Etiology, epidemiology, pathology, and advances in diagnosis, vaccine development, and treatment of Gallibacterium anatis infection in poultry: a review

Licorice Extract Supplementation Benefits Growth Performance, Blood Biochemistry and Hormones, Immune Antioxidant Status, Hindgut Fecal Microbial Community, and Metabolism in Beef Cattle

This study aimed to evaluate the effects of licorice extract (LE) on growth performance, nutrient apparent digestibility, serum index (biochemistry, hormones, humoral immunity, and antioxidant function), hindgut fecal microbiota, and metabolism in beef cattle. In total, 12 male yellow cattle aged 12 months were divided into two groups (6 cattle per group): the basal diet (CK group) and the basal diet supplemented with 2 g/kg LE (CHM group). The entire experimental phase lasted for 120 days, including a 30-day pre-feeding period. Compared to the CK group, the average daily gain, crude fiber, calcium, and crude protein nutrient digestibility were greater on d 30 than d 60 (p < 0.05) and the feed meat ratio was lower for LE addition (p < 0.01). In terms of serum indexes, the insulin and nitric oxide contents were enhanced on d 30, the alkaline phosphatase level was improved on d 60, and the levels of albumin, immunoglobulin A, and catalase were increased on d 90 (p < 0.05). In contrast, the cholesterol content was lower on d 60 for LE addition compared with the CK group (p < 0.05). The higher enrichment of [Eubacterium]-oxidoreducens-group, p-2534-18b5-gut-group, and Ileibacterium were observed in the CHM group (p < 0.05), while the relative abundances of Gallibacterium and Breznakia in the CHM group were lower compared with the CK group (p < 0.05). In addition, the differential metabolites related to healthy growth in the CHM group were increased compared with the CK group. And there was a close correlation between hindgut microbiota and metabolic differentials. In general, LE has a promoting effect on the growth performance and health status of beef cattle over a period (30 to 60 days).

Exploring the complexities of poultry respiratory microbiota: colonization, composition, and impact on health

An accurate understanding of the ecology and complexity of the poultry respiratory microbiota is of utmost importance for elucidating the roles of commensal or pathogenic microorganisms in the respiratory tract, as well as their associations with health or disease outcomes in poultry. This comprehensive review delves into the intricate aspects of the poultry respiratory microbiota, focusing on its colonization patterns, composition, and impact on poultry health. Firstly, an updated overview of the current knowledge concerning the composition of the microbiota in the respiratory tract of poultry is provided, as well as the factors that influence the dynamics of community structure and diversity. Additionally, the significant role that the poultry respiratory microbiota plays in economically relevant respiratory pathobiologies that affect poultry is explored. In addition, the challenges encountered when studying the poultry respiratory microbiota are addressed, including the dynamic nature of microbial communities, site-specific variations, the need for standardized protocols, the appropriate sequencing technologies, and the limitations associated with sampling methodology. Furthermore, emerging evidence that suggests bidirectional communication between the gut and respiratory microbiota in poultry is described, where disturbances in one microbiota can impact the other. Understanding this intricate cross talk holds the potential to provide valuable insights for enhancing poultry health and disease control. It becomes evident that gaining a comprehensive understanding of the multifaceted roles of the poultry respiratory microbiota, as presented in this review, is crucial for optimizing poultry health management and improving overall outcomes in poultry production.

GWAS and comparative genomics reveal candidate antibiotic resistance genes in the avian pathogen Gallibacterium anatis for six widespread antibiotics

Gallibacterium anatis is a Gram-negative bacterium found in the respiratory and genital tracts of various animals, primarily poultry. Its association with septicemia and high mortality in poultry, along with the rise in multidrug-resistant strains, has amplified concerns. Recent research uncovered significant variability in antibiotic resistance profiles among G. anatis isolates from different Austrian flocks, and even between different organs within the same bird. In response, in the present study 60 of these isolates were sequenced and a combination of comparative genomics and genome-wide association study (GWAS) analysis was applied to understand the genetic variability of G. anatis across flocks and organs and to identify genes related to antibiotic resistance. The results showed that each flock harbored one or two strains of G. anatis with only a few strains shared between flocks, demonstrating a great variability among flocks. We identified genes associated with resistance to nalidixic acid, trimethoprim, cefoxitin, tetracycline, ampicillin and sulfamethoxazole. Our findings revealed that G. anatis may develop antibiotic resistance through two mechanisms: single-nucleotide mutations and the presence of specific genes that confer resistance. Unexpectedly, some tetracycline-resistant isolates lacked all known tetracycline-associated genes, suggesting the involvement of novel mechanisms of tetracycline resistance that require additional exploration. Furthermore, our functional annotation of resistance genes highlighted the citric acid cycle pathway as a potential key modulator of antibiotic resistance in G. anatis. In summary, this study describes the first application of GWAS analysis to G. anatis and provides new insights into the acquisition of multidrug resistance in this important avian pathogen.

Antibiotic resistance of Gallibacterium anatis biovar haemolytica isolates from chickens

Introduction

Gallibacterium anatis is an opportunistic bacteria inducing a range of clinical signs in poultry. Gallibacterium anatis strains show multidrug resistance to antibacterial substances. The purpose of this study was to examine the susceptibility of G. anatis biovar haemolytica isolates collected from the respiratory, reproduction and gastrointestinal tracts of chickens to different antibiotics from various classes.

