Molecular epidemiology ofEnterococcus cecorumisolates recovered from enterococcal spondylitis outbreaks in the southeastern United States

Detection of Enterococcus cecorum to identify persistently contaminated locations using faecal and environmental samples in broiler houses of clinically healthy flocks

Worldwide outbreaks make infections with pathogenic strains of Enterococcus cecorum (EC) one of the most important diseases in the broiler industry. Although research has increased knowledge about the pathogen, the transmission is not fully understood. Samples from different locations were collected from two broiler farms in Germany over a total of six production cycles. Samples were collected at days 1, 5, 10, 15, 21, 27, 34, 41 post-hatch and after cleaning and disinfection (C&D). A total of 1017 samples were collected from 25 different locations on the farms. Samples were analysed in the laboratory for EC by quantitative real-time PCR. Overall, 7.5% of the samples were positive. The probabilities for positive and negative samples did not differ between the farms. The number of findings differed significantly between the cycles. Compared to other samples, the chances of detecting EC in faecal samples were significantly higher. Most positive samples were found in the last week of the production periods, indicating an accumulation of EC in the barn environment. After C&D, positive PCR results were obtained in four out of 14 locations. A re-introduction from contaminated environment seemed possible. However, one pooled faecal sample was positive 1 day post-hatch. The locations that showed positive results after C&D and the positive faecal sample 1 day post-hatch indicated the persistence of EC in broiler houses of clinically healthy flocks that could lead to potential horizontal transmission routes. The present study detected potential EC sources and may help to improve hygienic measures to avoid transmissions.RESEARCH HIGHLIGHTSMethodology is suitable to detect EC during production and after C&D.Locations were detected that may serve as a reservoir for EC.Cycles with fewer positive samples were observed.Cleaning and disinfection had a major impact on the detection of EC.

The Genetic Landscape of Antimicrobial Resistance Genes in Enterococcus cecorum Broiler Isolates

Enterococcus cecorum is associated with bacterial chondronecrosis with osteomyelitis (BCO) in broilers. Prophylactic treatment with antimicrobials is common in the poultry industry, and, in the case of outbreaks, antimicrobial treatment is needed. In this study, the minimum inhibitory concentrations (MICs) and epidemiological cutoff (ECOFF) values (COWT) for ten antimicrobials were determined in a collection of E. cecorum strains. Whole-genome sequencing data were analyzed for a selection of these E. cecorum strains to identify resistance determinants involved in the observed phenotypes. Wild-type and non-wild-type isolates were observed for the investigated antimicrobial agents. Several antimicrobial resistance genes (ARGs) were detected in the isolates, linking phenotypes with genotypes for the resistance to vancomycin, tetracycline, lincomycin, spectinomycin, and tylosin. These detected resistance genes were located on mobile genetic elements (MGEs). Point mutations were found in isolates with a non-wild-type phenotype for enrofloxacin and ampicillin/ceftiofur. Isolates showing non-wild-type phenotypes for enrofloxacin had point mutations within the GyrA, GyrB, and ParC proteins, while five amino acid changes in penicillin-binding proteins (PBP2x superfamily) were observed in non-wild-type phenotypes for the tested β-lactam antimicrobials. This study is one of the first that describes the genetic landscape of ARGs within MGEs in E. cecorum, in association with phenotypical resistance determination.

Enterococcus cecorum lesion strains are less sensitive to the hostile environment of albumen and more resistant to lysozyme compared to cloaca strains

RESEARCH HIGHLIGHTS

Egg albumen inhibits Enterococcus cecorum cloaca strains more than lesion strains.Enterococcus cecorum lesion strains are resistant to high concentrations of lysozyme.Lysozyme resistance could enhance survival in albumen and body fluids.

Serological monitoring of Enterococcus cecorum specific antibodies in chickens

Pathogenic Enterococcus cecorum (EC) has gained increasing importance as the cause of skeletal infections in meat-type chicken production. Since effective intervention strategies are scarce, it must be focused on preventive measures. Vaccination of meat-type breeder chicken flocks is common practice to protect the progeny against infection with EC. However, no data are available on seroconversion after infection or vaccination. The aim of the present study was the serological monitoring of chickens for EC-specific immunoglobulin Y (IgY) using a newly established EC-specific, indirect ELISA for chickens. Sera from previous infection studies were used for the establishment of the assay. Serum samples from confirmed EC-positive meat-type chicken flocks, vaccinated, and non-vaccinated meat-type chicken breeder flocks were analyzed for EC-specific IgY. Comparison of ELISA results with results from real-time PCR and/or bacteriological examination via culture revealed fair to substantial agreement. In infected chickens, more samples were classified as positive via ELISA than via real-time PCR and/or bacteriological examination via culture. Focusing on chickens experimentally infected at 1 day post-hatch (dph), the highest proportion of positive results and highest S/P ratios were found at 42 dph (p < 0.05). A similar trend was observed for the samples from naturally infected chickens (p < 0.05). Adjustment of the secondary antibody against immunoglobulin M (IgM) may open possibilities to use the assay during the early phase of the growing period, when there is still a chance to treat the infection. The examination of samples from vaccinated and non-vaccinated meat-type breeder chickens revealed no significant differences of S/P ratios independent of farm and autogenous vaccine used. In addition to that, monitoring of a non-vaccinated meat-type breeder chicken flock at 4, 10, 15, and 19 weeks post-hatch showed a continuous increase of ELISA-positive serum samples associated with an increase of S/P ratios. This may be explained by cross reactivity with antibodies to Enterococcus hirae or natural antibodies. The usage of EC-specific, recombinant proteins for coating of the plates may help to reduce unspecific background and increase the assay's specificity in future applications. In conclusion, the newly developed ELISA provides a suitable tool for serological monitoring of meat-type chickens during experimental studies with EC under standardized conditions. Remarkably, the assay is able to detect a higher proportion of EC-positive chickens than other methods, which are currently available. However, the assay is not yet suitable for the monitoring of breeder flocks due to high background.

