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.

Effects of different vaccine combinations against Mycoplasma gallisepticum on blood characteristics in commercial layer chickens.

Mycoplasma gallisepticum (MG) is a major and economically significant pathogen of avian species. When administered before lay, F-strain MG (FMG) can reduce egg production during lay, but the ts-11 strain of MG (ts11MG) does not exert this effect. Two trials were conducted to determine the effects of pre-lay vaccinations of ts11MG, MG-Bacterin (MGBac), or their combination, in conjunction with an FMG challenge overlay after peak production on the blood characteristics of commercial layers. In each trial, 160 mycoplasma-free Hy-Line W-36 layers were housed in negative-pressure biological isolation units (4 units per treatment, 10 birds per unit) from 9 through 52 wk of age (woa). The following vaccination treatments were administered at 10 woa: 1) Control (no vaccinations); 2) MGBac; 3) ts11MG; and 4) ts11MG and MGBac combination (ts11MG+MGBac). At 45 woa, half of the birds were challenged with a laboratory stock of high-passage FMG. Parameters measured in both trials were whole-blood hematocrit and serum concentrations of cholesterol (SCHOL), triglycerides, calcium, and total protein (STP). An age×treatment interaction (P=0.04) was observed for STP between 23 and 43 woa. The STP concentration in the ts11MG and ts11MG+MGBac groups was higher at 33 woa, but was lower at 43 woa, in comparison to the Control group. Also, at 38 woa, the STP of the ts11MG+MGBac group was higher than that of the MGBac group. Although use of the ts11MG vaccine alone or in combination with MGBac may influence circulating STP concentrations when administered before lay, it remains effective in protecting layers against the adverse effect of a post-peak challenge of FMG on egg production, as was observed in a previous companion study.

Effects of the In ovo Administration of the 6/85 Mycoplasma gallisepticum Vaccine on Layer Chicken Embryo Hatchability and Early Posthatch Performance.

In ovo administration as a possible alternative method of 6/85 MG vaccination was assessed. After 18 days of incubation (doi), the eggs were administered a particular dosage of a live attenuated 6/85 MG vaccine in either the air cell (AC) or amnion (AM). The treatments included non-injected eggs and eggs injected into the AC or AM with diluent alone as controls. Treatments also included eggs injected with diluent, which contained 1.73 × 102, or 1.73 × 104 CFU of 6/85 MG. Hatchability of viable injected eggs (HI) and residual embryonic mortality were determined at 22 doi. At hatch and at three weeks posthatch, one hatched chick per treatment replicate was bled and swabbed for the detection of 6/85 MG in the choanal cleft using PCR, serum plate agglutination (SPA), and ELISA methods. The results show that AC in ovo injection of 6/85 MG had no negative impacts on HI or on the live performance of pullets, but that it failed to provide adequate protection (p ≤ 0.0001) in hatchlings or three-week-old pullets. The 1.73 × 104 6/85 MG CFU dosage injected into the AM decreased the hatchability of injected eggs containing viable embryos (HI; p = 0.009) and was associated with a significant increase in late dead mortality (p = 0.001). Hatchling and three-week-old chick mortalities (p = 0.008) were significantly greater in the 1.73 × 104 CFU-AM treatment group in comparison with the other treatment groups. In addition, the 1.73 and 1.73 × 102 6/85 MG-AM treatments had no negative effects on the hatching process or on posthatch growth, and the 1.73 × 102 6/85 MG-AM treatment was more effective in the protection of pullets against MG (p ≤ 0.0001) as compared with the low dosage and non-injected treatment groups. Further research is needed to examine the influence of the 6/85 MG in ovo vaccine on layer immune competence.

Effects of the In Ovo Vaccination of the ts-11 Strain of Mycoplasma gallisepticum in Layer Embryos and Posthatch Chicks.

The transmission of the ts-11 strain of Mycoplasma gallisepticum (MG) vaccine (ts-11MGV) between incubated eggs and between hatchlings that was administrated via in ovo injection, and its subsequent effects on their posthatch performance were evaluated. Marek's disease diluent alone (sham-injected) or containing either 3.63 × 101, 102, 103, or 104 cfu of ts-11MGV was manually in ovo-injected into the amnion on 18 days of incubation. Egg residue analysis, percentage incubational egg weight loss, hatchability of viable injected eggs, and hatchling body weight (BW) were assessed. Selected hatchlings from each treatment replicate group were swabbed in the choanal cleft for MG DNA detection. Female chick live performance was also assessed through 21 days of posthatch age. Unexposed control sentinel chicks were allocated to each treatment replicate group to assess horizontal transmission. Birds were later swabbed and bled respectively, for detection of MG DNA and IgM production at 21 days posthatch. In all birds, no MG DNA was detected and SPA tests for IgM were negative. Among all variables, only 0 to 21 day BW gain was significantly affected by treatment and was lower in the 3.63 × 104 ts-11 MGV treatment in comparison to all the other treatments. Because ts-11MGV does not exhibit vertical or horizontal transmission capabilities under commercial conditions, it may not be a good candidate for in ovo injection.

