@article{troxell_mendoza_ali_koci_hassan_2020, title={Attenuated Salmonella enterica Serovar Typhimurium, Strain NC983, Is Immunogenic, and Protective against Virulent Typhimurium Challenges in Mice}, volume={8}, ISSN={["2076-393X"]}, DOI={10.3390/vaccines8040646}, abstractNote={Non-typhoidal Salmonella (NTS) serovars are significant health burden worldwide. Although much effort has been devoted to developing typhoid-based vaccines for humans, currently there is no NTS vaccine available. Presented here is the efficacy of a live attenuated serovar Typhimurium strain (NC983). Oral delivery of strain NC983 was capable of fully protecting C57BL/6 and BALB/c mice against challenge with virulent Typhimurium. Strain NC983 was found to elicit an anti-Typhimurium IgG response following administration of vaccine and boosting doses. Furthermore, in competition experiments with virulent S. Typhimurium (ATCC 14028), NC983 was highly defective in colonization of the murine liver and spleen. Collectively, these results indicate that strain NC983 is a potential live attenuated vaccine strain that warrants further development.}, number={4}, journal={VACCINES}, author={Troxell, Bryan and Mendoza, Mary and Ali, Rizwana and Koci, Matthew and Hassan, Hosni}, year={2020}, month={Dec} }
 @article{meinders_mendoza_dickey_scholl_hassan_2020, title={Complete Genome Sequences of Six Lactobacilli Isolated from American Quarter Horses}, volume={9}, ISSN={["2576-098X"]}, url={https://doi.org/10.1128/MRA.00997-20}, DOI={10.1128/MRA.00997-20}, abstractNote={We report the complete circular genome sequences of six Lactobacillus strains and their plasmids, if any, from the fecal material of quarter horses at different ages.}, number={47}, journal={MICROBIOLOGY RESOURCE ANNOUNCEMENTS}, publisher={American Society for Microbiology}, author={Meinders, Rachael I. and Mendoza, Mary and Dickey, Allison N. and Scholl, Elizabeth H. and Hassan, Hosni M.}, editor={Rasko, DavidEditor}, year={2020}, month={Nov} }
 @article{allali_arnold_roach_cadenas_butz_hassan_koci_ballou_mendoza_ali_et al._2017, title={A comparison of sequencing platforms and bioinformatics pipelines for compositional analysis of the gut microbiome}, volume={17}, ISSN={["1471-2180"]}, DOI={10.1186/s12866-017-1101-8}, abstractNote={Advancements in Next Generation Sequencing (NGS) technologies regarding throughput, read length and accuracy had a major impact on microbiome research by significantly improving 16S rRNA amplicon sequencing. As rapid improvements in sequencing platforms and new data analysis pipelines are introduced, it is essential to evaluate their capabilities in specific applications. The aim of this study was to assess whether the same project-specific biological conclusions regarding microbiome composition could be reached using different sequencing platforms and bioinformatics pipelines. Chicken cecum microbiome was analyzed by 16S rRNA amplicon sequencing using Illumina MiSeq, Ion Torrent PGM, and Roche 454 GS FLX Titanium platforms, with standard and modified protocols for library preparation. We labeled the bioinformatics pipelines included in our analysis QIIME1 and QIIME2 (de novo OTU picking [not to be confused with QIIME version 2 commonly referred to as QIIME2]), QIIME3 and QIIME4 (open reference OTU picking), UPARSE1 and UPARSE2 (each pair differs only in the use of chimera depletion methods), and DADA2 (for Illumina data only). GS FLX+ yielded the longest reads and highest quality scores, while MiSeq generated the largest number of reads after quality filtering. Declines in quality scores were observed starting at bases 150–199 for GS FLX+ and bases 90–99 for MiSeq. Scores were stable for PGM-generated data. Overall microbiome compositional profiles were comparable between platforms; however, average relative abundance of specific taxa varied depending on sequencing platform, library preparation method, and bioinformatics analysis. Specifically, QIIME with de novo OTU picking yielded the highest number of unique species and alpha diversity was reduced with UPARSE and DADA2 compared to QIIME. The three platforms compared in this study were capable of discriminating samples by treatment, despite differences in diversity and abundance, leading to similar biological conclusions. Our results demonstrate that while there were differences in depth of coverage and phylogenetic diversity, all workflows revealed comparable treatment effects on microbial diversity. To increase reproducibility and reliability and to retain consistency between similar studies, it is important to consider the impact on data quality and relative abundance of taxa when selecting NGS platforms and analysis tools for microbiome studies.