Material and Methods

Gallibacterium anatis biovar haemolytica was identified in tracheal swab and gastrointestinal and reproductive tract tissue samples from Polish layer and broiler chicken flocks. Twenty six isolates with β-haemolysis capability, each from a different flock, obtained from the respiratory (n = 8), reproductive (n = 10) and gastrointestinal (n = 8) tracts were selected and identified by matrix-assisted laser desorption/ionisation-time-of-flight mass spectrometry after culturing. A PCR method targeting the 16S genes was used for verification of isolates. The isolates' susceptibility to 20 antimicrobials was evaluated using the disc diffusion method for 8 drugs and the dilution method for the other 12. In addition, they were tested for the presence of the GtxA, gyrB and flfA virulence genes and blaROB, aphA, tetB and tetH antibiotic resistance genes by PCR.

Results

The most prevalent antibiotic resistance was to tilmicosin, tylosin and quinupristin/dalfopristin (all 100%), erythromycin (96.2%), tetracycline (96.2%), linezolid (92.3%) and teicoplanin (92.3%). Universal susceptibility was to only one antibiotic, chloramphenicol. Statistically significant differences were found between the resistance of gastrointestinal tract strains and that of strains from other tracts to daptomycin, gentamicin, ciprofloxacin and colistin. The GtxA and gyrB genes were detected in 100% of isolates and flfA in 19.2%. The isolates most frequently contained tetB and less frequently tetH and aphA, and did not contain blaROB.

Conclusion

Most G. anatis biovar haemolytica isolates were resistant to many classes of antibiotics. Therefore, it is necessary and important to be vigilant for the occurrence of these bacteria and thorough in their diagnosis.

Layer chicken microbiota: a comprehensive analysis of spatial and temporal dynamics across all major gut sections

BACKGROUND

The gut microbiota influences chicken health, welfare, and productivity. A diverse and balanced microbiota has been associated with improved growth, efficient feed utilisation, a well-developed immune system, disease resistance, and stress tolerance in chickens. Previous studies on chicken gut microbiota have predominantly focused on broiler chickens and have usually been limited to one or two sections of the digestive system, under controlled research environments, and often sampled at a single time point. To extend these studies, this investigation examined the microbiota of commercially raised layer chickens across all major gut sections of the digestive system and with regular sampling from rearing to the end of production at 80 weeks. The aim was to build a detailed picture of microbiota development across the entire digestive system of layer chickens and study spatial and temporal dynamics.

RESULTS

The taxonomic composition of gut microbiota differed significantly between birds in the rearing and production stages, indicating a shift after laying onset. Similar microbiota compositions were observed between proventriculus and gizzard, as well as between jejunum and ileum, likely due to their anatomical proximity. Lactobacillus dominated the upper gut in pullets and the lower gut in older birds. The oesophagus had a high proportion of Proteobacteria, including opportunistic pathogens such as Gallibacterium. Relative abundance of Gallibacterium increased after peak production in multiple gut sections. Aeriscardovia was enriched in the late-lay phase compared to younger birds in multiple gut sections. Age influenced microbial richness and diversity in different organs. The upper gut showed decreased diversity over time, possibly influenced by dietary changes, while the lower gut, specifically cecum and colon, displayed increased richness as birds matured. However, age-related changes were inconsistent across all organs, suggesting the influence of organ-specific factors in microbiota maturation.

CONCLUSION

Addressing a gap in previous research, this study explored the microbiota across all major gut sections and tracked their dynamics from rearing to the end of the production cycle in commercially raised layer chickens. This study provides a comprehensive understanding of microbiota structure and development which help to develop targeted strategies to optimise gut health and overall productivity in poultry production.

The intestinal microflora diversity of aboriginal chickens in Jiangxi province, China

Intestinal microbiota can coevolve with host to form symbiotic relationship and be participated in the regulation of host physiological function. At present, there is no clear explanation on the effect of intestinal microflora in Jiangxi aboriginal chickens. Here, we investigated the association between gut microbiota and host genome of Jiangxi local chickens using 16S rRNA sequencing and genome-wide association studies (GWAS). The results showed that the breeds and genders had important effects on the intestinal microbiota of chickens. A total of 28 SNPs in 14 regions of the chicken genome were related to the relative abundance of microorganisms in 5 genera: Clostridium_sensu_stricto_1, Enterococcus, Gallibacterium, Turicibacter, and Rikenellaceae_RC9_gut_group. A total of 17 candidate genes were identified composition of chicken microbiome and show an association between the host genome and the chicken intestinal microbiota, which also unveiled the diversity of intestinal microbes in Jiangxi chickens. Given the correlation between chicken genome and intestinal microbe found in the present study, a new idea for the protection of aboriginal chicken genetic resources in China could be provided.

Isolation and characterization of multidrug resistant Gallibacterium anatis biovar haemolytica strains from Polish geese and hens

Gallibacterium anatis biovar haemolytica is a bacterium that is frequently associated with infections of the reproductive tract and respiratory system in poultry. To assess the current prevalence and resistance profile of these bacteria in Poland, we collected and investigated 63 strains of Gallibacterium from diseased domestic poultry flocks including geese, laying hens, breeding hens and an ornamental hen. Detailed characterization of the isolates included the analysis of phenotypic antimicrobial resistance profiles and biofilm formation ability. Furthermore, the genetic background of 40 selected isolates regarding the presence of virulence and antimicrobial resistance genes and mobile genetic elements was determined. All investigated isolates were multidrug resistant, most prominently to β-lactams, fluoroquinolones, sulfonamides and macrolides. A total of 48 different resistance profiles were detected. Of all isolates, 50.8% formed a strong biofilm, where strains isolated from geese appeared to be better at biofilm formation than strains isolated from laying and breeding hens. Single-nucleotide polymorphism genotyping revealed that G. anatis bv. haemolytica strains are restricted in host and geographical distribution, and the geese isolates showed greater phylogenetic similarity. Whole genome sequencing enabled identification of 25 different antimicrobial resistance determinants. The most common resistance genes were tetB, blaROB-1, and blaTEM-1 which may be located on mobile genetic elements. All isolates possessed the toxin gene gtxA, and the fimbrial gene flfA was identified in 95% of strains. Our results indicated that all G. anatis bv. haemolytica isolates showed multidrug resistant phenotypes. Strains isolated from geese were characterized by the highest percentage of isolates resistant to selected antimicrobials, probably reflecting host-related adaptations.

