Biology subjects

Kariyawasam, S.

Publications and source records attributed to Kariyawasam, S..

7 recordsLinked to original sources

bioRxiv2026

Metagenomic Insights into the Fecal Microbiome, Resistome, and Mobilome of Beef Cattle in Cow-Calf Operations in Florida, United States

Food-producing animals are a focus of One Health approaches to antimicrobial resistance (AMR) as reservoirs of antimicrobial-resistant bacteria (ARB) and antimicrobial resistance genes (ARGs). We hypothesized that microbial composition, ARGs profiles, and mobile genetic element (MGE) profiles would differ by operation size and animal age group. Fecal samples from 162 cows and calves were combined into 54 composite samples, each comprising three animals of the same age group. Across operation sizes, Bacillota (51.4-64.9%), Bacteroidota (12.0-17.3%), Pseudomonadota (10.3-16.5%), and Actinomycetota (3.3-10.9%) were predominant phyla. Alpha diversity did not differ among operation sizes; however, cows exhibited greater observed richness, Shannon diversity, and Simpson diversity than calves (all P < 0.001). Microbial composition did not differ significantly among operation sizes (PERMANOVA, R{superscript 2} = 0.065, P = 0.609) but differed significantly between cows and calves (R{superscript 2} = 0.200, P < 0.001). Seventy-five ARGs representing 14 resistance classes were identified. Normalized ARG hit rates were higher in small operations (0.444) than in medium (0.278) and large operations (0.222; P = 0.088), whereas calves exhibited a higher estimated marginal mean normalized ARG hit rate than cows (0.383 vs. 0.247 hits/million reads; P < 0.001). Of 1,054 curated ARG hits, 23.9% occurred on predicted plasmid contigs, 0.9% on predicted viral contigs, and 7.1% on contigs containing insertion sequences. Overall findings demonstrate differences in fecal microbiome diversity and ARG abundance between cows and calves and indicate that predicted plasmids are associated with a notable proportion of ARG hits in Florida beef cow-calf operations.

microbiology↗

bioRxiv2026

Hepatic Transcriptomic Landscape of Chicken Reveals Host Responses to Spotty Liver Disease

Spotty Liver Disease (SLD) is an acute bacterial infection of layer chickens in production, caused by Campylobacter hepaticus, and occurs most frequently in barn-housed and free-range systems. The disease is characterized by a sharp decline in egg production and increased mortality. The hallmark pathological feature is 1-2 mm white to grey necrotic foci distributed across the liver surface. Despite its growing economic impact on commercial poultry, the molecular mechanisms underlying host responses to C. hepaticus infection remain poorly understood. To address this gap, we performed a comprehensive transcriptome analysis of liver tissue from chickens naturally infected with SLD compared to uninfected controls. High-throughput transcriptome sequencing, yielding 9,277 differentially expressed genes (DEG), of which 3,063 were upregulated and 6,214 were downregulated. Functional pathway enrichment analysis revealed significant alterations in immune and metabolic processes associated with SLD pathophysiology. Infected chickens exhibited significant activation of immune response pathways, particularly cytokine-cytokine receptor interactions involving interleukins IL-22, IL-21, and IL-6, along with enhanced cell signaling, and cell adhesion. Among the individual genes, C1QTNF1 and the adhesion molecule gene ADGRD1 were notably overexpressed, indicating enhanced inflammatory activity. In contrast, core hepatic metabolic functions were profoundly reduced, as evidenced by downregulation of oxidative phosphorylation, fatty acid metabolism, iron ion binding, and heme binding pathways. A marked increase in serum amyloid A gene (SAA) expression further confirmed robust acute-phase responses and compromised liver function during infection. Together, these findings demonstrate a complex interplay between inflammatory activation and metabolic dysregulation during SLD. The strong upregulation of acute-phase proteins and pro-inflammatory cytokines demonstrates the hosts vigorous attempt to combat bacterial infection, whereas the concurrent suppression of essential metabolic pathways reflects the pathological consequences of SLD. This study provides a transcriptomic characterization of host responses to C. hepaticus infection, offering insights into SLD pathogenesis and potential avenues for targeted intervention.

microbiology↗

bioRxiv2025

The Carbon Starvation-Inducible Lipoprotein (Slp) Influences Differential Adherence of Escherichia coli O157:H7 at the Bovine Rectoanal Junction.

