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Woyda R, Oladeinde A, Endale D, Strickland T, Plumblee Lawrence J, Abdo Z. Genetic Characteristics of Salmonella Isolates Recovered From Reused Broiler Litter Over Three Successive Flocks. J Food Prot 2024; 87:100236. [PMID: 38307462 PMCID: PMC11000695 DOI: 10.1016/j.jfp.2024.100236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 02/04/2024]
Abstract
Salmonella infections are a leading cause of bacterial food-borne illness worldwide. Infections are highly associated with the consumption of contaminated food, and in particular, chicken meat. The severity of Salmonella infections depends on the presence of antimicrobial resistance genes and virulence factors. While there are many studies which have investigated Salmonella strains isolated from postharvest chicken samples, there is a gap in our understanding of the genetic properties that influence the persistence of Salmonella in preharvest and in particular their makeup of antimicrobial resistance genes and virulence factors. We used whole genome sequencing and hierarchical clustering to characterize and classify the genetic diversity of Salmonella enterica isolates (n = 55) recovered from the litter of commercial broiler chicken raised in four colocated broiler houses of one integrated farm over three consecutive flocks. The chicken were raised under a newly adopted "No Antibiotics Ever" program, and copper sulfate was administered via drinking water. In-silico serovar prediction identified three S. enterica serovars: Enteritidis (n = 12), Kentucky (n = 40), and Senftenberg (n = 3). Antimicrobial susceptibility testing revealed that only one S. Kentucky isolate was resistant to streptomycin, while the remaining isolates were susceptible to all antibiotics tested. Metal resistance operons, including copper and silver, were identified chromosomally and on plasmids in serovar Senftenberg and Kentucky isolates, respectively, while serovar Enteritidis carried several virulence factors on plasmids. Serovar Kentucky isolates harboring metal resistance operons were the only Salmonella isolates recovered from the litter of third flock cohort. These results suggest that there might be environmental selection for Salmonella strains carrying plasmid-associated metal resistance and virulence genes, which could play a role in their persistence in litter.
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Affiliation(s)
- Reed Woyda
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA; Program of Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | | | - Dinku Endale
- Southeast Watershed Research, USDA, Tifton, Georgia, USA
| | | | | | - Zaid Abdo
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA; Program of Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA.
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Curtis BE, Abdo Z, Graham B, LaVoy A, Evans SJM, Santangelo K, Dean GA. An Aptamer-Based Proteomic Analysis of Plasma from Cats ( Felis catus) with Clinical Feline Infectious Peritonitis. Viruses 2024; 16:141. [PMID: 38257841 PMCID: PMC10819688 DOI: 10.3390/v16010141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 01/13/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
Feline infectious peritonitis (FIP) is a systemic disease manifestation of feline coronavirus (FCoV) and is the most important cause of infectious disease-related deaths in domestic cats. FIP has a variable clinical manifestation but is most often characterized by widespread vasculitis with visceral involvement and/or neurological disease that is typically fatal in the absence of antiviral therapy. Using an aptamer-based proteomics assay, we analyzed the plasma protein profiles of cats who were naturally infected with FIP (n = 19) in comparison to the plasma protein profiles of cats who were clinically healthy and negative for FCoV (n = 17) and cats who were positive for the enteric form of FCoV (n = 9). We identified 442 proteins that were significantly differentiable; in total, 219 increased and 223 decreased in FIP plasma versus clinically healthy cat plasma. Pathway enrichment and associated analyses showed that differentiable proteins were related to immune system processes, including the innate immune response, cytokine signaling, and antigen presentation, as well as apoptosis and vascular integrity. The relevance of these findings is discussed in the context of previous studies. While these results have the potential to inform diagnostic, therapeutic, and preventative investigations, they represent only a first step, and will require further validation.
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Affiliation(s)
| | | | | | | | | | | | - Gregg A. Dean
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA; (B.E.C.); (A.L.); (S.J.M.E.); (K.S.)
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Woyda R, Oladeinde A, Endale D, Strickland T, Plumblee Lawrence J, Abdo Z. Virulence factors and antimicrobial resistance profiles of Campylobacter isolates recovered from consecutively reused broiler litter. Microbiol Spectr 2023; 11:e0323623. [PMID: 37882583 PMCID: PMC10871742 DOI: 10.1128/spectrum.03236-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 09/19/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE Campylobacter is a leading cause of foodborne illness in the United States due to consumption of contaminated or mishandled food products, often associated with chicken meat. Campylobacter is common in the microbiota of avian and mammalian gut; however, acquisition of antimicrobial resistance genes (ARGs) and virulence factors (VFs) may result in strains that pose significant threat to public health. Although there are studies investigating the genetic diversity of Campylobacter strains isolated from post-harvest chicken samples, there are limited data on the genome characteristics of isolates recovered from preharvest broiler production. Here, we show that Campylobacter jejuni and Campylobacter coli differ in their carriage of antimicrobial resistance and virulence factors may also differ in their ability to persist in litter during consecutive grow-out of broiler flocks. We found that presence/absence of virulence factors needed for evasion of host defense mechanisms and gut colonization played an integral role in differentiating Campylobacter strains.
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Affiliation(s)
- Reed Woyda
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
- Program of Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | | | - Dinku Endale
- Southeast Watershed Research Laboratory, USDA, Tifton, Georgia, USA
| | | | | | - Zaid Abdo
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
- Program of Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
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Hopken MW, Piaggio AJ, Abdo Z, Chipman RB, Mankowski CP, Nelson KM, Hilton MS, Thurber C, Tsuchiya MTN, Maldonado JE, Gilbert AT. Are rabid raccoons ( Procyon lotor) ready for the rapture? Determining the geographic origin of rabies virus-infected raccoons using RADcapture and microhaplotypes. Evol Appl 2023; 16:1937-1955. [PMID: 38143904 PMCID: PMC10739080 DOI: 10.1111/eva.13613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 09/06/2023] [Accepted: 10/18/2023] [Indexed: 12/26/2023] Open
Abstract
North America is recognized for the exceptional richness of rabies virus (RV) wildlife reservoir species. Management of RV is accomplished through vaccination targeting mesocarnivore reservoir populations, such as the raccoon (Procyon lotor) in Eastern North America. Raccoons are a common generalist species, and populations may reach high densities in developed areas, which can result in contact with humans and pets with potential exposures to the raccoon variant of RV throughout the eastern United States. Understanding the spatial movement of RV by raccoon populations is important for monitoring and refining strategies supporting the landscape-level control and local elimination of this lethal zoonosis. We developed a high-throughput genotyping panel for raccoons based on hundreds of microhaplotypes to identify population structure and genetic diversity relevant to rabies management programs. Throughout the eastern United States, we identified hierarchical population genetic structure with clusters that were connected through isolation-by-distance. We also illustrate that this genotyping approach can be used to support real-time management priorities by identifying the geographic origin of a rabid raccoon that was collected in an area of the United States that had been raccoon RV-free for 8 years. The results from this study and the utility of the microhaplotype panel and genotyping method will provide managers with information on raccoon ecology that can be incorporated into future management decisions.
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Affiliation(s)
- Matthew W. Hopken
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife ServicesNational Wildlife Research CenterFort CollinsColoradoUSA
- Department of Microbiology, Immunology, and PathologyColorado State UniversityFort CollinsColoradoUSA
| | - Antoinette J. Piaggio
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife ServicesNational Wildlife Research CenterFort CollinsColoradoUSA
| | - Zaid Abdo
- Department of Microbiology, Immunology, and PathologyColorado State UniversityFort CollinsColoradoUSA
| | - Richard B. Chipman
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife ServicesNational Rabies Management ProgramConcordNew HampshireUSA
| | - Clara P. Mankowski
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife ServicesNational Wildlife Research CenterFort CollinsColoradoUSA
- Department of Microbiology, Immunology, and PathologyColorado State UniversityFort CollinsColoradoUSA
| | - Kathleen M. Nelson
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife ServicesNational Rabies Management ProgramConcordNew HampshireUSA
| | - Mikaela Samsel Hilton
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife ServicesNational Wildlife Research CenterFort CollinsColoradoUSA
| | - Christine Thurber
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife ServicesNational Rabies Management ProgramConcordNew HampshireUSA
| | - Mirian T. N. Tsuchiya
- Data Science Lab, Office of the Chief Information OfficerSmithsonian InstitutionWashingtonDCUSA
- Center for Conservation GenomicsSmithsonian National Zoo and Conservation Biology InstituteWashingtonDCUSA
| | - Jesús E. Maldonado
- Center for Conservation GenomicsSmithsonian National Zoo and Conservation Biology InstituteWashingtonDCUSA
| | - Amy T. Gilbert
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife ServicesNational Wildlife Research CenterFort CollinsColoradoUSA
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Gilfillan D, Vilander AC, Pan M, Goh YJ, O’Flaherty S, Feng N, Fox BE, Lang C, Greenberg HB, Abdo Z, Barrangou R, Dean GA. Lactobacillus acidophilus Expressing Murine Rotavirus VP8 and Mucosal Adjuvants Induce Virus-Specific Immune Responses. Vaccines (Basel) 2023; 11:1774. [PMID: 38140179 PMCID: PMC10747613 DOI: 10.3390/vaccines11121774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 11/14/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023] Open
Abstract
Rotavirus diarrhea-associated illness remains a major cause of global death in children under five, attributable in part to discrepancies in vaccine performance between high- and low-middle-income countries. Next-generation probiotic vaccines could help bridge this efficacy gap. We developed a novel recombinant Lactobacillus acidophilus (rLA) vaccine expressing rotavirus antigens of the VP8* domain from the rotavirus EDIM VP4 capsid protein along with the adjuvants FimH and FliC. The upp-based counterselective gene-replacement system was used to chromosomally integrate FimH, VP8Pep (10 amino acid epitope), and VP8-1 (206 amino acid protein) into the L. acidophilus genome, with FliC expressed from a plasmid. VP8 antigen and adjuvant expression were confirmed by flow cytometry and Western blot. Rotavirus naïve adult BALB/cJ mice were orally immunized followed by murine rotavirus strain ECWT viral challenge. Antirotavirus serum IgG and antigen-specific antibody-secreting cell responses were detected in rLA-vaccinated mice. A day after the oral rotavirus challenge, fecal antigen shedding was significantly decreased in the rLA group. These results indicate that novel rLA constructs expressing VP8 can be successfully constructed and used to generate modest homotypic protection from rotavirus challenge in an adult murine model, indicating the potential for a probiotic next-generation vaccine construct against human rotavirus.
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Affiliation(s)
- Darby Gilfillan
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA; (D.G.); (A.C.V.); (B.E.F.); (C.L.); (Z.A.)
| | - Allison C. Vilander
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA; (D.G.); (A.C.V.); (B.E.F.); (C.L.); (Z.A.)
| | - Meichen Pan
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC 27695, USA; (M.P.); (Y.J.G.); (S.O.); (R.B.)
| | - Yong Jun Goh
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC 27695, USA; (M.P.); (Y.J.G.); (S.O.); (R.B.)
| | - Sarah O’Flaherty
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC 27695, USA; (M.P.); (Y.J.G.); (S.O.); (R.B.)
| | - Ningguo Feng
- Departments of Medicine and Microbiology and Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA (H.B.G.)
- VA Palo Alto Health Care System, Department of Veterans Affairs, Palo Alto, CA 94304, USA
| | - Bridget E. Fox
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA; (D.G.); (A.C.V.); (B.E.F.); (C.L.); (Z.A.)
| | - Callie Lang
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA; (D.G.); (A.C.V.); (B.E.F.); (C.L.); (Z.A.)
| | - Harry B. Greenberg
- Departments of Medicine and Microbiology and Immunology, School of Medicine, Stanford University, Stanford, CA 94305, USA (H.B.G.)
- VA Palo Alto Health Care System, Department of Veterans Affairs, Palo Alto, CA 94304, USA
| | - Zaid Abdo
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA; (D.G.); (A.C.V.); (B.E.F.); (C.L.); (Z.A.)
| | - Rodolphe Barrangou
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC 27695, USA; (M.P.); (Y.J.G.); (S.O.); (R.B.)
| | - Gregg A. Dean
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA; (D.G.); (A.C.V.); (B.E.F.); (C.L.); (Z.A.)
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Fitzmeyer EA, Gallichotte EN, Weger-Lucarelli J, Kapuscinski ML, Abdo Z, Pyron K, Young MC, Ebel GD. Loss of West Nile virus genetic diversity during mosquito infection due to species-dependent population bottlenecks. iScience 2023; 26:107711. [PMID: 37701570 PMCID: PMC10494182 DOI: 10.1016/j.isci.2023.107711] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/13/2023] [Accepted: 08/23/2023] [Indexed: 09/14/2023] Open
Abstract
Vector competence (VC) refers to the efficiency of pathogen transmission by vectors. Each step in the infection of a mosquito vector constitutes a barrier to transmission that may impose bottlenecks on virus populations. West Nile virus (WNV) is maintained by multiple mosquito species with varying VC. However, the extent to which bottlenecks and VC are linked is poorly understood. Similarly, quantitative analyses of mosquito-imposed bottlenecks on virus populations are limited. We used molecularly barcoded WNV to quantify tissue-associated population bottlenecks in three variably competent WNV vectors. Our results confirm strong population bottlenecks during mosquito infection that are capable of dramatically reshaping virus population structure in a non-selective manner. In addition, we found that mosquitoes with differing VC uniquely shape WNV population structure: highly competent vectors are more likely to contribute to the maintenance of rare viral genotypes. These findings have important implications for arbovirus emergence and evolution.
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Affiliation(s)
- Emily A. Fitzmeyer
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Emily N. Gallichotte
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - James Weger-Lucarelli
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, USA
| | - Marylee L. Kapuscinski
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Zaid Abdo
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Kyra Pyron
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Michael C. Young
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Gregory D. Ebel
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
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Kozhar O, Sitz RA, Woyda R, Legg L, Ibarra Caballero JR, Pearse IS, Abdo Z, Stewart JE. Population genomic analysis of an emerging pathogen Lonsdalea quercina affecting various species of oaks in western North America. Sci Rep 2023; 13:14852. [PMID: 37684300 PMCID: PMC10491777 DOI: 10.1038/s41598-023-41976-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 09/04/2023] [Indexed: 09/10/2023] Open
Abstract
Understanding processes leading to disease emergence is important for effective disease management and prevention of future epidemics. Utilizing whole genome sequencing, we studied the phylogenetic relationship and diversity of two populations of the bacterial oak pathogen Lonsdalea quercina from western North America (Colorado and California) and compared these populations to other Lonsdalea species found worldwide. Phylogenetic analysis separated Colorado and California populations into two Lonsdalea clades, with genetic divergence near species boundaries, suggesting long isolation and populations that differ in genetic structure and distribution and possibly their polyphyletic origin. Genotypes collected from different host species and habitats were randomly distributed within the California cluster. Most Colorado isolates from introduced planted trees, however, were distinct from three isolates collected from a natural stand of Colorado native Quercus gambelii, indicating cryptic population structure. The California identical core genotypes distribution varied, while Colorado identical core genotypes were always collected from neighboring trees. Despite its recent emergence, the Colorado population had higher nucleotide diversity, possibly due to its long presence in Colorado or due to migrants moving with nursery stock. Overall, results suggest independent pathogen emergence in two states likely driven by changes in host-microbe interactions due to ecosystems changes. Further studies are warranted to understand evolutionary relationships among L. quercina from different areas, including the red oak native habitat in northeastern USA.