Prevalence, Identification and Antibiotic Resistance of Gallibacterium anatis Isolates from Chickens in Poland

The Gram-negative bacterium Gallibacterium anatis is part of the normal avian respiratory, intestinal and reproductive tract microflora and can be transmitted horizontally and vertically. With the coexistence of other relevant factors, G. anatis becomes an opportunistic pathogen, economically damaging to the poultry industry. This bacterium's prevalence and molecular epidemiology were investigated, and the antimicrobial treatment options for G. anatis infection in chicken flocks in Poland were assessed. Tracheal samples from 182 flocks were collected between April 2022 and March 2023. The bacterial prevalence was determined by PCR targeting the gyrB gene and 16-23S rRNA. Gallibacterium anatis was identified by matrix-assisted laser desorption/ionisation-time-of-flight mass spectrometry (MALDI-TOF) after culturing and PCR amplification. Isolates' susceptibility to 11 antimicrobials was assessed with a disc diffusion test. Isolates were also tested for gyrB, GtxA and flfA virulence genes and blaROB, aphA, tetB and tetH antibiotic resistance genes by PCR. Forty-one flocks (22.5%) were positive through PCR. Antibiotic resistance was most frequently observed against tilmicosin, tylosin, enrofloxacin, amoxicillin, tetracycline and doxycycline. Multiple resistance to at least eight antibiotics occurred in 20% of isolates and to at least four in 100%. The occurrence of gyrB was noted in 100%, GtxA was detected in 89%, and flfA was found in 14% of positive samples. The tetB gene was present in 61.0% of positive samples, tetH was in 36.0%, aphA was in 16.7%, and blaROB was in 5.6%. Significant differences were found in G. anatis isolates related to the presence of the virulence genes GtxA and gyrB and the presence of resistance genes (p < 0.05) associated with resistance to tetracyclines, β-lactams and aminoglycosides. The continued rise in the resistance of G. anatis to a broadening range of antibiotics is a major problem for the poultry industry worldwide, as well as for public health. The findings of this study may expand the knowledge of the pathogenicity of G. anatis in poultry.

Quinolone Resistance in Gallibacterium anatis Determined by Mutations in Quinolone Resistance-Determining Region

Control of the important pathogen, Gallibacterium anatis, which causes salpingitis and peritonitis in poultry, relies on treatment using antimicrobial compounds. Among these, quinolones and fluoroquinolones have been used extensively, leading to a rise in the prevalence of resistant strains. The molecular mechanisms leading to quinolone resistance, however, have not previously been described for G. anatis, which is the aim of this study. The present study combines phenotypic antimicrobial resistance data with genomic sequence data from a collection of G. anatis strains isolated from avian hosts between 1979 and 2020. Minimum inhibitory concentrations were determined for nalidixic acid, as well as for enrofloxacin for each included strain. In silico analyses included genome-wide queries for genes known to convey resistance towards quinolones, identification of variable positions in the primary structure of quinolone protein targets and structural prediction models. No resistance genes known to confer resistance to quinolones were identified. Yet, a total of nine positions in the quinolone target protein subunits (GyrA, GyrB, ParC and ParE) displayed substantial variation and were further analyzed. By combining variation patterns with observed resistance patterns, positions 83 and 87 in GyrA, as well as position 88 in ParC, appeared to be linked to increased resistance towards both quinolones included. As no notable differences in tertiary structure were observed between subunits of resistant and sensitive strains, the mechanism behind the observed resistance is likely due to subtle shifts in amino acid side chain properties.

The integrated analysis of digestive physiology and gastrointestinal microbiota structure in Changle goose

Changle goose in Fujian, China is a rare genetic resource and in urgent need to be protected. Understanding the characteristics of digestive physiology and spatial variation of gastrointestinal microbiota is crucial for developing nutritional intervention strategies to improve intestinal health and production performance of goose. Hence, histomorphological assay was used for observing development status of proventriculus, jejunum, and cecum in 70-day-old Changle geese, whereas digesta from 6 alimentary canal locations (crop, proventriculus, gizzard, jejunum, cecum, and rectum) were collected for 16S rRNA gene sequencing and short chain fatty acids (SCFAs) quantitative analysis. The histomorphological observation indicated that the jejunum and cecum of Changle goose were well developed. The alpha diversity analysis revealed that, except rectum, microbiota in other noncecum sections were in high diversity as cecum. The Nonmetric MultiDimensional Scaling (NMDS) analysis showed that microbial community of proventriculus, gizzard, and jejunum formed a cluster, which distinctly discrete with the microbiota of the other gastrointestinal locations. Additionally, the proportions of Proteobacteria, Bacteroidota, and Campilobacterota at the phylum level and Lactobacillus, Streptococcus, Helicobacter, and Subdoligranulum at the genus level exhibited tremendous alternations among different gastrointestinal locations. The characteristic bacterial composition in each section was further disclosed by analyzing the core and feature Amplicon Sequence Variants (ASVs) and SCFAs pattern. Importantly, 7 body-weight-associated ASVs and 2 cecum-development-related ASVs were identified via correlation analysis. In a whole, our findings provided the first insights into the specialized digestive physiology of Changle geese and distinctive regional distribution of gastrointestinal microbiota, which laid the important foundation for improving growth performance through microbiota manipulation in geese.

