Phylogeny of the family Pasteurellaceae based on rpoB sequences

Prevalence of Taxa of Pasteurellaceae Among Populations of Healthy Captive Psittacine Birds

Sixty-two strains of Pasteurellaceae-like bacteria were isolated from the tracheas of 87 clinically healthy psittacine birds in two Danish zoos. The isolates were identified by a combination of rpoB and 16S rRNA gene sequencing and by matrix-assisted laser desorption-ionization time of flight. Twenty-eight strains belonged to the genus Volucribacter or were related to this genus and to the unnamed taxon 34 of Bisgaard, and 28 strains were related to the unnamed taxon 44 of Bisgaard. Four strains were identified as Pasteurella multocida , two isolates were classified with the related taxon 45 of Bisgaard, and a single isolate was classified as Pasteurella sp. The investigation documented an unrecognized reservoir of rarely reported and unclassified or unnamed species of Pasteurellaceae-like bacteria in psittacine birds. The results were in accordance with a recent report on isolation of Pasteurellaceae from diseased psittacine birds, and the investigation documented that the same taxa of Pasteurellaceae-like bacteria can be isolated from apparently healthy birds as well as from diseased birds.

Neptuniibacter pectenicola sp. nov. and Neptuniibacter marinus sp. nov., two novel species isolated from a Great scallop (Pecten maximus) hatchery in Norway and emended description of the genus Neptuniibacter

Nine isolates obtained from a great scallop hatchery in Norway were characterized using a polyphasic approach. Strains were Gram-negative, aerobic and motile rods with oxidative metabolism. Phylogenetic analysis based on the sequences of 16S rRNA and rpoB genes showed that these strains formed two different groups associated with members of the genus Neptuniibacter. DNA-DNA hybridization (DDH) and Average Nucleotide Identity (ANI) demonstrated that the isolates constituted two novel species of this genus, which can be phenotypically differentiated from their closest relatives. The names Neptuniibacter marinus sp. nov. and Neptuniibacter pectenicola sp. nov are proposed, with ATR 1.1^T (=CECT 8938^T=DSM 100783^T) and LFT 1.8^T (=CECT 8936^T=DSM 100781^T) as respective type strains.

Exposure to pairs of Aeromonas strains enhances virulence in the Caenorhabditis elegans infection model

Aeromonad virulence remains poorly understood, and is difficult to predict from strain characteristics. In addition, infections are often polymicrobial (i.e., are mixed infections), and 5-10% of such infections include two distinct aeromonads, which has an unknown impact on virulence. In this work, we studied the virulence of aeromonads recovered from human mixed infections. We tested them individually and in association with other strains with the aim of improving our understanding of aeromonosis. Twelve strains that were recovered in pairs from six mixed infections were tested in a virulence model of the worm Caenorhabditis elegans. Nine isolates were weak worm killers (median time to death, TD50, ≥7 days) when administered alone. Two pairs showed enhanced virulence, as indicated by a significantly shortened TD50 after co-infection vs. infection with a single strain. Enhanced virulence was also observed for five of the 14 additional experimental pairs, and each of these pairs included one strain from a natural synergistic pair. These experiments indicated that synergistic effects were frequent and were limited to pairs that were composed of strains belonging to different species. The genome content of virulence-associated genes failed to explain virulence synergy, although some virulence-associated genes that were present in some strains were absent from their companion strain (e.g., T3SS). The synergy observed in virulence when two Aeromonas isolates were co-infected stresses the idea that consideration should be given to the fact that infection does not depend only on single strain virulence but is instead the result of a more complex interaction between the microbes involved, the host and the environment. These results are of interest for other diseases in which mixed infections are likely and in particular for water-borne diseases (e.g., legionellosis, vibriosis), in which pathogens may display enhanced virulence in the presence of the right partner. This study contributes to the current shift in infectiology paradigms from a premise that assumes a monomicrobial origin for infection to one more in line with the current pathobiome era.

The upper respiratory tract is a natural reservoir of haemolytic Mannheimia species associated with ovine mastitis

Lamb suckling has been suggested to be an important way of infecting a ewe's udder with different bacteria, including Mannheimia haemolytica. To test the potential role of lambs in transferring Mannheimia species to the ewe's udder, the restriction endonuclease cleavage patterns of isolates obtained from nasopharyngeal swabs were compared with those obtained from cases of mastitis. Sterile cotton swabs were used to collect nasopharyngeal samples from 50 ewes and 36 lambs from three flocks. M. haemolytica and Mannheimia glucosida as well as haemolytic Mannheimia ruminalis-like organisms were detected in the upper respiratory tract of lambs and ewes. Comparison of the restriction endonuclease cleavage patterns of the isolates suggested that the M. haemolytica isolates obtained from different milk samples from ewes with mastitis were more clonal than those obtained from the nasal swabs. However, some nasal isolates within both Mannheimia species had restriction endonuclease cleavage patterns identical to those obtained from milk samples from ewes with mastitis, indicating that lambs may have a role in transferring these organisms to the udder. More clonality was observed between the M. glucosida isolates than between M. haemolytica isolates.