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Affiliation(s)
- Olga Kozhar
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
| | - Rachael A Sitz
- Davey Resource Group, Inc., Urban & Community Forestry Services, Atascadero, CA, USA
| | - Reed Woyda
- Program of Cell and Molecular Biology, Colorado State University, Fort Collins, CO, USA
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Lillian Legg
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
| | | | - Ian S Pearse
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
| | - Zaid Abdo
- Program of Cell and Molecular Biology, Colorado State University, Fort Collins, CO, USA
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Jane E Stewart
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA.
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Hopken MW, Gilfillan D, Gilbert AT, Piaggio AJ, Hilton MS, Pierce J, Kimball B, Abdo Z. Biodiversity indices and Random Forests reveal the potential for striped skunk (Mephitis mephitis) fecal microbial communities to function as a biomarker for oral rabies vaccination. PLoS One 2023; 18:e0285852. [PMID: 37607164 PMCID: PMC10443867 DOI: 10.1371/journal.pone.0285852] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 04/24/2023] [Indexed: 08/24/2023] Open
Abstract
Wildlife disease surveillance and monitoring poses unique challenges when assessing rates of population vaccination, immunity, or infection prevalence. Non-invasively detected biomarkers can help reduce risk to both animal and field personnel during wildlife disease management activities. In this study, we investigated the utility of fecal microbiome data collected from captive striped skunks (Mephitis mephitis) in predicting rabies virus vaccination and infection status. We sequenced the hypervariable region 4 (V4) of the bacterial 16S gene and estimated alpha and beta diversity across timepoints in three groups of skunks: vaccination then rabies virus infection, sham vaccination then rabies virus infection, and rabies virus infected without vaccination. Alpha diversity did not differ among treatment groups but beta diversity between treatments was statistically significant. The phyla Firmicutes and Proteobacteria were dominant among all samples. Using Random Forests, we identified operational taxonomic units (OTUs) that greatly influenced classification of fecal samples into treatment groups. Each of these OTUs was correlated with fecal volatile organic compounds detected from the samples for companion treatment groups in another study. This research is the first to highlight striped skunk microbiome biodiversity as a vaccination biomarker which pushes the frontier on alternative methods for surveillance and monitoring of vaccination and disease in wildlife populations.
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Affiliation(s)
- Matthew W. Hopken
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, Colorado, United States of America
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Darby Gilfillan
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Amy T. Gilbert
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, Colorado, United States of America
| | - Antoinette J. Piaggio
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, Colorado, United States of America
| | - Mikaela Samsel Hilton
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, Colorado, United States of America
| | - James Pierce
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Bruce Kimball
- Monell Chemical Senses Center, Philadelphia, Pennsylvania, United States of America
| | - Zaid Abdo
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
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Woyda R, Oladeinde A, Endale D, Strickland T, Lawrence JP, Abdo Z. Broiler house environment and litter management practices impose selective pressures on antimicrobial resistance genes and virulence factors of Campylobacter. bioRxiv 2023:2023.02.02.526821. [PMID: 36778422 PMCID: PMC9915665 DOI: 10.1101/2023.02.02.526821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Campylobacter infections are a leading cause of bacterial diarrhea in humans globally. Infections are due to consumption of contaminated food products and are highly associated with chicken meat, with chickens being an important reservoir for Campylobacter. Here, we characterized the genetic diversity of Campylobacter species detected in broiler chicken litter over three consecutive flocks and determined their antimicrobial resistance and virulence factor profiles. Antimicrobial susceptibility testing and whole genome sequencing were performed on Campylobacter jejuni (n = 39) and Campylobacter coli (n = 5) isolates. All C. jejuni isolates were susceptible to all antibiotics tested while C. coli (n =4) were resistant to only tetracycline and harbored the tetracycline-resistant ribosomal protection protein (TetO). Virulence factors differed within and across grow houses but were explained by the isolates' flock cohort, species and multilocus sequence type. Virulence factors involved in the ability to invade and colonize host tissues and evade host defenses were absent from flock cohort 3 C. jejuni isolates as compared to flock 1 and 2 isolates. Our results show that virulence factors and antimicrobial resistance genes differed by the isolates' multilocus sequence type and by the flock cohort they were present in. These data suggest that the house environment and litter management practices performed imposed selective pressures on antimicrobial resistance genes and virulence factors. In particular, the absence of key virulence factors within the final flock cohort 3 isolates suggests litter reuse selected for Campylobacter strains that are less likely to colonize the chicken host.
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Affiliation(s)
- Reed Woyda
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
- Program of Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | | | - Dinku Endale
- Southeast Watershed Research Laboratory, USDA, Tifton, GA, 31793
| | | | | | - Zaid Abdo
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
- Program of Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
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Zwirzitz B, Oladeinde A, Johnson J, Zock G, Milfort MC, Fuller AL, Ghareeb AFA, Foutz JC, Teran JA, Woyda R, Abdo Z, Looft T, Lawrence JP, Cudnik D, Aggrey SE. Temporal dynamics of the cecal and litter microbiome of chickens raised in two separate broiler houses. Front Physiol 2023; 14:1083192. [PMID: 36935743 PMCID: PMC10018173 DOI: 10.3389/fphys.2023.1083192] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 02/20/2023] [Indexed: 03/06/2023] Open
Abstract
In this study, we investigated the dynamics of the ceca and litter microbiome of chickens from post-hatch through pre-harvest. To achieve this, six hundred one-day old Cobb 500 broiler chicks were raised on floor pens for 49 days in two separate houses. We performed short-read and full-length sequencing of the bacterial 16S rRNA gene present in the meconium and in cecal and litter samples collected over the duration of the study. In addition, we determined the antimicrobial resistance (AMR) phenotype of Escherichia coli and Enterococcus spp. isolated from the meconium and the ceca of 49-day old chickens. We monitored the relative humidity, temperature, and ammonia in each house daily and the pH and moisture of litter samples weekly. The overall microbial community structure of the ceca and litter consistently changed throughout the course of the grow-out and correlated with some of the environmental parameters measured (p < 0.05). We found that the ceca and litter microbiome were similar in the two houses at the beginning of the experiment, but over time, the microbial community separated and differed between the houses. When we compared the environmental parameters in the two houses, we found no significant differences in the first half of the growth cycle (day 0-21), but morning temperature, morning humidity, and ammonia significantly differed (p < 0.05) between the two houses from day 22-49. Lastly, the prevalence of AMR in cecal E. coli isolates differed from meconium isolates (p < 0.001), while the AMR phenotype of cecal Enterococcus isolates differed between houses (p < 0.05).
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Affiliation(s)
- Benjamin Zwirzitz
- Department of Food Science and Technology, Institute of Food Science, University of Natural Resources and Life Sciences, Vienna, Austria
- Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Tulln, Austria
| | - Adelumola Oladeinde
- USDA-ARS, U.S. National Poultry Research Center, Athens, GA, United States
- *Correspondence: Adelumola Oladeinde, ; Samuel E. Aggrey,
| | - Jasmine Johnson
- Department of Poultry Science, University of Georgia, Athens, GA, United States
| | - Gregory Zock
- Department of Poultry Science, University of Georgia, Athens, GA, United States
| | - Marie C. Milfort
- Department of Poultry Science, University of Georgia, Athens, GA, United States
| | | | - Ahmed F. A. Ghareeb
- Department of Poultry Science, University of Georgia, Athens, GA, United States
| | - James C. Foutz
- Department of Poultry Science, University of Georgia, Athens, GA, United States
| | - Jose Alexis Teran
- College of Engineering, University of Georgia, Athens, GA, United States
| | - Reed Woyda
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States
- Program of Cell and Molecular Biology, Colorado State University, Fort Collins, CO, United States
| | - Zaid Abdo
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, United States
- Program of Cell and Molecular Biology, Colorado State University, Fort Collins, CO, United States
| | - Torey Looft
- USDA-ARS, National Animal Disease Center, Ames, IA, United States
| | | | - Denice Cudnik
- USDA-ARS, U.S. National Poultry Research Center, Athens, GA, United States
| | - Samuel E. Aggrey
- Department of Poultry Science, University of Georgia, Athens, GA, United States
- *Correspondence: Adelumola Oladeinde, ; Samuel E. Aggrey,
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11
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Ullal TV, Lakin S, Gallagher B, Sbardellati N, Abdo Z, Twedt DC. Demographic and histopathologic features of dogs with abnormally high concentrations of hepatic copper. J Vet Intern Med 2022; 36:2016-2027. [DOI: 10.1111/jvim.16580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Affiliation(s)
| | - Steven Lakin
- Colorado State University Fort Collins Colorado USA
| | | | | | - Zaid Abdo
- Colorado State University Fort Collins Colorado USA
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Fox BE, Vilander AC, Gilfillan D, Dean GA, Abdo Z. Oral Vaccination Using a Probiotic Vaccine Platform Combined with Prebiotics Impacts Immune Response and the Microbiome. Vaccines (Basel) 2022; 10:vaccines10091465. [PMID: 36146543 PMCID: PMC9504555 DOI: 10.3390/vaccines10091465] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 08/29/2022] [Accepted: 08/31/2022] [Indexed: 11/26/2022] Open
Abstract
Unique to mucosal vaccination is the reciprocal influence of the microbiome and mucosal immune responses, where the immune system is constantly balancing between the clearance of pathogens and the tolerance of self-antigen, food, and the microbiota. Secretory IgA plays a major role in maintaining the homeostasis of a healthy gut microbiome. Natural polyreactive IgA often coats members of the commensal microbiota to aid in their colonization, while high-affinity specific IgA binds to pathogens resulting in their clearance. We developed a probiotic-based mucosal vaccination platform using the bacterium Lactobacillus acidophilus (rLA) with the potential to influence this balance in the IgA coating. In this study, we sought to determine whether repeated administration of rLA alters the host intestinal microbial community due to the immune response against the rLA vaccine. To address this, IgA-seq was employed to characterize shifts in IgA-bound bacterial populations. Additionally, we determined whether using rice bran as a prebiotic would influence the immunogenicity of the vaccine and/or IgA-bound bacterial populations. Our results show that the prebiotic influenced the kinetics of rLA antibody induction and that the rLA platform did not cause lasting disturbances to the microbiome.
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McClure KM, Bastille‐Rousseau G, Davis AJ, Stengel CA, Nelson KM, Chipman RB, Wittemyer G, Abdo Z, Gilbert AT, Pepin KM. Accounting for animal movement improves vaccination strategies against wildlife disease in heterogeneous landscapes. Ecol Appl 2022; 32:e2568. [PMID: 35138667 PMCID: PMC9285612 DOI: 10.1002/eap.2568] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 08/28/2021] [Accepted: 10/15/2021] [Indexed: 06/14/2023]
Abstract
Oral baiting is used to deliver vaccines to wildlife to prevent, control, and eliminate infectious diseases. A central challenge is how to spatially distribute baits to maximize encounters by target animal populations, particularly in urban and suburban areas where wildlife such as raccoons (Procyon lotor) are abundant and baits are delivered along roads. Methods from movement ecology that quantify movement and habitat selection could help to optimize baiting strategies by more effectively targeting wildlife populations across space. We developed a spatially explicit, individual-based model of raccoon movement and oral rabies vaccine seroconversion to examine whether and when baiting strategies that match raccoon movement patterns perform better than currently used baiting strategies in an oral rabies vaccination zone in greater Burlington, Vermont, USA. Habitat selection patterns estimated from locally radio-collared raccoons were used to parameterize movement simulations. We then used our simulations to estimate raccoon population rabies seroprevalence under currently used baiting strategies (actual baiting) relative to habitat selection-based baiting strategies (habitat baiting). We conducted simulations on the Burlington landscape and artificial landscapes that varied in heterogeneity relative to Burlington in the proportion and patch size of preferred habitats. We found that the benefits of habitat baiting strongly depended on the magnitude and variability of raccoon habitat selection and the degree of landscape heterogeneity within the baiting area. Habitat baiting improved seroprevalence over actual baiting for raccoons characterized as habitat specialists but not for raccoons that displayed weak habitat selection similar to radiocollared individuals, except when baits were delivered off roads where preferred habitat coverage and complexity was more pronounced. In contrast, in artificial landscapes with either more strongly juxtaposed favored habitats and/or higher proportions of favored habitats, habitat baiting performed better than actual baiting, even when raccoons displayed weak habitat preferences and where baiting was constrained to roads. Our results suggest that habitat selection-based baiting could increase raccoon population seroprevalence in urban-suburban areas, where practical, given the heterogeneity and availability of preferred habitat types in those areas. Our novel simulation approach provides a flexible framework to test alternative baiting strategies in multiclass landscapes to optimize bait-distribution strategies.
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Affiliation(s)
- Katherine M. McClure
- National Wildlife Research Center, Wildlife Services, Animal and Plant Health Inspection ServiceUnited States Department of AgricultureFort CollinsColoradoUSA
- Department of Microbiology, Immunology, and PathologyColorado State UniversityFort CollinsColoradoUSA
- Present address:
Hawai‘i Cooperative Studies UnitUniversity of Hawai‘i at HiloHiloHawai‘iUSA
| | - Guillaume Bastille‐Rousseau
- National Wildlife Research Center, Wildlife Services, Animal and Plant Health Inspection ServiceUnited States Department of AgricultureFort CollinsColoradoUSA
- Cooperative Wildlife Research LaboratorySouthern Illinois UniversityCarbondaleIllinoisUSA
| | - Amy J. Davis
- National Wildlife Research Center, Wildlife Services, Animal and Plant Health Inspection ServiceUnited States Department of AgricultureFort CollinsColoradoUSA
| | - Carolyn A. Stengel
- Wildlife Services, Animal and Plant Health Inspection ServiceUnited States Department of AgricultureConcordNew HampshireUSA
| | - Kathleen M. Nelson
- National Rabies Management Program, Wildlife Services, Animal and Plant Health Inspection ServiceUnited States Department of AgricultureConcordNew HampshireUSA
| | - Richard B. Chipman
- National Rabies Management Program, Wildlife Services, Animal and Plant Health Inspection ServiceUnited States Department of AgricultureConcordNew HampshireUSA
| | - George Wittemyer
- Fish, Wildlife, and Conservation BiologyColorado State UniversityFort CollinsColoradoUSA
| | - Zaid Abdo
- Department of Microbiology, Immunology, and PathologyColorado State UniversityFort CollinsColoradoUSA
| | - Amy T. Gilbert
- National Wildlife Research Center, Wildlife Services, Animal and Plant Health Inspection ServiceUnited States Department of AgricultureFort CollinsColoradoUSA
| | - Kim M. Pepin
- National Wildlife Research Center, Wildlife Services, Animal and Plant Health Inspection ServiceUnited States Department of AgricultureFort CollinsColoradoUSA
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14
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Fox BE, Vilander A, Abdo Z, Dean GA. NOD2 signaling in CD11c + cells is critical for humoral immune responses during oral vaccination and maintaining the gut microbiome. Sci Rep 2022; 12:8491. [PMID: 35589853 PMCID: PMC9119386 DOI: 10.1038/s41598-022-12469-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 05/11/2022] [Indexed: 11/09/2022] Open
Abstract
Nucleotide-binding oligomerization domain containing 2 (NOD2) is a critical regulator of immune responses within the gastrointestinal tract. This innate immune receptor is expressed by several cell types, including both hematopoietic and nonhematopoietic cells within the gastrointestinal tract. Vaccination targeting the gastrointestinal mucosal immune system is especially difficult due to both physical and mechanistic barriers to reaching inductive sites. The use of lactic acid bacteria is appealing due to their ability to persist within harsh conditions, expression of selected adjuvants, and manufacturing advantages. Recombinant Lactobacillus acidophilus (rLA) has shown great promise in activating the mucosal immune response with minimal impacts on the resident microbiome. To better classify the kinetics of mucosal vaccination with rLA, we utilized mice harboring knockouts of NOD2 expression specifically within CD11c + cells. The results presented here show that NOD2 signaling in CD11c + cells is necessary for mounting a humoral immune response against exogenous antigens expressed by rLA. Additionally, disruption of NOD2 signaling in these cells results in an altered bacterial microbiome profile in both control mice and mice receiving L. acidophilus strain NCK1895 and vaccine strain LaOVA.
