsp. II serovar 4,5,12:a:-) and demonstrated its ability to infect humans and cause clusters of cases. Whole-genome sequencing detection and surveillance of Salmonella can accurately define Salmonella classification and clonality, improve diagnosis, facilitate outbreak detection, and aid in the source tracing of salmonellosis epidemics.
Article
Agriculture, Dairy & Animal Science
Xin Yu, Hongwei Zhu, Yongheng Bo, Youzhi Li, Yue Zhang, Yang Liu, Jianlong Zhang, Linlin Jiang, Guozhong Chen, Xingxiao Zhang
Summary: The study investigated the prevalence and antimicrobial resistance of Salmonella enterica serovar Enteritidis in broiler chickens in Shandong Province, China. It found that S. Enteritidis was the predominant serovar with high antimicrobial resistance rates to several antibiotics. Multidrug resistance, particularly to fluoroquinolone, showed an increasing trend from 2013 to 2018. This study provides updated information on antimicrobial resistance data and risk assessment for Salmonella Enteritidis in broiler chickens in Shandong Province, which can be valuable for future surveillance activities to ensure chicken supply safety.
Article
Immunology
Jessica C. Allen, Franklin R. Toapanta, Scott M. Baliban, Marcelo B. Sztein, Sharon M. Tennant
Summary: Non-typhoidal Salmonella (NTS) is a significant cause of foodborne infections and deaths worldwide. We have developed a live attenuated vaccine, CVD 1926, against Salmonella enterica serovar Typhimurium. The study found that older mice had weaker immune responses to the vaccine and mucosal responses decrease with age.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Microbiology
Yu-feng Qiu, Reshma B. Nambiar, Xue-bin Xu, Shun-tai Weng, Hang Pan, Kui-cheng Zheng, Min Yue
Summary: Non-typhoidal Salmonella (NTS) is a common cause of gastroenteritis, with the invasive infection caused by an infrequently reported serovar Telelkebir strain FJ001 in China carrying antimicrobial-resistant and typhoidtoxin genes. Genomic investigation revealed a high relatedness among global S. Telelkebir isolates, suggesting potential rapid transmissions through international travels. This study highlights the importance of surveillance and understanding the threat posed by the unique combination of virulent and antimicrobial-resistant determinants in NTS infections.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Food Science & Technology
Guodong Zhang, Lijun Hu, Yan Luo, Sofia M. Santillana Farakos, Rhoma Johnson, Virginia N. Scott, Phillip Curry, David Melka, Eric W. Brown, Errol Strain, Vincent K. Bunning, Steven M. Musser, Thomas S. Hammack
Summary: This study aimed to estimate the prevalence, contamination level, and genetic diversity of Salmonella in selected raw, shelled tree nuts at retail markets in the United States. Results showed varying prevalence rates of Salmonella in different types of nuts, with most samples having low levels of the bacteria. There was no significant difference in Salmonella prevalence between nuts sourced from different types of retail stores and between organic and conventional nuts.
JOURNAL OF FOOD SCIENCE
(2021)
Article
Infectious Diseases
Gregory H. Tyson, Cong Li, Lucas B. Harrison, Gordon Martin, Chih-Hao Hsu, Heather Tate, Thu-Thuy Tran, Errol Strain, Shaohua Zhao
Summary: This study conducted short-read sequencing analysis of the ESI clone of Salmonella Infantis in poultry in the United States, finding that this clone first appeared in retail meats in Tennessee in 2014 and had spread nationwide by 2019, comprising 29% of all Salmonella isolated from retail chickens and 7% from retail turkey. Long-read sequencing data showed substantial recombination in the pESI plasmid, resulting in the presence of multiple resistance genes.
MICROBIAL DRUG RESISTANCE
(2021)
Article
Microbiology
Jay Noboru Worley, Kiran Javkar, Maria Hoffmann, Kristen Hysell, Amanda Garcia-Williams, Kaitlin Tagg, Sanjat Kanjilal, Errol Strain, Mihai Pop, Marc Allard, Louise Francois Watkins, Lynn Bry
Summary: MDR Shigella infections are a global concern among MSM, with new macrolide-resistant strains complicating treatment. Genomic analyses reveal resistant genes in US Shigella isolates and the receptivity of certain strains to plasmid acquisition. Leveraging integrated genomic-epidemiologic analyses can guide targeted clinical actions and public health efforts to combat the spread of multidrug-resistant Shigella.
