@misc{obe_kiess_nannapaneni_2024, title={Antimicrobial Tolerance in <i>Salmonella</i>: Contributions to Survival and Persistence in Processing Environments}, volume={14}, ISSN={["2076-2615"]}, DOI={10.3390/ani14040578}, abstractNote={Salmonella remains a top bacterial pathogen implicated in several food-borne outbreaks, despite the use of antimicrobials and sanitizers during production and processing. While these chemicals have been effective, Salmonella has shown the ability to survive and persist in poultry processing environments. This can be credited to its microbial ability to adapt and develop/acquire tolerance and/or resistance to different antimicrobial agents including oxidizers, acids (organic and inorganic), phenols, and surfactants. Moreover, there are several factors in processing environments that can limit the efficacy of these antimicrobials, thus allowing survival and persistence. This mini-review examines the antimicrobial activity of common disinfectants/sanitizers used in poultry processing environments and the ability of Salmonella to respond with innate or acquired tolerance and survive exposure to persists in such environments. Instead of relying on a single antimicrobial agent, the right combination of different disinfectants needs to be developed to target multiple pathways within Salmonella.}, number={4}, journal={ANIMALS}, author={Obe, Tomi and Kiess, Aaron S. and Nannapaneni, Ramakrishna}, year={2024}, month={Feb} }
 @article{jia_hsu_zhang_li_schilling_peebles_kiess_wamsley_zhang_2024, title={Changes in gene expression in the intestinal mucus of broilers with woody breast myopathy}, volume={103}, ISSN={["1525-3171"]}, DOI={10.1016/j.psj.2023.103398}, abstractNote={Previous work has shown that dietary treatments affect woody breast (WB) incidence differently, which indicates that gut conditions such as gut barrier function, inflammation, and oxidative stress are likely related to WB. In this study, dietary supplementation with antibiotics (bacitracin) or probiotics (Bacillus subtilis) was investigated for their effects on the expression of transcripts related to gut barrier function, inflammation, and oxidative stress in the mucus lining of the jejunum from broilers with or without WB. A split-plot experimental design was used in this study. The dietary treatments served as the main plot factor and the breast muscle condition was the subplot factor. On day 41, jejunum mucus was collected from one bird from each of 3 replicate pens in each 3 dietary treatment groups that exhibited WB and an additional bird that contained a normal breast (3 biological replicates/treatment/phenotype; 3 × 3 × 2, total N = 18). Total RNA was extracted using a commercial RNA extraction kit. The expression levels of CLDN1, MUC6, TLR2A, TLR2B, TLR4, IFN-γ, IL-1β, IL-8L1, IL-10, NOS2, and SOD were determined using two-step RT-qPCR analysis. The gene expression difference in ΔCt values was determined after normalizing with the chicken 18S rRNA gene. When the significant differences occurred between treatments, the relative fold change was calculated using the ΔΔCt method and the significance level was calculated. The PROC GLM procedure of SAS 9.4 was used, and the level of significance was set at P ≤ 0.05. There were no significant interactive effects between diet and the breast muscle condition on the expression of any of the genes tested. However, birds with WB exhibited higher MUC6 (P < 0.0001) gene expression levels than birds with normal breast muscles. In addition, the expression of SOD decreased in birds that were fed the antibiotic diet when compared to birds that were fed the probiotic diet (P = 0.014). In conclusion, WB identified in broilers tested in the current study is attributed to increased expression of mucin, indicating a correlation between WB incidence and gel-forming mucin secretion and pathogen signaling.}, number={3}, journal={POULTRY SCIENCE}, author={Jia, Linan and Hsu, Chuan-Yu and Zhang, Xue and Li, Xiaofei and Schilling, M. Wes and Peebles, E. David and Kiess, Aaron S. and Wamsley, Kelley G. S. and Zhang, Li}, year={2024}, month={Mar} }