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Affiliation(s)
- B E Fox
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA.
| | - A Vilander
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Z Abdo
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA.
| | - G A Dean
- Department of Microbiology, Immunology and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA.
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15
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Oladeinde A, Abdo Z, Zwirzitz B, Woyda R, Lakin SM, Press MO, Cox NA, Thomas JC, Looft T, Rothrock MJ, Zock G, Plumblee Lawrence J, Cudnik D, Ritz C, Aggrey SE, Liachko I, Grove JR, Wiersma C. Litter Commensal Bacteria Can Limit the Horizontal Gene Transfer of Antimicrobial Resistance to Salmonella in Chickens. Appl Environ Microbiol 2022; 88:e0251721. [PMID: 35416680 PMCID: PMC9107613 DOI: 10.1128/aem.02517-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 03/06/2022] [Indexed: 12/15/2022] Open
Abstract
Fostering a "balanced" gut microbiome through the administration of beneficial microbes that can competitively exclude pathogens has gained a lot of attention and use in human and animal medicine. However, little is known about how microbes affect the horizontal gene transfer of antimicrobial resistance (AMR). To shed more light on this question, we challenged neonatal broiler chicks raised on reused broiler chicken litter-a complex environment made up of decomposing pine shavings, feces, uric acid, feathers, and feed-with Salmonella enterica serovar Heidelberg (S. Heidelberg), a model pathogen. Neonatal chicks challenged with S. Heidelberg and raised on reused litter were more resistant to S. Heidelberg cecal colonization than chicks grown on fresh litter. Furthermore, chicks grown on reused litter were at a lower risk of colonization with S. Heidelberg strains that encoded AMR on IncI1 plasmids. We used 16S rRNA gene sequencing and shotgun metagenomics to show that the major difference between chicks grown on fresh litter and those grown on reused litter was the microbiome harbored in the litter and ceca. The microbiome of reused litter samples was more uniform and enriched in functional pathways related to the biosynthesis of organic and antimicrobial molecules than that in fresh litter samples. We found that Escherichia coli was the main reservoir of plasmids encoding AMR and that the IncI1 plasmid was maintained at a significantly lower copy per cell in reused litter compared to fresh litter. These findings support the notion that commensal bacteria play an integral role in the horizontal transfer of plasmids encoding AMR to pathogens like Salmonella. IMPORTANCE Antimicrobial resistance spread is a worldwide health challenge, stemming in large part from the ability of microorganisms to share their genetic material through horizontal gene transfer. To address this issue, many countries and international organizations have adopted a One Health approach to curtail the proliferation of antimicrobial-resistant bacteria. This includes the removal and reduction of antibiotics used in food animal production and the development of alternatives to antibiotics. However, there is still a significant knowledge gap in our understanding of how resistance spreads in the absence of antibiotic selection and the role commensal bacteria play in reducing antibiotic resistance transfer. In this study, we show that commensal bacteria play a key role in reducing the horizontal gene transfer of antibiotic resistance to Salmonella, provide the identity of the bacterial species that potentially perform this function in broiler chickens, and also postulate the mechanism involved.
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Affiliation(s)
| | - Zaid Abdo
- Department of Microbiology, Immunology and Pathology, Colorado State Universitygrid.47894.36, Fort Collins, Colorado, USA
| | - Benjamin Zwirzitz
- Institute of Food Science, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Reed Woyda
- Department of Microbiology, Immunology and Pathology, Colorado State Universitygrid.47894.36, Fort Collins, Colorado, USA
| | - Steven M Lakin
- Department of Microbiology, Immunology and Pathology, Colorado State Universitygrid.47894.36, Fort Collins, Colorado, USA
| | | | - Nelson A Cox
- U.S. National Poultry Research Center, USDA-ARS, Athens, Georgia, USA
| | - Jesse C Thomas
- Division of STD Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Torey Looft
- National Animal Disease Center, USDA-ARS, Ames, Iowa, USA
| | | | - Gregory Zock
- Department of Poultry Science, University of Georgia, Athens, Georgia, USA
| | | | - Denice Cudnik
- U.S. National Poultry Research Center, USDA-ARS, Athens, Georgia, USA
| | - Casey Ritz
- Department of Poultry Science, University of Georgia, Athens, Georgia, USA
| | - Samuel E Aggrey
- Department of Poultry Science, University of Georgia, Athens, Georgia, USA
| | | | | | - Crystal Wiersma
- Department of Microbiology, Immunology and Pathology, Colorado State Universitygrid.47894.36, Fort Collins, Colorado, USA
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16
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Vilander AC, Hess A, Abdo Z, Ibrahim H, Doumbia L, Douyon S, Koné K, Boré A, Zambrana LE, Vilchez S, Koita O, Ryan EP. A Randomized Controlled Trial of Dietary Rice Bran Intake on Microbiota Diversity, Enteric Dysfunction, and Fecal Secretory IgA in Malian and Nicaraguan Infants. J Nutr 2022; 152:1792-1800. [PMID: 35441218 PMCID: PMC9258582 DOI: 10.1093/jn/nxac087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/09/2021] [Accepted: 04/11/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Malnutrition and diarrhea are leading causes of death in children aged <5 y. Rice bran is a nutrient-dense prebiotic available globally. OBJECTIVES The objective of this secondary analysis was to evaluate the effects of daily rice bran supplementation on environmental enteric dysfunction (EED) markers, total fecal secretory IgA (sIgA), and microbiota in infants at high risk of malnutrition. METHODS Six-month-old Malian and Nicaraguan infants were randomly assigned to control or daily rice bran supplementation cohorts (1 to 5 g/d). Feces were collected monthly for 6 mo to evaluate fecal sIgA, markers of EED, and microbiota diversity. Statistical methods included linear mixed models, generalized mixed models, Spearman correlation, and Wilcoxon rank-sum tests. RESULTS Six-month-old Malian infants had significantly elevated sIgA (4.0× higher, P < 0.001), fecal myeloperoxidase (31.6× higher, P < 0.001), fecal α1-antitrypsin (1.8× higher, P = 0.006), and lower fecal neopterin (0.13× higher, P < 0.001) than the age-matched Nicaraguan infants. In the Nicaraguan rice bran cohort from 6 to 12 mo of age, there was a significant decrease in sIgA concentrations (0.4×, P < 0.05) and a correlation between sIgA and the EED marker α1-antitrypsin (0.523, P < 0.0001) at 12 mo of age. In Malian infants, daily rice bran ingestion resulted in decreased EED scores (0.71×, P = 0.02) and a stable sIgA concentration over time. The rice bran group of Malian infants also had correlation between sIgA and the EED marker neopterin (0.544, P < 0.001) at 12 mo of age and a significant (P < 0.05) increase in microbiota α-diversity at a younger age (9 mo with rice bran compared with 10 mo in control group), which supports earlier microbiota maturation. CONCLUSIONS These results support rice bran as a functional food ingredient targeting gut mucosa in children at high-risk of malnutrition.
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Affiliation(s)
- Allison C Vilander
- Department of Microbiology, Immunology, and Pathology; College of Veterinary Medicine and Veterinary Science; Colorado State University, Fort Collins, CO, USA
| | - Ann Hess
- Department of Statistics, Colorado State University, Fort Collins, CO, USA
| | - Zaid Abdo
- Department of Microbiology, Immunology, and Pathology; College of Veterinary Medicine and Veterinary Science; Colorado State University, Fort Collins, CO, USA
| | - Hend Ibrahim
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA,Department of Medical Biochemistry, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Lassina Doumbia
- Laboratoire de Biologie Moléculaire Appliquée, Campus de Badalabougou, Université des Sciences, des Techniques et des Technologies de Bamako, Bamako, Mali
| | - Seydou Douyon
- Laboratoire de Biologie Moléculaire Appliquée, Campus de Badalabougou, Université des Sciences, des Techniques et des Technologies de Bamako, Bamako, Mali
| | - Karim Koné
- Laboratoire de Biologie Moléculaire Appliquée, Campus de Badalabougou, Université des Sciences, des Techniques et des Technologies de Bamako, Bamako, Mali
| | - Abdoulaye Boré
- Laboratoire de Biologie Moléculaire Appliquée, Campus de Badalabougou, Université des Sciences, des Techniques et des Technologies de Bamako, Bamako, Mali
| | - Luis E Zambrana
- Center of Infectious Diseases, Department of Microbiology and Parasitology, Faculty of Medicine Sciences, National Autonomous University of Nicaragua, Leόn, Nicaragua
| | - Samuel Vilchez
- Center of Infectious Diseases, Department of Microbiology and Parasitology, Faculty of Medicine Sciences, National Autonomous University of Nicaragua, Leόn, Nicaragua
| | - Ousmane Koita
- Laboratoire de Biologie Moléculaire Appliquée, Campus de Badalabougou, Université des Sciences, des Techniques et des Technologies de Bamako, Bamako, Mali
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17
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Cummings JE, Abdo Z, Slayden RA. OUP accepted manuscript. JAC Antimicrob Resist 2022; 4:dlac028. [PMID: 35350133 PMCID: PMC8947225 DOI: 10.1093/jacamr/dlac028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 02/27/2022] [Indexed: 12/03/2022] Open
Abstract
Background NIAID has a programme for testing drug candidates against biodefense and emerging bacterial pathogens that uses defined strain panels consisting of standard laboratory reference strains and strains of clinical origin. Objectives The current studies were performed to assess the activity of standard-of-care drugs, determine benchmark criteria for new investigational antibacterial candidate prioritization and identify reduced non-redundant strain panels for candidate performance classification. Methods The susceptibilities of each strain in the screening panels to 40 standard-of-care drugs and clinical drug combinations were determined by percentage growth inhibition using multiple concentrations, a method commonly used in efficient high-throughput screening efforts. The drug susceptibility of each strain was categorized based on interpretive criteria to benchmark the activity of each standard-of-care drug and drug combination, followed by confirmation of select active drugs. Exact match and clustering analyses defined focused non-redundant species and pan-species screening panels. Results This process revealed a broad spectrum of susceptibilities among strains in each species, with important differences between the standard laboratory reference strains and strains of clinical origin. Exact match and clustering analyses identified subsets of non-redundant strains that can more efficiently classify drug activity resulting in individual species screening panels, a pan-species screening panel and a pan-species maximum resistance panel. Conclusions This study resulted in improved non-redundant species screening panels for benchmarking the performance of new investigational antibacterial candidates with the greatest potential for efficacy against clinically relevant Category A and B priority and emerging pathogens.
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Affiliation(s)
- Jason E. Cummings
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, 80523-2025 CO, USA
| | - Zaid Abdo
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, 80523-2025 CO, USA
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18
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Oh KP, Shiels AB, Shiels L, Blondel DV, Campbell KJ, Saah JR, Lloyd AL, Thomas PQ, Gould F, Abdo Z, Godwin JR, Piaggio AJ. Population genomics of invasive rodents on islands: Genetic consequences of colonization and prospects for localized synthetic gene drive. Evol Appl 2021; 14:1421-1435. [PMID: 34025776 PMCID: PMC8127709 DOI: 10.1111/eva.13210] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 02/15/2021] [Accepted: 02/16/2021] [Indexed: 12/22/2022] Open
Abstract
Introduced rodent populations pose significant threats worldwide, with particularly severe impacts on islands. Advancements in genome editing have motivated interest in synthetic gene drives that could potentially provide efficient and localized suppression of invasive rodent populations. Application of such technologies will require rigorous population genomic surveys to evaluate population connectivity, taxonomic identification, and to inform design of gene drive localization mechanisms. One proposed approach leverages the predicted shifts in genetic variation that accompany island colonization, wherein founder effects, genetic drift, and island-specific selection are expected to result in locally fixed alleles (LFA) that are variable in neighboring nontarget populations. Engineering of guide RNAs that target LFA may thus yield gene drives that spread within invasive island populations, but would have limited impacts on nontarget populations in the event of an escape. Here we used pooled whole-genome sequencing of invasive mouse (Mus musculus) populations on four islands along with paired putative source populations to test genetic predictions of island colonization and characterize locally fixed Cas9 genomic targets. Patterns of variation across the genome reflected marked reductions in allelic diversity in island populations and moderate to high degrees of differentiation from nearby source populations despite relatively recent colonization. Locally fixed Cas9 sites in female fertility genes were observed in all island populations, including a small number with multiplexing potential. In practice, rigorous sampling of presumptive LFA will be essential to fully assess risk of resistance alleles. These results should serve to guide development of improved, spatially limited gene drive design in future applications.
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Affiliation(s)
- Kevin P. Oh
- National Wildlife Research CenterUSDA APHIS Wildlife ServicesFort CollinsColoradoUSA
- Department of Microbiology, Immunology and PathologyColorado State UniversityFort CollinsColoradoUSA
| | - Aaron B. Shiels
- National Wildlife Research CenterUSDA APHIS Wildlife ServicesFort CollinsColoradoUSA
| | - Laura Shiels
- National Wildlife Research CenterUSDA APHIS Wildlife ServicesFort CollinsColoradoUSA
| | - Dimitri V. Blondel
- Department of Biological SciencesNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Karl J. Campbell
- Island ConservationPuerto AyoraEcuador
- School of Agriculture and Food SciencesThe University of QueenslandGattonQueenslandAustralia
| | - J. Royden Saah
- Island ConservationPuerto AyoraEcuador
- Genetic Engineering and Society CenterNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Alun L. Lloyd
- Genetic Engineering and Society CenterNorth Carolina State UniversityRaleighNorth CarolinaUSA
- Biomathematics Graduate Program and Department of MathematicsNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Paul Q. Thomas
- The Robinson Research Institute and School of MedicineThe University of AdelaideAdelaideSouth AustraliaAustralia
| | - Fred Gould
- Genetic Engineering and Society CenterNorth Carolina State UniversityRaleighNorth CarolinaUSA
- Department of Entomology and Plant PathologyNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Zaid Abdo
- Department of Microbiology, Immunology and PathologyColorado State UniversityFort CollinsColoradoUSA
| | - John R. Godwin
- Department of Biological SciencesNorth Carolina State UniversityRaleighNorth CarolinaUSA
- Genetic Engineering and Society CenterNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Antoinette J. Piaggio
- National Wildlife Research CenterUSDA APHIS Wildlife ServicesFort CollinsColoradoUSA
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Hopken MW, Reyes-Torres LJ, Scavo N, Piaggio AJ, Abdo Z, Taylor D, Pierce J, Yee DA. Temporal and Spatial Blood Feeding Patterns of Urban Mosquitoes in the San Juan Metropolitan Area, Puerto Rico. Insects 2021; 12:insects12020129. [PMID: 33540671 PMCID: PMC7913113 DOI: 10.3390/insects12020129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/25/2021] [Accepted: 01/29/2021] [Indexed: 11/21/2022]
Abstract
Simple Summary Understanding the biodiversity of urban ecosystems is critical for management of invasive and pest species, conserving native species, and disease control. Mosquitoes (Culicidae) are ubiquitous and abundant in urban ecosystems, and rely on blood meals taken from vertebrates. We used DNA from freshly blood-fed mosquitoes to characterize the diversity of vertebrate host species in the San Juan Metropolitan Area, Puerto Rico. We collected two mosquito species that fed on a variety of vertebrates. Culex quinquefasciatus fed on 17 avian taxa (81.2% of blood meals), seven mammalian taxa (17.9%), and one reptilian taxon (0.85%). Aedes aegypti blood meals were from a less diverse group, with two avian taxa (11.1%) and three mammalian taxa (88.9%) identified. Domestic chickens dominated the blood meals of Cx. quinquefasciatus, both temporally and spatially, and no statistically significant shift from birds to mammals was detected. The species we detected from the mosquito blood meals provided a snapshot of the vertebrate community in the San Juan Metropolitan Area, most of which were domestic species. However, we also identified a variety of native and nonnative wild species. These results add knowledge about potential ecological factors that impact vector-borne disease management in urban habitats. Abstract Urban ecosystems are a patchwork of habitats that host a broad diversity of animal species. Insects comprise a large portion of urban biodiversity which includes many pest species, including those that transmit pathogens. Mosquitoes (Diptera: Culicidae) inhabit urban environments and rely on sympatric vertebrate species to complete their life cycles, and in this process transmit pathogens to animals and humans. Given that mosquitoes feed upon vertebrates, they can also act as efficient samplers that facilitate detection of vertebrate species that utilize urban ecosystems. In this study, we analyzed DNA extracted from mosquito blood meals collected temporally in multiple neighborhoods of the San Juan Metropolitan Area, Puerto Rico to evaluate the presence of vertebrate fauna. DNA was collected from 604 individual mosquitoes that represented two common urban species, Culex quinquefasciatus (n = 586) and Aedes aegypti (n = 18). Culex quinquefasciatus fed on 17 avian taxa (81.2% of blood meals), seven mammalian taxa (17.9%), and one reptilian taxon (0.85%). Domestic chickens dominated these blood meals both temporally and spatially, and no statistically significant shift from birds to mammals was detected. Aedes aegypti blood meals were from a less diverse group, with two avian taxa (11.1%) and three mammalian taxa (88.9%) identified. The blood meals we identified provided a snapshot of the vertebrate community in the San Juan Metropolitan Area and have potential implications for vector-borne pathogen transmission.