Article
Biotechnology & Applied Microbiology
Jayanthi Gangiredla, Hugh Rand, Daniel Benisatto, Justin Payne, Charles Strittmatter, Jimmy Sanders, William J. Wolfgang, Kevin Libuit, James B. Herrick, Melanie Prarat, Magaly Toro, Thomas Farrell, Errol Strain
Summary: GalaxyTrakr is a customized instance of the Galaxy platform designed for laboratory scientists conducting food safety regulatory research. It provides tools for quality assessment, linking clinical isolates with food/environmental samples, and exploring new methodologies like metagenomics. With over 600 registered users and 450,000 analytical jobs processed, it promotes collaboration across public health laboratories and supports consistent interpretation of results.
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
Biotechnology & Applied Microbiology
Seth Commichaux, Kiran Javkar, Padmini Ramachandran, Niranjan Nagarajan, Denis Bertrand, Yi Chen, Elizabeth Reed, Narjol Gonzalez-Escalona, Errol Strain, Hugh Rand, Mihai Pop, Andrea Ottesen
Summary: Integration of long and short read sequencing can expedite the reconstruction of high-quality pathogen genomes, with long reads spanning repetitive regions and short reads accurately analyzing core genes. However, long reads have lower accuracy while short reads result in fragmented assemblies.
Article
Microbiology
Lucas Harrison, Sampa Mukherjee, Chih-Hao Hsu, Shenia Young, Errol Strain, Qijing Zhang, Glenn E. Tillman, Cesar Morales, Jovita Haro, Shaohua Zhao
Summary: Utilizing core genome multilocus sequence typing and minimal multilocus distance methodology, the relative contribution of different sources of C. coli to human infections can be evaluated, serving as an indicator of antimicrobial resistance.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Cong Li, Gregory H. Tyson, Chih-Hao Hsu, Lucas Harrison, Errol Strain, Thu-Thuy Tran, Glenn E. Tillman, Uday Dessai, Patrick F. McDermott, Shaohua Zhao
Summary: This study used long-read sequencing to investigate the genomic heterogeneity and antimicrobial resistance mechanisms of Salmonella isolated from retail meats and food animals. It found significant genetic variation among different serotypes, with the presence of plasmids playing a key role in genomic variability. Moreover, the bacteria's resistance mechanisms may be associated with plasmid types, sources, and serotypes.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Kiran Javkar, Hugh Rand, Maria Hoffmann, Yan Luo, Saul Sarria, Nagarajan Thirunavukkarasu, Christine A. Pillai, Patrick McGann, J. Kristie Johnson, Errol Strain, Mihai Pop
Summary: This large-scale whole-genome genotype-phenotype association study on 349 A. baumannii isolates identified 10 known resistance genes significantly associated with resistance to imipenem and revealed a conserved chromosomal region exclusive to imipenem-susceptible isolates. These findings provide new hypotheses for future research in understanding the genetic factors underlying carbapenem resistance in A. baumannii.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Genetics & Heredity
Patrick K. Mitchell, Leyi Wang, Bryce J. Stanhope, Brittany D. Cronk, Renee Anderson, Shipra Mohan, Lijuan Zhou, Susan Sanchez, Paula Bartlett, Carol Maddox, Vanessa DeShambo, Rinosh Mani, Lindsy M. Hengesbach, Sarah Gresch, Katie Wright, Sunil Mor, Shuping Zhang, Zhenyu Shen, Lifang Yan, Rebecca Mackey, Rebecca Franklin-Guild, Yan Zhang, Melanie Prarat, Katherine Shiplett, Akhilesh Ramachandran, Sai Narayanan, Justin Sanders, Andree A. Hunkapiller, Kevin Lahmers, Amanda A. Carbonello, Nicole Aulik, Ailam Lim, Jennifer Cooper, Angelica Jones, Jake Guag, Sarah M. Nemser, Gregory H. Tyson, Ruth Timme, Errol Strain, Renate Reimschuessel, Olgica Ceric, Laura B. Goodman
Summary: There is a growing need for public health and veterinary laboratories to perform whole genome sequencing (WGS) for monitoring antimicrobial resistance (AMR) and protecting the safety of people and animals. The iSeq platform, with its smaller size and affordability, is a viable option for small laboratories interested in genomic surveillance of microbial pathogens. The Illumina DNA Prep library preparation kit produced high-quality assemblies and nearly complete AMR gene annotations, making it an effective choice for generating WGS data.
