Mannheimia indoligenes sp. nov., proposed for clade V organisms of Mannheimia.

A set of 25 strains belonging to clade V of Mannheimia mainly isolated from cattle was investigated and is proposed to represent Mannheimia indoligenes sp. nov. The species can be separated from the other validly published species of the genus by pheno- and genotype. Only indole separates M. indoligenes and Mannheimia varigena while two to seven characters separate M. indoligenes from other species of Mannheimia. Thirteen strains belonging to biogroups 6, 7, 8C, 9, 10, 12 and UG5 formed a monophyletic group based on 16S rRNA gene sequence comparisons with 98-100 % similarity. Eight of these strains were further included in the whole genome comparison. Digital DNA-DNA hybridization showed that the similarities between the suggested type strain M14.4T and the other strains of M. indoligenes were 62.9 % or higher. The average nucleotide identity was 95.5 % or higher between M14.4T and the other strains of the species. The rpoB gene sequence similarity was 95-100 % within M. indoligenes. MALDI-TOF allowed a clear separation from other Mannheimia species further supporting classification as a novel species and making it the diagnostic identification tool of choice for M. indoligenes. The type strain is M14.4T (=CCUG 77347T=DSM 116804T) isolated from a cattle tongue in Scotland.

The best of both worlds: a proposal for further integration of Candidatus names into the International Code of Nomenclature of Prokaryotes.

The naming of prokaryotes is governed by the International Code of Nomenclature of Prokaryotes (ICNP) and partially by the International Code of Nomenclature for Algae, Fungi and Plants (ICN). Such codes must be able to determine names of taxa in a universal and unambiguous manner, thus serving as a common language across different fields and activities. This unity is undermined when a new code of nomenclature emerges that overlaps in scope with an established, time-tested code and uses the same format of names but assigns different nomenclatural status values to the names. The resulting nomenclatural confusion is not beneficial to the wider scientific community. Such ambiguity is expected to result from the establishment of the 'Code of Nomenclature of Prokaryotes Described from DNA Sequence Data' ('SeqCode'), which is in general and specific conflict with the ICNP and the ICN. Shortcomings in the interpretation of the ICNP may have exacerbated the incompatibility between the codes. It is reiterated as to why proposals to accept sequences as nomenclatural types of species and subspecies with validly published names, now implemented in the SeqCode, have not been implemented by the International Committee on Systematics of Prokaryotes (ICSP), which oversees the ICNP. The absence of certain regulations from the ICNP for the naming of as yet uncultivated prokaryotes is an acceptable scientific argument, although it does not justify the establishment of a separate code. Moreover, the proposals rejected by the ICSP are unnecessary to adequately regulate the naming of uncultivated prokaryotes. To provide a better service to the wider scientific community, an alternative proposal to emend the ICNP is presented, which would result in Candidatus names being regulated analogously to validly published names. This proposal is fully consistent with previous ICSP decisions, preserves the essential unity of nomenclature and avoids the expected nomenclatural confusion.

Classification of Bisgaard taxon 6 and taxon 10 as Exercitatus varius gen. nov., sp. nov.

Forty-one isolates of Bisgaard taxon 6 obtained from guinea pigs, pandas, pigs and muskrat and isolates of taxon 10 from horses and horse bites in humans were subjected phenotypic characterization. Production of acid from (-)-d-mannitol, (-)-d-sorbitol and (+)-d-glycogen separated taxon 10 (positive) from taxon 6 (negative), while from two to 11 phenotypic characteristics separated taxa 6 and 10 from the 32 genera of Pasteurellaceae reported so far. Forty-four strains were genetically characterized. Sequencing of 16S rRNA genes documented a monophyletic relationship at the species level and the highest 16S rRNA gene sequence similarity of 95.6 % to other species was found between strain CCUG 15568T and the type strain of Mannheimia glucosida (CCUG 38457T). Digital DNA-DNA hybridization (dDDH) values predicted from whole genomic sequences between CCUG 15568T and other characterized strains of taxa 6 and 10 were 69.3-99.9 %. The average nucleotide identity values were higher than 95 % for all strains. The highest dDDH value of 29 % outside the taxa 6 and 10 group was obtained with the genome of the type strain of [Actinobacillus] succinogenes, indicating a separate taxonomic status at species level to taxa 6 and 10. The phylogenetic comparison of concatenated conserved protein sequences showed the unique position of the taxa investigated in the current study which qualified for the status of a new genus since the highest identity was found with Basfia with 79 %, well below the upper threshold between genera of 85 %. Based upon the low genetic similarity to other genera of the family Pasteurellaceae and a unique phenotype, we suggest that Bisgaard taxa 6 and 10 should be classified as Exercitatus varius gen. nov., sp. nov. The G+C of the type strain of Exercitatus varius, 8.5T (=CCUG 15568T=DSM 115565T), is 46.2 mol%, calculated from the whole genome.