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Affiliation(s)
- Matthew W. Hopken
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA; (Z.A.); (J.P.)
- United States Department of Agriculture National Wildlife Research Center, Fort Collins, CO 80521, USA; (A.J.P.); (D.T.)
- Correspondence:
| | - Limarie J. Reyes-Torres
- School of Biological, Environmental, & Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA; (L.J.R.-T.); (N.S.); (D.A.Y.)
| | - Nicole Scavo
- School of Biological, Environmental, & Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA; (L.J.R.-T.); (N.S.); (D.A.Y.)
| | - Antoinette J. Piaggio
- United States Department of Agriculture National Wildlife Research Center, Fort Collins, CO 80521, USA; (A.J.P.); (D.T.)
| | - Zaid Abdo
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA; (Z.A.); (J.P.)
| | - Daniel Taylor
- United States Department of Agriculture National Wildlife Research Center, Fort Collins, CO 80521, USA; (A.J.P.); (D.T.)
| | - James Pierce
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA; (Z.A.); (J.P.)
| | - Donald A. Yee
- School of Biological, Environmental, & Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA; (L.J.R.-T.); (N.S.); (D.A.Y.)
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Geldert C, Abdo Z, Stewart JE, H S A. Dietary supplementation with phytochemicals improves diversity and abundance of honey bee gut microbiota. J Appl Microbiol 2020; 130:1705-1720. [PMID: 33058297 DOI: 10.1111/jam.14897] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 09/21/2020] [Accepted: 10/10/2020] [Indexed: 12/20/2022]
Abstract
AIM Determine the impact of beneficial phytochemicals on diversity and abundance of the gut microbiome in the honey bee (Apis mellifera). METHODS AND RESULTS Eight-day-old honey bee workers were fed 25 ppm of phytochemical (caffeine, gallic acid, p-coumaric acid or kaempferol) in 20% sucrose. Guts of bees collected at 3 and 6 days were excised and subjected to next-generation sequencing for bacterial 16S and fungal ITS regions. Although phytochemical supplementation fostered gut microbial diversity and abundance, the patterns differed between phytochemicals and there was a temporal stabilization of the bacterial community. While bacterial and fungal communities responded differently, all phytochemical treatments displayed increased abundance of the most represented bacterial genera, Snodgrassella sp. and Lactobacillus sp. CONCLUSIONS Phytochemical supplementation improves gut microbial diversity and abundance, reiterating the need for diverse habitats that provide bees with access to pollen and nectar rich in these micronutrients. Diverse gut microbiota can provide a strong line of defense for bees against biotic stressors while improving worker bee lifespan. SIGNIFICANCE AND IMPACT OF THE STUDY This is the first report on the impact of phytochemical supplementation on gut microbiota in honey bees and these findings have implications for strategic hive management through standardization of effective phytochemical and probiotic feed supplements.
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Affiliation(s)
- C Geldert
- College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Z Abdo
- College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - J E Stewart
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, USA
| | - Arathi H S
- USDA/ARS, WRRC Invasive Species and Pollinator Health Research Unit, Davis, CA, USA
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21
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Radwan S, Gilfillan D, Eklund B, Radwan HM, El Menofy NG, Lee J, Kapuscinski M, Abdo Z. A comparative study of the gut microbiome in Egyptian patients with Type I and Type II diabetes. PLoS One 2020; 15:e0238764. [PMID: 32903276 PMCID: PMC7480833 DOI: 10.1371/journal.pone.0238764] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 08/24/2020] [Indexed: 12/12/2022] Open
Abstract
INTRODUCTION Diabetes remains a growing public health concern in Egypt, as prevalence of Type II diabetes (TIID) has nearly tripled there in the last two decades. Egypt was ranked ninth worldwide in number of diabetes cases, with prevalence of 15.56% among adults. Recent studies have proposed that disturbance of gut microbiota could influence TIID development and indicated associations between a reduced diversity in microbiomes and Type I diabetes (TID). In the present study, we investigated the composition and abundance of the bacterial microbiome in disease state (TID and TIID) of Egyptian patients. Our goal in this study was to characterize features of the gut microbiota and possible differences associated with TID and TIID in this population. METHODS DNA was extracted from fecal samples taken from 22 TID and 18 TIID outpatients of Al-Hussein hospital, Cairo, Egypt. 16S rRNA amplicon sequencing was used to characterize the bacterial taxa and these reads were processed using the software mothur with analysis utilizing packages vegan, phyloseq and metagenomSeq in R. RESULTS AND CONCLUSIONS Our results highlighted a significant increase in abundance of Gram negative, potentially opportunistic pathogenic taxa (Pseudomonas, Prevotella) in all diabetic groups, compared to the control. Lipopolysccharide (LPS), a component of the gram-negative bacterial wall, can activate local immune response and may result in low-grade systemic inflammation contributing to insulin resistance. The gram-positive Gemella, which is associated with increased risk to diabetes, also had a significant increase in abundance in all diabetic groups, compared to the control. In contrast, the commensal bacterial taxa Turicibacter, Terrisporobacter and Clostridium were found to be more abundant in the control group than in TID. Further studies are needed to understand the role of these taxa in health and disease. Lower Richness and low Shannon diversity, though not statistically significant, were observed for TID subjects with no glucose control and with onset of liver disease or hypertension compared to other subjects. In addition, large variation in alpha diversity within the control group could also be observed. Future studies will include larger samples sizes to further elucidate these findings, as well as possible metagenomic studies to examine the intriguing function of significant microbes.
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Affiliation(s)
- Sahar Radwan
- Microbiology and Immunology Department, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt
| | - Darby Gilfillan
- Department of Microbiology Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Bridget Eklund
- Department of Microbiology Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Hend M. Radwan
- Microbiology and Immunology Department, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt
| | - Nagwan G. El Menofy
- Microbiology and Immunology Department, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt
| | - Justin Lee
- Department of Microbiology Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Marylee Kapuscinski
- Department of Microbiology Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Zaid Abdo
- Department of Microbiology Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
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22
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Hopken MW, Piaggio AJ, Pabilonia KL, Pierce J, Anderson T, Pierce C, Abdo Z. Population genomic transformations induced by isolation of wild bird avian influenza viruses (Orthomyxoviridae) in embryonated chicken eggs. Infect Genet Evol 2020; 90:104505. [PMID: 32827730 DOI: 10.1016/j.meegid.2020.104505] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/09/2020] [Accepted: 08/13/2020] [Indexed: 12/21/2022]
Abstract
Isolation and cultivation of wild-type viruses in model organism cells or tissues is standard practice in virology. Oftentimes, the virus host species is distantly related to the species from which the culture system was developed. Thus, virus culture in these tissues and cells basically constitutes a host jump, which can lead to genomic changes through genetic drift and/or adaptation to the culture system. We directly sequenced 70 avian influenza virus (Orthomyxoviridae) genomes from oropharyngeal/cloacal swabs collected from wild bird species and paired virus isolates propagated from the same samples following isolation in specific-pathogen-free embryonated chicken eggs. The data were analyzed using population genetic approaches including evaluation of single nucleotide polymorphism (SNP) frequencies and divergence with pooled-sequencing analyses, consensus sequence placement in neighbor-joining trees, and haplotype reconstruction and networks. We found that propagation of virus in eggs leads to skewed SNP mutation spectra with some SNPs going to fixation. Both synonymous and nonsynonmous SNP frequencies shifted. We found multiple consensus sequences that differed between the swabs and the isolates, with some sequences from the same sample falling into divergent genetic clusters. Twenty of 23 coinfections detected had different dominant subtypes following virus isolation, thus sequences from both the swab and isolate were needed to obtain full subtype data. Haplotype networks revealed haplotype frequency shifts and the appearance or loss of low-frequency haplotypes following isolation. The results from this study revealed that isolation of wild bird avian influenza viruses in chicken eggs leads to skewed populations that are different than the input populations. Consensus sequence changes from virus isolation can lead to flawed phylogenetic inferences, and subtype detection is biased. These results suggest that for genomic studies of wild bird influenza viruses the biological field should move away from chicken egg isolation towards directly sequencing the virus from host samples.
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Affiliation(s)
- Matthew W Hopken
- Department of Microbiology, Immunology, and Pathology, College of Veterinary and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA; United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, CO 80521, USA.
| | - Antoinette J Piaggio
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, CO 80521, USA
| | - Kristy L Pabilonia
- Department of Microbiology, Immunology, and Pathology, College of Veterinary and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA; Veterinary Diagnostics Laboratories, College of Veterinary and Biomedical Sciences, Colorado State University, Fort Collins, CO 80526, USA
| | - James Pierce
- Department of Microbiology, Immunology, and Pathology, College of Veterinary and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Theodore Anderson
- Veterinary Diagnostics Laboratories, College of Veterinary and Biomedical Sciences, Colorado State University, Fort Collins, CO 80526, USA
| | - Courtney Pierce
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, CO 80521, USA
| | - Zaid Abdo
- Department of Microbiology, Immunology, and Pathology, College of Veterinary and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA
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Bucher MG, Zwirzitz B, Oladeinde A, Cook K, Plymel C, Zock G, Lakin S, Aggrey SE, Ritz C, Looft T, Lipp E, Agga GE, Abdo Z, Sistani KR. Reused poultry litter microbiome with competitive exclusion potential against Salmonella Heidelberg. J Environ Qual 2020; 49:869-881. [PMID: 33016484 DOI: 10.1002/jeq2.20081] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 03/20/2020] [Accepted: 04/03/2020] [Indexed: 05/24/2023]
Abstract
The success of poultry litter reuse in U.S. poultry production can be attributed to the efficient treatment methods used by producers during downtimes (the time lapse between consecutive flocks, during which the broiler house is empty). During this period, reused litter may be decaked, tilled/windrowed, or treated with acid-based amendments to reduce ammonia and bacteria levels. Competitive exclusion, pH, and temperature are proposed factors that influence the level of pathogens and the overall litter microbiome during downtimes. We previously reported on the bacterial genetic factors associated with the fitness of two strains of Salmonella enterica serovar Heidelberg (SH) incubated for 14 d in reused litter. Here, we investigated the physicochemical parameters and the microbiome of the litter correlating with SH abundance during this period. We used 16S ribosomal RNA gene sequencing to determine the litter microbiome and whole genome sequencing to characterize bacteria with competitive exclusion potential against SH. The β diversity of the litter microbiome was significantly affected by the duration of incubation, microcosm, and microcosm plus Heidelberg strain combinations. In addition, β diversity was significantly affected by litter parameters, including NH4 , pH, moisture, water activity, and aluminum. The major phyla observed in the reused litter throughout the 14-d incubation experiment were Firmicutes and Actinobacteria, although their abundance differed by microcosm and time. Amplicon-specific variants homologous to the members of the genera Nocardiopsis and Lentibacillus and the family Bacillaceae_2 were found to significantly correlate with the abundance of Salmonella. A consortium of Bacillus subtilis strains isolated from the litter microcosms reduced the growth of SH in vitro.
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Affiliation(s)
| | - Benjamin Zwirzitz
- Institute of Food Safety, Food Technology and Veterinary Public Health, Univ. of Veterinary Medicine, Vienna, 1210, Austria
- Austrian Competence Centre for Feed and Food Quality, Safety and Innovation FFoQSI GmbH, Tulln, 3430, Austria
| | | | - Kimberly Cook
- USDA-ARS, U.S. National Poultry Research Center, Athens, GA, USA
| | - Caroline Plymel
- Environmental Health Sciences Dep., Univ. of Georgia, Athens, GA, 30602, USA
| | - Gregory Zock
- USDA-ARS, U.S. National Poultry Research Center, Athens, GA, USA
| | - Steven Lakin
- Dep. of Microbiology, Immunology and Pathology, Colorado State Univ., Fort Collins, CO, 80523, USA
| | - Samuel E Aggrey
- Dep. of Poultry Science, Univ. of Georgia, Athens, GA, 30602, USA
| | - Casey Ritz
- Dep. of Poultry Science, Univ. of Georgia, Athens, GA, 30602, USA
| | - Torey Looft
- USDA-ARS, National Animal Disease Center, Ames, IA, 50010, USA
| | - Erin Lipp
- Environmental Health Sciences Dep., Univ. of Georgia, Athens, GA, 30602, USA
| | - Getahun E Agga
- USDA-ARS, Food Animal Environmental Systems Research, Bowling Green, KY, 42101, USA
| | - Zaid Abdo
- Dep. of Microbiology, Immunology and Pathology, Colorado State Univ., Fort Collins, CO, 80523, USA
| | - Karamat R Sistani
- USDA-ARS, Food Animal Environmental Systems Research, Bowling Green, KY, 42101, USA
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Pepin KM, Golnar AJ, Abdo Z, Podgórski T. Ecological drivers of African swine fever virus persistence in wild boar populations: Insight for control. Ecol Evol 2020; 10:2846-2859. [PMID: 32211160 PMCID: PMC7083705 DOI: 10.1002/ece3.6100] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 01/12/2020] [Indexed: 12/12/2022] Open
Abstract
Environmental sources of infection can play a primary role in shaping epidemiological dynamics; however, the relative impact of environmental transmission on host-pathogen systems is rarely estimated. We developed and fit a spatially explicit model of African swine fever virus (ASFV) in wild boar to estimate what proportion of carcass-based transmission is contributing to the low-level persistence of ASFV in Eastern European wild boar. Our model was developed based on ecological insight and data from field studies of ASFV and wild boar in Eastern Poland. We predicted that carcass-based transmission would play a substantial role in persistence, especially in low-density host populations where contact rates are low. By fitting the model to outbreak data using approximate Bayesian computation, we inferred that between 53% and 66% of transmission events were carcass-based that is, transmitted through contact of a live host with a contaminated carcass. Model fitting and sensitivity analyses showed that the frequency of carcass-based transmission increased with decreasing host density, suggesting that management policies should emphasize the removal of carcasses and consider how reductions in host densities may drive carcass-based transmission. Sensitivity analyses also demonstrated that carcass-based transmission is necessary for the autonomous persistence of ASFV under realistic parameters. Autonomous persistence through direct transmission alone required high host densities; otherwise re-introduction of virus periodically was required for persistence when direct transmission probabilities were moderately high. We quantify the relative role of different persistence mechanisms for a low-prevalence disease using readily collected ecological data and viral surveillance data. Understanding how the frequency of different transmission mechanisms vary across host densities can help identify optimal management strategies across changing ecological conditions.