}, journal={BMC MICROBIOLOGY}, author={Allali, Imane and Arnold, Jason W. and Roach, Jeffrey and Cadenas, Maria Belen and Butz, Natasha and Hassan, Hosni M. and Koci, Matthew and Ballou, Anne and Mendoza, Mary and Ali, Rizwana and et al.}, year={2017}, month={Sep} }
 @article{azcarate-peril_butz_cadenas_koci_ballou_mendoza_ali_hassan_2017, title={An Attenuated
                    Salmonella enterica
                    Serovar Typhimurium Strain and Galacto-Oligosaccharides Accelerate Clearance of
                    Salmonella
                    Infections in Poultry through Modifications to the Gut Microbiome}, volume={84}, ISSN={0099-2240 1098-5336}, url={http://dx.doi.org/10.1128/AEM.02526-17}, DOI={10.1128/aem.02526-17}, abstractNote={ABSTRACT Salmonella is estimated to cause one million foodborne illnesses in the United States every year. Salmonella -contaminated poultry products are one of the major sources of salmonellosis. Given the critical role of the gut microbiota in Salmonella transmission, a manipulation of the chicken intestinal microenvironment could prevent animal colonization by the pathogen. In Salmonella , the global regulator gene fnr ( f umarate n itrate r eduction) regulates anaerobic metabolism and is essential for adapting to the gut environment. This study tested the hypothesis that an attenuated Fnr mutant of Salmonella enterica serovar Typhimurium (attST) or prebiotic galacto-oligosaccharides (GOS) could improve resistance to wild-type Salmonella via modifications to the structure of the chicken gut microbiome. Intestinal samples from a total of 273 animals were collected weekly for 9 weeks to evaluate the impact of attST or prebiotic supplementation on microbial species of the cecum, duodenum, jejunum, and ileum. We next analyzed changes to the gut microbiome induced by challenging the animals with a wild-type Salmonella serovar 4,[5],12:r:− (Nal r ) strain and determined the clearance rate of the virulent strain in the treated and control groups. Both GOS and the attenuated Salmonella strain modified the gut microbiome but elicited alterations of different taxonomic groups. The attST produced significant increases of Alistipes and undefined Lactobacillus , while GOS increased Christensenellaceae and Lactobacillus reuteri . The microbiome structural changes induced by both treatments resulted in a faster clearance after a Salmonella challenge. IMPORTANCE With an average annual incidence of 13.1 cases/100,000 individuals, salmonellosis has been deemed a nationally notifiable condition in the United States by the Centers for Disease Control and Prevention (CDC). Earlier studies demonstrated that Salmonella is transmitted by a subset of animals (supershedders). The supershedder phenotype can be induced by antibiotics, ascertaining an essential role for the gut microbiota in Salmonella transmission. Consequently, modulation of the gut microbiota and modification of the intestinal microenvironment could assist in preventing animal colonization by the pathogen. Our study demonstrated that a manipulation of the chicken gut microbiota by the administration of an attenuated Salmonella strain or prebiotic galacto-oligosaccharides (GOS) can promote resistance to Salmonella colonization via increases of beneficial microorganisms that translate into a less hospitable gut microenvironment.}, number={5}, journal={Applied and Environmental Microbiology}, publisher={American Society for Microbiology}, author={Azcarate-Peril, M. Andrea and Butz, Natasha and Cadenas, Maria Belen and Koci, Matthew and Ballou, Anne and Mendoza, Mary and Ali, Rizwana and Hassan, Hosni}, editor={Schottel, Janet L.Editor}, year={2017}, month={Dec} }