Characterizing the impact of Enterococcus cecorum infection during late embryogenesis on disease progression, cecal microbiome composition, and early performance in broiler chickens

Enterococcus cecorum (EC) has been associated with septicemia and early mortality in broiler chickens. There is limited research investigating the pathogenicity of EC field strains obtained from affected birds. The purpose of this study was to evaluate the effect of in-ovo administration into the amnion with different EC field isolates at d 18 of embryogenesis (DOE18). In Exp 1, 7 EC field isolates alone or in combination (EC1-EC3, EC4-EC5, EC6, and EC7) were selected based on phenotypic characteristics and evaluated at different concentrations (1 × 102, 1 × 104, and 1 × 106 CFU/200 µL/embryo) to assess the impact on early performance and macroscopic lesions. Three isolates (n = 3; EC2, EC5, EC7) were selected for additional evaluation based on the significant (P < 0.05) BWG reduction (d 0-21) compared to the negative control (NC) and the presence of macroscopic lesions observed during posting sessions at d 14 and d 21. An additional isolate associated with enterococcal spondylitis was included in Exp 2 (EC11B). Treatment groups for Exp 2 include: 1) NC, 2) EC2, 3) EC5, 4) EC7, and 5) EC11B (n = 90-120/embryos/group). Groups 2 to 5 were challenged at 1 × 102 CFU/200 µL/embryo by in-ovo injection into the amnion at DOE18. Chicks were placed in battery cages for the duration of the study (21 d), and pen weights were recorded at d 0, d 7, d 14, and d 21 to calculate average BW and BWG. At d 14 and d 21 posthatch, liver, spleen, free thoracic vertebrae (FTV), and femoral head (FH) were aseptically collected to enumerate Enterococcus spp. using Chromagar Orientation as the selective media. Cecal contents were collected at d 21 to evaluate the effect of EC challenge on the cecal microbiome composition. There was a significant (P < 0.05) reduction in BW at d 21, and BWG from d 14 to 21 and d 0 to 21, for EC7 and EC11B. Enterococcus cecorum was recovered from the FTV of all challenged groups at d 14 and d 21. The most representative lesions were pericarditis, hydropericardium, focal heart necrosis, and FH osteomyelitis. However, lesions were not uniform across challenged groups or ages (d 14 and d 21). Alpha diversity of the cecal contents was markedly lower in EC5 and EC11B compared to all treatment groups suggesting that EC exposure during late embryogenesis affect the cecal microbiome up to 21 d posthatch. Additionally, these results highlight the differences in pathogenicity of EC strains isolated from field cases and suggest that hatchery exposure to EC during late embryogenesis is a potential route of introduction into a flock.

Study of the effect of administration of narasin or antibiotics on in vivo selection of a narasin- and multidrug-resistant Enterococcus cecorum strain

Enterococcus cecorum is a member of the normal poultry gut microbiota and an emerging poultry pathogen. Some strains are resistant to key antibiotics and coccidiostats. We evaluated the impact on chicken excretion and persistence of a multidrug-resistant E. cecorum of administering narasin or antibiotics. E. cecorum CIRMBP-1294 (Ec1294) is non-wild-type to many antimicrobials, including narasin, levofloxacin, oxytetracycline and glycopeptides, it has a low susceptibility to amoxicillin, and carries a chromosomal vanA operon. Six groups of 15 chicks each were orally inoculated with Ec1294 and two groups were left untreated. Amoxicillin, oxytetracycline or narasin were administered orally to one group each, either at the recommended dose for five days (amoxicillin, oxytetracycline) or continuously (narasin). Faecal samples were collected weekly and caecal samples were obtained from sacrificed birds on day 28. Ec1294 titres were evaluated by culture on vancomycin- and levofloxacin-supplemented media in 5 % CO₂. For inoculated birds given narasin, oxytetracycline or no antimicrobials, vancomycin-resistant enterococci were searched by culture on vancomycin-supplemented media incubated in air, and a PCR was used to detect the vanA gene. Ec1294 persisted in inoculated chicks up to day 28. Compared to the control group, the Ec1294 titre was significantly lower in the amoxicillin- and narasin-receiving groups on days 21 and 28, but was unexpectedly higher in the oxytetracycline-receiving group before and after oxytetracycline administration, preventing a conclusion for this group. No transfer of the vanA gene to other enterococci was detected. Other trials in various experimental conditions should now be conducted to confirm this apparent absence of co-selection of the multi-drug-resistant E. cecorum by narasin or amoxicillin administration.

Determination of Epidemiological Cutoff Values for Antimicrobial Resistance of Enterococcus cecorum

Enterococcus cecorum, a commensal Gram-positive bacterium of the chicken gut, has emerged as a worldwide cause of lameness in poultry, particularly in fast-growing broilers. It is responsible for osteomyelitis, spondylitis, and femoral head necrosis, causing animal suffering, mortality, and antimicrobial use. Research on the antimicrobial resistance of E. cecorum clinical isolates in France is scarce, and epidemiological cutoff (ECOFF) values are unknown. To determine tentative ECOFF (COWT) values for E. cecorum and to investigate the antimicrobial resistance patterns of isolates from mainly French broilers, we tested the susceptibility of a collection of commensal and clinical isolates (n = 208) to 29 antimicrobials by the disc diffusion (DD) method. We also determined the MICs of 23 antimicrobials by the broth microdilution method. To detect chromosomal mutations conferring antimicrobial resistance, we investigated the genomes of 118 E. cecorum isolates obtained mainly from infectious sites and described previously in the literature. We determined the COWT values for more than 20 antimicrobials and identified two chromosomal mutations explaining fluoroquinolone resistance. The DD method appears better suited for detecting E. cecorum antimicrobial resistance. Although tetracycline and erythromycin resistances were persistent in clinical and nonclinical isolates, we found little or no resistance to medically important antimicrobials.