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Affiliation(s)
- Kim M. Pepin
- National Wildlife Research CenterUSDAAPHISFort CollinsCOUSA
| | | | - Zaid Abdo
- Microbiology, Immunology, and PathologyColorado State UniversityFort CollinsCOUSA
| | - Tomasz Podgórski
- Mammal Research InstitutePolish Academy of SciencesBiałowieżaPoland
- Department of Game Management and Wildlife BiologyFaculty of Forestry and Wood SciencesCzech University of Life SciencesPraha 6Czech Republic
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25
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Martiny JBH, Whiteson KL, Bohannan BJM, David LA, Hynson NA, McFall-Ngai M, Rawls JF, Schmidt TM, Abdo Z, Blaser MJ, Bordenstein S, Bréchot C, Bull CT, Dorrestein P, Eisen JA, Garcia-Pichel F, Gilbert J, Hofmockel KS, Holtz ML, Knight R, Mark Welch DB, McDonald D, Methé B, Mouncey NJ, Mueller NT, Pfister CA, Proctor L, Sachs JL. The emergence of microbiome centres. Nat Microbiol 2019; 5:2-3. [DOI: 10.1038/s41564-019-0644-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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26
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Abdo Z, LeCureux J, LaVoy A, Eklund B, Ryan EP, Dean GA. Impact of oral probiotic Lactobacillus acidophilus vaccine strains on the immune response and gut microbiome of mice. PLoS One 2019; 14:e0225842. [PMID: 31830087 PMCID: PMC6907787 DOI: 10.1371/journal.pone.0225842] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 11/13/2019] [Indexed: 02/07/2023] Open
Abstract
The potential role of probiotic bacteria as adjuvants in vaccine trials led to their use as nonparenteral live mucosal vaccine vectors. Yet, interactions between these vectors, the host and the microbiome are poorly understood. This study evaluates impact of three probiotic, Lactobacillus acidophilus, vector strains, and their interactions with the host's immune response, on the gut microbiome. One strain expressed the membrane proximal external region from HIV-1 (MPER). The other two expressed MPER and either secreted interleukin-1ß (IL-1ß) or expressed the surface flagellin subunit C (FliC) as adjuvants. We also used MPER with rice bran as prebiotic supplement. We observed a strain dependent, differential effect suggesting that MPER and IL-1β induced a shift of the microbiome while FliC had minimal impact. Joint probiotic and prebiotic use resulted in a compound effect, highlighting a potential synbiotic approach to impact efficacy of vaccination. Careful consideration of constitutive adjuvants and use of prebiotics is needed depending on whether or not to target microbiome modulation to improve vaccine efficacy. No clear associations were observed between total or MPER-specific IgA and the microbiome suggesting a role for other immune mechanisms or a need to focus on IgA-bound, resident microbiota, most affected by an immune response.
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Affiliation(s)
- Zaid Abdo
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Jonathan LeCureux
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Alora LaVoy
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Bridget Eklund
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Elizabeth P. Ryan
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado, United States of America
| | - Gregg A. Dean
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
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27
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Hopken MW, Piaggio AJ, Pabilonia KL, Pierce J, Anderson T, Abdo Z. Predicting whole genome sequencing success for archived avian influenza virus (Orthomyxoviridae) samples using real-time and droplet PCRs. J Virol Methods 2019; 276:113777. [PMID: 31730870 DOI: 10.1016/j.jviromet.2019.113777] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 11/05/2019] [Accepted: 11/10/2019] [Indexed: 01/01/2023]
Abstract
Long-term viral archives are valuable sources of research data. Each archive can store hundreds of thousands of diverse sample types. In the current era of whole genome sequencing, archived samples become a rich source of evolutionary and epidemiological data that can span years, and even decades. However, the ability to obtain high quality viral whole genome sequences from samples of various types, age, and quality is inconsistent. A minimum quality threshold that helps predict the best success of obtaining high quality genomic sequences for both recent and archived samples is highly valuable. Real-time reverse transcription PCR (rrt-PCR) and droplet digital PCR (ddPCR) are useful tools to evaluate nucleic acid integrity. We hypothesized that diagnostic rrt-PCR and ddPCR data for avian influenza virus (AIV) can predict viral whole genome sequencing success. To test this hypothesis we used RNA extracted from cloacal and oropharyngeal swabs stored in the USDA-APHIS National Wildlife Disease Program Wildlife Tissue Archive. We determined that a specific rrt-PCR Cq value or ddPCR copies/μL resulted in recovery of complete sequences of all eight AIV gene segments. We used logistic regression to estimate probabilities of whole genome recovery at 0.95 (Cq = 15, copies/μL = 49,350), 0.75 (Cq = 24, copies/μL = 16,800), 0.50 (Cq = 29, copies/μL = <1), and 0.25 (Cq = 235, copies/μL = <1). We also identified values at which we predictably recovered HA and NA segments for diagnosing subtypes (Cq = 27.29; copies/μL = 757.50). This approach will allow researchers to assess the potential success of AIV whole genome recovery from diagnostic samples collected in routine AIV surveillance.
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Affiliation(s)
- Matthew W Hopken
- Department of Microbiology, Immunology, and Pathology, College of Veterinary and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA; United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, CO, 80521, USA
| | - Antoinette J Piaggio
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Fort Collins, CO, 80521, USA
| | - Kristy L Pabilonia
- Department of Microbiology, Immunology, and Pathology, College of Veterinary and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA; Veterinary Diagnostics Laboratory, College of Veterinary and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80526, USA
| | - James Pierce
- Department of Microbiology, Immunology, and Pathology, College of Veterinary and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Theodore Anderson
- Veterinary Diagnostics Laboratory, College of Veterinary and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80526, USA
| | - Zaid Abdo
- Department of Microbiology, Immunology, and Pathology, College of Veterinary and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA.
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28
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Pepin KM, Hopken MW, Shriner SA, Spackman E, Abdo Z, Parrish C, Riley S, Lloyd-Smith JO, Piaggio AJ. Improving risk assessment of the emergence of novel influenza A viruses by incorporating environmental surveillance. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180346. [PMID: 31401963 PMCID: PMC6711309 DOI: 10.1098/rstb.2018.0346] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Reassortment is an evolutionary mechanism by which influenza A viruses (IAV) generate genetic novelty. Reassortment is an important driver of host jumps and is widespread according to retrospective surveillance studies. However, predicting the epidemiological risk of reassortant emergence in novel hosts from surveillance data remains challenging. IAV strains persist and co-occur in the environment, promoting co-infection during environmental transmission. These conditions offer opportunity to understand reassortant emergence in reservoir and spillover hosts. Specifically, environmental RNA could provide rich information for understanding the evolutionary ecology of segmented viruses, and transform our ability to quantify epidemiological risk to spillover hosts. However, significant challenges with recovering and interpreting genomic RNA from the environment have impeded progress towards predicting reassortant emergence from environmental surveillance data. We discuss how the fields of genomics, experimental ecology and epidemiological modelling are well positioned to address these challenges. Coupling quantitative disease models and natural transmission studies with new molecular technologies, such as deep-mutational scanning and single-virus sequencing of environmental samples, should dramatically improve our understanding of viral co-occurrence and reassortment. We define observable risk metrics for emerging molecular technologies and propose a conceptual research framework for improving accuracy and efficiency of risk prediction. This article is part of the theme issue 'Dynamic and integrative approaches to understanding pathogen spillover'.
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Affiliation(s)
- Kim M. Pepin
- National Wildlife Research Center, USDA-APHIS, Fort Collins, CO 80521, USA
- e-mail:
| | - Matthew W. Hopken
- National Wildlife Research Center, USDA-APHIS, Fort Collins, CO 80521, USA
- Colorado State University, Fort Collins, CO 80523, USA
| | - Susan A. Shriner
- National Wildlife Research Center, USDA-APHIS, Fort Collins, CO 80521, USA
| | - Erica Spackman
- Exotic and Emerging Avian Viral Diseases Research, USDA-ARS, Athens, GA 30605, USA
| | - Zaid Abdo
- Colorado State University, Fort Collins, CO 80523, USA
| | - Colin Parrish
- Baker Institute for Animal Health, Department of Microbiology and Immunology, Cornell University, Ithaca, NY 14853, USA
| | - Steven Riley
- MRC Centre for Global Infectious Disease Analysis, Imperial College, London, SW7 2AZ, UK
| | - James O. Lloyd-Smith
- UCLA, Los Angeles, CA 90095, USA
- Department of Ecology and Evolutionary Biology, Fogarty International Center, National Institutes of Health, Bethesda MD 20892, USA
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29
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Zambrana LE, McKeen S, Ibrahim H, Zarei I, Borresen EC, Doumbia L, Boré A, Cissoko A, Douyon S, Koné K, Perez J, Perez C, Hess A, Abdo Z, Sangaré L, Maiga A, Becker-Dreps S, Yuan L, Koita O, Vilchez S, Ryan EP. Rice bran supplementation modulates growth, microbiota and metabolome in weaning infants: a clinical trial in Nicaragua and Mali. Sci Rep 2019; 9:13919. [PMID: 31558739 PMCID: PMC6763478 DOI: 10.1038/s41598-019-50344-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 09/11/2019] [Indexed: 12/12/2022] Open
Abstract
Rice bran supplementation provides nutrients, prebiotics and phytochemicals that enhance gut immunity, reduce enteric pathogens and diarrhea, and warrants attention for improvement of environmental enteric dysfunction (EED) in children. EED is a subclinical condition associated with stunting due to impaired nutrient absorption. This study investigated the effects of rice bran supplementation on weight for age and length for age z-scores (WAZ, LAZ), EED stool biomarkers, as well as microbiota and metabolome signatures in weaning infants from 6 to 12 months old that reside in Nicaragua and Mali. Healthy infants were randomized to a control (no intervention) or a rice bran group that received daily supplementation with increasing doses at each month (1–5 g/day). Stool microbiota were characterized using 16S rDNA amplicon sequencing. Stool metabolomes were analyzed using ultra-high-performance liquid-chromatography tandem mass-spectrometry. Statistical comparisons were completed at 6, 8, and 12 months of age. Daily consumption of rice bran was safe and feasible to support changes in LAZ from 6–8 and 8–12 months of age in Nicaragua and Mali infants when compared to control. WAZ was significantly improved only for Mali infants at 8 and 12 months. Mali and Nicaraguan infants showed major differences in the overall gut microbiota and metabolome composition and structure at baseline, and thus each country cohort demonstrated distinct microbial and metabolite profile responses to rice bran supplementation when compared to control. Rice bran is a practical dietary intervention strategy that merits development in rice-growing regions that have a high prevalence of growth stunting due to malnutrition and diarrheal diseases. Rice is grown as a staple food, and the bran is used as animal feed or wasted in many low- and middle-income countries where EED and stunting is prevalent.
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Affiliation(s)
- Luis E Zambrana
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, 80523, USA.,Center of Infectious Diseases, Department of Microbiology and Parasitology, Faculty of Medical Sciences, National Autonomous University of Nicaragua, León (UNAN-León), León, Nicaragua
| | - Starin McKeen
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Hend Ibrahim
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, 80523, USA.,Department of Medical Biochemistry, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Iman Zarei
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Erica C Borresen
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Lassina Doumbia
- Laboratoire de Biologie Moléculaire Appliquée, Campus de Badalabougou, Université des Sciences, des Techniques et des Technologies de Bamako, BP: 1805, Bamako, Mali
| | - Abdoulaye Boré
- Laboratoire de Biologie Moléculaire Appliquée, Campus de Badalabougou, Université des Sciences, des Techniques et des Technologies de Bamako, BP: 1805, Bamako, Mali
| | - Alima Cissoko
- Laboratoire de Biologie Moléculaire Appliquée, Campus de Badalabougou, Université des Sciences, des Techniques et des Technologies de Bamako, BP: 1805, Bamako, Mali
| | - Seydou Douyon
- Laboratoire de Biologie Moléculaire Appliquée, Campus de Badalabougou, Université des Sciences, des Techniques et des Technologies de Bamako, BP: 1805, Bamako, Mali
| | - Karim Koné
- Laboratoire de Biologie Moléculaire Appliquée, Campus de Badalabougou, Université des Sciences, des Techniques et des Technologies de Bamako, BP: 1805, Bamako, Mali
| | - Johann Perez
- Center of Infectious Diseases, Department of Microbiology and Parasitology, Faculty of Medical Sciences, National Autonomous University of Nicaragua, León (UNAN-León), León, Nicaragua
| | - Claudia Perez
- Center of Infectious Diseases, Department of Microbiology and Parasitology, Faculty of Medical Sciences, National Autonomous University of Nicaragua, León (UNAN-León), León, Nicaragua
| | - Ann Hess
- Department of Statistics, Colorado State University, Fort Collins, CO, 80523, USA
| | - Zaid Abdo
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, 80521, USA
| | - Lansana Sangaré
- Laboratoire de Biologie Moléculaire Appliquée, Campus de Badalabougou, Université des Sciences, des Techniques et des Technologies de Bamako, BP: 1805, Bamako, Mali
| | - Ababacar Maiga
- Laboratoire de Biologie Moléculaire Appliquée, Campus de Badalabougou, Université des Sciences, des Techniques et des Technologies de Bamako, BP: 1805, Bamako, Mali
| | - Sylvia Becker-Dreps
- Departments of Family Medicine and Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599-7595, USA
| | - Lijuan Yuan
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Ousmane Koita
- Laboratoire de Biologie Moléculaire Appliquée, Campus de Badalabougou, Université des Sciences, des Techniques et des Technologies de Bamako, BP: 1805, Bamako, Mali.
| | - Samuel Vilchez
- Center of Infectious Diseases, Department of Microbiology and Parasitology, Faculty of Medical Sciences, National Autonomous University of Nicaragua, León (UNAN-León), León, Nicaragua.
| | - Elizabeth P Ryan
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, 80523, USA.
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Lakin SM, Kuhnle A, Alipanahi B, Noyes NR, Dean C, Muggli M, Raymond R, Abdo Z, Prosperi M, Belk KE, Morley PS, Boucher C. Hierarchical Hidden Markov models enable accurate and diverse detection of antimicrobial resistance sequences. Commun Biol 2019; 2:294. [PMID: 31396574 PMCID: PMC6684577 DOI: 10.1038/s42003-019-0545-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 07/08/2019] [Indexed: 12/13/2022] Open
Abstract
The characterization of antimicrobial resistance genes from high-throughput sequencing data has become foundational in public health research and regulation. This requires mapping sequence reads to databases of known antimicrobial resistance genes to determine the genes present in the sample. Mapping sequence reads to known genes is traditionally accomplished using alignment. Alignment methods have high specificity but are limited in their ability to detect sequences that are divergent from the reference database, which can result in a substantial false negative rate. We address this shortcoming through the creation of Meta-MARC, which enables detection of diverse resistance sequences using hierarchical, DNA-based Hidden Markov Models. We first describe Meta-MARC and then demonstrate its efficacy on simulated and functional metagenomic datasets. Meta-MARC has higher sensitivity relative to competing methods. This sensitivity allows for detection of sequences that are divergent from known antimicrobial resistance genes. This functionality is imperative to expanding existing antimicrobial gene databases.
