Genomic diversity, pathogenicity and antimicrobial resistance of Escherichia coli isolated from poultry in the southern United States.

Escherichia coli (E. coli) are typically present as commensal bacteria in the gastro-intestinal tract of most animals including poultry species, but some avian pathogenic E. coli (APEC) strains can cause localized and even systematic infections in domestic poultry. Emergence and re-emergence of antimicrobial resistant isolates (AMR) constrain antibiotics usage in poultry production, and development of an effective vaccination program remains one of the primary options in E. coli disease prevention and control for domestic poultry. Thus, understanding genetic and pathogenic diversity of the enzootic E. coli isolates, particularly APEC, in poultry farms is the key to designing an optimal vaccine candidate and to developing an effective vaccination program. This study explored the genomic and pathogenic diversity among E. coli isolates in southern United States poultry. A total of nine isolates were recovered from sick broilers from Mississippi, and one from Georgia, with epidemiological variations among clinical signs, type of housing, and bird age. The genomes of these isolates were sequenced by using both Illumina short-reads and Oxford Nanopore long-reads, and our comparative analyses suggested data from both platforms were highly consistent. The 16 s rRNA based phylogenetic analyses showed that the 10 bacteria strains are genetically closer to each other than those in the public database. However, whole genome analyses showed that these 10 isolates encoded a diverse set of reported virulence and AMR genes, belonging to at least nine O:H serotypes, and are genetically clustered with at least five different groups of E. coli isolates reported by other states in the United States. Despite the small sample size, this study suggested that there was a large extent of genomic and serological diversity among E. coli isolates in southern United States poultry. A large-scale comprehensive study is needed to understand the overall genomic diversity and the associated virulence, and such a study will be important to develop a broadly protective E. coli vaccine.

Bovine viral diarrhea virus infection affects the expression of proteins related to professional antigen presentation in bovine monocytes.

The complete annotation of the cattle genome allows reliable protein identification by tandem mass spectrometry (MS(2)) and greatly facilitates proteomics. Previously, we reported that differential detergent fractionation (DDF) analysis of bovine monocytes reveals proteins related to antigen pattern recognition, uptake and presentation to immunocompetent lymphocytes. Here we have identified 47 bovine proteins, involved in immune function of professional antigen-presenting cells (APC) that have been significantly altered after cytopathic (cp) Bovine Viral Diarrhea Virus (BVDV) infection. In particular, proteins related to immune responses such as cell adhesion, apoptosis, antigen uptake, processing and presentation, acute phase response proteins, MHC class I- and II-related proteins and other molecules involved in immune function of professional antigen presentation have been significantly altered after BVDV infection. Our data suggest that cp BVDV, while promoting monocyte activation and differentiation, is inhibiting their antigen presentation to immunocompetent T cells, thus resulting in the uncontrolled inflammation mediated by activated macrophages, enhanced viral spread, and impaired anti-viral defense mechanisms in the host.

Prevalence of and risk factors associated with shedding of Cryptosporidium felis in domestic cats of Mississippi and Alabama.

The prevalence of and risk factors associated with the shedding of cryptosporidial oocysts were determined for domestic cats in northeastern Mississippi and northwestern Alabama. Cryptosporidial oocysts were found in a single fecal samples from 30 of 250 cats using a centrifugal concentration technique followed by an immunofluorescent assay. The odds of a cat shedding oocysts were increased when another cat shedding oocysts was present in the household. Logistic regression analysis showed only concurrent shedding of Giardia cysts to be significantly associated with the presence of Cryptosporidium oocysts in the feces. Oocysts from 12 cats were successfully genotyped, based on sequencing of a fragment of the 18S rRNA gene, all isolates were Cryptosporidium felis.

Genotypic analysis of Giardia duodenalis in domestic cats.

BACKGROUND: Giardia duodenalis is an intestinal flagellated protozoan that affects many mammalian species often causing severe diarrheal disease. Several different genotypes have been identified (Assemblages A-G). Most isolates recovered from domestic cats have been assigned to either Assemblage A, the zoonotic form of the parasite, or Assemblage F, identified thus far only in cats. Genotypic variation within G. duodenalis may influence clinical presentation and course of disease. Therefore, host-adapted genotypes may not be responsible for diarrheal disease (eg, Assemblage F in cats). HYPOTHESIS: Multiple Giardia genotypes will be present in domestic cats, including Assemblage F, which will not be correlated with clinical signs. ANIMALS: 250 domestic cats from eastern Mississippi and northwestern Alabama. METHODS: Prevalence survey. Fecal samples evaluated for cysts using a centrifugation concentration technique and a commercially available direct immunoflourescent antibody kit. Giardia isolates were characterized by PCR amplification and sequencing of the glutamate dehydrogenase gene. RESULTS: Both Assemblage A-I (6/17) and Assemblage F (11/17) were identified. Although Assemblage was significantly associated with age and housing, no association was detected between Assemblage and a variety of other factors including the presence of gastrointestinal signs (acute vomiting, diarrhea, and constipation). CONCLUSIONS AND CLINICAL IMPORTANCE: The presence of diarrhea in domestic cats with Giardia cannot be used as a predictor of the presence of zoonotic genotypes in animals within the study area. Although Assemblage A was associated with age and housing, veterinarians should consider any isolation of Giardia from domestic cats as potentially zoonotic.