Comparative Genome Analysis of Enterococcus cecorum Reveals Intercontinental Spread of a Lineage of Clinical Poultry Isolates

Enterococcus cecorum is an emerging pathogen responsible for osteomyelitis, spondylitis, and femoral head necrosis causing animal suffering and mortality and requiring antimicrobial use in poultry. Paradoxically, E. cecorum is a common inhabitant of the intestinal microbiota of adult chickens. Despite evidence suggesting the existence of clones with pathogenic potential, the genetic and phenotypic relatedness of disease-associated isolates remains little investigated. Here, we sequenced and analyzed the genomes and characterized the phenotypes of more than 100 isolates, the majority of which were collected over the last 10 years from 16 French broiler farms. Comparative genomics, genome-wide association studies, and the measured susceptibility to serum, biofilm-forming capacity, and adhesion to chicken type II collagen were used to identify features associated with clinical isolates. We found that none of the tested phenotypes could discriminate the origin of the isolates or the phylogenetic group. Instead, we found that most clinical isolates are grouped phylogenetically, and our analyses selected six genes that discriminate 94% of isolates associated with disease from those that are not. Analysis of the resistome and the mobilome revealed that multidrug-resistant clones of E. cecorum cluster into a few clades and that integrative conjugative elements and genomic islands are the main carriers of antimicrobial resistance. This comprehensive genomic analysis shows that disease-associated clones of E. cecorum belong mainly to one phylogenetic clade. IMPORTANCE Enterococcus cecorum is an important pathogen of poultry worldwide. It causes a number of locomotor disorders and septicemia, particularly in fast-growing broilers. Animal suffering, antimicrobial use, and associated economic losses require a better understanding of disease-associated E. cecorum isolates. To address this need, we performed whole-genome sequencing and analysis of a large collection of isolates responsible for outbreaks in France. By providing the first data set on the genetic diversity and resistome of E. cecorum strains circulating in France, we pinpoint an epidemic lineage that is probably also circulating elsewhere that should be targeted preferentially by preventive strategies in order to reduce the burden of E. cecorum-related diseases.

Bacterial chondronecrosis with osteomyelitis related Enterococcus cecorum isolates are genetically distinct from the commensal population and are more virulent in an embryo mortality model

Bacterial chondronecrosis with osteomyelitis (BCO) is a common cause of broiler lameness. Bacteria that are found in BCO lesions are intestinal bacteria that are proposed to have translocated through the intestinal epithelium and have spread systemically. One of the specific bacterial species frequently isolated in BCO cases is Enterococcus cecorum. In the current study, caecal isolates were obtained from birds derived from healthy flocks (12 isolates from 6 flocks), while isolates derived from caeca, colon, pericardium, caudal thoracic vertebrae, coxo-femoral joint, knee joint and intertarsal joint (hock) were obtained from broilers derived from BCO outbreaks (111 isolates from 10 flocks). Pulsed field gel electrophoresis was performed to determine similarity. Clonal E. cecorum populations were isolated from different bones/joints and pericardium from animals within the same flock, with intestinal strains carrying the same pulsotype, pointing to the intestinal origin of the systemically present bacteria. Isolates from the intestinal tract of birds from healthy flocks clustered away from the BCO strains. Isolates from the gut, bones/joints and pericardium of affected animals contained a set of genes that were absent in isolates from the gut of healthy animals, such as genes encoding for enterococcal polysaccharide antigens (epa genes), cell wall structural components and nutrient transporters. Isolates derived from the affected birds induced a significant higher mortality in the embryo mortality model as compared to the isolates from the gut of healthy birds, pointing to an increased virulence.

Assessment of the best inoculation route for virulotyping Enterococcus cecorum strains in a chicken embryo lethality assay

AbstractThe study aim was to determine the best inoculation route for virulotyping Enterococcus cecorum in a chicken embryo lethality assay (ELA). Twenty-eight genetically different strains were used. Fourteen strains were isolated from cloaca swabs of broiler reproduction chickens (cloaca strains) and fourteen strains from broilers with E. cecorum lesions (lesion strains). In all ELAs, 12 days incubated embryonated broiler eggs were inoculated with approximately 100 colony forming units of E. cecorum/egg. Twenty embryos per inoculation route and strain were used in each of three experiments. In Experiment 1, four cloaca and four lesion strains were inoculated via various routes, i.e. albumen, amniotic cavity, allantoic cavity, chorioallantoic membrane, intravenous or air chamber. The albumen inoculation route showed low mortality with cloaca strains, high mortality with lesion strains and the largest difference in mortality between these groups of strains (≥60%). This route was therefore used in subsequent experiments. In Experiment 2, the same strains were used to test reproducibility, which proved to be generally good. All 28 strains were thereafter used in Experiment 3. In the three experiments, mortality by cloaca and lesion strains ranged from 0 to 25% and from 15 to 100%, respectively. Recovery rates, assessed in all experiments after albumen inoculation, were significantly lower from eggs inoculated with cloaca strains, compared to lesion strains inoculated eggs (P <0.05). However, the bacterial load of eggs with positive recovery was similar in both groups. In conclusion: the albumen inoculation route appeared to be the best to virulotype E. cecorum strains.

Chicken embryo lethality assay for determining the lethal dose, tissue distribution and pathogenicity of clinical Enterococcus cecorum isolates from poultry

Enterococcus cecorum is a well-known component of the normal poultry intestinal microbiota and an important bacterial pathogen. Infections caused by E. cecorum have negative effects on the poultry production worldwide. In this study we used the SPF-chicken embryo lethality assay (ELA) to assess the pathogenic potential of E. cecorum. A total of 23 isolates were used: 19 clinical isolates from field outbreaks in different poultry groups (CB – broiler chickens, BB – broiler breeders, CL – layers, T– turkeys, W – waterfowl) and 4 commensal isolates. The cumulative mortality caused by all clinical isolates was higher (53.4%) than that of the commensals (38.9%). The highest mortality was induced by CB isolates (68.9%), followed by CL (60.4%), all chicken isolates (59.2%; CB, BB, CL), BB (45.8%), T (41.7%), non-chicken isolates (40.7%; T, W), and W isolates (39.8%). Most of the embryos that died, did die on the 1st day post-infection (dpi), except those infected with CB, CL (on 2 dpi). The median lethal dose (LD₅₀) of E. cecorum ranged from 6.07 × 10² cfu/ml (CB isolates) and 1.42 × 10⁴ cfu/ml (all clinical isolates) to 4.8 × 10⁵ cfu/ml (commensal isolates). This study provides the first evidence of a wide tissue distribution and multiplication of E. cecorum in embryos. Dead embryos showed scattered petechiae, hemorrhages, aggregates of bacteria in blood vessels, multiple organ necrosis, and encephalomalacia. Our data indicate that surviving embryos were able to elicit innate immune response to infection. On the other hand, reisolation of viable bacteria from surviving embryos may suggest that E. cecorum could evade or resist immune mechanisms in order to persist in organs. Furthermore, body mass of surviving embryos was affected by the strain type, not the dose (bacterial concentration) used, and was lower for the infection with clinical strains. The results indicated the highest pathogenicity of clinical E. cecorum isolates from CB and CL flocks.