 @article{barbalho_castaneda_araujo_kiess_carvalho_barbalho_borges_bonato_2023, title={B-glucans and MOS, essential oil, and probiotics in diets of broilers challenged with Eimeria spp. and Clostridium perfringens}, volume={102}, ISSN={["1525-3171"]}, DOI={10.1016/j.psj.2023.102541}, abstractNote={The aim of this study was to evaluate the effectiveness of β-glucans and MOS, essential oil (mixture of carvacrol and thymol), and the probiotic based on Saccharomyces boulardi, as an alternative to anticoccidial agents. In this experiment, six hundred seventy-two 1-day-old male broiler chicks were housed in batteries for 28 d. The experimental design of 4 randomized blocks with 24 cages each, and 7 birds per cage, consisted of an initial phase from 1 to 14 d of age, and a growth phase, from 15 to 28 d of age. The rations were formulated based on corn and soybean meal as energy and protein ingredients, respectively. All birds were inoculated with Eimeria spp and C. Perfringes at 14 d of age, and with C. Perfringes only at 21 d of age. The results showed the best weight gain in the initial phase when the anticoccidial agent was applied, whereas the use of additives in growth and entire experimental phases showed superior results in all treatments for this parameter. The birds that did not receive additives in the rations had the worst feed conversion in both phases and along raising. The results showed no significant differences between the treatments for the scores of lesions in the digestive tract and counts in the cecum, however, the red lesions increased numerically in the duodenum and jejunum of birds fed diets without the inclusion of additives. The use of additives indicated effectiveness for the parameters of performance in broilers challenged with C. Perfringes and Eimeria spp. at 14 d of age, and with C. Perfringes at 21 d of age.}, number={4}, journal={POULTRY SCIENCE}, author={Barbalho, Ricardo L. do C. and Castaneda, Claudia and Araujo, Lucio F. and Kiess, Aaron S. and Carvalho, Rachel S. B. and Barbalho, Caio B. and Borges, Liliana L. and Bonato, Melina A.}, year={2023}, month={Apr} }
 @article{poudel_jia_ii_hsu_thrash_sukumaran_adhikari_kiess_zhang_2023, title={In silico prediction and expression analysis of vaccine candidate genes of Campylobacter jejuni}, volume={102}, ISSN={["1525-3171"]}, DOI={10.1016/j.psj.2023.102592}, abstractNote={Campylobacter jejuni (C. jejuni) is the most common food-borne pathogen that causes human gastroenteritis in the United States. Consumption of contaminated poultry products is considered as the major source of human Campylobacter infection. An effective vaccine would be a promising alternative to antibiotic supplements to curb C. jejuni colonization in poultry gastrointestinal (GI) tract. However, the genetic diversity among the C. jejuni isolates makes vaccine production more challenging. Despite many attempts, an effective Campylobacter vaccine is not yet available. This study aimed to identify suitable candidates to develop a subunit vaccine against C. jejuni, which could reduce colonization in the GI tract of the poultry. In the current study, 4 C. jejuni strains were isolated from retail chicken meat and poultry litter samples and their genomes were sequenced utilizing next-generation sequencing technology. The genomic sequences of C. jejuni strains were screened to identify potential antigens utilizing the reverse vaccinology approach. In silico genome analysis predicted 3 conserved potential vaccine candidates (phospholipase A [PldA], TonB dependent vitamin B12 transporter [BtuB], and cytolethal distending toxin subunit B [CdtB]) suitable for the development of a vaccine. Furthermore, the expression of predicted genes during host-pathogen interaction was analyzed by an infection study using an avian macrophage-like immortalized cell line (HD11). The HD11 was infected with C. jejuni strains, and the RT-qPCR assay was performed to determine the expression of the predicted genes. The expression difference was analyzed using ΔΔCt methods. The results indicate that all 3 predicted genes, PldA, BtuB, and CdtB, were upregulated in 4 tested C. jejuni strains irrespective of their sources of isolation. In conclusion, in silico prediction and gene expression analysis during host-pathogen interactions identified 3 potential vaccine candidates for C. jejuni.}, number={5}, journal={POULTRY SCIENCE}, author={Poudel, Sabin and Jia, Linan and Ii, Mark A. Arick and Hsu, Chuan-Yu and Thrash, Adam and Sukumaran, Anuraj T. and Adhikari, Pratima and Kiess, Aaron S. and Zhang, Li}, year={2023}, month={May}, pages={1–10} }