Mannheimia cairinae sp. nov., a novel species of Mannheimia obtained from Muscovy ducks (Cairina moschata) and reclassification of Mannheimia ovis as heterotypic synonym of Mannheimia pernigra.

During a screening study for Pasteurella multocida in two unrelated flocks of Muscovy ducks pharyngeal and cloacal swabs were collected. A total of 59 Pasteurellaceae-like isolates sharing the same colony morphology were subcultured and subsequently characterized. Colonies on bovine blood agar were nonhaemolytic, regular, circular, slightly raised, shiny, intransparent with an entire margin, greyish and had an unguent-like consistency. Isolate AT1T was characterized by 16S rRNA gene sequencing and showed the highest similarity of 96.1 % to the type strain of Mannheimia caviae and 96.0 % to the type strain of Mannheimia bovis, respectively. In addition, rpoB and recN gene sequences also showed the highest similarity to the genus Mannheimia. The phylogenetic comparison of concatenated conserved protein sequences also showed a unique position of AT1T compared to other species of Mannheimia. Full phenotypic characterization of the isolates showed that between two (Mannheimia ruminalis) and 10 (Mannheimia glucosida) phenotypic characteristics separate the taxon isolated from Muscovy ducks from the accepted species of Mannheimia. Whole genomic sequences of two strains analysed by the type strain genome server showed the highest similarity of 24.9 % to the genome of the type strain of Pasteurella multocida and 23.0 % to the genome of the type strain of Mannheimia haemolytica. The species Mannheimia cairinae sp. nov. is proposed based on the phenotypic and genotypic similarity to Mannheimia as well as differences to the other validly published species of the genus. The leukotoxin protein was not predicted in the genome of AT1T. The G+C content of the type strain of M. cairinae sp. nov., AT1T (=CCUG 76754T=DSM 115341T) is 37.99 mol%, calculated from the whole genome. The investigation further proposes that Mannheimia ovis is reclassified as a later heterotypic synonym of Mannheimia pernigra, since M. ovis and M. pernigra are closely genetically related, and M. pernigra was validly published before M. ovis.

Prevalence of Potential Pathogenic and Antimicrobial Resistant Escherichia coli in Danish Broilers.

Avian pathogenic Escherichia coli (APEC) are important bacteria in broiler production in terms of economy, welfare, and use of antibiotics. During a previous outbreak of APEC in the Nordic countries, it was suggested that the pathogenic clones of E. coli causing the outbreak originated from grandparent stock and were transmitted to the offspring, causing increased first week mortality. This study investigated whether the pathogenic potential of E. coli at the parent and broiler level differs in relation to pathogenic potential described by the level of virulence-associated genes and pattern of antimicrobial resistance. The hypothesis was that, due to higher biosecurity at the parent level, the E. coli population will show a lower level of antimicrobial resistance and carry fewer virulence-associated genes, as a result of fewer E. coli infections observed. From four parent flocks and eight broiler flocks, 715 E. coli were isolated from cloacal swabs of newly hatched chickens (Ross 308). The isolated E. coli were characterized by eight virulence-associated genes and phenotypic resistance against six antimicrobials. It was found that the prevalence of virulence-associated genes and phenotypic antimicrobial resistance varied significantly between flocks, and the virulence-associated genes papC and irp2 and resistance against ampicillin were significantly more prevalent in breeder flocks compared to broiler flocks.