Assessment of listing and categorisation of animal diseases within the framework of the Animal Health Law (Regulation (EU) No 2016/429): antimicrobial-resistant Enterococcus cecorum in poultry

Enterococcus cecorum (E. cecorum) was identified among the most relevant antimicrobial-resistant (AMR) bacteria in the EU for poultry in a previous scientific opinion. Thus, it has been assessed according to the criteria of the Animal Health Law (AHL), in particular criteria of Article 7 on disease profile and impacts, Article 5 on its eligibility to be listed, Annex IV for its categorisation according to disease prevention and control rules as in Article 9, and Article 8 for listing animal species related to the bacterium. The assessment has been performed following a methodology previously published. The outcome is the median of the probability ranges provided by the experts, which indicates whether each criterion is fulfilled (lower bound ≥ 66%) or not (upper bound ≤ 33%), or whether there is uncertainty about fulfilment. Reasoning points are reported for criteria with uncertain outcome. According to the assessment here performed, it is uncertain whether AMR E. cecorum can be considered eligible to be listed for Union intervention according to Article 5 of the AHL (33-75% probability). According to the criteria in Annex IV, for the purpose of categorisation related to the level of prevention and control as in Article 9 of the AHL, the AHAW Panel concluded that the bacterium does not meet the criteria in Sections 1, 2 and 4 (Categories A, B and D; 0-5%, 5-10% and 10-33% probability of meeting the criteria, respectively) and the AHAW Panel is uncertain whether it meets the criteria in Sections 3 and 5 (Categories C and E, 33-66% and 33-75% probability of meeting the criteria, respectively). The animal species to be listed for AMR E. cecorum according to Article 8 criteria are mostly birds belonging to the families of Anatidae, Columbidae and Phasianidae.

Influence of lincomycin-spectinomycin treatment on the outcome of Enterococcus cecorum infection and on the cecal microbiota in broilers

Background

Enterococcus cecorum (EC) is one of the main reasons for skeletal disease in meat type chickens. Intervention strategies are still rare and focus mainly on early antibiotic treatment of the disease, although there are no data available concerning the effectivity of this procedure. The present study aimed to investigate the effectivity of early lincomycin-spectinomycin treatment during the first week of life after EC-infection. Furthermore, the impact of lincomycin-spectinomycin treatment and EC infection on the development of cecal microbiota was investigated.

Methods

A total of 383 day-old broiler chicks were randomly assigned to four groups (non-infected and non-treated, non-infected and treated, EC-infected and non-treated, and EC-infected and treated). The EC-infected groups were inoculated orally with an EC suspension at the day of arrival and at study day 3. The treatment groups were treated with lincomycin-spectinomycin via the drinking water for six consecutive days, starting two hours after the first inoculation. Necropsy of 20 chickens per group was performed at study days 7, 14, 21, and 42. Bacteriological examination via culture and real-time PCR was performed to detect EC in different extraintestinal organs. Cecal samples of nine chickens per group and necropsy day were analyzed to characterize the composition of the cecal microbiota.

Results

No clinical signs or pathologic lesions were found at necropsy, and EC was not detected in extraintestinal organs of the EC-infected and treated birds. Lincomycin-spectinomycin promoted the growth of the bacterial genus Escherichia/Shigella and reduced the amount of potentially beneficial Lactobacillus spp. in the ceca regardless of EC-infection. Unexpectedly, the highest abundances of the genus Enterococcus were found directly after ending antibiotic treatment in both treatment groups, suggesting the growth of resistant enterococcal species. EC was not detected among the most abundant members of the genus Enterococcus. Oral EC-infection at the first day of life did not influence the development of cecal microbiota in the present study.

Conclusions

Lincomycin-spectinomycin treatment during the first week of life can prevent the EC-associated disease in broiler type chickens and has a direct impact on the development of the cecal microbiota. The low abundance of EC in the ceca of infected chickens underlines the pathogenic nature of the disease-causing EC strains. Further research on alternative prevention and intervention strategies is needed with regard to current efforts on reducing the use of antibiotics in livestock animals.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13099-021-00467-9.

Different virulence levels of Enterococcus cecorum strains in experimentally infected meat-type chickens

In recent years, pathogenic strains of Enterococcus cecorum (EC) have emerged as a causing agent of septicemia and skeletal infection in broiler chickens with a high economic impact worldwide. Although research has been conducted, many aspects of the pathogenesis of the EC-associated disease are still unknown. In the present study, an experimental infection model was established in broiler chickens. Two different EC strains (EC14 and EC15) were compared in two different concentrations of each strain (2 × 106 and 2 × 108 colony-forming units per milliliter (CFU/mL)) after oral infection of one-day-old chicks. Clinical signs and gross lesions of the EC-associated disease were monitored in the following seven weeks. Although both EC strains were originally isolated from clinical disease outbreaks and had a high embryonic lethality, only EC14 successfully induced the typical course of the EC-associated disease with characteristic clinical signs and gross lesions. In total, 23% of the birds in the two EC14-groups were EC-positive in extraintestinal organs on culture, and no differences were found between the two infectious doses. EC14 was frequently detected via real-time PCR in the free thoracic vertebra (FTV) and femoral heads without any detectable gross lesions. The number of EC positive spleens from infected broilers was comparable using bacterial isolation and a specific real-time PCR. Interestingly, EC15 was not detected in extraintestinal organs, although birds in the EC15 groups were colonized by EC in the ceca after experimental infection. The present study represents first proof that virulence differs among EC strains in experimentally infected chickens, and emphasizes the need to further characterize virulence factors and pathogenic mechanisms of EC. The strain EC14 at a dose of 106 CFU is suitable for reproduction of the EC-associated disease. The experimental infection model reported here provides the basis for further research on the EC pathogenesis and possible prevention and intervention strategies.