Prevalence and factors associated with fecal shedding of Giardia spp. in domestic cats.

The prevalence of cats shedding Giardia cysts (13.6%) in the present study was found to be higher than previously reported (1% to 11%) and may reflect a higher sensitivity for the diagnostic test used. The presence of Cryptosporidium spp. oocysts, coccidial oocysts, and a clinical history of chronic (>2 weeks) gastrointestinal signs were significantly associated with the presence of Giardia spp. cysts in the feces. There were no associations between the presence of Giardia spp. cysts and type of housing, acute gastrointestinal signs, vomiting, gender, source of cat (i.e., animal shelter versus private breeder), or gastrointestinal parasites other than Cryptosporidium spp. and intestinal coccidial agents.

Antigenic Characterization of H3 Subtypes of Avian Influenza A Viruses from North America.

Besides humans, H3 subtypes of influenza A viruses (IAVs) can infect various animal hosts, including avian, swine, equine, canine, and sea mammal species. These H3 viruses are both antigenically and genetically diverse. Here, we characterized the antigenic diversity of contemporary H3 avian IAVs recovered from migratory birds in North America. Hemagglutination inhibition (HI) assays were performed on 37 H3 isolates of avian IAVs recovered from 2007 to 2011 using generated reference chicken sera. These isolates were recovered from samples taken in the Atlantic, Mississippi, Central, and Pacific waterfowl migration flyways. Antisera to all the tested H3 isolates cross-reacted with each other and, to a lesser extent, with those to H3 canine and H3 equine IAVs. Antigenic cartography showed that the largest antigenic distance among the 37 avian IAVs is about four units, and each unit corresponds to a 2 log 2 difference in the HI titer. However, none of the tested H3 IAVs cross-reacted with ferret sera derived from contemporary swine and human IAVs. Our results showed that the H3 avian IAVs we tested lacked significant antigenic diversity, and these viruses were antigenically different from those circulating in swine and human populations. This suggests that H3 avian IAVs in North American waterfowl are antigenically relatively stable.

Confirmation of vertical transmission of bovine immunodeficiency virus in naturally infected dairy cattle using the polymerase chain reaction.

The purpose of this study was to determine whether bovine immunodeficiency virus (BIV) is vertically transmitted in naturally infected dairy cattle. Twenty-two dam/calf pairs from a Mississippi Agriculture and Forestry Experiment Station dairy were the study group. Blood samples were collected following delivery of calves, the peripheral blood leukocytes were purified from these samples, and the leukocyte DNA was used in polymerase chain reactions targeting the pol gene region of the BIV provirus. Southern blotting and hybridization were used to confirm the BIV specificity of the amplified fragments. BIV provirus was detected in 14 of 22 calves (64%), demonstrating vertical transmission. Eight of the calves were disqualified from the final interpretation of transplacental transfer because they may have nursed their mothers prior to blood collection, allowing the possibility of lactogenic transfer of the virus. Transplacental transmission of BIV was identified in 6 of 22 calves (27%).

Use of serological and mucosal immune responses to Mycoplasma hyopneumoniae antigens P97R1, P46 and P36 in the diagnosis of infection.

Currently available ELISAs used to diagnose Mycoplasma hyopneumoniae infection in pigs have high specificity but low sensitivity. To develop more sensitive assays, the kinetics of specific serum IgG and respiratory mucosal sIgA responses against three M. hyopneumoniae antigens, namely, P97R1 (an adhesin protein), P46 (a membrane protein), and P36 (a cytosolic protein), were characterised over 133 days following experimental infection. Immunoglobulin G against the three proteins remained at high concentrations from 28 to 133 days post-infection (dpi), although IgG against P97R1 was detected earlier and was more reactive than the other two antigens under assessment. Mucosal sIgA appeared earlier than serum IgG but did not persist as long; sIgA concentrations against P97R1 were the highest. Seroconversion was detected 2 weeks earlier with the P97R1-based ELISA than with a commercially available ELISA. On analysis of serum samples from five pig farms that did not use a M. hyopneumoniae vaccine, the P97R1-based IgG ELISA demonstrated a 73.6% coincidence rate with the commercial kit. Moreover, this more specific P97R1-based ELISA detected more positive samples than the commercial kit (52.8% vs. 39.2%). It was concluded that the systemic immune response to M. hyopneumoniae infection in pigs was delayed in onset but persistent whereas the mucosal response developed more rapidly but was less sustained. The P97R1 antigen was identified as a suitable serological marker for diagnosing M. hyopneumoniae infection in pigs, particularly early stage infection.