Fluorescent microspheres as a positive indicator in an intratracheal infection model.

Animal models testing the ability of vaccines and therapeutic agents to prevent pathology from induced respiratory infection are an important means of testing and validating the vaccines and therapeutic agents. However, the lack of induced pathology in test subjects could be either indicative of protection or a problem with the animal model system. This work describes the improvement of a chicken model system of intratracheal infection using fluorescent microspheres as a positive indicator of infection. It was shown that fluorescent microspheres and Mycoplasma gallisepticum bacteria both dispersed to the same areas of the chicken respiratory system and that the microspheres remained detectable in the chicken lung tissue for at least 7 days following infection. The microspheres used are detectable using a black light, allowing for visualization during necropsy. Using the updated model system, three live M. gallisepticum vaccines were tested both for their ability to elicit a humoral immune response following vaccination, and for their ability to protect from air sac lesion pathology at two different time points following vaccination. Results showed the protective effects of the different M. gallisepticum vaccines prevented the induction of pathology, consistent with previous results. The presence of the fluorescent microspheres provided a positive method of identifying the properly infected chickens and a means of differentiating failed experimental infections so that those samples could be removed, resulting in improved consistency in infection results.

Complete Genome Sequences of Two Vaccine Strains and One Field Isolate of Mycoplasma gallisepticum.

Mycoplasma gallisepticum infection of poultry can cause significant losses for poultry producers. Live attenuated M. gallisepticum vaccines mitigate the losses caused by infection, although the antigens that lead to immune protection have not been identified. Here, we report the sequencing of two vaccine strains and one field strain.

Complete Genome Sequences of Two Mycoplasma gallisepticum F-Strain Variants.

Mycoplasma gallisepticum pathology in poultry is preventable by vaccination with live M. gallisepticum vaccines. Research has suggested possible differences in host response between F-strain-based vaccines. The genomes of the AviPro vaccine and F99 parent strains were sequenced for comparison with the already sequenced F-strain vaccine.

Transcriptomic analysis of early B-cell development in the chicken embryo.

The chicken bursa of Fabricius is a primary lymphoid tissue important for B-cell development. Our long-term goal is to understand the role of bursal microenvironment in an early B-cell differentiation event initiating repertoire development through immunoglobulin gene conversion in the chick embryo. We hypothesize that early bursal B-cell differentiation is guided by signals through cytokine receptors. Our theory is based on previous evidence for expression of the receptor tyrosine kinase superfamily members and interleukin receptors in unseparated populations of bursal B-cells and bursal tissue. Knowledge of the expressed genes that are responsible for B-cell differentiation is a prerequisite for understanding the bursal microenvironment's function. This project uses transcriptomic analysis to evaluate gene expression across early B-cell development. RNA-seq was performed with total RNA isolated from bursal B-cells at embryonic day (ED) 16 and ED 19 (n = 3). Approximately 90 million high-quality clean reads were obtained from the cDNA libraries. The analysis revealed differentially expressed genes involved in the Jak-STAT pathway, Wnt signaling pathway, MAPK signaling pathway, metabolic pathways including tyrosine metabolism, Toll-like receptor signaling pathway, and cell-adhesion molecules. The genes predicted to encode surface receptors, signal transduction proteins, and transcription factors identified in this study represent gene candidates for controlling B-cell development in response to differentiation factors in the bursal microenvironment.

The netB-positive Clostridium perfringens in the experimental induction of necrotic enteritis with or without predisposing factors.