Prediction of Pasteurella multocida serotypes based on whole genomic sequences.

The serotypes of Pasteurella multocida were predicted based on whole genomic sequences (WGS) with specific genes of the capsular and liposaccharide (LPS) outer core polysaccharide regions as targets. A total of 56 strains were whole genomic sequenced and in addition all assembled genomes from NCBI were included for comparison. BIGSdb (Bacterial Isolate Genome Sequence Database) was installed on a Linux server and targets for capsular types A, B, D, E and F were defined as gene sequences of hyaD, bcbD, dcbF, ecbJ and fcbD, respectively and targets for LPS groups 1, 2, 3, 4, 5, 6, 7 and 8 were defined as gene sequences of pcgB, nctA, gatF, latB, rmlA, nctB, ppgB and natG, respectively. The serotypes of P. multocida were predicted from WGS by designating the capsular type and LPS group as well as subtype alleles to isolates. Comparisons between WGS predictions of capsular types and classical phenotypic typing showed correspondence in 87 % of cases whereas comparisons of WGS predictions of LPS groups to phenotypic typing corresponded for 82 % of the strains. In total 93 % and 94 % of the strains available with WGS could be capsular and LPS group typed, respectively. The server is free to access from https://ivsmlst.sund.ku.dk.

Prediction of Mannheimia haemolytica serotypes based on whole genomic sequences.

The aim of the investigation was to predict the serotypes of M. haemolytica based on whole genomic sequences with the capsular gene region as target. A total of 22 strains selected to have been serotyped and to represent all serotypes were investigated by whole genomic sequencing. The BIGSdb (Bacterial Isolate Genome Sequence Database) was downloaded and installed on a Linux server. Here the sequence database was setup with unique loci at serotype level. The server allows serotypes of M. haemolytica to be predicted from whole genomic sequences and the service is available to the public for free from https://ivsmlst.sund.root.ku.dk.

Reclassification of [Haemophilus] haemoglobinophilus as Canicola haemoglobinophilus gen. nov., comb. nov. including Bisgaard taxon 35.

[Haemophilus] haemoglobinophilus and the unpublished Bisgaard taxon 35 are associated with respiratory and urogenital tract infections in dogs. A total of 21 strains including the type strain of [Haemophilus] haemoglobinophilus were included in the investigation. Strains of [Haemophilus] haemoglobinophilus and taxon 35 formed a monophyletic group demonstrating at least 97.8 and 96.5% similarities within the group based upon 16S rRNA and rpoB gene sequence comparisons, respectively. Glaesserella australis was the most closely related species to [Haemophilus] haemoglobinophilus and taxon 35 with 96.1 % 16S rRNA gene sequence similarity which is slightly higher than the 95 % separating most genera of the family Pasteurellaceae. However, the conserved protein sequence phylogeny documented a unique position of [Haemophilus] haemoglobinophilus with only 81 % identity to the most closely related species, genomospecies 1 of the genus Rodentibacter which is lower than the 85 % separating most genera of the family Pasteurellaceae. The conserved protein sequence identity to Haemophilus influenzae, the type species of the genus, was 77%, demonstrating that [Haemophilus] haemoglobinophilus is not properly classified as a member of the genus Haemophilus. On the basis of the phylogenetic comparisons, the taxa [Haemophilus] haemoglobinophilus and taxon 35 are proposed to be included with a novel genus Canicola with one species, Canicola haemoglobinophilus which is reclassified from [Haemophilus] haemoglobinophilus. Phenotypic characters obtained with isolates genetically approved to represent Canicola haemoglobinophilus were in accordance with those of the members of the family Pasteurellaceae, and the novel genus can be separated from most of the existing genera by a positive catalase reaction, lack of V-factor requirement for growth, lack of haemolysis of blood agar and negative Voges-Proskauer and urease tests. The novel genus cannot be separated by biochemical and physiological characteristics alone from the genera Aggregatibacter, Avibacterium, Frederiksenia and Spirabiliibacterium. However, MALDI-TOF mass spectroscopy and also RpoB amino acid signatures allowed a clear separation from these taxa, supporting the existence of a novel genus. The DNA G+C content is 37.0-37.8 mol% for the genus, based on the whole genomic sequences. The type strain of Canicola haemoglobinophilus is CCUG 3714T (=ATCC 19416T=NCTC 1659T) isolated in 1901 from the prepuce of a dog in Germany.

