Publications by authors named "Zaid Abdo"

62 Publications

Complete Genome Sequences of Eight Streptococcus equi subsp. Strains Isolated from Mares in Estrus with Endometritis.

Microbiol Resour Announc 2021 Jul 1;10(26):e0132120. Epub 2021 Jul 1.

Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA.

Eight isolates of Streptococcus equi subsp. were isolated from mares with clinical cases of endometritis. S. equi subsp. strains were chosen for sequencing based on differing levels of biofilm production . Using Illumina short-read sequencing in conjunction with MinION sequencing, we report the genomes of eight isolates.
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http://dx.doi.org/10.1128/MRA.01321-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8248867PMC
July 2021

Population genomics of invasive rodents on islands: Genetic consequences of colonization and prospects for localized synthetic gene drive.

Evol Appl 2021 May 10;14(5):1421-1435. Epub 2021 Mar 10.

National Wildlife Research Center USDA APHIS Wildlife Services Fort Collins Colorado USA.

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 () 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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http://dx.doi.org/10.1111/eva.13210DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8127709PMC
May 2021

Temporal and Spatial Blood Feeding Patterns of Urban Mosquitoes in the San Juan Metropolitan Area, Puerto Rico.

Insects 2021 Feb 2;12(2). Epub 2021 Feb 2.

School of Biological, Environmental, & Earth Sciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA.

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, ( = 586) and ( = 18). 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. 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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http://dx.doi.org/10.3390/insects12020129DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7913113PMC
February 2021

An Open-Source Program (Haplo-ST) for Whole-Genome Sequence Typing Shows Extensive Diversity among Listeria monocytogenes Isolates in Outdoor Environments and Poultry Processing Plants.

Appl Environ Microbiol 2020 12 17;87(1). Epub 2020 Dec 17.

Institute of Bioinformatics, University of Georgia, Athens, Georgia, USA.

A reliable and standardized classification of is important for accurate strain identification during outbreak investigations. Current whole-genome sequencing (WGS)-based approaches for strain characterization are either difficult to standardize, rendering them less suitable for data exchange, or are not freely available. Thus, we developed a portable and open-source tool, Haplo-ST, to improve standardization and provide maximum discriminatory potential to WGS data tied to a multilocus sequence typing (MLST) framework. Haplo-ST performs whole-genome MLST (wgMLST) for while allowing for data exchangeability worldwide. This tool takes in (i) raw WGS reads as input, (ii) cleans the raw data according to user-specified parameters, (iii) assembles genes across loci by mapping to genes from reference strains, and (iv) assigns allelic profiles to assembled genes and provides a wgMLST subtyping for each isolate. Data exchangeability relies on the tool assigning allelic profiles based on a centralized nomenclature defined by the widely used BIGSdb- database. Tests of Haplo-ST's performance with simulated reads from reference strains demonstrated high sensitivity (97.5%), and coverage depths of ≥20× were found to be sufficient for wgMLST profiling. We then used Haplo-ST to characterize and differentiate between two groups of isolates derived from the natural environment and poultry processing plants. Phylogenetic reconstruction identified lineages within each group, and no lineage specificity was observed with isolate phenotypes (transient versus persistent) or origins. Genetic differentiation analyses between isolate groups identified 21 significantly differentiated loci, potentially enriched for adaptation and persistence of within poultry processing plants. We have developed an open-source tool (https://github.com/swarnalilouha/Haplo-ST) that provides allele-based subtyping of isolates at the whole-genome level. Along with allelic profiles, this tool also generates allele sequences and identifies paralogs, which is useful for phylogenetic tree reconstruction and deciphering relationships between closely related isolates. More broadly, Haplo-ST is flexible and can be adapted to characterize the genome of any haploid organism simply by installing an organism-specific gene database. Haplo-ST also allows for scalable subtyping of isolates; fewer reference genes can be used for low-resolution typing, whereas higher resolution can be achieved by increasing the number of genes used in the analysis. Our tool enabled clustering of isolates into lineages and detection of potential loci for adaptation and persistence in food processing environments. Findings from these analyses highlight the effectiveness of Haplo-ST in subtyping and evaluating relationships among isolates in studies of bacterial population genetics.
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http://dx.doi.org/10.1128/AEM.02248-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7755245PMC
December 2020

Reused poultry litter microbiome with competitive exclusion potential against Salmonella Heidelberg.

J Environ Qual 2020 Jul 28;49(4):869-881. Epub 2020 May 28.