Genetic Organization of Acquired Antimicrobial Resistance Genes and Detection of Resistance-Mediating Mutations in a Gallibacterium anatis Isolate from a Calf Suffering from a Respiratory Tract Infection

Gallibacterium (G.) anatis isolates associated with respiratory diseases in calves and harboring acquired antimicrobial resistance genes have been described in Belgium. The aim of this study was to analyze the genetic organization of acquired resistance genes in the G. anatis isolate IMT49310 from a German calf suffering from a respiratory tract infection. The isolate was submitted to antimicrobial susceptibility testing, and a closed genome was obtained by a hybrid assembly of Illumina MiSeq short-reads and MinION long-reads. Isolate IMT49310 showed elevated MIC values for macrolides, aminoglycosides, florfenicol, tetracyclines, and trimethoprim/sulfamethoxazole. The acquired resistance genes catA1, floR, aadA1, aadB, aphA1, strA, tet(M), tet(B), erm(B), and sul2 were identified within three resistance gene regions in the genome, some of which were associated with IS elements, such as ISVsa5-like or IS15DII. Furthermore, nucleotide exchanges within the QRDRs of gyrA and parC, resulting in amino acid exchanges S83F and D87A in GyrA and S80I in ParC, were identified. Even if the role in the pathogenesis of respiratory tract infections in cattle needs to be further investigated, the identification of a G. anatis isolate with reduced susceptibility to regularly used antimicrobial agents in cases of fatal bovine respiratory tract infections is worrisome, and such isolates might also act as a reservoir for antimicrobial resistance genes.

Dietary Epimedium extract supplementation improves intestinal functions and alters gut microbiota in broilers

BACKGROUND

Growth-promoting antibiotics have been banned by law in the livestock and poultry breeding industry in many countries. Various alternatives to antibiotics have been investigated for using in livestock. Epimedium (EM) is an herb rich in flavonoids that has many beneficial effects on animals. Therefore, this study was planned to explore the potential of EM as a new alternative antibiotic product in animal feed.

METHODS

A total of 720 1-day-old male broilers (Arbor Acres Plus) were randomly divided into six groups and fed basal diet (normal control; NC), basal diet supplemented with antibiotic (75 mg/kg chlortetracycline; CTC), and basal diet supplemented with 100, 200, 400 or 800 mg/kg EM extract for 6 weeks (EM100, EM200, EM400 and EM800 groups). The growth performance at weeks 3 and 6 was measured. Serum, intestinal tissue and feces were collected to assay for antioxidant indexes, intestinal permeability, lactic acid and short-chain fatty acids (SCFAs) profiles, microbial composition, and expression of intestinal barrier genes.

RESULTS

The average daily feed intake in CTC group at 1-21 d was significantly higher than that in the NC group, and had no statistical difference with EM groups. Compared with NC group, average daily gain in CTC and EM200 groups increased significantly at 1-21 and 1-42 d. Compared with NC group, EM200 and EM400 groups had significantly decreased levels of lipopolysaccharide and D-lactic acid in serum throughout the study. The concentrations of lactic acid, acetic acid, propionic acid, butyric acid and SCFAs in feces of birds fed 200 mg/kg EM diet were significantly higher than those fed chlortetracycline. The dietary supplementation of chlortetracycline and 200 mg/kg EM significantly increased ileal expression of SOD1, Claudin-1 and ZO-1 genes. Dietary supplemented with 200 mg/kg EM increased the relative abundances of g_NK4A214_group and Lactobacillus in the jejunal, while the relative abundances of Microbacterium, Kitasatospora, Bacteroides in the jejunal and Gallibacterium in the ileum decreased.

CONCLUSION

Supplementation with 200 mg/kg EM extract improved the composition of intestinal microbiota by regulating the core bacterial genus Lactobacillus, and increased the concentration of beneficial metabolites lactic acid and SCFAs in the flora, thereby improving the antioxidant capacity and intestinal permeability, enhancing the function of tight junction proteins. These beneficial effects improved the growth performance of broilers.

Identification, 16S rRNA-based characterization, and antimicrobial profile of Gallibacterium isolates from broiler and layer chickens

Gallibacterium spp., particularly G. anatis, have received much attention as poultry pathogens in recent years. We report here the presence and antimicrobial resistance profile of 69 Gallibacterium isolates obtained from 2,204 diagnostic submissions of broiler and layer chickens in 2019-2021. Gallibacterium-positive chickens had lesions primarily in the respiratory tract, reproductive tract, and related serosal surfaces. Gallibacterium spp. were initially identified based on their typical cultural characteristics on blood agar. The isolates were confirmed by a genus-specific PCR spanning 16S-23S rRNA and MALDI-TOF mass spectrometry. Phylogenetic analysis based on 16S rRNA gene sequence revealed distinct clades. Of the 69 isolates, 68 clustered with the reference strains of G. anatis and 1 with Gallibacterium genomospecies 1 and 2. Antimicrobial susceptibility testing of 58 of the 69 isolates by a MIC method showed variable responses to antimicrobials. The isolates were all susceptible to enrofloxacin, ceftiofur, florfenicol, and gentamicin. There was a high level of susceptibility to trimethoprim-sulfamethoxazole (98.0%), streptomycin (98.0%), amoxicillin (84.0%), sulfadimethoxine (71.0%), and neomycin (71.0%). All of the isolates were resistant to tylosin. There was resistance to penicillin (98.0%), erythromycin (95.0%), clindamycin (94.0%), novobiocin (90.0%), tetracycline (88.0%), oxytetracycline (76.0%), and sulfathiazole (53.0%). A high rate of intermediate susceptibility was observed for spectinomycin (67.0%) and sulfathiazole (40.0%). Our findings indicate a potential role of G. anatis as an important poultry pathogen and cause of subsequent disease, alone or in combination with other pathogens. Continuous monitoring and an antimicrobial susceptibility assay are recommended for effective treatment and disease control.