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Affiliation(s)
- Steven M Lakin
- 1Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523 USA
| | - Alan Kuhnle
- 2Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL 32611 USA
| | - Bahar Alipanahi
- 2Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL 32611 USA
| | - Noelle R Noyes
- 3Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN 55108 USA
| | - Chris Dean
- 1Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523 USA
| | - Martin Muggli
- 4Department of Computer Science, Colorado State University, Fort Collins, CO 80523 USA
| | - Rob Raymond
- 4Department of Computer Science, Colorado State University, Fort Collins, CO 80523 USA
| | - Zaid Abdo
- 1Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523 USA
| | - Mattia Prosperi
- 5Department of Epidemiology, University of Florida, Gainesville, FL 32611 USA
| | - Keith E Belk
- 6Department of Animal Sciences, Colorado State University, Fort Collins, CO 80523 USA
| | - Paul S Morley
- 7VERO Center, Texas A&M University and West Texas A&M University, Canyon, TX 79016 USA
| | - Christina Boucher
- 2Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL 32611 USA
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Huebner KL, Martin JN, Weissend CJ, Holzer KL, Parker JK, Lakin SM, Doster E, Weinroth MD, Abdo Z, Woerner DR, Metcalf JL, Geornaras I, Bryant TC, Morley PS, Belk KE. Effects of a Saccharomyces cerevisiae fermentation product on liver abscesses, fecal microbiome, and resistome in feedlot cattle raised without antibiotics. Sci Rep 2019; 9:2559. [PMID: 30796295 PMCID: PMC6385275 DOI: 10.1038/s41598-019-39181-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 01/09/2019] [Indexed: 01/15/2023] Open
Abstract
Liver abscesses in feedlot cattle form secondary to high concentrate feeds and rumen acidosis. Antimicrobial drugs are commonly included in cattle feed for prevention of liver abscesses, but concerns regarding antimicrobial resistance have increased the need for alternative treatments. A block randomized clinical trial was conducted to evaluate the effects of a Saccharomyces cerevisiae fermentation product (SCFP) on liver abscesses, fecal microbiomes, and resistomes in cattle raised without antibiotics in a Colorado feedlot. At enrollment, steers (n = 4,689) were sorted, by weight and source, into 2 pens comprising a block (n = 14 blocks, 28 pens); pens were randomly allocated to either the control group or the treatment group, where the diet was supplemented with SCFP. Prior to harvest, composited feces were collected for characterization of the microbiome and resistome using 16S rRNA gene and shotgun sequencing. At harvest, liver abscess severity was quantified for individual cattle. There were no statistical differences detected by treatment group in animal health, liver abscess prevalence or severity. Organisms classified to phylum, Elusimicrobia were more abundant in the feces of treated cattle, however, there were no differences in the resistome by treatment group. Both microbiome and resistome varied significantly among enrollment blocks.
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Affiliation(s)
- Katherine L Huebner
- Department of Clinical Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Jennifer N Martin
- Department of Animal Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Carla J Weissend
- Department of Animal Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Katlyn L Holzer
- Department of Animal Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Jennifer K Parker
- Department of Clinical Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Steven M Lakin
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Enrique Doster
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Margaret D Weinroth
- Department of Animal Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Zaid Abdo
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Dale R Woerner
- Department of Animal Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Jessica L Metcalf
- Department of Animal Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Ifigenia Geornaras
- Department of Animal Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Tony C Bryant
- Five Rivers Cattle Feeding, LLC, Kersey, Colorado, USA
| | - Paul S Morley
- Department of Clinical Sciences, Colorado State University, Fort Collins, Colorado, USA
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Keith E Belk
- Department of Animal Sciences, Colorado State University, Fort Collins, Colorado, USA.
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Stenkamp‐Strahm C, McConnel C, Magzamen S, Abdo Z, Reynolds S. Associations between
Escherichia coli
O157 shedding and the faecal microbiota of dairy cows. J Appl Microbiol 2018; 124:881-898. [DOI: 10.1111/jam.13679] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 12/01/2017] [Accepted: 12/15/2017] [Indexed: 12/20/2022]
Affiliation(s)
- C. Stenkamp‐Strahm
- College of Veterinary Medicine and Biomedical Sciences Colorado State University Fort Collins CO USA
| | - C. McConnel
- College of Veterinary Medicine and Biomedical Sciences Colorado State University Fort Collins CO USA
| | - S. Magzamen
- College of Veterinary Medicine and Biomedical Sciences Colorado State University Fort Collins CO USA
| | - Z. Abdo
- College of Veterinary Medicine and Biomedical Sciences Colorado State University Fort Collins CO USA
| | - S. Reynolds
- College of Veterinary Medicine and Biomedical Sciences Colorado State University Fort Collins CO USA
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Noyes N, Cho KC, Ravel J, Forney LJ, Abdo Z. Associations between sexual habits, menstrual hygiene practices, demographics and the vaginal microbiome as revealed by Bayesian network analysis. PLoS One 2018; 13:e0191625. [PMID: 29364944 PMCID: PMC5783405 DOI: 10.1371/journal.pone.0191625] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 01/06/2018] [Indexed: 12/13/2022] Open
Abstract
The vaginal microbiome plays an influential role in several disease states in reproductive age women, including bacterial vaginosis (BV). While demographic characteristics are associated with differences in vaginal microbiome community structure, little is known about the influence of sexual and hygiene habits. Furthermore, associations between the vaginal microbiome and risk symptoms of bacterial vaginosis have not been fully elucidated. Using Bayesian network (BN) analysis of 16S rRNA gene sequence results, demographic and extensive questionnaire data, we describe both novel and previously documented associations between habits of women and their vaginal microbiome. The BN analysis approach shows promise in uncovering complex associations between disparate data types. Our findings based on this approach support published associations between specific microbiome members (e.g., Eggerthella, Gardnerella, Dialister, Sneathia and Ruminococcaceae), the Nugent score (a BV diagnostic) and vaginal pH (a risk symptom of BV). Additionally, we found that several microbiome members were directly connected to other risk symptoms of BV (such as vaginal discharge, odor, itch, irritation, and yeast infection) including L. jensenii, Corynebacteria, and Proteobacteria. No direct connections were found between the Nugent Score and risk symptoms of BV other than pH, indicating that the Nugent Score may not be the most useful criteria for assessment of clinical BV. We also found that demographics (i.e., age, ethnicity, previous pregnancy) were associated with the presence/absence of specific vaginal microbes. The resulting BN revealed several as-yet undocumented associations between birth control usage, menstrual hygiene practices and specific microbiome members. Many of these complex relationships were not identified using common analytical methods, i.e., ordination and PERMANOVA. While these associations require confirmatory follow-up study, our findings strongly suggest that future studies of the vaginal microbiome and vaginal pathologies should include detailed surveys of participants' sanitary, sexual and birth control habits, as these can act as confounders in the relationship between the microbiome and disease. Although the BN approach is powerful in revealing complex associations within multidimensional datasets, the need in some cases to discretize the data for use in BN analysis can result in loss of information. Future research is required to alleviate such limitations in constructing BN networks. Large sample sizes are also required in order to allow for the incorporation of a large number of variables (nodes) into the BN, particularly when studying associations between metadata and the microbiome. We believe that this approach is of great value, complementing other methods, to further our understanding of complex associations characteristic of microbiome research.
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Affiliation(s)
- Noelle Noyes
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Kyu-Chul Cho
- Department of Statistics, University of Idaho, Moscow, Idaho, United States of America
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore Maryland, United States of America
| | - Larry J. Forney
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States of America
| | - Zaid Abdo
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
- * E-mail:
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Noyes NR, Weinroth ME, Parker JK, Dean CJ, Lakin SM, Raymond RA, Rovira P, Doster E, Abdo Z, Martin JN, Jones KL, Ruiz J, Boucher CA, Belk KE, Morley PS. Enrichment allows identification of diverse, rare elements in metagenomic resistome-virulome sequencing. Microbiome 2017; 5:142. [PMID: 29041965 PMCID: PMC5645900 DOI: 10.1186/s40168-017-0361-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 10/05/2017] [Indexed: 05/29/2023]
Abstract
BACKGROUND Shotgun metagenomic sequencing is increasingly utilized as a tool to evaluate ecological-level dynamics of antimicrobial resistance and virulence, in conjunction with microbiome analysis. Interest in use of this method for environmental surveillance of antimicrobial resistance and pathogenic microorganisms is also increasing. In published metagenomic datasets, the total of all resistance- and virulence-related sequences accounts for < 1% of all sequenced DNA, leading to limitations in detection of low-abundance resistome-virulome elements. This study describes the extent and composition of the low-abundance portion of the resistome-virulome, using a bait-capture and enrichment system that incorporates unique molecular indices to count DNA molecules and correct for enrichment bias. RESULTS The use of the bait-capture and enrichment system significantly increased on-target sequencing of the resistome-virulome, enabling detection of an additional 1441 gene accessions and revealing a low-abundance portion of the resistome-virulome that was more diverse and compositionally different than that detected by more traditional metagenomic assays. The low-abundance portion of the resistome-virulome also contained resistance genes with public health importance, such as extended-spectrum betalactamases, that were not detected using traditional shotgun metagenomic sequencing. In addition, the use of the bait-capture and enrichment system enabled identification of rare resistance gene haplotypes that were used to discriminate between sample origins. CONCLUSIONS These results demonstrate that the rare resistome-virulome contains valuable and unique information that can be utilized for both surveillance and population genetic investigations of resistance. Access to the rare resistome-virulome using the bait-capture and enrichment system validated in this study can greatly advance our understanding of microbiome-resistome dynamics.
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Affiliation(s)
- Noelle R Noyes
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Maggie E Weinroth
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
| | - Jennifer K Parker
- Department of Clinical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Chris J Dean
- Department of Computer Sciences, Colorado State University, Fort Collins, CO, USA
| | - Steven M Lakin
- Department of Clinical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Robert A Raymond
- Department of Computer Sciences, Colorado State University, Fort Collins, CO, USA
| | - Pablo Rovira
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
| | - Enrique Doster
- Department of Clinical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Zaid Abdo
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Jennifer N Martin
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
| | - Kenneth L Jones
- Department of Pediatrics, Section of Hematology Oncology and Bone Marrow Transplant, University of Colorado School of Medicine, Aurora, CO, USA
| | - Jaime Ruiz
- Department of Computer and Information Science and Engineering, University of Florida, Gainesville, Florida, USA
| | - Christina A Boucher
- Department of Computer and Information Science and Engineering, University of Florida, Gainesville, Florida, USA
| | - Keith E Belk
- Department of Animal Sciences, Colorado State University, Fort Collins, CO, USA
| | - Paul S Morley
- Department of Clinical Sciences, Colorado State University, Fort Collins, CO, USA.
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Huebner KL, Martin JN, Weinroth MD, Holzer KH, Weissend CJ, Abdo Z, Metcalf JL, Geornaras I, Parker JK, Morley PS, Belk KE. 263 Effects of in-feed administration of a Saccharomyces cerevisiae fermentation product on the liver abscess microbiome and liver abscess rate in cattle reared to produce natural-branded beef. J Anim Sci 2017. [DOI: 10.2527/asasann.2017.263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Susta L, He Y, Hutcheson JM, Lu Y, West FD, Stice SL, Yu P, Abdo Z, Afonso CL. Derivation of chicken induced pluripotent stem cells tolerant to Newcastle disease virus-induced lysis through multiple rounds of infection. Virol J 2016; 13:205. [PMID: 27919263 PMCID: PMC5139146 DOI: 10.1186/s12985-016-0659-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 11/25/2016] [Indexed: 12/29/2022] Open
Abstract
Background Newcastle disease (ND), caused by Newcastle disease virus (NDV), is a devastating disease of poultry and wild birds. ND is prevented by rigorous biocontainment and vaccination. One potential approach to prevent spread of the virus is production of birds that show innate resistance to NDV-caused disease. Induced pluripotent stem cell (iPSC) technology allows adult cells to be reprogrammed into an embryonic stem cell-like state capable of contributing to live offspring and passing on unique traits in a number of species. Recently, iPSC approaches have been successfully applied to avian cells. If chicken induced pluripotent stem cells (ciPSCs) are genetically or epigenetically modified to resist NDV infection, it may be possible to generate ND resistant poultry. There is limited information on the potential of ciPSCs to be infected by NDV, or the capacity of these cells to become resistant to infection. The aim of the present work was to assess the characteristics of the interaction between NDV and ciPSCs, and to develop a selection method that would increase tolerance of these cells to NDV-induced cellular damage. Results Results showed that ciPSCs were permissive to infection with NDV, and susceptible to virus-mediated cell death. Since ciPSCs that survived infection demonstrated the ability to recover quickly, we devised a system to select surviving cells through multiple infection rounds with NDV. ciPSCs that sustained 9 consecutive infections had a statistically significant increase in survival (up to 36 times) compared to never-infected ciPSCs upon NDV infection (tolerant cells). Increased survival was not caused by a loss of permissiveness to NDV replication. RNA sequencing followed by enrichment pathway analysis showed that numerous metabolic pathways where differentially regulated between tolerant and never-infected ciPSCs. Conclusions Results demonstrate that ciPSCs are permissive to NDV infection and become increasingly tolerant to NDV under selective pressure, indicating that this system could be applied to study mechanisms of cellular tolerance to NDV. Electronic supplementary material The online version of this article (doi:10.1186/s12985-016-0659-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Leonardo Susta
- US National Poultry Research Center, Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, Athens, GA, 30605, USA. .,Present address: Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, N1G 2 W1, Canada.
| | - Ying He
- Regenerative Bioscience Center, University of Georgia, Athens, GA, 30602, USA.,Present address: College of Animal Science and Technology, Guangxi University, Nanning, Guangxi, 53004, China
| | - Jessica M Hutcheson
- Regenerative Bioscience Center, University of Georgia, Athens, GA, 30602, USA.,Department of Animal and Dairy Science, University of Georgia, Athens, GA, 30602, USA
| | - Yangqing Lu
- Regenerative Bioscience Center, University of Georgia, Athens, GA, 30602, USA.,Department of Animal and Dairy Science, University of Georgia, Athens, GA, 30602, USA
| | - Franklin D West
- Regenerative Bioscience Center, University of Georgia, Athens, GA, 30602, USA.,Department of Animal and Dairy Science, University of Georgia, Athens, GA, 30602, USA
| | - Steven L Stice
- Regenerative Bioscience Center, University of Georgia, Athens, GA, 30602, USA.,Department of Animal and Dairy Science, University of Georgia, Athens, GA, 30602, USA
| | - Ping Yu
- Regenerative Bioscience Center, University of Georgia, Athens, GA, 30602, USA.,Department of Animal and Dairy Science, University of Georgia, Athens, GA, 30602, USA
| | - Zaid Abdo
- Department of Microbiology, Immunology, and Pathology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Claudio L Afonso
- US National Poultry Research Center, Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, Athens, GA, 30605, USA
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Lakin SM, Dean C, Noyes NR, Dettenwanger A, Ross AS, Doster E, Rovira P, Abdo Z, Jones KL, Ruiz J, Belk KE, Morley PS, Boucher C. MEGARes: an antimicrobial resistance database for high throughput sequencing. Nucleic Acids Res 2016; 45:D574-D580. [PMID: 27899569 PMCID: PMC5210519 DOI: 10.1093/nar/gkw1009] [Citation(s) in RCA: 212] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 10/11/2016] [Accepted: 10/28/2016] [Indexed: 01/18/2023] Open
Abstract
Antimicrobial resistance has become an imminent concern for public health. As methods for detection and characterization of antimicrobial resistance move from targeted culture and polymerase chain reaction to high throughput metagenomics, appropriate resources for the analysis of large-scale data are required. Currently, antimicrobial resistance databases are tailored to smaller-scale, functional profiling of genes using highly descriptive annotations. Such characteristics do not facilitate the analysis of large-scale, ecological sequence datasets such as those produced with the use of metagenomics for surveillance. In order to overcome these limitations, we present MEGARes (https://megares.meglab.org), a hand-curated antimicrobial resistance database and annotation structure that provides a foundation for the development of high throughput acyclical classifiers and hierarchical statistical analysis of big data. MEGARes can be browsed as a stand-alone resource through the website or can be easily integrated into sequence analysis pipelines through download. Also via the website, we provide documentation for AmrPlusPlus, a user-friendly Galaxy pipeline for the analysis of high throughput sequencing data that is pre-packaged for use with the MEGARes database.