The netB-positive Clostridium perfringens has been considered as the requisite to consistently induce necrotic enteritis (NE). However, use of a netB-positive strain did not guarantee consistent NE reproduction unless high protein diets or Eimeria, conceived as 2 major predisposing factors, was incorporated. To establish a refined model, the roles of dietary fishmeal inclusion, Eimeria inoculation, and netB-positive C. perfringens challenge in NE induction and the confounding effects of Eimeria infection on NE were examined. The results showed that the use of netB-positive C. perfringens without a predisposing factor failed to induce NE. Fishmeal incorporation promoted the occurrence of NE but did not significantly affect the incidence of the disease in conjunction with challenge of netB-positive C. perfringens. However, the additional participation of Eimeria infection in the same induction procedure produced significantly higher numbers of NE cases and promoted more severe lesions in chickens (P < 0.05). Inoculation of Eimeria resulted in a significant higher incidence of NE compared to the non-Eimeria treated group (P < 0.05). The results demonstrated that both netB-positive C. perfringens and predisposing factors were required for the reproduction of disease. Mild-to-moderate coccidial infection (coccidial lesion score ≤ 2) was noted in NE cases in this model but severe coccidial infection did not correlate with the occurrence of NE, indicating mild coccidial infection may be beneficial for the development of NE. If multiple species infection of Eimeria precedes the challenge of C. perfringens, days 19 to 21 (1 to 3 D after the last clostridial challenge) was the time period favorable for observations of NE lesions. The time after this period may be subject to bias of severity, incidence, or mortality of NE owing to the profound coccidial lesions in the intestinal region. This study demonstrated that the co-infection with netB-positive C. perfringens and Eimeria species under fishmeal incorporation produced a desirable NE model, being of value in studying the effectiveness of novel feed additives and alternative mitigation strategies to prevent NE.

The impact of vaccination route on Mycoplasma gallisepticum vaccine efficacy.

Mycoplasma gallisepticum infection can lead to major financial losses for poultry producers. Control of M. gallisepticum infection in the layer industry is generally obtained through vaccination due to the nature of the multi-aged flocks in the facilities. Live vaccines can provide significant protection from the pathogenic effects of M. gallisepticum infection. However, differing management practices, including vaccination procedures, can lead to significant variations in the efficacy of the same vaccine. The site of vaccine deposition has been shown to be one important factor significantly influencing the vaccination outcome. Previous research has shown that vaccine applied to the eyes or sprayed on the head is significantly more effective than when sprayed on the body. Vaccine application to the eyes, through the nares (nasal), and 2 routes through the oral cavity were studied to further characterize the most efficient route for delivery. Results of this work demonstrate that eye drop vaccination is significantly more effective than nasal vaccination, and vaccine delivered through the oral cavity has a negligible contribution to overall vaccination outcome.

Induction of a mycoplasma gallisepticum pMGA gene in the chicken tracheal ring organ culture model.

Genetic and molecular methods to investigate the pathogenesis of the poultry respiratory pathogen Mycoplasma gallisepticum are quite limited. Therefore, the objective of this study was to design and evaluate a functional genomics approach to identify M. gallisepticum genes involved in colonization of the poultry respiratory tract. To serve as a transcriptional reporter, a promoterless lacZ gene from Escherichia coli was cloned into the Tn4001 transposon. The transposon was used to randomly mutagenize the chromosome of the M. gallisepticum S6 strain, and a bank of 1386 transposon mutants containing lacZ fusions to mycoplasma chromosomal DNA was assembled. Each mycoplasma clone containing the lacZ reporter was independently screened in the chicken tracheal ring organ culture (TROC) model system for increased production of beta-galactosidase. A twofold or greater increase in beta-galactosidase was consistently observed for eight mutants. In one of the mutants, the transposon was inserted in a pMGA gene encoding a cell surface adhesin involved in hemagglutination. Therefore, these data indicate that screening of a M. gallisepticum transposon reporter bank with a chicken TROC model is useful for the identification of genes induced during poultry colonization and virulence.

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.

Identification and initial characterization of a putative Mycoplasma gallinarum leucine aminopeptidase gene.

Aminopeptidases (APN) may play a role in host colonization of M. gallinarum. Characterization of endogenous APN activity suggests that the leucine APN (LAP) of M. gallinarum is a metallo-aminopeptidase activated by Mn2+ and is present in the cytosol and possibly associated with the inner leaflet of the membrane. A 1.36-kb open reading frame (ORF) identified from overlapping genomic phage clones showed 68% nucleotide identity and 51% amino acid identity with the M. salivarium LAP gene. This ORF is expressed as a 1.5-kb monocistronic transcript and is present as a single copy in M. gallinarum. This gene sequence was modified to account for codon usage, and expression in E. coli produced a 51-kDa protein, which compares well with the product predicted from the ORF. This ORF is a strong candidate for contributing the LAP activity of M. gallinarum protein extracts.