Genomic Characterization of a Nalidixic Acid-Resistant Salmonella Enteritidis Strain Causing Persistent Infections in Broiler Chickens

Virulent strains of Salmonella enterica subsp. enterica serovar Enteritidis (SE) harbored by poultry can cause disease in poultry flocks and potentially result in human foodborne illness. Two broiler flocks grown a year apart on the same premises experienced mortality throughout the growing period due to septicemic disease caused by SE. Gross lesions predominantly consisted of polyserositis followed by yolk sacculitis, arthritis, osteomyelitis, and spondylitis. Tissues with lesions were cultured yielding 59 SE isolates. These were genotyped by Rep-PCR followed by whole-genome sequencing (WGS) of 15 isolates which were clonal. The strain, SE_TAU19, was further characterized for antimicrobial susceptibility and virulence in a broiler embryo lethality assay. SE_TAU19 was resistant to nalidixic acid and sulfadimethoxine and was virulent to embryos with 100% mortality of all challenged broiler embryos within 3.5 days. Screening the SE_TAU19 whole-genome sequence revealed seven antimicrobial resistance (AMR) genes, 120 virulence genes, and two IncF plasmid replicons corresponding to a single, serovar-specific pSEV virulence plasmid. The pef, spv, and rck virulence genes localized to the plasmid sequence assembly. We report phenotypic and genomic features of a virulent SE strain from persistently infected broiler flocks and present a workflow for SE characterization from isolate collection to genome assembly and sequence analysis. Further SE surveillance and investigation of SE virulence in broiler chickens is warranted.

Tenacity of Enterococcus cecorum at different environmental conditions

AIMS

Our aim was to analyse the survival of Enterococcus cecorum (EC) at various temperatures, relative air humidities and on different substrates commonly existing in broiler houses.

METHODS AND RESULTS

A pathogenic EC isolate (EC14) was used to inoculate sterile litter, polyvinyl chloride (PVC) and dust samples. Incubation at 37, 25 or 15°C with either 32% relative humidity (RH) or 78% RH followed. At defined time points (0-4272 h post-inoculation), samples were examined in triplicate for the total viable count. Selected combinations were repeated for a non-pathogenic and two additional pathogenic EC strains. For EC14, the measured survival time ranged from 48 to 4272 h (178 days) depending on the substrate-humidity-temperature combination. The longevity was the highest on litter, followed by dust and then PVC. Lower temperatures facilitated its survival, lower relative air humidity favoured the survival only in combination with 25 or 15°C. All three pathogenic strains showed longer survival times (up to 432 h, 18 days) compared to the non-pathogenic EC strain (168 h, 7 days) under the same conditions.

CONCLUSIONS

Enterococcus cecorum demonstrates a high persistence in the environment especially at 15°C and 32% RH.

SIGNIFICANCE AND IMPACT OF THE STUDY

Hygiene management plans should consider the durability of EC and the risk of a carry-over to control consecutive EC outbreaks.

The role of Enterococcus faecalis during co-infection with avian pathogenic Escherichia coli in avian colibacillosis

Enterococcus spp. (ENT) are frequently co-isolated with avian pathogenic E. coli (APEC) from poultry with colibacillosis, a leading cause of flock mortality. Although largely overlooked, ENT may play an active role in these infections. To assess the frequency of ENT co-isolation in colibacillosis, cultures were collected from birds with gross lesions of omphalitis, polyserositis, and septicaemia over a 3-year period from three turkey flocks and three broiler flocks. In birds diagnosed with colibacillosis based on gross findings and isolation of E. coli, ENT were co-isolated with APEC in 35.7% (n = 41/115) of colibacillosis mortality and 3.7% of total mortality (n = 41/1122). Co-isolated APEC and ENT pairs (n = 41) were further characterized using antimicrobial resistance phenotyping and in vitro co-culture assays. E. faecalis (EF) was the most commonly co-isolated species (68% n = 28/41) and tetracycline resistance was the resistance phenotype most commonly found among APEC (51% n = 21/41) and ENT (93% n = 38/41). Under iron-restricted conditions, EF enhanced APEC growth in a proximity-dependent manner and APEC grown in mixed culture with EF exhibited a significant growth and survival advantage (P ≤ 0.01). In an embryo lethality assay, APEC co-infection with EF resulted in decreased survival of broiler embryos compared to mono-infections (P ≤ 0.05). These data demonstrate that EF augmented APEC survival and growth under iron limiting conditions, possibly translating to the increased virulence of APEC in broiler embryos. Thus, ENT co-infections may be a previously unrecognized contributor to colibacillosis-related mortality. Further investigations into the mechanism of this interaction are warranted. RESEARCH HIGHLIGHTS Enterococcus is frequently co-isolated with avian pathogenic E. coli (APEC). Enterococcus faecalis (EF) enhances survival of APEC in iron restricted conditions. EF co-infection increases APEC virulence in broiler embryos.

Comparison of Antimicrobial Resistance and Pan-Genome of Clinical and Non-Clinical Enterococcus cecorum from Poultry Using Whole-Genome Sequencing

Enterococcus cecorum is an emerging avian pathogen, particularly in chickens, but can be found in both diseased (clinical) and healthy (non-clinical) poultry. To better define differences between E. cecorum from the two groups, whole-genome sequencing (WGS) was used to identify and compare antimicrobial resistance genes as well as the pan-genome among the isolates. Eighteen strains selected from our previous study were subjected to WGS using Illumina MiSeq and comparatively analyzed. Assembled contigs were analyzed for resistance genes using ARG-ANNOT. Resistance to erythromycin was mediated by ermB, ermG, and mefA, in clinical isolates and ermB and mefA, in non-clinical isolates. Lincomycin resistance genes were identified as linB, lnuB, lnuC, and lnuD with lnuD found only in non-clinical E. cecorum; however, lnuB and linB were found in only one clinical isolate. For both groups of isolates, kanamycin resistance was mediated by aph3-III, while tetracycline resistance was conferred by tetM, tetO, and tetL. No mutations or known resistance genes were found for isolates resistant to either linezolid or chloramphenicol, suggesting possible new mechanisms of resistance to these drugs. A comparison of WGS results confirmed that non-clinical isolates contained more resistance genes than clinical isolates. The pan-genome of clinical and non-clinical isolates resulted in 3651 and 4950 gene families, respectively, whereas the core gene sets were comprised of 1559 and 1534 gene families in clinical and non-clinical isolates, respectively. Unique genes were found more frequently in non-clinical isolates than clinical. Phylogenetic analysis of the isolates and all the available complete and draft genomes showed no correlation between healthy and diseased poultry. Additional genomic comparison is required to elucidate genetic factors in E. cecorum that contribute to disease in poultry.