In silico detection and characterization of novel virulence proteins of the emerging poultry pathogen Gallibacterium anatis

The pathogen Gallibacterium anatis has caused heavy economic losses for commercial poultry farms around the world. However, despite its importance, the functions of its hypothetical proteins (HPs) have been poorly characterized. The present study analyzed the functions and structures of HPs obtained from Gallibacterium anatis (NCTC11413) using various bioinformatics tools. Initially, all the functions of HPs were predicted using the VICMpred tool, and the physicochemical properties of the identified virulence proteins were then analyzed using Expasy's ProtParam server. A virulence protein (WP_013745346.1) that can act as a potential drug target was further analyzed for its secondary structure, followed by homology modeling and three-dimensional (3D) structure determination using the Swiss-Model and Phyre2 servers. The quality assessment and validation of the 3D model were conducted using ERRAT, Verify3D, and PROCHECK programs. The functional and phylogenetic analysis was conducted using ProFunc, STRING, KEGG servers, and MEGA software. The bioinformatics analysis revealed 201 HPs related to cellular processes (n = 119), metabolism (n = 61), virulence (n = 11), and information/storage molecules (n = 10). Among the virulence proteins, three were detected as drug targets and six as vaccine targets. The characterized virulence protein WP_013745346.1 is proven to be stable, a drug target, and an enzyme related to the citrate cycle in the present pathogen. This enzyme was also found to facilitate other metabolic pathways, the biosynthesis of secondary metabolites, and the biosynthesis of amino acids.

An urban diet differentially alters the gut microbiome and metabolomic profiles compared with a seed diet in mourning doves

Urbanization influences food quality and availability for many avian species, with increased access to human refuse and food subsidies in built environments. In relation to such nutritional intakes and their presumed impact on microbes harbored in the intestinal tract and metabolic profiles of host physiological systems, our overall knowledge of the role of gut microbiome (GM) and metabolomic expression in the avian host lags far behind our understanding of mammals. Therefore, the objective of this investigation was to examine the potential differential effect of an urban modeled versus control (i.e., bird seed) diet on the GM, the metabolic profiles of plasma, liver, adipose, kidney, and muscle tissues, and circulating endotoxin and inflammatory factors in urban-caught mourning doves (Zenaida macroura). We hypothesized that the urban diet would differently impact the profiles of the GM and tissue metabolomes and increase plasma lipopolysaccharide (LPS) and proinflammatory factors compared with animals fed a seed diet. After a 4-wk-diet period, contents of the large intestine were sequenced to profile the microbiome, metabolomic analyses were performed on plasma and tissue homogenates, and circulating LPS and inflammatory markers were assessed. The composition of the GM was significantly dissimilar between diets, with greater abundance of Erysipelatoclostridiaceae, Sanguibacteraceae, Oribacterium, and Sanguibacter and decreased circulating LPS in the urban-fed birds. These differences were largely not reflected in the surveyed metabolomes and plasma inflammatory markers. This research supports the notion that the microbial composition in urban doves is impacted by diet, though may only weakly associate with host physiology.

Sequence Analysis, Antibiogram Profile, Virulence and Antibiotic Resistance Genes of XDR and MDR Gallibacterium anatis Isolated from Layer Chickens in Egypt

Background

Gallibacterium anatis is incriminated frequently in severe economic losses and mortalities in the poultry industry. This study aimed to detect the prevalence of G. anatis in layer chickens, sequence analysis, the antibiogram profiles, and PCR screening of virulence determinants and antibiotic resistance genes.

Methods

Accordingly, 300 samples (tracheal swabs, ovary and oviduct, and lung) were randomly collected from 100 diseased layer chickens from private commercial layer farms at Elsharkia Governorate, Egypt. The bacteriological examination was carried out. The retrieved isolates were tested for 16S rRNA-23S rRNA gene sequencing, antibiogram profiling, PCR screening of virulence (gtxA, fifA, and gyrB), and antibiotic resistance genes (bla_ROB, aphA1, tetB, and tetH).

Results

The prevalence of G. anatis was 25% in the examined diseased layer chickens. The sequence analyses emphasized that the tested strains derived from a common ancestor and exhibited a notable genetic similarity with other G. anatis strains from USA, China, and Denmark. The isolated G. anatis strains were highly resistant to sulfamethoxazole-trimethoprim, oxytetracycline, penicillin, ampicillin, kanamycin, neomycin, and erythromycin. The PCR revealed that the retrieved G. anatis strains carried gtxA, gyrB, and fifA virulence genes with a prevalence of 100%, 100%, and 38.3%, respectively. Approximately 30.1% of the retrieved G. anatis isolates were XDR to six antimicrobial classes and harbored bla_ROB, aphA1, and tetB resistance genes. Moreover, 20.5% of the isolated G. anatis strains were MDR to three different classes and carried bla_ROB and tetH resistance genes.

Conclusion

Briefly, this study emphasized the existence of XDR and MDR G. anatis strains in poultry. Florfenicol and norfloxacin displayed a promising antimicrobial effect against the emerging XDR and MDR G. anatis in poultry. The emergence of XDR and MDR G. anatis is considered a public health alarm.