 @article{jia_zhang_li_schilling_peebles_kiess_zhai_zhang_2022, title={Bacitracin, Bacillus subtilis, and Eimeria spp. challenge exacerbates woody breast incidence and severity in broilers}, volume={101}, ISSN={["1525-3171"]}, DOI={10.1016/j.psj.2021.101512}, abstractNote={Woody breast (WB) is a myopathy that is related to the increasing growth rate. Understanding the influence of management factors on WB formation and development is important to minimize WB. This study was conducted to define how management factors affect broiler growth performance, processing yield, and WB incidence. Ross × Ross 708 chicks were randomly assigned to a 3 (diet) × 2 (cocci challenge) × 2 (sex) factorial arrangement of treatments. The 3 dietary treatments were: control diet (corn-soybean meal basal diet), antibiotic diet (basal diet + 6.075 mg bacitracin /kg feed), and probiotic diet (basal diet + 2.2 × 108 CFU Bacillus subtilis PB6/kg feed). Birds in cocci challenge treatments received 20 × live cocci vaccine on d 14. The hardness of breast muscle in live birds was determined by palpation and grouped into Normal, Slight, Moderate, and Severe categories. Across diet and sex treatments, the cocci challenge resulted in decreases in body weight (BW) on d 29 and 35 (P < 0.0001 and = 0.032) in body weight gain (BWG) from d 14 to 29 (P < 0.0001). However, an increase of BW occurred on d 35 (P = 0.032) and an increase of BWG occurred from d 29 to 35 and d 35 to 43 (P = 0.0001 and 0.002), and the cocci challenge increased WB incidence on d 29 (P = 0.043) and d 43 (P = 0.013). Across challenge and sex treatments, birds fed the antibiotic diet exhibited a higher growth rate (GR) than those fed the control or probiotic diet from d 0 to 14 (P = 0.016), but not after d 14 (P > 0.05). Across sex, the antibiotic and probiotic diets increased WB incidence for those birds that did not receive a cocci challenge on d 43 (P = 0.040). Across challenge and diet treatments, males exhibited a higher BW, BWG, and GR throughout all growth phases, and males showed a higher WB incidence on d 29, 35, and 43 (P = 0.002, P < 0.0001, and P = 0.0002, respectively). In conclusion, bacitracin and Eimeria spp. increased WB incidence, BW, and GR. However, Bacillus subtilis increased WB incidence in male broilers without affecting BW and GR.}, number={1}, journal={POULTRY SCIENCE}, author={Jia, Linan and Zhang, Xue and Li, Xiaofei and Schilling, Wes and Peebles, E. David and Kiess, Aaron S. and Zhai, Wei and Zhang, Li}, year={2022}, month={Jan} }
 @article{poudel_li_arick_hsu_thrash_sukumaran_adhikari_kiess_zhang_2022, title={Complete Genome Sequences of Four Campylobacter jejuni Strains Isolated from Retail Chicken Meat and Broiler Feces}, ISSN={["2576-098X"]}, DOI={10.1128/mra.00898-22}, abstractNote={
            Campylobacter jejuni
            is the leading pathogen that causes foodborne infections. Here, we report the complete genome sequences of four
            C. jejuni
            strains isolated from retail chicken meat and broiler feces samples. Genes encoding type VI secretion and antibiotic resistance were detected among these isolates.
          }, journal={MICROBIOLOGY RESOURCE ANNOUNCEMENTS}, author={Poudel, Sabin and Li, Tianmin and Arick, Mark A. and Hsu, Chuan-Yu and Thrash, Adam and Sukumaran, Anuraj T. and Adhikari, Pratima and Kiess, Aaron S. and Zhang, Li}, year={2022}, month={Sep} }
 @article{jia_zhang_li_schilling_peebles_kiess_zhang_2022, title={Internal organ and skeletal muscle development in commercial broilers with woody breast myopathy}, volume={101}, ISSN={["1525-3171"]}, DOI={10.1016/j.psj.2022.102012}, abstractNote={Increasing growth rate, body weight, and breast muscle yield have been linked to broiler muscle problems such as woody breast (WB). The aim of this study was to investigate the internal organ and skeletal muscle development of broilers with WB myopathy under dietary and Eimeria challenge treatments. A 3 diet (control, antibiotic, or probiotic) × 2 challenge (control or Eimeria) × 2 sex factorial arrangement of treatments was used in a randomized complete block design. Ross × Ross 708 chicks were randomly assigned to 96 floor pens with 12 treatment combinations (8 replicates per treatment). Internal organs were sampled on d 13 and 41. Skeletal muscles were sampled on d 41. Internal organ and skeletal muscle weights were analyzed using a 3-way analysis of variance (ANOVA). Relationships between WB and internal organ and skeletal muscle weights were analyzed