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Affiliation(s)
- Steven M Lakin
- Department of Clinical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Chris Dean
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Noelle R Noyes
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Adam Dettenwanger
- Department of Computer Science, Colorado State University, Fort Collins, CO 80523, USA
| | - Anne Spencer Ross
- Department of Computer Science, Colorado State University, Fort Collins, CO 80523, USA
| | - Enrique Doster
- Department of Clinical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Pablo Rovira
- Department of Animal Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Zaid Abdo
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA
| | - Kenneth L Jones
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, CO 80045, USA
| | - Jaime Ruiz
- Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL 32611, USA
| | - Keith E Belk
- Department of Animal Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Paul S Morley
- Department of Clinical Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Christina Boucher
- Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL 32611, USA
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Guard J, Abdo Z, Byers SO, Kriebel P, Rothrock MJ. Subtyping of Salmonella enterica Subspecies I Using Single-Nucleotide Polymorphisms in Adenylate Cyclase. Foodborne Pathog Dis 2016; 13:350-62. [PMID: 27035032 PMCID: PMC4939371 DOI: 10.1089/fpd.2015.2088] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Methods to rapidly identify serotypes of Salmonella enterica subspecies I are of vital importance for protecting the safety of food. To supplement the serotyping method dkgB-linked intergenic sequence ribotyping (ISR), single-nucleotide polymorphisms were characterized within adenylate cyclase (cyaA). The National Center for Biotechnology Information (NCBI) database had 378 cyaA sequences from S. enterica subspecies I, which included 42 unique DNA sequences and 19 different amino acid sequences. Five representative isolates, namely serotypes Typhimurium, Kentucky, Enteritidis phage type PT4, and two variants of Enteritidis phage type PT13a, were differentiated within a microsphere-based fluidics system in cyaA by allele-specific primer extension. Validation against 25 poultry-related environmental Salmonella isolates representing 11 serotypes yielded a ∼89% success rate at identifying the serotype of the isolate, and a different region could be targeted to achieve 100%. When coupled with ISR, all serotypes were differentiated. Phage lineages of serotype Enteritidis 13a and 4 were identified, and a biofilm-forming strain of PT13a was differentiated from a smooth phenotype within phage type. Comparative ranking of mutation indices to genes such as the tRNA transferases, the diguanylate cyclases, and genes used for multilocus sequence typing indicated that cyaA is an appropriate gene for assessing epidemiological trends of Salmonella because of its relative stability in nucleotide composition.
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Affiliation(s)
- Jean Guard
- 1 U.S. National Poultry Research Center , U.S. Department of Agriculture, Athens, Georgia
| | - Zaid Abdo
- 1 U.S. National Poultry Research Center , U.S. Department of Agriculture, Athens, Georgia
| | | | - Patrick Kriebel
- 2 Department of Statistics, University of Georgia , Athens, Georgia
| | - Michael J Rothrock
- 1 U.S. National Poultry Research Center , U.S. Department of Agriculture, Athens, Georgia
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Jones DR, Guard J, Gast RK, Buhr RJ, Fedorka-Cray PJ, Abdo Z, Plumblee JR, Bourassa DV, Cox NA, Rigsby LL, Robison CI, Regmi P, Karcher DM. Influence of commercial laying hen housing systems on the incidence and identification of Salmonella and Campylobacter. Poult Sci 2016; 95:1116-24. [PMID: 26976901 PMCID: PMC4876611 DOI: 10.3382/ps/pew036] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 01/05/2016] [Indexed: 11/30/2022] Open
Abstract
The housing of laying hens is important for social, industrial, and regulatory aspects. Many studies have compared hen housing systems on the research farm, but few have fully examined commercial housing systems and management strategies. The current study compared hens housed in commercial cage-free aviary, conventional cage, and enriched colony cage systems. Environmental and eggshell pool samples were collected from selected cages/segments of the housing systems throughout the production cycle and monitored for Salmonella and Campylobacter prevalence. At 77 wk of age, 120 hens per housing system were examined for Salmonella and Campylobacter colonization in the: adrenal glands, spleen, ceca, follicles, and upper reproductive tract. All isolates detected from environmental swabs, eggshell pools, and tissues were identified for serotype. Two predominant Salmonella were detected in all samples: S. Braenderup and S. Kentucky. Campylobacter coli and C. jejuni were the only Campylobacter detected in the flocks. Across all housing systems, approximately 7% of hens were colonized with Salmonella, whereas > 90% were colonized with Campylobacter. Salmonella Braenderup was the isolate most frequently detected in environmental swabs (P < 0.0001) and housing system impacted Salmonella spp. shedding (P < 0.0001). Campylobacter jejuni was the isolate most frequently found in environmental swabs (P < 0.01), while housing system impacted the prevalence of C. coli and jejuni in ceca (P < 0.0001). The results of this study provide a greater understanding of the impact of hen housing systems on hen health and product safety. Additionally, producers and academia can utilize the findings to make informed decisions on hen housing and management strategies to enhance hen health and food safety.
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Affiliation(s)
- D R Jones
- USDA, Agricultural Research Service, US National Poultry Research Center, Athens, GA 30605
| | - J Guard
- USDA, Agricultural Research Service, US National Poultry Research Center, Athens, GA 30605
| | - R K Gast
- USDA, Agricultural Research Service, US National Poultry Research Center, Athens, GA 30605
| | - R J Buhr
- USDA, Agricultural Research Service, US National Poultry Research Center, Athens, GA 30605
| | - P J Fedorka-Cray
- USDA, Agricultural Research Service, US National Poultry Research Center, Athens, GA 30605
| | - Z Abdo
- USDA, Agricultural Research Service, US National Poultry Research Center, Athens, GA 30605
| | - J R Plumblee
- USDA, Agricultural Research Service, US National Poultry Research Center, Athens, GA 30605
| | - D V Bourassa
- USDA, Agricultural Research Service, US National Poultry Research Center, Athens, GA 30605
| | - N A Cox
- USDA, Agricultural Research Service, US National Poultry Research Center, Athens, GA 30605
| | - L L Rigsby
- USDA, Agricultural Research Service, US National Poultry Research Center, Athens, GA 30605
| | - C I Robison
- Department of Animal Science, Michigan State University, East Lansing, MI 48824
| | - P Regmi
- Department of Animal Science, Michigan State University, East Lansing, MI 48824
| | - D M Karcher
- Department of Animal Science, Michigan State University, East Lansing, MI 48824
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Marques de Carvalho L, Benda ND, Vaughan MM, Cabrera AR, Hung K, Cox T, Abdo Z, Allen LH, Teal PEA. Mi-1-Mediated Nematode Resistance in Tomatoes is Broken by Short-Term Heat Stress but Recovers Over Time. J Nematol 2015; 47:133-40. [PMID: 26170475 PMCID: PMC4492288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Indexed: 06/04/2023] Open
Abstract
Tomato (Solanum lycopersicum L.) is among the most valuable agricultural products, but Meloidogyne spp. (root-knot nematode) infestations result in serious crop losses. In tomato, resistance to root-knot nematodes is controlled by the gene Mi-1, but heat stress interferes with Mi-1-associated resistance. Inconsistent results in published field and greenhouse experiments led us to test the effect of short-term midday heat stress on tomato susceptibility to Meloidogyne incognita race 1. Under controlled day/night temperatures of 25°C/21°C, 'Amelia', which was verified as possessing the Mi-1 gene, was deemed resistant (4.1 ± 0.4 galls/plant) and Rutgers, which does not possess the Mi-1 gene, was susceptible (132 ± 9.9 galls/plant) to M. incognita infection. Exposure to a single 3 hr heat spike of 35°C was sufficient to increase the susceptibility of 'Amelia' but did not affect Rutgers. Despite this change in resistance, Mi-1 gene expression was not affected by heat treatment, or nematode infection. The heat-induced breakdown of Mi-1 resistance in 'Amelia' did recover with time regardless of additional heat exposures and M. incognita infection. These findings would aid in the development of management strategies to protect the tomato crop at times of heightened M. incognita susceptibility.
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Affiliation(s)
| | - Nicole D Benda
- Entomology and Nematology Department, University of Florida, Gainesville, FL. ; These authors contributed equally to this work
| | - Martha M Vaughan
- National Center for Agricultural Utilization Research USDA-ARS, Peoria, IL
| | - Ana R Cabrera
- Entomology and Nematology Department, University of Florida, Gainesville, FL
| | - Kaddie Hung
- Center for Medical and Veterinary Entomology USDA-ARS, Gainesville, FL
| | - Thomas Cox
- Center for Medical and Veterinary Entomology USDA-ARS, Gainesville, FL
| | - Zaid Abdo
- Area Directors Office USDA-ARS, Athens, GA
| | - L Hartwell Allen
- Center for Medical and Veterinary Entomology USDA-ARS, Gainesville, FL
| | - Peter E A Teal
- Center for Medical and Veterinary Entomology USDA-ARS, Gainesville, FL
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de Carvalho SA, de Carvalho Nunes WM, Belasque J, Machado MA, Croce-Filho J, Bock CH, Abdo Z. Comparison of Resistance to Asiatic Citrus Canker Among Different Genotypes of Citrus in a Long-Term Canker-Resistance Field Screening Experiment in Brazil. Plant Dis 2015; 99:207-218. [PMID: 30699570 DOI: 10.1094/pdis-04-14-0384-re] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Asiatic citrus canker (ACC) is caused by Xanthomonas citri subsp. citri. The disease results in yield loss and renders fruit unfit for the fresh market. A 6-year study in Paraná State, Brazil, was conducted to compare the susceptibility of 186 genotypes of citrus representing sweet orange (Citrus sinensis), mandarin (C. reticulata), Mediterranean mandarin (C. deliciosa), Clementine mandarin (C. clementina), Satsuma mandarin (C. unshiu), sour orange (C. aurantium), lemon (C. limon), sweet lime (C. aurantifolia), grapefruit (C. paradisi), and four hybrids (C. reticulata × Citrus sp., C. reticulata × C. paradisi, C. reticulata × C. sinensis, and C. unshiu × C. sinensis). Sweet orange (C. sinensis) was represented by the most genotypes (n = 141). The number of lesions per leaf was assessed 18 times from 2005 to 2010 (up to 4 times per year). The data were analyzed using mixed-model analysis of fixed and random effects, which showed a total of six resistance-susceptibility groupings of species and hybrids. Based on species, the most resistant genotypes, on average, included Satsuma and lemon (mean lesions per leaf = 4.32 and 4.26, respectively), and the most susceptible genotypes were grapefruit and sweet lime, with 14.84 and 10.96 lesions per leaf, respectively. Genotypes of mandarin, sour orange, Mediterranean mandarin, and sweet orange had intermediate severity (5.48 to 9.56 lesions per leaf). The hybrids also showed a range of ACC severity but all were in the more resistant groupings (5.26 to 7.35 lesions per leaf). No genotype was immune to ACC. The most resistant genotype was 'Muscia' (C. reticulata) and the most susceptible was 'Valencia Frost' (C. sinensis) (1.86 and 14.78 lesions per leaf, respectively). Approximately one-sixth of the genotypes showed a negative relationship of mean lesions per leaf with time, suggesting increasing resistance as they aged, due to a reduction in either new flush or plant size and structure. These results of the relative susceptibility of different citrus genotypes can be used in future research and to assist in varietal selection or for breeding purposes both within Brazil and other regions where ACC is an issue.
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Affiliation(s)
- Sérgio Alves de Carvalho
- Centro de Citricultura "Sylvio Moreira", Instituto Agronômico de Campinas (IAC), 13490-970, Cordeirópolis, SP, Brazil
| | | | - José Belasque
- Departamento de Fitopatologia e Nematologia, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Piracicaba, SP, Brazil
| | | | - José Croce-Filho
- Secretaria de Estado da Agricultura e do Abastecimento do Paraná, Maringá, PR, Brazil
| | - Clive H Bock
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS)-SEFTNRL, Byron, GA 31008
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Karcher DM, Jones DR, Abdo Z, Zhao Y, Shepherd TA, Xin H. Impact of commercial housing systems and nutrient and energy intake on laying hen performance and egg quality parameters. Poult Sci 2015; 94:485-501. [PMID: 25630672 PMCID: PMC4990894 DOI: 10.3382/ps/peu078] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The US egg industry is exploring alternative housing systems for laying hens. However, limited published research related to cage-free aviary systems and enriched colony cages exists related to production, egg quality, and hen nutrition. The laying hen's nutritional requirements and resulting productivity are well established with the conventional cage system, but diminutive research is available in regards to alternative housing systems. The restrictions exist with limited availability of alternative housing systems in research settings and the considerable expense for increased bird numbers in a replicate due to alternative housing system design. Therefore, the objective of the current study was to evaluate the impact of nutrient and energy intake on production and egg quality parameters from laying hens housed at a commercial facility. Lohmann LSL laying hens were housed in three systems: enriched colony cage, cage-free aviary, and conventional cage at a single commercial facility. Daily production records were collected along with dietary changes during 15 production periods (28-d each). Eggs were analyzed for shell strength, shell thickness, Haugh unit, vitelline membrane properties, and egg solids each period. An analysis of covariance (ANCOVA) coupled with a principal components analysis (PCA) approach was utilized to assess the impact of nutritional changes on production parameters and monitored egg quality factors. The traits of hen-day production and mortality had a response only in the PCA 2 direction. This finds that as house temperature and Met intake increases, there is an inflection point at which hen-day egg production is negatively effected. Dietary changes more directly influenced shell parameters, vitelline membrane parameters, and egg total solids as opposed to laying hen housing system. Therefore, further research needs to be conducted in controlled research settings on laying hen nutrient and energy intake in the alternative housing systems and resulting impact on egg quality measures.