Characterization of pathogenic Enterococcus cecorum from different poultry groups: Broiler chickens, layers, turkeys, and waterfowl

Enterococcus cecorum (EC) is known as a commensal in the intestines of mammals and birds. However, it has been described as an emerging pathogen in poultry industry worldwide. The aim of this study was to analyze and compare EC isolated from clinical material collected from poultry groups with different production purposes. The genetic diversity among pathogenic EC in relation to each specific poultry type was examined. In total, 148 isolates from independent infection outbreaks (2011–2016) were used: 76 broiler chickens (CB), 37 broiler breeders (BB), 23 layers (CL), 7 waterfowl (W) and 5 turkey (T) flocks (1 isolate/1 flock). We provided age ranges at diagnosis of EC-infection for 5 poultry groups. Isolates obtained from CB were significantly more frequently retrieved from bone marrow, joints, spine, and contrary to BB, CL less frequently retrieved from respiratory system. The study showed differences between EC of various poultry types in relation to 10/32 (31.3%) biochemical parameters. EC isolates from CB were significantly more often positive for βGAL, βNAG, MLZ, and less often positive for PAL and βMAN than isolates from other poultry types. However, BB and W isolates showed higher ability to metabolise mannitol than CB, CL, and T. CB isolates showed lower ability to survive at 60°C. Only chicken EC-isolates harbored virulence genes: CB (8.1%) > BB (3.4%) > CL (2%). No specific pulsotype of EC was associated with a specific poultry. One or several various (up to 6) genetic types of EC may be involved in outbreaks in CB flocks within one year in one region. Outbreaks reported in following years in the same region were usually caused by a distinct set of EC-genetic types. PFGE results indicated at the genetic heterogeneity among pathogenic isolates involved in outbreaks in relation to each poultry type. To our best knowledge, this is the first study which provides a comparison between clinical EC from 5 poultry groups. The study provides a new insight into EC as pathogen of different bird species. The obtained data may be useful in further studies on EC-infections more focused on a specific type of poultry.

Disease surveillance in England and Wales, December 2016

Current and emerging issues: avian influenza and Schmallenberg virusHighlights from the scanning surveillance networkUpdate on international disease threatsCongenital tremor associated with atypical porcine pestivirus These are among matters discussed in the Animal and Plant Health Agency's (APHA's) disease surveillance report for December 2016.

Comparison of pathogenic and non-pathogenic Enterococcus cecorum strains from different animal species

Background

Enterococcus cecorum (EC) infection currently is one of the most important bacterial diseases of modern broiler chickens but can also affect ducks or other avian species. However, little is known concerning pathogenesis of EC and most studies concentrate on examinations of EC strains from broilers only. The objective of this study was to compare pathogenic and commensal EC strains from different animal species concerning different phenotypic and genotypic traits.

Results

Pathogenic and commensal EC strains were not clearly separated from each other in a phylogenetic tree based on partial sequences of the 16S-rRNA-gene and also based on the fatty acid profile determined with gas chromatography. C_12:0, C_14:0, C_15:0, C_16:0, C_17:0, C_18:0, C_18:1 w7c, C_18:1 w9c and C_20:4 w6,9,12,15c were detected as the major fatty acids. None of the 21 pathogenic EC strains was able to utilize mannitol, while 9 of 29 commensal strains were mannitol positive. In a dendrogram based on MALDI-TOF MS data, pathogenic strains were not clearly separated from commensal isolates. However, significant differences concerning the prevalence of several mass peaks were confirmed between the two groups. Two different antisera were produced but none of the serotypes was predominantly found in the pathogenic or commensal EC isolates. Enterococcal virulence factors gelE, esp, asa1, ccf, hyl and efaAfs were only detected in single isolates via PCR. No virulence factor was found significantly more often in the pathogenic isolates. The chicken embryo lethality of the examined EC isolates varied from 0 up to 100%. The mean embryo lethality in the pathogenic EC isolates was 39.7%, which was significantly higher than the lethality of the commensal strains, which was 18.9%. Additionally, five of the commensal isolates showed small colony variant growth, which was never reported for EC before.

Conclusions

Pathogenic and commensal EC isolates from different animal species varied in chicken embryo lethality, in their ability to metabolize mannitol and probably showed divergent mass peak patterns with MALDI-TOF MS. These differences may be explained by a separate evolution of pathogenic EC isolates. Furthermore, different serotypes of EC were demonstrated for the first time.

Impact of Enteric Health and Mucosal Permeability on Skeletal Health and Lameness in Poultry

Intestinal barrier leakage and/or altered gut microbial composition has been shown to markedly impact both osteoblast and osteoclast activities, systemically through circulation of gut immune cells and cytokines and locally by causing inflammation of extraintestinal organs such as the liver and bone marrow. Mild cases of heightened intestinal inflammation can cause bone loss in male mice in the absence of any overt nutritional deficiencies or weight loss, which has also been shown in chickens that have been infected with Salmonella. For poultry, ingredients selected for feed formulation have also a significant impact on gut health, intestinal microbiota, bone quality, and performance parameters. Consumption of diets with a high content of soluble non-starch polysaccharides (NSP) can affect bone quality parameters by reducing the amount of conjugated bile acids in the intestine, therefore diminishing the absorption of fat-soluble vitamins such as vitamin D and minerals like calcium and phosphorus. Recent enteric inflammation studies have shown that high NSP-containing diets have effects on intestinal viscosity, bone mineral content, and breaking strength, along with increased fluorescein isothiocyanate-dextran (FITC-d) leakage. Other skeletal diseases, such as bacterial chondronecrosis with osteomyelitis and enterococcal spondylitis, have a microbial component that is associated with increased mucosal permeability of the gut. Probiotics targeted toward control of enteric inflammation, either created through infectious disease or poor diet, may serve as a strategy for control of predisposing factors that lead to bone disorders.