Mannheimia pernigra sp. nov., isolated from bovine respiratory tract.

Over a period of 1 year, 270 isolates identified as Taxon 39 of Bisgaard were obtained from the nasopharynx of veal calves at 11 epidemiologically independent Swiss fattening farms. Two isolates from each farm and the Australian Taxon 39 reference strain BNO311 were further characterized by genetic and phenotypic methods. Phylogenetic analysis of 16S rRNA and recN gene sequences placed the isolates in a single, distinct cluster within the genus Mannheimia. As to the rpoB gene, most isolates clustered together, but four strains formed a separate cluster close to Mannheimia varigena. Genome sequence analysis of isolates from both rpoB clusters confirmed their species status, with an average nucleotide identity (ANI) >98.9 % between isolates and <84 % to the closest species, M. varigena. Based upon whole genome sequences, the G+C content was determined as 39.1 mol%. Similarly, analysis of MALDI-TOF MS reference spectra clustered the isolates clearly separated from the other Mannheimia species, making this the method of choice for identification. In addition, numerous biochemical markers based on classical as well as commercial identification schemes were determined, allowing separation from other Mannheimia species and identification of the new taxon. Major fatty acids for strain 17CN0883T are C14 : 0, C16 : 0, C16 : 1 ω7c and C18 : 1 ω7c. Major respiratory quinones are ubiquinone-7 and ubiquinone-8. We propose the name Mannheimia pernigra sp. nov. for former Taxon 39 of Bisgaard. The type strain is 17CN0883T (=CCUG 74657T=DSM 111153T) isolated from a veal calf in Switzerland.

Molecular and serological characterization of Riemerella isolates associated with poultry in Australia.

A total of 62 isolates of Riemerella-like organisms, originally isolated from Australian poultry (10 from chickens, 46 from ducks, five from unknown hosts and one vaccine strain), were included in this study. On the basis of two published polymerase chain reaction (PCR) assays that are reported to be specific for Riemerella anatipestifer, 51 of the isolates were identified as R. anatipestifer. Forty-six of these isolates had a detailed history and were sourced from ducks, while five were of unknown origin. The 11 remaining isolates failed to yield a positive reaction in either PCR with 10 originating from chickens and one from a duck. Amplification and sequencing of the 16S rRNA gene of these isolates identified the duck isolate as Moraxella lacunta. Phylogenetic analysis of the 10 chicken isolates identified one as R. columbina and the remaining nine isolates as Riemerella-like taxon 2. The 51 Australian R. anatipestifer isolates were assigned by gel diffusion test to serovars 1 (26 isolates), 6 (seven isolates), 8 (five isolates), 9 (two isolates), 13 (one isolate) and 14 (one isolate) while nine isolates gave no reaction to any antiserum. A commercial system was used to perform DNA fingerprinting using rep-PCR analysis, which revealed different clusters with a lack of a clear relationship between the clusters and the serovars.

New strategies to prevent and control avian pathogenic Escherichia coli (APEC).