Shiga toxin-producing Escherichia coli O157:H7 (O157), a foodborne human pathogen, persists at the rectoanal junction (RAJ) of the bovine intestinal tract, in asymptomatic cattle reservoirs. Identifying mechanisms used by O157 for initial adherence before persistence at the RAJ could help develop effective O157 control modalities. We recently established the role of carbon starvation-inducible lipoprotein (Slp) in initial adherence of O157 to Caco-2 cells, with the human polymeric immunoglobulin receptor (pIgR) protein as the Slp-receptor. Here, we evaluated the role of Slp in O157 adherence to the bovine RAJ using the RAJ squamous epithelial (RSE) cell- and RAJ-In vitro Organ Culture (IVOC)- adherence assays. The wild-type O157 strain EDL932 (EDL932-WT), its isogenic slp deletion mutant (EDL932 {Delta}slp), and the slp complemented mutant (EDL932 {Delta}slp-p:slp), were tested with no bacteria controls. Adherence was verified by culture and immunofluorescence (IF) staining of O157. Tissue integrity was determined using nuclear/cell staining dyes and histopathological examination. All test strains adhered in a diffuse-moderate pattern on RSE cells. However, differential adherence was observed on the RAJ-IVOC with the strains preferentially adhering to the columnar cells. Additionally, EDL932- WT and EDL932 {Delta}slp-p:slp strains adhered in slightly greater numbers than the EDL932 {Delta}slp strain to the RAJ-IVOC, causing disruptions primarily in the columnar region of otherwise intact RAJ-IVOC tissues. Interestingly, pIgR was also predominantly detected by IF microscopy and RNAscope in situ hybridization at the columnar region of the RAJ-IVOC tissue. In silico modeling demonstrated the possibility of a bovine pIgR- bacterial Slp interaction. Hence, our observations support the role for Slp in the initial adherence of O157 to the columnar cells at the bovine RAJ, unlike the squamous cells where the loss of slp did not impact attachment. In addition, a possible mucosal immune-interference resulting from the bovine pIgR-Slp interaction could contribute towards long-term O157 colonization of cattle. AUTHOR SUMMARYEscherichia coli O157:H7 (O157) is a foodborne pathogen that causes disease in humans with symptoms ranging from watery/bloody diarrhea to kidney failure. Cattle are the main reservoirs of this human pathogen, where O157 tends to persist at the rectoanal junction (RAJ) of the bovine gastrointestinal tract. However, the exact mechanisms by which O157 adheres and persists at the bovine RAJ is not fully understood. Here, we identified that the O157 carbon starvation-inducible lipoprotein (Slp) allows O157 to attach to cells at the RAJ using polymeric immunoglobulin receptor (pIgR) protein as the Slp-receptor. Not only does this attachment of Slp to the cattle receptor allow O157 to colonize cattle, but the interaction could potentially interfere with intestinal immune responses, further promoting long-term O157 colonization of cattle. This makes Slp an attractive target for therapeutic interventions, such as vaccines that could interfere with O157 attachment to cattle intestinal cells.

microbiology↗

bioRxiv2024

Exploring Transcriptomic Changes in Antibiotic-Resistant Salmonella Heidelberg Modulated by Commensal Escherichia coli in Vitro

Nontyphoidal Salmonella (NTS) are major foodborne pathogens primarily transmitted to humans through contaminated poultry products. The increase in antibiotic-resistant NTS, including Salmonella Heidelberg, has recently become a public health issue. Current control measures are inadequate, emphasizing the need for novel approaches to mitigate NTS colonization in poultry and contamination of poultry products. We hypothesized that commensal Escherichia coli can reduce antibiotic-resistant NTS colonization in the chicken intestines by modulating the fitness, virulence, and antibiotic resistance (AMR) potential of Salmonella. To test this hypothesis, we co-cultured commensal E. coli 47-1826 and antibiotic-resistant S. Heidelberg 18-9079 strains isolated from poultry and analyzed their transcriptomes using RNA sequencing. Our analysis revealed 4,890 differentially expressed genes in S. Heidelberg 18-9079 when co-cultured with E. coli 47-1826. After filtering the expression data, we found 193 genes were significantly upregulated while 202 genes were downregulated. Notably, several genes involved in bacterial growth, pathogenicity and virulence, biofilm formation, metal-ion hemostasis, signal transduction and chemotaxis, stress response, transmembrane transport of xenobiotics, and cellular metabolism were down-regulated by as much as eighty-six folds in S. Heidelberg as compared to the control. Further, the study revealed the downregulation of genes associated with AMR and drug efflux in S. Heidelberg 18-9079 by up to twelvefold. These findings highlight that commensal E. coli 47-1826 may reduce the fitness, persistence, virulence, and antimicrobial resistance (AMR) dissemination of S. Heidelberg 18-9079, implying that E. coli strain 47-1826 could be utilized as a strategy to mitigate antibiotic-resistant S. Heidelberg in poultry, ultimately enhancing food safety. ImportanceNontyphoidal Salmonella, commonly transmitted to humans through contaminated poultry meat and eggs, is one of the most frequent causes of foodborne illness. Augmenting the situation, foodborne outbreaks of antibiotic-resistant NTS have become an additional food safety and public health concern. Evaluation of growth changes and transcriptomic profiling of antibiotic-resistant S. Heidelberg and commensal E. coli in a mixed culture of the two will provide insight into the ability of commensal E. coli to reduce S. Heidelberg colonization of chicken intestines and the genes involved in that change. Our study showed that commensal E. coli strain 47-1826 significantly reduced antibiotic-resistant S. Heidelberg 18-9079 counts and expression of Salmonella genes, which play a vital role in the growth and persistence of nontyphoidal Salmonella in poultry intestines. The study results suggest the potential use of commensal E. coli strain 47-1826 to control antibiotic-resistant S. Heidelberg colonization in poultry, leading to improved food safety through reduced NTS contamination of foods of poultry origin and reduced dissemination of antibiotic-resistant Salmonella and their resistant determinants to humans via the food chain.