USDA-ARS, Food Animal Environmental Systems Research, Bowling Green, KY, 42101, USA.

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 NH , 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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http://dx.doi.org/10.1002/jeq2.20081DOI Listing
July 2020

A comparative study of the gut microbiome in Egyptian patients with Type I and Type II diabetes.

PLoS One 2020 9;15(9):e0238764. Epub 2020 Sep 9.

Department of Microbiology Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America.

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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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0238764PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7480833PMC
November 2020

Population genomic transformations induced by isolation of wild bird avian influenza viruses (Orthomyxoviridae) in embryonated chicken eggs.

Infect Genet Evol 2021 Jun 20;90:104505. Epub 2020 Aug 20.

Department of Microbiology, Immunology, and Pathology, College of Veterinary and Biomedical Sciences, Colorado State University, Fort Collins, CO 80523, USA.

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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http://dx.doi.org/10.1016/j.meegid.2020.104505DOI Listing
June 2021

Ecological drivers of African swine fever virus persistence in wild boar populations: Insight for control.

Ecol Evol 2020 Mar 18;10(6):2846-2859. Epub 2020 Feb 18.

Mammal Research Institute Polish Academy of Sciences Białowieża Poland.

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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http://dx.doi.org/10.1002/ece3.6100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7083705PMC
March 2020

Impact of oral probiotic Lactobacillus acidophilus vaccine strains on the immune response and gut microbiome of mice.

PLoS One 2019 12;14(12):e0225842. Epub 2019 Dec 12.

Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America.

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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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0225842PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6907787PMC
March 2020

Predicting whole genome sequencing success for archived avian influenza virus (Orthomyxoviridae) samples using real-time and droplet PCRs.

J Virol Methods 2020 02 12;276:113777. Epub 2019 Nov 12.

Department of Microbiology, Immunology, and Pathology, College of Veterinary and Biomedical Sciences, Colorado State University, Fort Collins, CO, 80523, USA. Electronic address:

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 C 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 (C = 15, copies/μL = 49,350), 0.75 (C = 24, copies/μL = 16,800), 0.50 (C = 29, copies/μL = <1), and 0.25 (C = 235, copies/μL = <1). We also identified values at which we predictably recovered HA and NA segments for diagnosing subtypes (C = 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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http://dx.doi.org/10.1016/j.jviromet.2019.113777DOI Listing
February 2020

Rice bran supplementation modulates growth, microbiota and metabolome in weaning infants: a clinical trial in Nicaragua and Mali.

Sci Rep 2019 09 26;9(1):13919. Epub 2019 Sep 26.

Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, 80523, USA.

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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http://dx.doi.org/10.1038/s41598-019-50344-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6763478PMC
September 2019

Horizontal Gene Transfer and Acquired Antibiotic Resistance in Salmonella enterica Serovar Heidelberg following Incubation in Broiler Ceca.

Appl Environ Microbiol 2019 11 30;85(22). Epub 2019 Oct 30.

Department of Environmental Health Science, University of Georgia, Athens, Georgia, USA.

The chicken gastrointestinal tract harbors microorganisms that play a role in the health and disease status of the host. The cecum is the part of the gut that carries the highest microbial densities, has the longest residence time of digesta, and is a vital site for urea recycling and water regulation. Therefore, the cecum provides a rich environment for bacteria to horizontally transfer genes between one another via mobile genetic elements such as plasmids and bacteriophages. In this study, we used broiler chicken cecum as a model to investigate antibiotic resistance genes that can be transferred from cecal flora to serovar Heidelberg. We used whole-genome sequencing and resistome enrichment to decipher the interactions between Heidelberg, the gut microbiome, and acquired antibiotic resistance. After 48 h of incubation of ceca under microaerophilic conditions, we recovered one Heidelberg isolate with an acquired IncK2 plasmid (88 kb) carrying an extended-spectrum-β-lactamase gene ( ). , this plasmid was transferable between and Heidelberg strains but transfer was unsuccessful between Heidelberg strains. An in-depth genetic characterization of transferred plasmids suggests that they share significant homology with P1-like phages. This study contributes to our understanding of horizontal gene transfer between an important foodborne pathogen and the chicken gut microbiome. Heidelberg is a clinically important serovar, linked to foodborne illness and among the top 5 serovars isolated from poultry in the United States and Canada. Acquisition of new genetic material from the microbial flora in the gastrointestinal tract of food animals, including broilers, may contribute to increased fitness of pathogens like Heidelberg and may increase their level of antibiotic tolerance. Therefore, it is critical to gain a better understanding of the interactions that occur between important pathogens and the commensals present in the animal gut and other agroecosystems. In this report, we show that the native flora in broiler ceca were capable of transferring mobile genetic elements carrying the AmpC β-lactamase ( ) gene to an important foodborne pathogen, Heidelberg. The potential role for bacteriophage transduction is also discussed.
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http://dx.doi.org/10.1128/AEM.01903-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6821953PMC
November 2019

Improving risk assessment of the emergence of novel influenza A viruses by incorporating environmental surveillance.