Avian pathogenic Escherichia coli (APEC) infections are associated with major economical losses and decreased animal welfare. In broiler production, APEC infections have traditionally been controlled by antibiotics, resulting in an increased prevalence of antibiotic-resistant E. coli. Concerns have been raised that transfer of antibiotic-resistant APEC via the food chain may result in risks for extra-intestinal infection of humans related to zoonotic transfer and increased difficulties in the treatment of human infections caused APEC-related E. coli types. In this review, the risks associated with APEC are presented based on new knowledge on transmission, virulence and antibiotic resistance of APEC. A major new change in our understanding of APEC is the high degree of genuine vertical transfer of APEC from parents to offspring. A new strategy for controlling APEC, including control of antibiotic-resistant APEC, has to focus on limiting vertical transfer from parents to offspring, and subsequent horizontal transmission within and between flocks and farms, by using all-in-all-out production systems and implementing a high level of biosecurity. Vaccination and the use of competitive exclusion are important tools to be considered. A specific reduction of antibiotic-resistant APEC can be obtained by implementing culling strategies, only allowing the use of antibiotics in cases where animal welfare is threatened. Strategies to reduce APEC, including antibiotic-resistant APEC, need to be implemented in the whole production pyramid, but it has to start at the very top of the production pyramid.

Whole genome sequence comparison of avian pathogenic Escherichia coli from acute and chronic salpingitis of egg laying hens.

BACKGROUND: Infection in the oviduct (salpingitis) is the most common bacterial infection in egg laying hens and is mainly caused by Escherichia coli. The disease is responsible for decreased animal welfare, considerable economic loss as well as a risk of horizontal and vertical transmission of pathogenic E. coli. The outcome of salpingitis may be either acute or chronic. It has not yet been clarified whether the pathological manifestation is a result of the characteristics of the E. coli or whether the manifestation is associated with host factors such as host immunity. RESULTS: From the core- and accessory genome analysis and comparison of 62 E. coli no genetic markers were found to be associated to either acute or chronic infection. Twenty of the 62 genomes harboured at least one antimicrobial resistance gene with resistance against sulfonamides being the most common. The increased serum survival and iron chelating genes iss and iroN were highly prevalent in genomes from both acute and chronic salpingitis. CONCLUSION: Our analysis revealed that no genetic markers could differentiate the E. coli isolated from acute versus chronic salpingitis in egg laying hens. The difference in pathological outcome may be related to other factors such as immunological status, genetics and health of the host. These data indicate that salpingitis is another manifestation of colibacillosis.

Correlation between footpad lesions and systemic bacterial infections in broiler breeders.

Footpad lesions are an important factor in evaluation of animal welfare in broilers regulated by law; however, no legal requirements have been set for the parent birds. Nevertheless, the present study confirms that foot health in broiler breeders declines significantly with increasing age, thus potentially impairing the animal welfare due to pain and discomfort from footpad dermatitis. Furthermore, this is the first report demonstrating a correlation between the presence of footpad lesions and systemic bacterial infections with Gram-positive cocci in broiler breeder birds.

Development of multi locus sequence typing (MLST) of Rodentibacter pneumotropicus.

The aim of the investigation was to develop a definitive typing system for Rodentibacter pneumotropicus. A total of 79 strains including the type strain of R. pneumotropicus, all associated with rodents were used to develop a multi-locus sequence typing scheme (MLST). Primers were designed for conserved regions of seven house-keeping genes (atpG, frdB, gdh, pgi, pmi, recA, zwf) and internal fragments of 399-839 bp were sequenced for all strains. The genes were also extracted in full length from whole genomic sequences of 14 strains of which 10 were sequenced in the current study. The number of alleles at the different loci ranged from 5 to 7 and a total of 20 allelic profiles or sequence types were recognized amongst the 79 strains. Analysis of the MLST data showed that some STs have been stable over many years probably circulating in the same colonies and probably transferred between colonies. We assume that this MLST scheme may provide a high level of resolution and might be an excellent tool for studying the population structure and epidemiology of R. pneumotropicus. Further development of the scheme is expected by including more genes and more strains and involve whole genomic sequencing.

Microbiota encompassing putative spoilage bacteria in retail packaged broiler meat and commercial broiler abattoir.