using one-way ANOVA as all treatments were pooled together and regrouped according to WB scores. On d 41, absolute and relative heart weights were greater in males when they were averaged over diet and challenge treatments (P < 0.001 and P = 0.026, respectively). The birds with WB score 3 had greater absolute heart (P = 0.0002) and spleen weights (P = 0.016), but there was no difference in relative spleen weight (P > 0.05). When averaged over diet and challenge treatments, males have greater absolute duodenum, jejunum, and ileum weights (for all P < 0.0001). Compared with birds with normal breasts, the birds with WB scores 1, 2, and 3 had a greater live weight (for all P < 0.0001) and absolute and relative breast weights (for all P < 0.0001). The birds with WB score 1, 2, and 3 had greater (P < 0.0001) absolute but lower (P < 0.0001) relative drumstick, thigh, and wing weights. Results indicated that broilers with WB had lower relative proventriculus and gizzard weights and greater relative breast meat weight with lower relative drumstick, thigh, and wing muscle weights.}, number={9}, journal={POULTRY SCIENCE}, author={Jia, Linan and Zhang, Xue and Li, Xiaofei and Schilling, M. Wes and Peebles, David and Kiess, Aaron S. and Zhang, Li}, year={2022}, month={Sep} }
 @article{poudel_li_chen_zhang_cheng_sukumaran_kiess_zhang_2022, title={Prevalence, Antimicrobial Resistance, and Molecular Characterization of Campylobacter Isolated from Broilers and Broiler Meat Raised without Antibiotics}, ISSN={["2165-0497"]}, DOI={10.1128/spectrum.00251-22}, abstractNote={
            Campylobacter
            is one of the main bacterial pathogens that cause campylobacteriosis in the United States. Poultry is considered a major reservoir for the transmission of
            Campylobacter
            to humans.
          }, journal={MICROBIOLOGY SPECTRUM}, author={Poudel, Sabin and Li, Tianmin and Chen, Saijuan and Zhang, Xue and Cheng, Wen-Hsing and Sukumaran, Anuraj T. and Kiess, Aaron S. and Zhang, Li}, year={2022}, month={May} }
 @article{thames_fancher_colvin_mcanally_tucker_zhang_kiess_dinh_sukumaran_2022, title={Spoilage Bacteria Counts on Broiler Meat at Different Stages of Commercial Poultry Processing Plants That Use Peracetic Acid}, volume={12}, ISSN={["2076-2615"]}, DOI={10.3390/ani12111439}, abstractNote={In poultry processing, spoilage microbes are persistent microorganisms, which affect the quality of broiler meat. Peracetic acid (PAA) is the most common antimicrobial used by commercial processing plants, which can reduce the prevalence of these microbes. The goal of this study was to determine the concentrations of aerobic bacteria, coliforms, lactic acid bacteria, and Pseudomonas on broiler meat in processing plants that use peracetic acid in various concentrations as the primary antimicrobial. Samples were collected from three processing plants at five processing steps: post-pick (defeathering), pre-chill, post-chill, mechanically deboned meat (MDM), and drumsticks. Samples were rinsed in buffered peptone water for bacteria isolation. Over six log CFU/sample of aerobic plate counts (APC), lactic acid bacteria, and coliforms were detected on post-pick samples. All spoilage bacteria were reduced to nondetectable levels on post-chill samples (p < 0.001). However, the presence of all bacteria on mechanically deboned meat (MDM) samples indicated varying degrees of cross contamination from post-chill and MDM samples. These results suggest PAA effectively reduces spoilage microbes in chilling applications irrespective of differences in PAA concentrations. However, due to the levels of spoilage microbes detected in MDM, it may be worth investigating the potential interventions for this stage of processing.}, number={11}, journal={ANIMALS}, author={Thames, Hudson T. and Fancher, Courtney A. and Colvin, Mary G. and McAnally, Mika and Tucker, Emily and Zhang, Li and Kiess, Aaron S. and Dinh, Thu T. N. and Sukumaran, Anuraj T.}, year={2022}, month={Jun} }
