Biology subjects

Woyda, R.

Publications and source records attributed to Woyda, R..

6 recordsLinked to original sources

bioRxiv2023

CAMPER: curated annotations for profiling microbial polyphenol metabolic potential

SummaryPolyphenols are diverse and abundant carbon sources across ecosystems-having important roles in host-associated and terrestrial systems alike. However, the microbial genes encoding polyphenol metabolic enzymes are poorly represented in commonly used annotation databases, limiting widespread surveying of this metabolism. Here we present CAMPER, a tool that combines custom annotation searches with database-derived searches to both annotate and summarize polyphenol metabolism genes for a wide audience. With CAMPER, users will identify potential polyphenol-active genes and genomes to more broadly understand microbial carbon cycling in their datasets. Availability and ImplementationCAMPER is implemented in Python and is published under the GNU General Public License Version 3. It is available as both a standalone tool and as a database in DRAM v.1.5+. The source code and full documentation is available on GitHub at https://github.com/WrightonLabCSU/CAMPER.

bioinformatics↗

bioRxiv2023

Management factors influence Salmonella persistence in reused poultry litter over three successive flocks

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. Understanding how management practices and environmental factors influence Salmonella populations in broiler chicken production may aid in reducing the risk of food-borne illness in humans. Utilizing whole genome sequencing with antimicrobial and heavy metal resistance, virulence factor and plasmid identification, we have characterized the genetic diversity of Salmonella enterica isolates (n = 55) obtained from broiler chicken litter. S. enterica isolates were recovered from the litter of broiler chickens over three consecutive flocks in four broiler houses on a single integrated farm in Georgia, USA. The chickens 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. Serovar Kentucky isolates harboring metal resistance operons were the only Salmonella isolates recovered from the litter of third flock cohort. These results suggest the addition of copper sulfate to drinking water may have selected for S. Kentucky isolates harboring plasmid-borne copper resistance genes and may explain their persistence in litter from flock to flock. ImportanceSalmonella foodborne illnesses are the leading cause of hospitalizations and deaths, resulting in a high economic burden on the healthcare system. Globally, chicken meat is one of the highest consumed meats and is a predominant source of foodborne illness. 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 post-harvest chicken samples, there is a gap in our understanding of the prevalence and persistence of Salmonella in pre-harvest and in particular their makeup of antibiotic resistance genes, virulence factors and metal resistance genes. The objective of this study was to determine how on-farm management practices and environmental factors influence Salmonella persistence, as well as the antimicrobial resistance genes and virulence factors they harbor. In this study we demonstrate that broiler chickens raised without antibiotics are less likely to harbor antibiotic resistance, however the practice of adding acidified copper sulfate to drinking water may select for strains carrying metal resistant genes.

genomics↗

bioRxiv2023

Broiler house environment and litter management practices impose selective pressures on antimicrobial resistance genes and virulence factors of Campylobacter

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. ImportanceCampylobacter is a leading cause of foodborne illness in the United States due to the consumption of contaminated food products or from mishandling of food products, often associated with chicken meat. Campylobacter is common in the microbiota of avian and mammalian gut; however, the acquisition of antimicrobial resistance genes and virulence factors may result in strains that pose a significant threat to public health. Although there are studies that have investigated the genetic diversity of Campylobacter strains isolated from post-harvest chicken samples, there is limited data on the genome characteristics of isolates recovered from pre-harvest broiler production. In this study, we show that Campylobacter jejuni and Campylobacter coli that differ in their carriage of antimicrobial resistance and virulence factors may differ in their ability to evade host defense mechanisms and colonize the gut of chickens and humans. Furthermore, we found that differences in virulence factor profiles were explained by the species of Campylobacter and its multilocus sequence type.

genetics↗

bioRxiv2023

Population genomic analysis of an emerging pathogen Lonsdalea quercina affecting various species of oaks in western North America