 @article{troxell_petri_daron_pereira_mendoza_hassan_koci_2015, title={Poultry Body Temperature Contributes to Invasion Control through Reduced Expression of Salmonella Pathogenicity Island 1 Genes in Salmonella enterica Serovars Typhimurium and Enteritidis}, volume={81}, ISSN={0099-2240 1098-5336}, url={http://dx.doi.org/10.1128/AEM.02622-15}, DOI={10.1128/aem.02622-15}, abstractNote={ABSTRACT Salmonella enterica serovars Typhimurium ( S . Typhimurium) and Enteritidis ( S . Enteritidis) are foodborne pathogens, and outbreaks are often associated with poultry products. Chickens are typically asymptomatic when colonized by these serovars; however, the factors contributing to this observation are uncharacterized. Whereas symptomatic mammals have a body temperature between 37°C and 39°C, chickens have a body temperature of 41°C to 42°C. Here, in vivo experiments using chicks demonstrated that numbers of viable S . Typhimurium or S . Enteritidis bacteria within the liver and spleen organ sites were ≥4 orders of magnitude lower than those within the ceca. When similar doses of S . Typhimurium or S . Enteritidis were given to C3H/HeN mice, the ratio of the intestinal concentration to the liver/spleen concentration was 1:1. In the avian host, this suggested poor survival within these tissues or a reduced capacity to traverse the host epithelial layer and reach liver/spleen sites or both. Salmonella pathogenicity island 1 (SPI-1) promotes localization to liver/spleen tissues through invasion of the epithelial cell layer. Following in vitro growth at 42°C, SPI-1 genes sipC , invF , and hilA and the SPI-1 rtsA activator were downregulated compared to expression at 37°C. Overexpression of the hilA activators fur , fliZ , and hilD was capable of inducing hilA-lacZ at 37°C but not at 42°C despite the presence of similar levels of protein at the two temperatures. In contrast, overexpression of either hilC or rtsA was capable of inducing hilA and sipC at 42°C. These data indicate that physiological parameters of the poultry host, such as body temperature, have a role in modulating expression of virulence.}, number={23}, journal={Applied and Environmental Microbiology}, publisher={American Society for Microbiology}, author={Troxell, Bryan and Petri, Nicholas and Daron, Caitlyn and Pereira, Rafaela and Mendoza, Mary and Hassan, Hosni M. and Koci, Matthew D.}, editor={Elkins, C. A.Editor}, year={2015}, month={Sep}, pages={8192–8201} }
 @article{husain_jones-carson_liu_song_saah_troxell_mendoza_hassan_vazquez-torresa_2014, title={Ferric Uptake Regulator-Dependent Antinitrosative Defenses in Salmonella enterica Serovar Typhimurium Pathogenesis}, volume={82}, ISSN={["1098-5522"]}, DOI={10.1128/iai.01201-13}, abstractNote={ABSTRACT Herein we report an important role for the ferric uptake regulator (Fur) in the resistance of Salmonella enterica serovar Typhimurium to the reactive nitrogen species produced by inducible nitric oxide (NO) synthase in an NRAMP1 r murine model of acute systemic infection. The expression of fur protected Salmonella grown under normoxic and hypoxic conditions against the bacteriostatic activity of NO. The hypersusceptibility of fur -deficient Salmonella to the cytotoxic actions of NO coincides with a marked repression of respiratory activity and the reduced ability of the bacteria to detoxify NO. A fur mutant Salmonella strain contained reduced levels of the terminal quinol oxidases of the electron transport chain. Addition of the heme precursor δ-aminolevulinic acid restored the cytochrome content, respiratory activity, NO consumption, and wild-type growth in bacteria undergoing nitrosative stress. The innate antinitrosative defenses regulated by Fur added to the adaptive response associated with the NO-detoxifying activity of the flavohemoprotein Hmp. Our investigations indicate that, in addition to playing a critical role in iron homeostasis, Fur is an important antinitrosative determinant of Salmonella pathogenesis.}, number={1}, journal={INFECTION AND IMMUNITY}, author={Husain, Maroof and Jones-Carson, Jessica and Liu, Lin and Song, Miryoung and Saah, J. Royden and Troxell, Bryan and Mendoza, Mary and Hassan, Hosni and Vazquez-Torresa, Andres}, year={2014}, month={Jan}, pages={333–340} }