Development and validation of an attenuated Mycoplasma hyopneumoniae aerosol vaccine.

Mycoplasma hyopneumoniae (M. hyopneumoniae) causes a chronic respiratory disease with high morbidity and low mortality in swine, and has been presented as a major cause of growth retardation in the swine industry. Aerosol vaccination presents a needle free, high throughput, and efficient platform for vaccine delivery, and has been widely applied in poultry vaccination. However, aerosol vaccines have rarely been used in swine vaccination primarily because the long and curving respiratory track of swine presents a barrier for vaccine particle delivery. To develop an effective M. hyopneumoniae aerosol vaccine, three major barriers need to be overcome: to optimize particle size for aerosol delivery, to maintain the viability of mycoplasma cells in the vaccine, and to optimize the environmental conditions for vaccine delivery. In this study, an aerosol mycoplasma vaccine was successfully developed based on a conventional live attenuated M. hyopneumoniae vaccine. Specifically, the Pari LCD nebulizer was used to produce an aerosol vaccine particle size less than 5 µm; and a buffer with 5% glycerol was developed and optimized to prevent inactivation of M. hyopneumoniae caused by aerosolization and evaporation. Before nebulization, the room temperature and relative humidity were control to 20-25 °C and 70-75%, respectively, which helped maintain the viability of aerosol vaccine. Animal experiments demonstrated that this newly developed aerosol vaccine was effectively delivered to swine low respiratory track, being confirmed by nested-PCR, in situ hybridization and scanning electron microscope. Moreover, M. hyopneumoniae specific sIgA secretion was detected in the nasal swab samples at 14 days post-immunization. To our knowledge, this is the first report on a live M. hyopneumoniae aerosol vaccine.

Proteomics inference of genes involved in host adaptation of Mycoplasma gallinarum.

Different from most other host-specific mycoplasmas, Mycoplasma gallinarum has been isolated from various hosts, such as poultry, pig, cattle, and sheep. The wide distribution among different hosts, the low pathogenesis, and the weak host immunological responses suggest this mycoplasma has a unique host adaptation mechanism. In this study, we applied two-dimensional liquid chromatography electrospray ionization tandem mass spectrometry (2D LC-MS/MS) to characterize the protein profiling of M. gallinarum. Our results suggest that M. gallinarum possesses homologs of cytadhesin proteins found in other mycoplasmas lacking an organized tip organelle. Our results showed that there are possibly multiple aminopeptidase gene homologs present in M. gallinarum, which might be involved in nutrient acquisition of M. gallinarum. The information present here would be useful for future studies to identify genes responsible for the colonization and host adaptation properties of M. gallinarum.

Modeling a whole organ using proteomics: the avian bursa of Fabricius.

While advances in proteomics have improved proteome coverage and enhanced biological modeling, modeling function in multicellular organisms requires understanding how cells interact. Here we used the chicken bursa of Fabricius, a common experimental system for B cell function, to model organ function from proteomics data. The bursa has two major functional cell types: B cells and the supporting stromal cells. We used differential detergent fractionation-multidimensional protein identification technology (DDF-MudPIT) to identify 5198 proteins from all cellular compartments. Of these, 1753 were B cell specific, 1972 were stroma specific and 1473 were shared between the two. By modeling programmed cell death (PCD), cell differentiation and proliferation, and transcriptional activation, we have improved functional annotation of chicken proteins and placed chicken-specific death receptors into the PCD process using phylogenetics. We have identified 114 transcription factors (TFs); 42 of the bursal B cell TFs have not been reported before in any B cells. We have also improved the structural annotation of a newly sequenced genome by confirming the in vivo expression of 4006 "predicted", and 6623 ab initio, ORFs. Finally, we have developed a novel method for facilitating structural annotation, "expressed peptide sequence tags" (ePSTs) and demonstrate its utility by identifying 521 potential novel proteins from the chicken "unassigned chromosome".

Differential detergent fractionation for non-electrophoretic eukaryote cell proteomics.

Differential detergent fractionation (DDF), which relies on detergents to sequentially extract proteins from eukaryotic cells, has been used to increase proteome coverage of 2D-PAGE. Here, we used DDF extraction in conjunction with the nonelectrophoretic proteomics method of liquid chromatography and electrospray ionization tandem mass spectrometry. We demonstrate that DDF can be used with 2D-LC ESI MS2 for comprehensive cellular proteomics, including a large proportion of membrane proteins. Compared to some published methods designed to isolate membrane proteins specifically, DDF extraction yields comprehensive proteomes which include twice as many membrane proteins. Two-thirds of these membrane proteins have more than one trans-membrane domain. Since DDF separates proteins based upon their physicochemistry and subcellular localization, this method also provides data useful for functional genome annotation. As more genome sequences are completed, methods which can aid in functional annotation will become increasingly important.