Previously unrecognized diseases continue to threaten the health of forest ecosystems globally. 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 within 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 well supported clades within the genus Lonsdalea, with an average nucleotide identity between them near species boundaries (95.31%) for bacteria, suggesting long isolation. Populations comprise distinct patterns in genetic structure and distribution. Genotypes collected from different host species and habitats were randomly distributed within the California cluster, while most Colorado isolates from introduced planted trees were distinct from isolates collected from a natural stand of CO native Q. gambelii, indicating the presence of cryptic population structure. The distribution of clones in California varied, while Colorado clones were always collected from neighboring trees. Despite its recent emergence, the Colorado population had higher nucleotide diversity, possibly 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 conditions changes. To our knowledge, this is the first study on L. quercina population structure. Further studies are warranted to understand evolutionary relationships among L. quercina populations from different areas, including the native habitat of red oak in northeastern USA. ImportanceBacterial pathogens from genus Lonsdalea severely affect oak forest ecosystems worldwide. In Colorado, USA, L. quercina is one of the causal agents of drippy blight disease on introduced red oak trees. Prior to discovery of drippy blight in Colorado, L. quercina was reported on oak trees in California, causing drippy nut on acorns of native oaks. Due to its recent emergence in Colorado, the origin and movement of L. quercina are unknown. In this study we investigated evolutionary relationships within genus Lonsdalea worldwide and L. quercina population structure in western USA. Our results demonstrate that L. quercina Colorado and California populations comprise distinct patterns of genetic structure and distribution, suggesting that accidental pathogen introduction from California to Colorado is unlikely. Higher nucleotide diversity in a recently emerged Colorado population suggests the bacterial strains might be migrants that initially moved with nursery stock from other areas in the last century. For example, Colorado strains of L. quercina may have moved from native stands of red oaks in the northeastern or southern USA. Curiously, however, this disease is not known in native red oak in the northeastern USA. Initial causes of recent disease emergence are likely driven by environmental/ecosystem changes since isolates for this study were collected from established mature trees. Results presented here give a better understanding of population biology of the bacterial oak pathogen and provide a framework for investigation of evolutionary relationships among pathogen populations from different areas.

evolutionary biology↗

bioRxiv2021

Competition is a determinant of multidrug resistant plasmid acquisition in Salmonella

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 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 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 fresh litter samples. We found that E. 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/SignificanceAntimicrobial 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 organization 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 and provide the identity of the bacterial species that potentially perform this function in broiler chickens and also postulate the mechanism involved.

microbiology↗

bioRxiv2021

Gene flux and acid-imposed selection are the main drivers of antimicrobial resistance in broiler chicks infected with Salmonella enterica serovar Heidelberg

Antimicrobial resistance (AR) spread is a worldwide health challenge, stemming in large part, from the ability of microbes to share their genetic material through horizontal gene transfer (HGT). Overuse and misuse of antibiotics in clinical settings and in food production have been linked to this increased prevalence and spread of AR. Consequently, public health and consumer concerns have resulted in a remarkable recent reduction in antibiotics used for food animal production. This is driven by the assumption that removing this selective pressure will favor the recovery of antibiotic susceptible taxa and will limit AR sharing through HGT, allowing the currently available antibiotic arsenal to be effective for a longer period. In this study we used broiler chicks raised antibiotic-free and Salmonella enterica serovar Heidelberg (SH), as a model food pathogen, to test this hypothesis. Our results show that neonatal broiler chicks challenged with an antibiotic susceptible SH strain and raised without antibiotics carried susceptible and multidrug resistance SH strains 14 days after challenge. SH infection perturbed the microbiota of broiler chicks and gavaged chicks acquired antibiotic resistant SH at a higher rate. We determined that the acquisition of a plasmid from commensal Escherichia coli population conferred multidrug resistance phenotype to SH recipients and carriage of this plasmid increased the fitness of SH under acidic selection pressure. These results suggest that HGT of AR shaped the evolution of SH and that antibiotic use reduction alone is insufficient to limit antibiotic resistance transfer from commensal bacteria to Salmonella. ImportanceThe reported increase in antibiotic resistant bacteria in humans have resulted in a major shift away from antibiotics use in food animal production. This has been driven by the assumption that removing antibiotics will select for antibiotic susceptible bacterial taxa, and this in turn will allow the currently available antibiotic arsenal to be more effective. This shift in practice has highlighted new questions that need to be answered to assess the effectiveness of antibiotic removal in reducing the spread of antibiotic resistance bacteria. This research demonstrates that antibiotic susceptible Salmonella Heidelberg strains can acquire multidrug resistance from commensal bacteria present in the gut of neonatal broiler chicks, even in the absence of antibiotic selection. We demonstrate that exposure to acidic pH drove the horizontal transfer of antimicrobial resistance plasmids and suggests that simply removing antibiotics from food-animal production might not be sufficient to limit the spread of antimicrobial resistance.

microbiology↗