Philos Trans R Soc Lond B Biol Sci 2019 09 12;374(1782):20180346. Epub 2019 Aug 12.

National Wildlife Research Center, USDA-APHIS, Fort Collins, CO 80521, USA.

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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http://dx.doi.org/10.1098/rstb.2018.0346DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6711309PMC
September 2019

Hierarchical Hidden Markov models enable accurate and diverse detection of antimicrobial resistance sequences.

Commun Biol 2019 6;2:294. Epub 2019 Aug 6.

2Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL 32611 USA.

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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http://dx.doi.org/10.1038/s42003-019-0545-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6684577PMC
April 2020

Effects of a Saccharomyces cerevisiae fermentation product on liver abscesses, fecal microbiome, and resistome in feedlot cattle raised without antibiotics.

Sci Rep 2019 02 22;9(1):2559. Epub 2019 Feb 22.

Department of Animal Sciences, Colorado State University, Fort Collins, Colorado, USA.

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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http://dx.doi.org/10.1038/s41598-019-39181-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6385275PMC
February 2019

Applications of the FIV Model to Study HIV Pathogenesis.

Viruses 2018 04 20;10(4). Epub 2018 Apr 20.

Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO 80523, USA.

Feline immunodeficiency virus (FIV) is a naturally-occurring retrovirus that infects domestic and non-domestic feline species, producing progressive immune depletion that results in an acquired immunodeficiency syndrome (AIDS). Much has been learned about FIV since it was first described in 1987, particularly in regard to its application as a model to study the closely related lentivirus, human immunodeficiency virus (HIV). In particular, FIV and HIV share remarkable structure and sequence organization, utilize parallel modes of receptor-mediated entry, and result in a similar spectrum of immunodeficiency-related diseases due to analogous modes of immune dysfunction. This review summarizes current knowledge of FIV infection kinetics and the mechanisms of immune dysfunction in relation to opportunistic disease, specifically in regard to studying HIV pathogenesis. Furthermore, we present data that highlight changes in the oral microbiota and oral immune system during FIV infection, and outline the potential for the feline model of oral AIDS manifestations to elucidate pathogenic mechanisms of HIV-induced oral disease. Finally, we discuss advances in molecular biology, vaccine development, neurologic dysfunction, and the ability to apply pharmacologic interventions and sophisticated imaging technologies to study experimental and naturally occurring FIV, which provide an excellent, but often overlooked, resource for advancing therapies and the management of HIV/AIDS.
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http://dx.doi.org/10.3390/v10040206DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5923500PMC
April 2018

Associations between sexual habits, menstrual hygiene practices, demographics and the vaginal microbiome as revealed by Bayesian network analysis.

PLoS One 2018 24;13(1):e0191625. Epub 2018 Jan 24.

Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America.

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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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0191625PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5783405PMC
March 2018

Enrichment allows identification of diverse, rare elements in metagenomic resistome-virulome sequencing.

Microbiome 2017 10 17;5(1):142. Epub 2017 Oct 17.

Department of Clinical Sciences, Colorado State University, Fort Collins, CO, USA.

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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http://dx.doi.org/10.1186/s40168-017-0361-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5645900PMC
October 2017

Whole-Genome Sequencing and Concordance Between Antimicrobial Susceptibility Genotypes and Phenotypes of Bacterial Isolates Associated with Bovine Respiratory Disease.

G3 (Bethesda) 2017 09 7;7(9):3059-3071. Epub 2017 Sep 7.