Litter Management Strategies and Their Impact on the Environmental and Respiratory Microbiome Might Influence Health in Poultry

Aerial and respiratory tract-associated bacterial diversity has been scarcely studied in broiler production systems. This study examined the relationship between the environmental air and birds’ respiratory microbiome, considering a longitudinal sampling. Total viable bacteria and coliforms in the air were quantified, and the 16S rRNA gene was sequenced from tracheal and air samples obtained through a novelty protocol. Air results showed a decrease in coliforms over time. However, at week 3, we reported an increase in coliforms (from 143 to 474 CFUc/m3) associated with litter management. Additionally, 16S rRNA gene results indicated a distinctive air microbial community, associated primarily with Bacillota phylum particularly of the Bacilli class (>58%), under all conditions. Tracheal results indicated a predominance of Escherichia coli/Shigella at the beginning of the productive cycle, shifting toward the middle and end of the cycle to Gallibacterium. However, at week 3, the dominance of Escherichia coli/Shigella (>99.5%) associated with litter aeration by tumbling stood out. Tracheal and air samples displayed a statistically different community structure, but shared differentially abundant features through time: Enterococcus, Gallibacterium, and Romboutsia ilealis. These results indicate the impact of production management protocols on the birds’ respiratory system that should be considered a breakpoint in poultry farm health.

Molecular epidemiological studies on avian pathogenic Escherichia coli associated with septicemia in chickens in India

Bacterial septicemia causes huge economic losses in the poultry industry and there is no systematic research available in India on the connection of various pathogens associated with septicemia. The present molecular epidemiological study was conducted to investigate the association of different bacterial and immunosuppressive viral pathogens in septicemia suspected chickens. A total of 443 chicken carcasses with septicemic conditions from 71 different flocks were included in this study. Heart blood swabs were subjected to bacterial culture for Salmonella spp., Pasteurella multocida, Escherichia coli, and Gallibacterium anatis. Of these 51 flocks tested for E. coli, 49 (96.1%) flocks were found positive. Among flocks tested for Salmonella spp., 2 flocks were found positive. All tested flocks were found negative for G. anatis and P. multocida as well as air sac swabs tested negative for Mycoplasma spp. Bacterial cultural examination revealed that majority of septicemic chickens were found to be infected with E. coli and these E. coli isolates showed the highest resistance to vancomycin (60%), followed by erythromycin (50%) and cefotaxime (38%) and maximum sensitivity to cefotaxime and clavulanic acid combinations (81.5%), followed by chloramphenicol (69.6%) and ertapenem (67.2%). Among the 5 avian pathogenic E. coli (APEC) virulence genes were detected in 36 flocks and highest frequency of iss (100%), followed by ompT or iutA (97.2%), hly (61.1%) and iroN (47.2%) genes. On polymerase chain reaction (PCR) screening, 10.5, 4.5, 52.2, 19.4, 9.0, 4.5, 20.1 and 19.4% of the flocks were positive for G. anatis, Ornithobacterium rhinotracheale, APEC, Salmonella spp., Mycoplasma gallisepticum, Mycoplasma synoviae, chicken infectious anemia virus and Marek's disease virus, respectively. To our knowledge, the present study is first on the etiology of septicemia in chicken flocks in India. The present study infers that the majority of septicemic deaths in broiler chickens less than 8 weeks have been connected with APEC and majority of E. coli isolates are multidrug resistance, suggesting the need for surveillance and intervention to curb the inadvertent use of antibiotics. Although, incidence of G. anatis association with septicemia was reported, still requires a rigorous epidemiological study to determine the actual prevalence. However, more detailed studies encompassing vast geographical area with large sample size and long duration of the studies are necessary to provide a clear picture of the interaction of different pathogens causing septicemia in chicken.

Comparative Genomics Analyses Support the Reclassification of Bisgaard Taxon 40 as Mergibacter gen. nov., With Mergibacter septicus sp. nov. as Type Species: Novel Insights Into the Phylogeny and Virulence Factors of a Pasteurellaceae Family Member Associated With Mortality Events in Seabirds

The Pasteurellaceae family has been associated with fatal diseases in numerous avian species. Several new taxa within this family, including Bisgaard taxon 40, have been recently described in wild birds, but their genomic characteristics and pathogenicity are not well understood. We isolated Bisgaard taxon 40 from four species of seabirds, including one sampled during a mass, multi-species mortality event in Florida, United States. Here, we present a comprehensive phenotypic and genetic characterization of Bisgaard taxon 40 and comparative genomic analysis with reference strains from the Pasteurellaceae family, aiming at determining its phylogenetic position, antimicrobial susceptibility profile, and identifying putative virulence factors. In silico multilocus sequence-based and whole-genome-based phylogenetic analysis clustered all Bisgaard taxon 40 strains together on a distinct branch separated from the other members of the Pasteurellaceae family, indicating that Bisgaard taxon 40 could represent a new genus. These findings were further supported by protein similarity analyses using the concatenation of 31 conserved proteins and other taxonomic approaches such as the percentage of conserved protein test. Additionally, several putative virulence factors were identified, including those associated with adhesion (capsule, ompA, ompH) and colonization (exbD, fur, galU, galE, lpxA, lpxC, and kdsA) of the host and a cytolethal distending toxin (cdt), which may have played a role in disease development leading to the mortality event. Considerably low minimum inhibitory concentrations (MICs) were found for all the drugs tested, in concordance with the absence of antimicrobial resistance genes in these genomes. The novel findings of this study highlight genomic and phenotypic characteristics of this bacterium, providing insights into genome evolution and pathogenicity. We propose a reclassification of these organisms within the Pasteurellaceae family, designated as Mergibacter gen. nov., with Mergibacter septicus sp. nov. as the type species. The type strain is Mergibacter septicus A25201^T (=DSM 112696).