Vertebral osteomyelitis associated with single and mixed bacterial infection in broilers

Vertebral osteomyelitis (VO) is a worldwide emerging disease that affects broilers. The objective of this study was to determine the frequency and aetiology of VO in broilers in a highly productive broiler region. For this, 608 broilers with locomotory problems were analysed from 18 farms. Clinical signs were recorded, necropsy was performed and samples were collected from vertebral bodies with gross changes for molecular and histopathological analysis and for bacterial isolation. From broilers with locomotory changes, 5.1% (31/608) had VO and, of these, 93.5% were 40 days old or older and 89.7% were males. The birds with VO presented varying degrees of limited mobility and this was related to the level of compression to the spinal cord. Bacterial species of the genus Enterococcus (DNA detected in 53.6%) were the aetiological agents involved in most VO cases. Enterococcus faecalis was detected most frequently (35.7%), but Enterococcus hirae was also present in some lesions (7.1%). Escherichia coli was detected in 35.7% of vertebral lesions and co-infection with E. faecalis was confirmed in 7.1% cases. Staphylococcus aureus was involved in 14.3% of the cases, being 7.1% in co-infection with Enterococcus spp. or E. hirae. Our study has indicated that, in Brazil, VO in broilers may not be caused by a single infectious agent and has a lower frequency than recently reported in other countries. This study suggests that there are geographical differences between Brazil and other countries concerning the frequency and aetiology of VO.

Pathogenesis of Enterococcal Spondylitis Caused by Enterococcus cecorum in Broiler Chickens

Enterococcal spondylitis (ES) is a disease of commercial broiler chickens, with a worldwide distribution. Symmetrical hind limb paralysis typical of ES results from infection of the free thoracic vertebra (FTV) by pathogenic strains of Enterococcus cecorum . To determine the pathogenesis of ES, birds with natural and experimental ES were studied over time. In natural disease, case birds (n = 150) from an affected farm and control birds (n = 100) from an unaffected farm were evaluated at weeks 1–6. In control birds, intestinal colonization by E. cecorum began at week 3. In case birds, E. cecorum was detected in intestine and spleen at week 1, followed by infection of the FTV beginning at week 3. E. cecorum isolates recovered from intestine, spleen, and FTV of case birds had matching genotypes, confirming that intestinal colonization with pathogenic strains precedes bacteremia and infection of the FTV. Clinical intestinal disease was not required for E. cecorum bacteremia. In 1- to 3-week-old case birds, pathogenic E. cecorum was observed within osteochondrosis dissecans (OCD) lesions in the FTV. To determine whether OCD of the FTV was a risk factor for ES, 214 birds were orally infected with E. cecorum, and the FTV was evaluated histologically at weeks 1–7. Birds without cartilage clefts of OCD in the FTV did not develop ES; while birds with OCD scores ≥3 were susceptible to lesion development. These findings suggest that intestinal colonization, bacteremia, and OCD of the FTV in early life are crucial to the pathogenesis of ES.

Phenotypic and genotypic characterization of Enterococcus cecorum strains associated with infections in poultry

Background

From the beginning of the 21^st century Enterococcus cecorum has emerged as a significant health problem for poultry raised under intensive production systems. To obtain new insights into this bacterial species, we investigated 82 clinical isolates originating from different poultry flocks in Poland between 2011 and 2014.

Results

Phenotypically, isolates from clinical cases showed ability to growth at low temperatures (4 °C, 10 °C), and differences in growth at 45 °C (74.4 %). Survival at high temperatures (60 °C, 70 °C) was observed for 15, 30 min. More than half of strains survived at 60 °C even after prolonged incubation (1 h), but none survived after 1 h at 70 °C. Total growth inhibition was observed on agar supplemented with tergitol or potassium tellurite. Relatively high number of isolates gave positive reactions for β-galactosidase (βGAL 80 %), Voges Proskauer test (60 %), less for β-mannosidase (17 %), glycogen and mannitol (12 %). The metabolic fingerprinting for E. cecorum obtained in Biolog system revealed ability to metabolise 22 carbon sources. Only 27/82 strains contained ≥ 1 virulence genes of tested 7, however 2.4 % isolates carried 6. Increased antimicrobial resistance was observed to enrofloxacin (87 %), teicoplanin (85 %), doxycycline (83 %), erythromycin (46 %). Most strains (75/82) showed multidrug resistance. The single isolate was resistant to vancomycin (VRE) and high level gentamicin (HLGR). Linezolid resistance among clinical isolates was not found. PFGE revealed diversity of E. cecorum from cases. It could be assumed that transmission of pathogenic strains between flocks regardless of type of production or geographical region may be possible.

Conclusions

Clinical infections in poultry caused by E. cecorum may indicated on new properties of this bacterial species, previously known as a commensal. Despite many common phenotypic features, differences were found among clinical isolates. Several, widely distributed pathogenic E. cecorum strains seemed to be responsible for infection cases found in different poultry types.

Electronic supplementary material

The online version of this article (doi:10.1186/s12917-016-0761-1) contains supplementary material, which is available to authorized users.

Antimicrobial Susceptibility Patterns of Enterococcus faecalis and Enterococcus faecium Isolated from Poultry Flocks in Germany

Between 2010 and 2011, 145 Enterococcus isolates (Enterococcus faecalis, n = 127; Enterococcus faecium, n = 18) were collected during routine bacteriologic diagnostics from broilers, layers, and fattening turkeys in Germany showing various clinical signs. The susceptibility to 24 antimicrobial agents was investigated by broth microdilution test to determine minimum inhibitory concentrations (MICs). All E. faecalis isolates (n = 127) were susceptible to the beta-lactam antibiotics ampicillin, amoxicillin-clavulanic acid, and penicillin. Corresponding MIC with 50% inhibition (MIC50) and MIC with 90% inhibition (MIC90) values of these antimicrobial agents were at the lower end of the test range (≤ 4 μg/ml). In addition, no vancomycin-resistant enterococci (VRE) were found. High resistance rates were identified in both Enterococcus species for lincomycin (72%-99%) and tetracycline (67%-82%). Half or more than half of Enterococcus isolates were resistant to gentamicin (54%-72%) and the macrolide antibiotics erythromycin (44%-61%) and tylosin-tartate (44%-56%). Enterococcus faecalis isolated from fattening turkeys showed the highest prevalence of antimicrobial resistance compared to other poultry production systems. Eighty-nine out of 145 Enterococcus isolates were resistant to three or more antimicrobial classes. Again, turkeys stood out with 42 (8 1%) multiresistant isolates. The most-frequent resistance patterns of E. faecalis were gentamicin, lincomycin, and tetracycline in all poultry production systems.