Department of Animal Science, University of California, Davis, California 95616

Extended laboratory culture and antimicrobial susceptibility testing timelines hinder rapid species identification and susceptibility profiling of bacterial pathogens associated with bovine respiratory disease, the most prevalent cause of cattle mortality in the United States. Whole-genome sequencing offers a culture-independent alternative to current bacterial identification methods, but requires a library of bacterial reference genomes for comparison. To contribute new bacterial genome assemblies and evaluate genetic diversity and variation in antimicrobial resistance genotypes, whole-genome sequencing was performed on bovine respiratory disease-associated bacterial isolates (, , , and ) from dairy and beef cattle. One hundred genomically distinct assemblies were added to the NCBI database, doubling the available genomic sequences for these four species. Computer-based methods identified 11 predicted antimicrobial resistance genes in three species, with none being detected in While computer-based analysis can identify antibiotic resistance genes within whole-genome sequences (genotype), it may not predict the actual antimicrobial resistance observed in a living organism (phenotype). Antimicrobial susceptibility testing on 64 , , and isolates had an overall concordance rate between genotype and phenotypic resistance to the associated class of antimicrobials of 72.7% ( < 0.001), showing substantial discordance. Concordance rates varied greatly among different antimicrobial, antibiotic resistance gene, and bacterial species combinations. This suggests that antimicrobial susceptibility phenotypes are needed to complement genomically predicted antibiotic resistance gene genotypes to better understand how the presence of antibiotic resistance genes within a given bacterial species could potentially impact optimal bovine respiratory disease treatment and morbidity/mortality outcomes.
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http://dx.doi.org/10.1534/g3.117.1137DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5592931PMC
September 2017

Determining the distribution of fitness effects using a generalized Beta-Burr distribution.

Theor Popul Biol 2018 07 12;122:88-96. Epub 2017 Jul 12.

Department of Microbiology, Immunology and Pathology, Colorado State University, Ft. Collins, CO 80523, United States. Electronic address:

In Beisel et al. (2007), a likelihood framework, based on extreme value theory (EVT), was developed for determining the distribution of fitness effects for adaptive mutations. In this paper we extend this framework beyond the extreme distributions and develop a likelihood framework for testing whether or not extreme value theory applies. By making two simple adjustments to the Generalized Pareto Distribution (GPD) we introduce a new simple five parameter probability density function that incorporates nearly every common (continuous) probability model ever used. This means that all of the common models are nested. This has important implications in model selection beyond determining the distribution of fitness effects. However, we demonstrate the use of this distribution utilizing likelihood ratio testing to evaluate alternative distributions to the Gumbel and Weibull domains of attraction of fitness effects. We use a bootstrap strategy, utilizing importance sampling, to determine where in the parameter space will the test be most powerful in detecting deviations from these domains and at what sample size, with focus on small sample sizes (n<20). Our results indicate that the likelihood ratio test is most powerful in detecting deviation from the Gumbel domain when the shape parameters of the model are small while the test is more powerful in detecting deviations from the Weibull domain when these parameters are large. As expected, an increase in sample size improves the power of the test. This improvement is observed to occur quickly with sample size n≥10 in tests related to the Gumbel domain and n≥15 in the case of the Weibull domain. This manuscript is in tribute to the contributions of Dr. Paul Joyce to the areas of Population Genetics, Probability Theory and Mathematical Statistics. A Tribute section is provided at the end that includes Paul's original writing in the first iterations of this manuscript. The Introduction and Alternatives to the GPD sections were obtained from the last iteration that Paul and I have worked on, with some adjustments. I hope that the rest gives justice to his thoughts and possible conclusions that he might have wanted to portray.
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http://dx.doi.org/10.1016/j.tpb.2017.07.001DOI Listing
July 2018

Derivation of chicken induced pluripotent stem cells tolerant to Newcastle disease virus-induced lysis through multiple rounds of infection.

Virol J 2016 12 5;13(1):205. Epub 2016 Dec 5.

US National Poultry Research Center, Exotic and Emerging Avian Viral Diseases Research Unit, Southeast Poultry Research Laboratory, Athens, GA, 30605, USA.

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.
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http://dx.doi.org/10.1186/s12985-016-0659-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5139146PMC
December 2016

MEGARes: an antimicrobial resistance database for high throughput sequencing.

Nucleic Acids Res 2017 01 28;45(D1):D574-D580. Epub 2016 Nov 28.

Department of Computer and Information Science and Engineering, University of Florida, Gainesville, FL 32611, USA

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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http://dx.doi.org/10.1093/nar/gkw1009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210519PMC
January 2017

Subtyping of Salmonella enterica Subspecies I Using Single-Nucleotide Polymorphisms in Adenylate Cyclase.