Kurthia gibsonii, a novel opportunistic pathogen in poultry

Kurthia gibsonii (H. Kurth, 1883) was isolated on 10 unrelated laying hen farms over a period of 15 months. Farmers reported elevated morbidity and mortality rates, and suspected of colibacillosis based on the necropsy findings. The most frequently found lesions were perihepatitis, fibrinous peritonitis, salpingitis and oophoritis. Necropsy findings and bacteriological results allowed the diagnosis of colibacillosis. In addition, K. gibsonii was isolated from the ovarian follicles (44.44 %), liver (22.22%), peritoneum (16.67%), bone marrow (5.56%), spleen (5.56%), and duodenum (5.56%). On all farms, coinfection with E. coli was detected, while on some farms other common avian pathogens were found as well. In total, 18 K. gibsonii strains were identified and phylogenetically analysed based on the 16S rRNA gene sequences. The results showed some variability of the strains originating from the same farm, although the overall phylogenetic diversity was low, regardless of the geographical location of the farm, age of the flock or date of collection. Embryo lethality assay showed K. gibsonii is not able to cause a primary infection. We conclude that Kurthia gibsonii may play a role as an opportunistic pathogen for poultry. This is the first report of coinfection of Kurthia gibsonii and E. coli in laying hens.

Respiratory and Reproductive Impairment of Commercial Layer Chickens After Experimental Infection with Gallibacterium anatis Biovar haemolytica

The prevalence of Gallibacterium anatis in poultry production has increased over the last two decades. However, only a few studies have explored the pathogenicity of this bacterium in commercial layer chickens. This trial studied the aspects of the pathogenicity of a Gallibacterium anatis biovar haemolytica local Egyptian isolate (previously registered as strain B14 with GenBank accession no. KJ026147). We used 500 base pairs of a 16S ribosomal RNA gene and the 16S-23S ribosomal RNA intergenic spacer, partial sequence in an experimental infection trial in commercial White Shaver layer chickens aged 19 wk. The hens were divided into three groups of 40 birds each. The hens in Groups 1 and 2 were experimentally infected through the intranasal (IN) and intravenous (IV) routes, respectively, with a dose of 0.2 ml/bird containing 1.2 × 109 colony-forming units/ml. In contrast, Group 3 was kept as a noninfected control group. Both IN and IV infections resulted in a delayed egg laying for 1 wk and a significant (P ≤ 0.05) drop in egg production by 7.81% and 10.28% compared with the control group over 7 wk. Severe lesions in the form of hemorrhagic pneumonia, catarrhal tracheitis, ovarian follicle and oviductal regression, and septicemia were evident on necropsy, demonstrating the pathogenicity of G. anatis as a primary pathogen.

Co-Infection of Escherichia coli, Enterococcus faecalis and Chlamydia psittaci Contributes to Salpingitis of Laying Layers and Breeder Ducks

Salpingitis is manifested as hemorrhagic follicular inflammation exudations and peritonitis, leading to reduced egg production and high culling of breeder flocks. From 2018 to 2021, increasing salpingitis during egg peak is threatening the poultry industry post-artificial insemination, both in breeder layers and breeder ducks across China. In our study, Escherichia coli (E. coli), Enterococcus faecalis(E. faecalis) and Chlamydia psittaci (C. psittaci) were isolated and identified from the diseased oviducts using biochemical tests and PCR. To identify and isolate pathogenicity, we inoculated the isolates into laying hens via an intravaginal route. Later, laying hens developed typical salpingitis after receiving the combination of the aforementioned three isolates (1 × 10⁵ IFU/mL of C. psittaci and 1 × 10⁶ CFU/mL of E. faecalis and E. coli, respectively), while less oviduct inflammation was observed in the layers inoculated with the above isolate alone. Furthermore, 56 breeder ducks were divided into seven groups, eight ducks per group. The birds received the combination of three isolates, synergic infection of E. coli and E. faecalis, and C. psittaci alone via vaginal tract, while the remaining ducks were inoculated with physiological saline as the control group. Egg production was monitored daily and lesions of oviducts and follicles were determined post-infection on day 6. Interestingly, typical salpingitis, degenerated follicles and yolk peritonitis were obviously found in the synergic infection of three isolates and the birds inoculated with C. psittaci alone developed hemorrhagic follicles and white exudates in oviducts, while birds with E. faecalis or E. coli alone did not develop typical salpingitis. Finally, higher E. coli loads were determined in the oviducts as compared to E. faecalis and C. psittaci infection. Taken together, the combination of E. coli and E. faecalis, and C. psittaci could induce typical salpingitis and yolk peritonitis both in laying hens and breeder ducks. Secondary infection of E. coli and E. faecalis via artificial insemination is urgently needed for investigation against salpingitis.

Detection of aerobic bacterial pathogens associated with early embryonic death in pregnant New Zealand female Rabbits in Egypt

Background and Aim:

Rabbits are a highly sensitive species and susceptible to various bacterial pathogens that may be causative agents for early embryonic death. This study aimed to explore the administration of different bacterial agents in does suffering from early embryonic death. Furthermore, identification of genes associated with virulence was performed to identify the phenotypic and genotypic antimicrobial resistance patterns that may increase the virulence of pathogens and lead to early embryonic death.