 @article{thames_fancher_colvin_mcanally_tucker_zhang_kiess_dinh_sukumaran_2022, title={The Prevalence of Salmonella and Campylobacter on Broiler Meat at Different Stages of Commercial Poultry Processing}, volume={12}, ISSN={["2076-2615"]}, DOI={10.3390/ani12182460}, abstractNote={In poultry processing, Salmonella and Campylobacter contaminations are major food safety concerns. Peracetic acid (PAA) is an antimicrobial commonly used in commercial poultry processing to reduce pathogen prevalence so as to meet the USDA-FSIS performance standards. The objective of this study was to determine the prevalence of Salmonella and Campylobacter on broiler meat in various steps of commercial poultry processing in plants that use PAA. Post-pick, pre-chill, post-chill, and drumstick chicken samples were collected from three processing plants and mechanically deboned meat (MDM) was collected from two of the three plants. Each plant was sampled thrice, and 10 samples were collected from each processing step during each visit. Among the 420 samples, 79 were contaminated with Salmonella and 155 were contaminated with Campylobacter. Salmonella and Campylobacter contamination on the post-pick samples averaged 32.2%. Significant reductions in Salmonella and Campylobacter were observed in pre-chill to post-chill samples, where the prevalence was reduced from 34% and 64.4% to nondetectable limits and 1.1%, respectively (p < 0.001). Salmonella and Campylobacter remained undetectable on the drumstick samples in all three processing plants. However, the prevalence of Salmonella and Campylobacter on MDM was similar to the post-pick prevalence, which suggests substantial cross-contamination from post-chill to MDM.}, number={18}, journal={ANIMALS}, author={Thames, Hudson T. and Fancher, Courtney A. and Colvin, Mary G. and McAnally, Mika and Tucker, Emily and Zhang, Li and Kiess, Aaron S. and Dinh, Thu T. N. and Sukumaran, Anuraj T.}, year={2022}, month={Sep} }
 @article{fancher_thames_colvin_smith_easterling_nuthalapati_zhang_kiess_dinh_sukumaran_2021, title={Prevalence and Molecular Characteristics of Avian Pathogenic Escherichia coli in "No Antibiotics Ever" Broiler Farms}, volume={9}, ISSN={["2165-0497"]}, DOI={10.1128/Spectrum.00834-21}, abstractNote={
            Avian pathogenic
            Escherichia coli
            causes one of the most detrimental bacterial diseases to the United States poultry industry, colibacillosis. Colibacillosis leads to decreased performance, early mortality, and subsequent production loss.
          }, number={3}, journal={MICROBIOLOGY SPECTRUM}, author={Fancher, Courtney A. and Thames, Hudson T. and Colvin, Mary Gates and Smith, Mercedes and Easterling, Alyssa and Nuthalapati, Nikhil and Zhang, Li and Kiess, Aaron and Dinh, Thu T. N. and Sukumaran, Anuraj Theradiyil}, year={2021}, month={Dec} }
 @article{fancher_thames_colvin_zhang_nuthalapati_kiess_dinh_sukumaran_2021, title={Research Note: Prevalence and molecular characteristics of Clostridium perfringens in "no antibiotics ever" broiler farms}, volume={100}, ISSN={["1525-3171"]}, DOI={10.1016/j.psj.2021.101414}, abstractNote={Clostridium perfringens (C. perfringens) is the etiological agent of necrotic enteritis and gangrenous dermatitis; 2 diseases that cause significant economic and welfare concerns to the broiler industry. Previously, Clostridium-related diseases were managed with the use of antimicrobial growth promoters fed to broilers that improved gut health and performance. The recent shift to no antibiotics ever (NAE) production has increased the incidence of Clostridium-related diseases. The objective of this study was to identify C. perfringens prevalence and toxinotypes in NAE farms. Samples of litter, feces, and cloacal swabs were collected from 4 NAE broiler farms in the summer of 2019, on d 28 and d 56 of one flock cycle. A total of 734 presumptive isolates were obtained from 192 samples collected in the study. Irrespective of the age of flock and sample type, all 192 samples contained at least one colony presumptively identified as C. perfringens on Perfringens agar plate with morphology as a single, round colony with opaque ring and black center. All isolates were further screened using PCR for confirmation, toxinotyping, and identification of virulence-associated genes. Only 9 isolates among the 734 presumptive isolates were confirmed as C. perfringens and all confirmed isolates were toxinotype A with variation in presence of netB, cpb2, and tpeL. More extensive studies are required to assess the prevalence and virulence of C. perfringens in NAE farms.}, number={11}, journal={POULTRY SCIENCE}, author={Fancher, Courtney A. and Thames, Hudson T. and Colvin, Mary G. and Zhang, Li and Nuthalapati, Nikhil and Kiess, Aaron and Dinh, Thu T. N. and Sukumaran, Anuraj T.}, year={2021}, month={Nov} }