It is well established, that certain bacteria within the Brochothrix, Carnobacterium, Lactobacillus, Lactococcus, and Leuconostoc genera have an important role in the spoilage of chill stored poultry meat packaged in modified atmosphere. However, little is known about the role of microorganisms that are difficult to culture and the microbiota during poultry spoilage. We combined traditional cultivation and culture-independent 16S rRNA amplicon sequencing to investigate the microbiota encompassing putative bacteria of whole broiler meat, packaged in modified atmosphere, during and exceeding shelf-life. Samples were taken from 6 flocks during independent slaughter days. Additional samples were analysed from the production line. There was a significant difference in the microbial community structure of 80%O2/20%CO2 retail packaged broiler meat during different times of shelf-life, mainly due to an increase of species within the Brochothrix, Carnobacterium, Vagococcus, and Janthinobacterium genera. These genera were already detected four to eight days after slaughter. However, no significant difference between flocks with respect to the microbiota encompassing putative spoilage bacteria was observed when examined in retail packaged broilers, slaughtered at the same abattoir on different days. Our study also showed that lactic acid bacteria within the Vagococcus genus can constitute a dominating part of the later shelf-life microbiota in fresh whole broiler meat packaged in 80%O2/20%CO2 modified atmosphere. A single operational taxonomic unit (OTU) assigned as Janthinobacterium lividum, an occasional spoiler of meat products, was identified as a major part of the microbiota in late shelf life broiler meat and swab samples in the cooling facility at the slaughter house production line. The combination of traditional cultivation and culture-independent methods provided a great insight into the microbiota of broiler meat during shelf-life and identified a potential point of contamination in the production line for cold tolerant Janthinobacterium.

Diversity and Population Overlap between Avian and Human Escherichia coli Belonging to Sequence Type 95.

Avian-pathogenic Escherichia coli (APEC) is a subgroup of extraintestinal pathogenic E.coli (ExPEC) presumed to be zoonotic and to represent an external reservoir for extraintestinal infections in humans, including uropathogenic E. coli (UPEC) causing urinary tract infections. Comparative genomics has previously been applied to investigate whether APEC and human ExPEC are distinct entities. Even so, whole-genome-based studies are limited, and large-scale comparisons focused on single sequence types (STs) are not available yet. In this study, comparative genomic analysis was performed on 323 APEC and human ExPEC genomes belonging to sequence type 95 (ST95) to investigate whether APEC and human ExPEC are distinct entities. Our study showed that APEC of ST95 did not constitute a unique ExPEC branch and was genetically diverse. A large genetic overlap between APEC and certain human ExPEC was observed, with APEC located on multiple branches together with closely related human ExPEC, including nearly identical APEC and human ExPEC. These results illustrate that certain ExPEC clones may indeed have the potential to cause infection in both poultry and humans. Previously described ExPEC-associated genes were found to be encoded on ColV plasmids. These virulence-associated plasmids seem to be crucial for ExPEC strains to cause avian colibacillosis and are strongly associated with strains of the mixed APEC/human ExPEC clusters. The phylogenetic analysis revealed two distinct branches consisting of exclusively closely related human ExPEC which did not carry the virulence-associated plasmids, emphasizing a lower avian virulence potential of human ExPEC in relation to an avian host.IMPORTANCE APEC causes a range of infections in poultry, collectively called colibacillosis, and is the leading cause of mortality and is associated with major economic significance in the poultry industry. A growing number of studies have suggested APEC as an external reservoir of human ExPEC, including UPEC, which is a reservoir. ExPEC belonging to ST95 is considered one of the most important pathogens in both poultry and humans. This study is the first in-depth whole-genome-based comparison of ST95 E. coli which investigates both the core genomes as well as the accessory genomes of avian and human ExPEC. We demonstrated that multiple lineages of ExPEC belonging to ST95 exist, of which the majority may cause infection in humans, while only part of the ST95 cluster seem to be avian pathogenic. These findings further support the idea that urinary tract infections may be a zoonotic infection.

Reclassification of Bisgaard taxon 37 and taxon 44 as Psittacicella melopsittaci gen. nov., sp. nov., Psittacicella hinzii sp. nov. and Psittacicella gerlachiana sp. nov. within Psittacicellaceae fam. nov. of the order Pasteurellales.