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Affiliation(s)
- D M Karcher
- Department of Animal Science, Michigan State University, East Lansing, MI 48824
| | - D R Jones
- Egg Safety and Quality Research Unit
| | - Z Abdo
- South Atlantic Area, USDA Agricultural Research Service, Athens, GA 30605
| | - Y Zhao
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA 50011
| | - T A Shepherd
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA 50011
| | - H Xin
- Department of Agricultural and Biosystems Engineering, Iowa State University, Ames, IA 50011
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Li R, Baysal-Gurel F, Abdo Z, Miller SA, Ling KS. Evaluation of disinfectants to prevent mechanical transmission of viruses and a viroid in greenhouse tomato production. Virol J 2015; 12:5. [PMID: 25623384 PMCID: PMC4312592 DOI: 10.1186/s12985-014-0237-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 12/30/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In recent years, a number of serious disease outbreaks caused by viruses and viroids on greenhouse tomatoes in North America have resulted in significant economic losses to growers. The objectives of this study were to evaluate the effectiveness of commercial disinfectants against mechanical transmission of these pathogens, and to select disinfectants with broad spectrum reactivity to control general virus and viroid diseases in greenhouse tomato production. METHODS A total of 16 disinfectants were evaluated against Pepino mosaic virus (PepMV), Potato spindle tuber viroid (PSTVd), Tomato mosaic virus (ToMV), and Tobacco mosaic virus (TMV). The efficacy of each disinfectant to deactivate the pathogen's infectivity was evaluated in replicate experiments from at least three independent experiments. Any infectivity that remained in the treated solutions was assessed through bioassays on susceptible tomato plants through mechanical inoculation using inocula that had been exposed with the individual disinfectant for three short time periods (0-10 sec, 30 sec and 60 sec). A positive infection on the inoculated plant was determined through symptom observation and confirmed with enzyme-linked immunosorbent assay (PepMV, ToMV, and TMV) and real-time reverse transcription-PCR (PSTVd). Experimental data were analyzed using Logistic regression and the Bayesian methodology. RESULTS Statistical analyses using logistic regression and the Bayesian methodology indicated that two disinfectants (2% Virkon S and 10% Clorox regular bleach) were the most effective to prevent transmission of PepMV, PSTVd, ToMV, and TMV from mechanical inoculation. Lysol all-purpose cleaner (50%) and nonfat dry milk (20%) were also effective against ToMV and TMV, but with only partial effects for PepMV and PSTVd. CONCLUSION With the broad spectrum efficacy against three common viruses and a viroid, several disinfectants, including 2% Virkon S, 10% Clorox regular bleach and 20% nonfat dry milk, are recommend to greenhouse facilities for consideration to prevent general virus and viroid infection on tomato plants.
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Affiliation(s)
- Rugang Li
- USDA-Agricultural Research Service, U.S. Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC, 29414, USA.
| | - Fulya Baysal-Gurel
- Department of Plant Pathology, The Ohio State University, OARDC, 1680 Madison Avenue, Wooster, OH, 44691, USA.
| | - Zaid Abdo
- USDA-ARS, South Atlantic Area, 950 College Station Road, Athens, GA, 30605, USA.
| | - Sally A Miller
- Department of Plant Pathology, The Ohio State University, OARDC, 1680 Madison Avenue, Wooster, OH, 44691, USA.
| | - Kai-Shu Ling
- USDA-Agricultural Research Service, U.S. Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC, 29414, USA.
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Carmody LA, Zhao J, Kalikin LM, LeBar W, Simon RH, Venkataraman A, Schmidt TM, Abdo Z, Schloss PD, LiPuma JJ. The daily dynamics of cystic fibrosis airway microbiota during clinical stability and at exacerbation. Microbiome 2015; 3:12. [PMID: 25834733 PMCID: PMC4381400 DOI: 10.1186/s40168-015-0074-9] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 02/24/2015] [Indexed: 05/21/2023]
Abstract
BACKGROUND Recent work indicates that the airways of persons with cystic fibrosis (CF) typically harbor complex bacterial communities. However, the day-to-day stability of these communities is unknown. Further, airway community dynamics during the days corresponding to the onset of symptoms of respiratory exacerbation have not been studied. RESULTS Using 16S rRNA amplicon sequencing of 95 daily sputum specimens collected from four adults with CF, we observed varying degrees of day-to-day stability in airway bacterial community structures during periods of clinical stability. Differences were observed between study subjects with respect to the degree of community changes at the onset of exacerbation. Decreases in the relative abundance of dominant taxa were observed in three subjects at exacerbation. We observed no relationship between total bacterial load and clinical status and detected no viruses by multiplex PCR. CONCLUSION CF airway microbial communities are relatively stable during periods of clinical stability. Changes in microbial community structure are associated with some, but not all, pulmonary exacerbations, supporting previous observations suggesting that distinct types of exacerbations occur in CF. Decreased abundance of species that are dominant at baseline suggests a role for less abundant taxa in some exacerbations. Daily sampling revealed patterns of change in microbial community structures that may prove useful in the prediction and management of CF pulmonary exacerbations.
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Affiliation(s)
- Lisa A Carmody
- />Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Jiangchao Zhao
- />Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Linda M Kalikin
- />Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - William LeBar
- />Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Richard H Simon
- />Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Arvind Venkataraman
- />Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Thomas M Schmidt
- />Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Zaid Abdo
- />USDA-ARS, South Atlantic Area, Athens, GA USA
| | - Patrick D Schloss
- />Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - John J LiPuma
- />Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, MI 48109 USA
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Jones DR, Cox NA, Guard J, Fedorka-Cray PJ, Buhr RJ, Gast RK, Abdo Z, Rigsby LL, Plumblee JR, Karcher DM, Robison CI, Blatchford RA, Makagon MM. Microbiological impact of three commercial laying hen housing systems. Poult Sci 2014; 94:544-51. [PMID: 25480737 PMCID: PMC4990896 DOI: 10.3382/ps/peu010] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Hen housing for commercial egg production continues to be a societal and regulatory concern. Controlled studies have examined various aspects of egg safety, but a comprehensive assessment of commercial hen housing systems in the US has not been conducted. The current study is part of a holistic, multidisciplinary comparison of the diverse aspects of commercial conventional cage, enriched colony cage, and cage-free aviary housing systems and focuses on environmental and egg microbiology. Environmental swabs and eggshell pools were collected from all housing systems during 4 production periods. Total aerobes and coliforms were enumerated, and the prevalence of Salmonella and Campylobacter spp. was determined. Environmental aerobic and coliform counts were highest for aviary drag swabs (7.5 and 4.0 log cfu/mL, respectively) and enriched colony cage scratch pad swabs (6.8 and 3.8 log cfu/mL, respectively). Aviary floor and system wire shell pools had the greatest levels of aerobic contamination for all eggshell pools (4.9 and 4.1 log cfu/mL, respectively). Hens from all housing systems were shedding Salmonella spp. (89–100% of manure belt scraper blade swabs). The dry belt litter removal processes for all housing systems appear to affect Campylobacter spp. detection (0–41% of manure belt scraper blade swabs) considering detection of Campylobacter spp. was much higher for other environmental samples. Aviary forage area drag swabs were 100% contaminated with Campylobacter spp., whereas enriched colony cage scratch pads had a 93% positive rate. There were no differences in pathogen detection in the shell pools from the 3 housing systems. Results indicate egg safety is enhanced when hens in alternative housing systems use nest boxes. Additionally, current outcomes indicate the use of scratch pads in hen housing systems needs to be more thoroughly investigated for effects on hen health and egg safety.
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Affiliation(s)
- D R Jones
- USDA, Agricultural Research Service, Russell Research Center, Athens, GA 30605
| | - N A Cox
- USDA, Agricultural Research Service, Russell Research Center, Athens, GA 30605
| | - J Guard
- USDA, Agricultural Research Service, Russell Research Center, Athens, GA 30605
| | - P J Fedorka-Cray
- USDA, Agricultural Research Service, Russell Research Center, Athens, GA 30605
| | - R J Buhr
- USDA, Agricultural Research Service, Russell Research Center, Athens, GA 30605
| | - R K Gast
- USDA, Agricultural Research Service, Russell Research Center, Athens, GA 30605
| | - Z Abdo
- USDA, Agricultural Research Service, Russell Research Center, Athens, GA 30605
| | - L L Rigsby
- USDA, Agricultural Research Service, Russell Research Center, Athens, GA 30605
| | - J R Plumblee
- USDA, Agricultural Research Service, Russell Research Center, Athens, GA 30605
| | - D M Karcher
- Department of Animal Science, Michigan State University, East Lansing 48824
| | - C I Robison
- Department of Animal Science, Michigan State University, East Lansing 48824
| | - R A Blatchford
- Department of Animal Science, University of California, Davis 95616
| | - M M Makagon
- Department of Animal Science, Michigan State University, East Lansing 48824
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Ammar ED, Richardson ML, Abdo Z, Hall DG, Shatters RG. Differences in stylet sheath occurrence and the fibrous ring (sclerenchyma) between xCitroncirus plants relatively resistant or susceptible to adults of the Asian citrus psyllid Diaphorina citri (Hemiptera: Liviidae). PLoS One 2014; 9:e110919. [PMID: 25343712 PMCID: PMC4208817 DOI: 10.1371/journal.pone.0110919] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 09/26/2014] [Indexed: 11/19/2022] Open
Abstract
The Asian citrus psyllid (ACP, Diaphorina citri, Hemiptera: Liviidae), is the principal vector of the phloem-limited bacteria strongly associated with huanglongbing (HLB), the world's most serious disease of citrus. Host plant resistance may provide an environmentally safe and sustainable method of controlling ACP and/or HLB. Two xCitroncirus accessions (hybrids of Poncirus trifoliata and Citrus spp.), that are relatively resistant (UN-3881) or relatively susceptible (Troyer-1459) to ACP adults with regard to adult longevity, were compared in relation to ACP feeding behavior and some structural features of the leaf midrib. The settling (putative feeding/probing) sites of ACP adults on various parts of the leaf were not influenced primarily by plant accession. However, fewer ACP stylet sheaths were found in the midrib and fewer stylet sheath termini reached the vascular bundle (phloem and/or xylem) in UN-3881 compared to Troyer-1459 plants. Furthermore, in midribs of UN-3881 leaves the fibrous ring (sclerenchyma) around the phloem was significantly wider (thicker) compared to that in midribs of Troyer-1459 leaves. Our data indicate that feeding and/or probing by ACP adults into the vascular bundle is less frequent in the more resistant (UN-3881) than in the more susceptible (Troyer-1459) accessions. Our results also suggest that the thickness of the fibrous ring may be a barrier to stylet penetration into the vascular bundle, which is important for successful ACP feeding on the phloem and for transmitting HLB-associated bacteria. These results may help in the development of citrus plants resistant to ACP, which in turn could halt or slow the spread of the HLB-associated bacteria by this vector.
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Affiliation(s)
- El-Desouky Ammar
- United States Department of Agriculture-Agricultural Research Service, Horticultural Research Laboratory, Fort Pierce, Florida, United States of America
- * E-mail:
| | - Matthew L. Richardson
- United States Department of Agriculture-Agricultural Research Service, Horticultural Research Laboratory, Fort Pierce, Florida, United States of America
| | - Zaid Abdo
- United States Department of Agriculture-Agricultural Research Service, South Atlantic Area, Athens, Georgia, United States of America
| | - David G. Hall
- United States Department of Agriculture-Agricultural Research Service, Horticultural Research Laboratory, Fort Pierce, Florida, United States of America
| | - Robert G. Shatters
- United States Department of Agriculture-Agricultural Research Service, Horticultural Research Laboratory, Fort Pierce, Florida, United States of America
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Ni X, Toews MD, Buntin GD, Carpenter JE, Huffaker A, Schmelz EA, Cottrell TE, Abdo Z. Influence of brown stink bug feeding, planting date and sampling time on common smut infection of maize. Insect Sci 2014; 21:564-571. [PMID: 24963742 DOI: 10.1111/1744-7917.12149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/10/2014] [Indexed: 06/03/2023]
Abstract
Phytopathogen infections are frequently influenced by both biotic and abiotic factors in a crop field. The effect of brown stink bug, Euschistus servus (Hemiptera: Pentatomidae), feeding and planting date and sampling time on common smut (Ustilago maydis) infection percentage of maize plants was examined in 2005 and 2006, and 2010 and 2011, respectively. Brown stink bug adult feeding on maize hybrid "DKC6971" at flowering in 2005 and 2006 did not influence smut infection percentage when examined using 3 treatments (i.e., 0 adult, 5 adults, and 5 adults mixed with the smut spores). The smut infection percentages were <3% (n = 12) in the 3 treatments. The smut infection percentage among the 4 weekly samplings was the same, so was natural aflatoxin contamination at harvest among the treatments. The 2nd experiment showed that planting date did not affect the smut infection percentage in either 2010 or 2011. But, the smut infection percentage from the postflowering sampling was greater than preflowering sampling in both years. The smut infection percentage varied among the germplasm lines in 2010, but not in 2011. This study demonstrated that brown stink bug feeding at flowering had no effect on smut infection in maize, and the best time for smut evaluation would be after flowering. The temperature and precipitation might have also influenced the percentage of smut-infected maize plants during the 4 years when the experiments were conducted. The similarity between kernel-colonizing U. maydis and Aspergillus flavus infections and genotype × environment interaction were also discussed.
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Affiliation(s)
- Xinzhi Ni
- USDA-ARS, Crop Genetics and Breeding Research Unit, Tifton, GA, 31793
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49
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Hou D, Zhou X, Zhong X, Settles ML, Herring J, Wang L, Abdo Z, Forney LJ, Xu C. Microbiota of the seminal fluid from healthy and infertile men. Fertil Steril 2013; 100:1261-9. [PMID: 23993888 DOI: 10.1016/j.fertnstert.2013.07.1991] [Citation(s) in RCA: 143] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 06/21/2013] [Accepted: 07/15/2013] [Indexed: 02/05/2023]
Abstract
OBJECTIVE To explore potential causes of male infertility by determining the composition and structure of commensal bacterial communities in seminal fluids. DESIGN Microscopy of Gram-stained semen samples and classification of 16S rRNA gene sequences to determine the species composition of semen bacterial communities. SETTING Clinical andrology laboratory and academic research laboratories. PATIENT(S) Nineteen sperm donors and 58 infertility patients. INTERVENTION(S) None. MAIN OUTCOME MEASURE(S) Classification of 16S rRNA gene sequences, clustering of seminal microbial communities, and multiple statistical tests. RESULT(S) High numbers of diverse kinds of bacteria were present in most samples of both sperm donors and infertility patients. The bacterial communities varied widely among subjects, but they could be clustered into six groups based on similarities in composition and the rank abundances of taxa. Overall, there were no significant differences between sperm donors and infertility patients. However, multiple statistical tests showed a significant negative association between sperm quality and the presence of Anaerococcus. The results also indicated that many of the bacterial taxa identified in semen also occur in the vaginal communities of some women, especially those with bacterial vaginosis, which suggests that heterosexual sex partners may share bacteria. CONCLUSION(S) Diverse kinds of bacteria were present in the human semen, but there were no significant differences between sperm donors and infertility patients. The presence of Anaerococcus might be a biomarker for low sperm quality.
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Affiliation(s)
- Dongsheng Hou
- Department of Histology and Embryology, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China; Shanghai Key Laboratory of Reproductive Medicine, Shanghai, People's Republic of China
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Hickey RJ, Abdo Z, Zhou X, Nemeth K, Hansmann M, Osborn TW, Wang F, Forney LJ. Effects of tampons and menses on the composition and diversity of vaginal microbial communities over time. BJOG 2013; 120:695-704; discussion 704-6. [DOI: 10.1111/1471-0528.12151] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2012] [Indexed: 11/27/2022]
Affiliation(s)
| | | | | | - K Nemeth
- FemCare Product Safety and Regulatory Affairs; The Procter & Gamble Company; Cincinnati; OH; USA
| | - M Hansmann
- FemCare Product Safety and Regulatory Affairs; The Procter & Gamble Company; Cincinnati; OH; USA
| | - TW Osborn
- FemCare Product Development; The Procter & Gamble Company; Cincinnati; OH; USA
| | - F Wang
- FemCare Product Development; The Procter & Gamble Company; Cincinnati; OH; USA
| | - LJ Forney
- Institute for Bioinformatics and Evolutionary Studies; University of Idaho; Moscow; ID; USA
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