Foodborne Pathog Dis 2016 07 1;13(7):350-62. Epub 2016 Apr 1.

1 U.S. National Poultry Research Center , U.S. Department of Agriculture, Athens, Georgia .

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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http://dx.doi.org/10.1089/fpd.2015.2088DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4939371PMC
July 2016

Draft Genome Sequence of Cercospora arachidicola, Causal Agent of Early Leaf Spot in Peanuts.

Genome Announc 2015 Nov 5;3(6). Epub 2015 Nov 5.

National Peanut Research Laboratory, Dawson, Georgia, USA

Cercospora arachidicola, causal agent of early leaf spot, is an economically important peanut pathogen. Lack of genetic information about this fungus prevents understanding the role that potentially diverse genotypes may have in peanut breeding programs. Here, we report for the first time a draft genome sequence of C. arachidicola.
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http://dx.doi.org/10.1128/genomeA.01281-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4645201PMC
November 2015

Maize death acids, 9-lipoxygenase-derived cyclopente(a)nones, display activity as cytotoxic phytoalexins and transcriptional mediators.

Proc Natl Acad Sci U S A 2015 Sep 24;112(36):11407-12. Epub 2015 Aug 24.

Section of Cell and Developmental Biology, University of California at San Diego, La Jolla, CA 92093-0380;

Plant damage promotes the interaction of lipoxygenases (LOXs) with fatty acids yielding 9-hydroperoxides, 13-hydroperoxides, and complex arrays of oxylipins. The action of 13-LOX on linolenic acid enables production of 12-oxo-phytodienoic acid (12-OPDA) and its downstream products, termed "jasmonates." As signals, jasmonates have related yet distinct roles in the regulation of plant resistance against insect and pathogen attack. A similar pathway involving 9-LOX activity on linolenic and linoleic acid leads to the 12-OPDA positional isomer, 10-oxo-11-phytodienoic acid (10-OPDA) and 10-oxo-11-phytoenoic acid (10-OPEA), respectively; however, physiological roles for 9-LOX cyclopentenones have remained unclear. In developing maize (Zea mays) leaves, southern leaf blight (Cochliobolus heterostrophus) infection results in dying necrotic tissue and the localized accumulation of 10-OPEA, 10-OPDA, and a series of related 14- and 12-carbon metabolites, collectively termed "death acids." 10-OPEA accumulation becomes wound inducible within fungal-infected tissues and at physiologically relevant concentrations acts as a phytoalexin by suppressing the growth of fungi and herbivores including Aspergillus flavus, Fusarium verticillioides, and Helicoverpa zea. Unlike previously established maize phytoalexins, 10-OPEA and 10-OPDA display significant phytotoxicity. Both 12-OPDA and 10-OPEA promote the transcription of defense genes encoding glutathione S transferases, cytochrome P450s, and pathogenesis-related proteins. In contrast, 10-OPEA only weakly promotes the accumulation of multiple protease inhibitor transcripts. Consistent with a role in dying tissue, 10-OPEA application promotes cysteine protease activation and cell death, which is inhibited by overexpression of the cysteine protease inhibitor maize cystatin-9. Unlike jasmonates, functions for 10-OPEA and associated death acids are consistent with specialized roles in local defense reactions.
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http://dx.doi.org/10.1073/pnas.1511131112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4568653PMC
September 2015

Mi-1-Mediated Nematode Resistance in Tomatoes is Broken by Short-Term Heat Stress but Recovers Over Time.

J Nematol 2015 Jun;47(2):133-40

Center for Medical and Veterinary Entomology USDA-ARS, Gainesville, FL.

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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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4492288PMC
June 2015

The daily dynamics of cystic fibrosis airway microbiota during clinical stability and at exacerbation.

Microbiome 2015 1;3:12. Epub 2015 Apr 1.

Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, MI 48109 USA.

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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http://dx.doi.org/10.1186/s40168-015-0074-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4381400PMC
April 2015

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 Feb;99(2):207-218

USDA-ARS-SAA, Athens, GA 30605.

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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http://dx.doi.org/10.1094/PDIS-04-14-0384-REDOI Listing
February 2015

Evaluation of disinfectants to prevent mechanical transmission of viruses and a viroid in greenhouse tomato production.

Virol J 2015 Jan 27;12. Epub 2015 Jan 27.

USDA-Agricultural Research Service, U.S. Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC, 29414, USA.

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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http://dx.doi.org/10.1186/s12985-014-0237-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4312592PMC
January 2015
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