Bacteria isolated from lesions as well as apparently normal tissues of psittacine birds have previously been reported as taxon 37 and taxon 44 of Bisgaard. 16S rRNA gene sequence comparisons revealed a distant relationship to members of Pasteurellaceae at the species, genus and family levels. The polar lipid profile consisted of the major components phosphatidylethanolamine and phosphatidylglycerol. A new family Psittacicellaceae fam. nov. is proposed with the type genus Psittacicella gen. nov. The new genus Psittacicella includes the type species Psittacicella melopsittaci sp. nov. with type strain B96/4T (=CCUG 70858T=DSM 105476T), Psittacicella hinzii sp. nov. with type strain 111T (=CCUG 52861T=CCM 8842T) and Psittacicella gerlachiana sp. nov. with type strain EEAB3T1T (=CCUG 70857T=DSM 105477T). In addition to the major polar lipids, strain 111T possessed the non-identified aminophospholipids APL1 and APL2 and trace amounts of four lipids (L1-L4) whereas strain B94/4T showed the minor unidentified aminophospholipids APL3 and APL2 and trace amounts of unidentified lipid L3. These results demonstrate that strain B96/4T can be distinguished from 111T based on presence/absence of the unidentified lipids APL1 and APL3. The total polar lipid profile of strain EEAB3T1T differed from B96/4Tonly in one minor lipid. Strain B96/4T can further be distinguished from 111T by acid formation from trehalose and raffinose and the α-glucosidase test. Strains 111T and EEAB3T1T can be separated based on acid formation from trehalose and the α-glucosidase test. Strains B96/4T and EEAB3T1T can be separated by acid formation from raffinose and eight signature indels in the RpoB protein.

Longitudinal Study on Causes of Mortality in Danish Broiler Breeders.

Broiler production is highly dependent on good health in the parent flocks. The so-called normal mortality in these flocks remains to be addressed to further reduce mortality of the breeders and to improve the quality of broilers. The aim of the present study, therefore, was to investigate the etiology of this breeder mortality to map out possible critical periods during production in relation to possible risks of importance to the offspring. Dead birds from four flocks were subjected to postmortem and bacteriologic examination from onset of lay until slaughter (20-60 weeks). Causes of mortality were divided into noninfectious and infectious etiology. The infectious group could be subdivided into suppurative salpingitis/peritonitis caused by Escherichia coli and other infections (e.g., sepsis, endocarditis, and arthritis) mainly caused by Gram-positive cocci. Data analysis showed that 41% of the birds died from noninfectious causes, while 55% died from infectious causes, and 4% had no known cause of death. The prevalence of noninfectious mortality was highest in the youngest birds and lowest in the oldest birds. In contrast, the infectious mortality was lowest in the young birds and highest at the end of production. Within each age group, the prevalence of salpingitis/ peritonitis was 26% in young birds (20-29 weeks) and progressed throughout production to 41% in the oldest birds (≥50 weeks of age). Mortality due to other infections was low at onset of production (12%), peaking at 40-49 weeks of age (25%). Consequently, 40-49 weeks of age is identified as a critical period with regard to causes of mortality, possible vertical transmission of E. coli to the offspring, and increased risk of Gram-positive coccal infections.