Materials and Methods:

We isolated and identified bacterial agents in 106 samples from live and dead female rabbits that had undergone early embryonic death, including liver and intestine tissue, aborted fetuses, discharges, and vaginal swabs. Conventional polymerase chain reaction (PCR) was conducted to confirm the identity of the isolated bacterial strains and their virulence. Moreover, antibiotic resistance was studied phenotypically and genotypically.

Results:

We isolated Escherichia coli, Salmonella, Staphylococcus aureus, Pasteurella multocida, and Listeria monocytogenes. PCR confirmed typical identification except in P. multocida, which was confirmed as Gallibacterium spp. in some cases. The final percentage of detection was 34%, 30.2%, 16.9%, 13.2%, and 11.3%, respectively. Virulence properties were investigated using different designated genes. All Salmonella strains harbored invA, stn, avrA, and ompf genes, while the sopE gene was identified in 31.25%. E. coli strains harboring the iss gene lacked the shiga toxin (stx1) gene. L. monocytogenes and S. aureus strains harbored the hemolysin gene (66.7% and 33.4%, respectively). Multidrug resistance was detected phenotypically and genotypically in most strains. Each bacterial pathogen had a different antibiotic resistance profile.

Conclusion:

Multiple bacterial species may contribute to early embryonic death in does. Furthermore, the combined infection could be the main cause of early embryonic death. Thus, monitoring programs should bear this in mind and focus on the early detection of these bacterial agents in female rabbits to avoid embryonic death.

Antibacterial Activity of Lactic Acid Producing Leuconostoc mesenteroides QZ1178 Against Pathogenic Gallibacterium anatis

Lactic acid bacteria (LAB) convert carbohydrates into organic acids [mainly lactic acid (LA)], which reportedly have bactericidal activities. Gallibacterium anatis is a Gram-negative bacteria which infects birds, and causes significant economic losses. In this study, we investigated the antibacterial activity of the LA producing, Leuconostoc mesenteroides QZ1178 from Qula (fermented food), against G. anatis, using the Oxford cup method. Our data showed that L. mesenteroides QZ1178 inhibited G. anatis isolates from different origins; however, L. mesenteroides QZ1178 antibacterial activity dropped dramatically at pH 5.5–pH 6. The LA concentration and pH of the liquid broth containing L. mesenteroides QZ1178 after 24 h culture was 29 mg/mL and 3.6, respectively. This concentration (29 mg/mL at pH 3.6) and the antibiotic, cefotaxime (minimum inhibitory concentration (MIC) 2.5 μg/mL) effectively inhibited G. anatis (GAC026) growth as observed by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). Gallibacterium anatis treated with LA exhibited extensive cell surface collapse, increased cell damage, cell membrane disruption, and cytoplasmic leakage, indicative of cell lysis. We suggest L. mesenteroides QZ1178 exerts potential antibacterial effects against the poultry pathogen, G. anatis via LA.

Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture

BACKGROUND

The chicken is the most abundant food animal in the world. However, despite its importance, the chicken gut microbiome remains largely undefined. Here, we exploit culture-independent and culture-dependent approaches to reveal extensive taxonomic diversity within this complex microbial community.

RESULTS

We performed metagenomic sequencing of fifty chicken faecal samples from two breeds and analysed these, alongside all (n = 582) relevant publicly available chicken metagenomes, to cluster over 20 million non-redundant genes and to construct over 5,500 metagenome-assembled bacterial genomes. In addition, we recovered nearly 600 bacteriophage genomes. This represents the most comprehensive view of taxonomic diversity within the chicken gut microbiome to date, encompassing hundreds of novel candidate bacterial genera and species. To provide a stable, clear and memorable nomenclature for novel species, we devised a scalable combinatorial system for the creation of hundreds of well-formed Latin binomials. We cultured and genome-sequenced bacterial isolates from chicken faeces, documenting over forty novel species, together with three species from the genus Escherichia, including the newly named species Escherichia whittamii.

CONCLUSIONS

Our metagenomic and culture-based analyses provide new insights into the bacterial, archaeal and bacteriophage components of the chicken gut microbiome. The resulting datasets expand the known diversity of the chicken gut microbiome and provide a key resource for future high-resolution taxonomic and functional studies on the chicken gut microbiome.

Clonal spread of multi-resistant Gallibacterium anatis isolates among Iranian broilers and layers

Gallibacterium anatis is a common cause of reproductive tract infection in chickens, which leads to reduced egg production and increased mortality. This study was undertaken to investigate prevalence of G. anatis in 12 poultry flocks originating from Iranian provinces with leading chicken production and to determine genetic diversity, antimicrobial resistance, and the presence of major antigens of the isolates investigated. Out of the 120 chicken tracheal samples collected and tested, 84 (70%) were positive for G. anatis. Genotyping by Pulse Field Gel Electrophoresis and genome sequencing revealed a total of 24 pulsotypes for 71 strains (at a 87% similarity level) and seven genome clusters comprising 21 strains (97% similarity level), respectively. The combination of the two typing methods confirmed the presence of several genotypes originating from a common ancestor affecting poultry yet also suggested that identical clones were shared among chickens within farms and between different farms. The latter finding is to our knowledge the first example of clonal presence of G. anatis in epidemiologically unrelated farms. The 21 sequenced strains were characterized against a panel of commonly used antibiotics and showed lowered sensitivity to tetracycline (76.2%) and enrofloxacin (90.5%). The widespread presence of multiresistant G. anatis isolates calls for non-antibiotic prophylactics. Three major immunogen genes, gtxA, Gab_1309 and Gab_2312 were detected in the isolates indicating these antigens likely represent effective vaccine targets. A conserved sequence of the gtxA gene across a range of epidemiologically independent strains suggests the use of GtxA for future vaccine development purposes.