microbiology↗

bioRxiv2024

Pangenomic analysis of Helcococcus ovis reveals widespread tetracycline resistance and a novel bacterial species, Helcococcus bovis.

Helcococcus ovis (H. ovis) is an opportunistic bacterial pathogen of a wide range of animal hosts including domestic ruminants, swine, avians, and humans. In this study, we sequenced the genomes of 35 Helcococcus sp. clinical isolates from the uterus of dairy cows and explored their antimicrobial resistance and biochemical phenotypes. Phylogenetic and average nucleotide identity analyses placed four Helcococcus isolates within a cryptic clade-representing an undescribed species, for which we propose the name Helcococcus bovis sp. nov. We applied whole genome comparative analyses to explore the pangenome, resistome, virulome, and taxonomic diversity of the remaining 31 H. ovis isolates. H. ovis was more often isolated from cows with metritis, however, there was no associations between H. ovis gene clusters and uterine infection. The phylogenetic distribution of high-virulence determinants of H. ovis is consistent with convergent gene loss in the species. The majority of H. ovis strains (30/31) contain mobile tetracycline resistance genes, leading to higher minimum inhibitory concentrations of tetracyclines in vitro. In summary, this study showed that the presence of H. ovis is associated with uterine infection in dairy cows, that mobile genetic element-mediated tetracycline resistance is widespread in H. ovis, and that there is evidence of co-occurring virulence factors across clades suggesting convergent gene loss in the species. Finally, we introduced a novel Helcococcus species closely related to H. ovis, called H. bovis sp. nov. HighlightsO_LIThe presence of Helcococcus ovis is associated with uterine infection in dairy cows C_LIO_LIMobile genetic element-mediated tetracycline resistance is widespread in H. ovis C_LIO_LICo-occurring virulence factors across clades suggest convergent gene loss in the species C_LIO_LIHelcococcus bovis is a novel species closely related to Helcococcus ovis C_LI

microbiology↗

bioRxiv2022

Feline Coronavirus Infection of Domestic Cats Causes Development of Cross-Reactive Antibodies to SARS-CoV-2 Receptor Binding Domain

The current study was initiated when our specific pathogen-free laboratory toms developed unexpectedly high levels of cross-reactive antibodies to human SARS-CoV-2 (SCoV2) receptor binding domain (RBD) upon mating with feline coronavirus (FCoV)-positive queens. Multi-sequence alignment analyses of SCoV2 Wuhan RBD and four strains each from FCoV serotypes 1 and 2 (FCoV1, FCoV2) demonstrated amino acid sequence identity of 11.5% and similarity of 31.8% with FCoV1 RBD, as well as 12.2% identity and 36.5% similarity for FCoV2 RBD. The sera from all three toms and three mated queens cross-reacted with SCoV2 RBD and reacted with FCoV1 RBD and FCoV2 spike-2, nucleocapsid, and membrane proteins of FCoV2 whole-virus, but not with FCoV2 RBD. Additionally, the plasma from all six FCoV2-inoculated laboratory cats reacted with FCoV2 and SCoV2 RBDs, but not with FCoV1 RBD. In another study, eight group-housed laboratory cats from a different lineage had a range of serum cross-reactivity to SCoV2 RBD even 15 months later. Such cross-reactivity was also observed in FCoV1-positive group-housed pet cats. The SCoV2 RBD at a high non-toxic dose and FCoV2 RBD at a 60-400-fold lower dose blocked the in vitro FCoV2 infection of the feline cells, demonstrating their close structural conformations essential as vaccine immunogens. Furthermore, such cross-reactivity to SCoV2 RBD was also detected by the peripheral blood mononuclear cells of both transient and chronically FCoV1-infected cats. Overall, the cross-reactivity with SCoV2 RBD by the sera from both serotypes of FCoV-infected cats also suggests that the cross-reactive epitope(s) on FCoV1 and FCoV2 RBDs may be similar to those of SCoV2 RBD and provides essential insights to developing a pan-CoV vaccine. Author SummaryTo date, there are no reports on the sera from feline coronavirus (FCoV)-infected cats cross-reacting with either SARS-CoV-1 or SARS-CoV2 (SCoV2) receptor binding domains (RBDs). This report describes the presence of cross-reactive antibodies to SCoV2 RBD in the sera of FCoV-infected laboratory cats, even though SCoV2 RBD and each FCoV serotype (FCoV1, FCoV2) RBD had minimal sequence similarity. However, this observation of serum cross-reactivity to SCoV2 RBD was confirmed by more stringent antibody-based assays and viral assays. Furthermore, both serotypes of FCoV-infected cats, including FCoV1-infected pet cats, produced the cross-reactive antibodies, and such cross-reactivity to SCoV2 RBD was also detected, most likely, by the T cells in peripheral blood mononuclear cells of both transient and chronically FCoV1-infected cats. Since SCoV2 RBD is essential component for current vaccines against COVID-19 disease, our findings should provide essential insights to developing a pan-coronavirus vaccine that induces full-scale immunity to completely prevent SCoV2 infection in humans and pet animals.