Comparative genomic analysis identifies divergent genomic features of pathogenic Enterococcus cecorum including a type IC CRISPR-Cas system, a capsule locus, an epa-like locus, and putative host tissue binding proteins

Enterococcus cecorum (EC) is the dominant enteric commensal of adult chickens and contributes to the gut consortia of many avian and mammalian species. While EC infection is an uncommon zoonosis, like other enterococcal species it can cause life-threating nosocomial infection in people. In contrast to other enterococci which are considered opportunistic pathogens, emerging pathogenic strains of EC cause outbreaks of musculoskeletal disease in broiler chickens. Typical morbidity and mortality is comparable to other important infectious diseases of poultry. In molecular epidemiologic studies, pathogenic EC strains were found to be genetically clonal. These findings suggested acquisition of specific virulence determinants by pathogenic EC. To identify divergent genomic features and acquired virulence determinants in pathogenic EC; comparative genomic analysis was performed on genomes of 3 pathogenic and 3 commensal strains of EC. Pathogenic isolates had smaller genomes with a higher GC content, and they demonstrated large regions of synteny compared to commensal isolates. A molecular phylogenetic analysis demonstrated sequence divergence in pathogenic EC genomes. At a threshold of 98% identity, 414 predicted proteins were identified that were highly conserved in pathogenic EC but not in commensal EC. Among these, divergent CRISPR-cas defense loci were observed. In commensal EC, the type IIA arrangement typical for enterococci was present; however, pathogenic EC had a type IC locus, which is novel in enterococci but commonly observed in streptococci. Potential mediators of virulence identified in this analysis included a polysaccharide capsular locus similar to that recently described for E. faecium, an epa-like locus, and cell wall associated proteins which may bind host extracellular matrix. This analysis identified specific genomic regions, coding sequences, and predicted proteins which may be related to the divergent evolution and increased virulence of emerging pathogenic strains of EC.

Antimicrobial resistance, virulence determinants and genetic profiles of clinical and nonclinical Enterococcus cecorum from poultry

Enterococcus cecorum has been implicated as a possible cause of disease in poultry. However, the characteristics that contribute to pathogenesis of Ent. cecorum in poultry have not been defined. In this study, Ent. cecorum from carcass rinsates (n = 75) and diseased broilers and broiler breeders (n = 30) were compared based upon antimicrobial resistance phenotype, the presence of virulence determinants and genetic relatedness using pulsed-field gel electrophoresis (PFGE). Of the 16 antimicrobials tested, Ent. cecorum from carcass rinsates and clinical cases were resistant to ten and six of the antimicrobials, respectively. The majority of Ent. cecorum from carcass rinsates was resistant to lincomycin (54/75; 72%) and tetracycline (46/75; 61.3%) while the highest level of resistance among clinical Ent. cecorum was to tetracycline (22/30; 73.3%) and erythromycin (11/30; 36.7%). Multidrug resistance (resistance to ≥2 antimicrobials) was identified in Ent. cecorum from carcass rinsates (53/75; 70.7%) and diseased poultry (18/30; 60%). Of the virulence determinants tested, efaAfm was present in almost all of the isolates (104/105; 99%). Using PFGE, the majority of clinical isolates clustered together; however, a few clinical isolates grouped with Ent. cecorum from carcass rinsates. These data suggest that distinguishing the two groups of isolates is difficult based upon the characterization criteria used.

Amplicon pyrosequencing and ion torrent sequencing of wild duck eubacterial microbiome from fecal samples reveals numerous species linked to human and animal diseases

Our investigation into the composition of the wild duck,Aythya americana, eubacterial microbiome from a fecal sample using amplicon pyrosequencing revealed that the representative bacterial species were quite distinct from a pond water sample, and we were able to classify the major operational taxonomic units withFusobacterium mortiferum,Streptobacillus moniliformis,Lactobacillus intermedius,Actinomyces suimastitidis,Campylobacter Canadensis,Enterococcus cecorum,Lactobacillus aviarus,Actimomyces spp.,Pseudobutyrivibrio spp.and Helicobacter brantaerepresenting the majority of the eubacterial fecal microbiome.  Bacterial species present in the analysis revealed numerous organisms linked to human and animal diseases including septicemia, rat bite fever, pig mastitis, endocarditis, malar masses, genital infections, skin lesions, peritonitis, wound infections, septic arthritis, urocystitis, gastroenteritis and drinking water diseases.  In addition, to being known carriers of viral pathogens wild ducks should also be recognized as a potential source of a range of bacterial diseases.

Experimental reproduction of an Enterococcus cecorum infection in Pekin ducks

Enterococcus cecorum (EC) was thus far only known as a pathogen for broilers and broiler breeders. Recently there was evidence of EC field outbreaks in Pekin duck flocks in Germany. In this study we experimentally reproduced an EC infection in Pekin ducks. At 12 days post hatch, groups of Pekin ducks were infected orally, via the thoracic air sac or intravenously with 1.5 × 10(9) colony-forming units (CFU) of EC per bird or via the air sac with 8.5 × 10(5) or 8.5 × 10(7) CFU per bird. Ducks of the intravenously infected group showed 100% mortality after 2 days post infection. The air sac inoculated high-dose group exhibited a mortality rate of 67%. Birds that were infected with 8.5 × 10(5) and 8.5 × 10(7) CFU showed 6.7% mortality after 7 days post infection. Dead birds displayed pneumonia, airsacculitis, pericarditis and splenitis and EC was re-isolated from these organs. Surviving birds of all groups apart from the orally infected ducks demonstrated clinical signs such as huddling, reduced mobility and diarrhoea. Furthermore, they showed gross pathological lesions including airsacculitis and splenitis and lower bodyweights than the control group at necropsy on days 7, 14 and 21 post infection. The present study clearly confirms that EC is pathogenic for Pekin ducks after experimental infection via the intravenous route or the respiratory tract. EC therefore has to be considered as an emerging avian pathogen not only in broilers but also in Pekin ducks.