MICROBIAL GENOMICS
(2022)
Article
Microbiology
Heather Tate, Sherry Ayers, Epiphanie Nyirabahizi, Cong Li, Stacey Borenstein, Shenia Young, Crystal Rice-Trujillo, Sanchez Saint Fleurant, Sonya Bodeis-Jones, Xunde Li, Melissa Tobin-D'Angelo, Victoriya Volkova, Rachel Hardy, Lisa Mingle, Nkuchia M. M'ikanatha, Laura Ruesch, Chris A. Whitehouse, Gregory H. Tyson, Errol Strain, Patrick F. McDermott
Summary: In 2019, a survey in the United States found that shrimp was the most susceptible seafood to bacterial contamination, and seafood from Asia and Latin America was more likely to be contaminated compared to North American seafood. The resistance testing showed that most antibiotics were still effective against the bacteria, but some medically relevant antimicrobial resistance genes were detected.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Food Science & Technology
Lucas Harrison, Gregory H. Tyson, Errol Strain, Rebecca L. Lindsey, Nancy Strockbine, Olgica Ceric, Gamola Z. Fortenberry, Beth Harris, Sheryl Shaw, Glenn Tillman, Shaohua Zhao, Uday Dessai
Summary: This study used genomic data to assess potential sources of ExPEC strains and found a higher likelihood of human infection-related strains in food animals and companion animals. Additionally, strains in high relative risk groups were more commonly resistant to antimicrobial drugs. This study highlights the importance of a One Health approach in identifying and managing human pathogens.
Article
Food Science & Technology
Shenia R. Young, Kelly J. Domesle, Ryan C. McDonald, Kristen A. Lozinak, Pongpan Laksanalamai, Erin Harrell, Siddhartha Thakur, Claudine Kabera, Errol A. Strain, Patrick F. McDermott, Beilei Ge
Summary: The study evaluated a loop-mediated isothermal amplification (LAMP) assay for the rapid screening of Salmonella. The results showed 100% sensitivity for LAMP compared to culture, and the method was found to streamline the laboratory workflow.
FOODBORNE PATHOGENS AND DISEASE
(2022)
Article
Multidisciplinary Sciences
Guojie Cao, Shaohua Zhao, Dai Kuang, Chih-Hao Hsu, Lanlan Yin, Yan Luo, Zhao Chen, Xuebin Xu, Errol Strain, Patrick McDermott, Marc Allard, Eric Brown, Jianghong Meng, Jie Zheng
Summary: MDR Salmonella has been a persistent challenge in public health and food safety, with higher prevalence in China compared to the U.S. and other countries. A genomic analysis of 197 S. Enteritidis genomes revealed four major clades, with MDR isolates predominantly found in clades II and III. Chinese isolates carried specific antimicrobial resistance genes and plasmid types, while African isolates had their own pattern of resistance genes and plasmids. The study also identified differences in virulence operons, pathogenicity islands, and other accessory genes among the isolates. These findings provide valuable insights into the diversification of MDR S. Enteritidis.
SCIENTIFIC REPORTS
(2023)
Article
Biochemical Research Methods
Kiran Javkar, Hugh Rand, Errol Strain, Mihai Pop
Summary: This article presents PRAWNS, an efficient and scalable tool for multiple-genome analysis, which can handle large-scale genotype-phenotype association studies.