microbiology↗

bioRxiv2018

The Escherichia coli O157:H7 Carbon Starvation-Inducible Lipoprotein Slp Contributes to Initial Adherence In Vitro via the Human Polymeric Immunoglobulin Receptor

Escherichia coli O157:H7 is the most well-studied serotype of enterohemorrhagic E. coli (EHEC) class of E. coli intestinal pathogens, and is responsible for many outbreaks of serious food-borne illness worldwide each year. Adherence mechanisms are a critical component of its pathogenesis, persistence in natural reservoirs, and environmental contamination. E. coli O157:H7 has a highly effective virulence operon, the Locus of Enterocyte Effacement (LEE), and its encoded intimate adherence mechanism is well characterized. However, factors involved in the preceding initial attachment are not well understood. In this study, we propose a mechanism of initial adherence used by E. coli O157:H7 in vitro. We describe a bacterial protein not previously reported to be involved in adherence, Slp, and its interactions with the human host protein polymeric immunoglobulin receptor (pIgR). The human pIgR has previously been shown to act as an adherence receptor for some mucosal pathogens, and is highly expressed in the intestine. Following observation of significant colocalization between E. coli O157:H7 and pIgR location on Caco-2 cells, a co-immunoprecipitation (Co-IP) assay using a human recombinant Fc-tagged pIgR protein led to the identification of this protein. Disruption of Slp expression in E. coli O157:H7, through deletion of its encoding gene slp, produced a significant adherence deficiency to Caco-2 cells at early time points associated with initial adherence. Plasmid complementation of slp fully restored the wild-type phenotype. Furthermore, immunofluorescence microscopy revealed evidence that this interaction is specific to the pathogenic strains of E. coli tested, and not the nonpathogenic strain E. coli K12. Additionally, deletion of slp resulted in the absence of the corresponding protein band in further Co-IP assays, while the plasmid-encoded slp complementation of the deletion mutant strain restored the wild-type pattern. These data support the proposal that Slp directly contributes to initial adherence, with the pIgR protein as its proposed receptor.\n\nAuthor summaryEscherichia coli O157:H7 and other enterohemorrhagic E. coli (EHEC) are responsible for tens of thousands of cases of food-borne illness in the United States each year. E. coli O157:H7 has a particularly effective intimate adherence mechanism. However, the mechanisms of initial adherence, which facilitate attachment and virulence prior to the engagement of intimate adherence, are not well understood. In this study, we describe an initial adherence interaction between the E. coli O157:H7 Slp and the human polymeric immunoglobulin receptor (pIgR) expressed by the human colonic epithelial cell line Caco-2. The relationship was first demonstrated as a significant colocalization between the locations of E. coli O157:H7 bacterial cells and pIgR protein using immunofluorescence microscopy. The E. coli O157:H7 Slp protein was identified, and disruption of the slp gene resulted in a severe adherence deficiency to Caco-2 cells during initial adherence. This effect was reversed upon complementation of the {Delta}slp strain with a plasmid-encoded slp gene, and the constitutive over-expression of slp resulted in hyper-adherence exceeding that of the wild-type E. coli O157:H7. These data support the proposition that Slp directly contributes to initial adherence, with the pIgR protein as its proposed receptor.

microbiology↗