Estudio longitudinal sobre las causas de mortalidad en reproductores pesados daneses. La producción de pollo de engorde depende en gran medida de la buena salud de las parvadas de reproductores. La llamada mortalidad normal en estas parvadas aún debe analizarse para reducir aún más la mortalidad de los reproductores y mejorar la calidad del pollo de engorde. El objetivo del presente estudio, por lo tanto, fue investigar la etiología de esta mortalidad en los reproductores para determinar posibles períodos críticos durante la producción con relación con los posibles riesgos que sean de importancia para la progenie. Las aves muertas de cuatro parvadas se sometieron a un examen post mortem y bacteriológico desde el inicio de la postura hasta la edad de sacrificio (20­60 semanas). Las causas de mortalidad se dividieron en etiología no infecciosa e infecciosa. El grupo de causas de origen infeccioso se subdividió en salpingitis/peritonitis supurativa (SP) causada por Escherichia coli y otras infecciones (por ejemplo, sepsis, endocarditis y artritis) causadas principalmente por cocos Gram positivos. El análisis de los datos mostró que el 41% de las aves murieron por causas no infecciosas, mientras que el 55% murió por causas infecciosas y el 4% por causas desconocidas. La prevalencia de mortalidad no infecciosa fue más alta en las aves más jóvenes y más baja en las aves con mayor edad. En contraste, la mortalidad infecciosa fue más baja en las aves jóvenes y más alta al final de la producción. Dentro de cada grupo de edad, la prevalencia de salpingitis/peritonitis supurativa fue del 26% en aves jóvenes (20­29 semanas) y aumentó a lo largo de la producción hasta el 41% en las aves con más edad (≥50 semanas de edad). La mortalidad debida a otras infecciones fue baja al inicio de la producción (12%), alcanzando un máximo de 40 a 49 semanas de edad (25%). En consecuencia, la edad entre 40 a 49 semanas se identifica como un período crítico con respecto a las causas de mortalidad, con la posible transmisión vertical de E. coli a la progenie y con el aumento del riesgo de infecciones por cocos Gram positivos.

Classification of Bisgaard's taxa 14 and 32 and a taxon from kestrels demonstrating satellitic growth and proposal of Spirabiliibacterium gen. nov., including the description of three species: Spirabiliibacterium mucosae sp. nov., Spirabiliibacterium pneumoniae sp. nov. and Spirabiliibacterium falconis sp. nov.

Avian Pasteurella-like organisms tentatively named taxon 14 of Bisgaard have been obtained from different lesions in birds including ducks, turkeys, pigeons, geese and peafowl. Taxon 32 of Bisgaard was first reported from lesions in pigeon hawks (Accipiter gentiles). The taxon isolated from kestrels (Falco tinnunculus) was V-factor dependent and originally reported as Haemophilus-like. The results of 16S rRNA gene sequence based phylogenetic analysis recently indicated that the taxa 14 and 32 and the kestrel taxon were located in a monophyletic group distantly related to [Pasteurella] testudinis with 92-93 % 16S rRNA gene sequence similarity. Comparison of 41 conserved protein sequences confirmed the monophyletic nature of the three taxa. Partial rpoB gene sequencing of 43 strains of taxon 14, taxon 32 and the kestrel taxon showed a relationship between taxon 14 and 32 of 88.2-90.0 % similarity. Within taxon 14, 93.3-100 % similarity was found, whereas the two strains of taxon 32 showed 99.8 % rpoB similarity. Sequencing of 16S rRNA genes of strains representing the rpoB diversity outlined showed more than 98 % similarity within taxon 14 and 99.4 % within taxon 32, while the kestrel strains showed 100 % 16S rRNA gene sequence similarity. A new genus, Spirabiliibacterium gen. nov., is proposed to include taxon 14, taxon 32 and the kestrel taxon. Phenotypically, members of the genus Spirabiliibacterium can be separated from members of the genera Aggregatibacter, Avibacterium and Volucribacter by maltose, oxidase and methyl red, respectively. Two or more phenotypic characters separate members of the genus Spirabiliibacterium from members of the remaining 27 genera of the family Pasteurellaceae.The G+C content of DNA ranged from 42.9 to 51.2 % (genome sequence) for members of the genus Spirabiliibacterium. The type strain of Spirabiliibacterium mucosae (taxon 14 of Bisgaard) is 20609/3T (=CCUG 16499T=DSM 111429T=HIM 913-3T). The type strain of Spirabiliibacterium pneumoniae is HPA106T (=CCUG 74731T=DSM 111430T). The type strain of Spirabiliibacterium falconis (kestrel taxon) is IPDH 2176T (=NCTC 11878T=CCUG 28587T).