Reclassification of Actinobacillus muris as Muribacter muris gen. nov., comb. nov

To reinvestigate the taxonomy of [Actinobacillus] muris, 474 strains, mainly from mice and rats, were characterized by phenotype and 130 strains selected for genotypic characterization by 16S rRNA and partial rpoB gene sequencing. The type strain was further investigated by whole-genome sequencing. Phylogenetic analysis of the DNA sequences showed one monophyletic group with intragroup similarities of 96.7 and 97.2 % for the 16S rRNA and rpoB genes, respectively. The highest 16S rRNA gene sequence similarity to a taxon with a validly published name outside the group was 95.9 %, to the type strain of [Pasteurella] pneumotropica. The closest related taxon based on rpoB sequence comparison was ‘Haemophilus influenzae-murium’, with 88.4 % similarity. A new genus and a new combination, Muribacter muris gen. nov., comb. nov., are proposed based on a distinct phylogenetic position based on 16S rRNA and rpoB gene sequence comparisons, with major divergence from the existing genera of the family Pasteurellaceae. The new genus has the characteristics of [A.] muris with the emendation that acid formation from ( − )-d-mannitol and hydrolysis of aesculin are variable, while the α-glucosidase test is positive. There is no requirement for exogenously supplied NAD (V factor) for the majority of strains investigated; however, one strain was found to require NAD. The major fatty acids of the type strain of Muribacter muris were C14 : 0, C14 : 0 3-OH/iso-C16 : 1 I, C16 : 1ω7c and C16 : 0, which is in line with most genera of the Pasteurellaceae. The type strain of Muribacter muris is CCUG 16938T ( = NCTC 12432T = ATCC 49577T).

Human Wound Infection with Mannheimia glucosida following Lamb Bite

Mannheimia spp. are veterinary pathogens that can cause mastitis and pneumonia in domestic cattle and sheep. While Mannheimia glucosida can be found as normal flora in oral and respiratory mucosa in sheep, there have been no reported cases of human infection with this organism.

Ursidibacter maritimus gen. nov., sp. nov. and Ursidibacter arcticus sp. nov., two new members of the family Pasteurellaceae isolated from the oral cavity of bears

Thirty-three suspected strains of the family Pasteurellaceae isolated from the oral cavity of polar and brown bears were characterized by genotypic and phenotypic tests. Phylogenetic analysis of partial 16S rRNA gene and rpoB sequences showed that the investigated isolates formed two closely related monophyletic groups, representing two novel species of a new genus. Based on 16S rRNA gene sequence comparison Bibersteinia trehalosi was the closest related species with a validly published name, with 95.4 % similarity to the polar bear group and 94.4 % similarity to the brown bear group. Otariodibacter oris was the closest related species based on rpoB sequence comparison with a similarity of 89.8 % with the polar bear group and 90 % with the brown bear group. The new genus could be separated from existing genera of the family Pasteurellaceae by three to ten phenotypic characters, and the two novel species could be separated from each other by two phenotypic characters. It is proposed that the strains should be classified as representatives of a new genus, Ursidibacter gen. nov., with two novel species: the type species Ursidibacter maritimus sp. nov., isolated from polar bears (type strain Pb43106T = CCUG 65144T = DSM 28137T, DNA G+C content 39.3 mol%), and Ursidibacter arcticus sp. nov., isolated from brown bears (type strain Bamse61T = CCUG 65145T = DSM 28138T).

Gut dysbiosis in acute-on-chronic liver failure and its predictive value for mortality

BACKGROUND

Bacterial translocation from the gut plays an important role in the pathophysiology of acute-on-chronic liver failure (ACLF). However, gut dysbiosis in ACLF was not widely documented in previous studies.

AIM

This research characterized the fecal microbiota in patients with ACLF and analyzed the temporal stability of gut microbiota during illness.

METHODS

Fecal microbiota of 79 ACLF patients (42 patients were followed in the next 4 weeks after the first visit for longitudinal study) and 50 healthy controls was analyzed by 16S ribosomal DNA pyrosequencing.

RESULTS

There was a marked difference between the ACLF group and the control group. The overall microbial diversity and richness were significantly lower in ACLF than in controls. ACLF patients had lower abundance of Bacteroidaceae, Ruminococcaceae, and Lanchnospiraceae, but higher abundance of Pasteurellaceae, Streptococcaceae, and Enterecoccaceae. The relative abundance of Lachnospiraceae was obviously decreased in ACLF patients with hepatic encephalopathy. The gut microbiota kept relatively stable in a short term after the onset of ACLF. The use of antibiotics only showed moderate impacts on the gut microbiota. The relative abundance of Pasteurellaceae and Model of End Stage Liver Disease score were independent factors predicting mortality rate. Network analysis comparison showed robust correlations between specific bacterial families (Ruminococcaceae and Lachnospiraceae) and inflammatory cytokines (interleukin [IL]-6, tumor necrosis factor alpha, IL-2) in ACLF patients.

CONCLUSIONS

These data suggest gut dysbiosis in ACLF and its predictive value for mortality. The results thus open up the possibility of designing diagnostic biomarkers and targeted probiotics aimed at decreasing mortality in ACLF.

Sinobacterium norvegicum sp. nov., isolated from great scallop (Pecten maximus) broodstock and emended description of Sinobacterium caligoides

Six isolates were recovered from great scallop (Pecten maximus) broodstock in a hatchery in Bergen, Norway. The strains were thoroughly characterized by a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these strains are related to the genus Sinobacterium, showing sequence similarities between 96.97 and 97.63 % with the only species of the genus, Sinobacterium caligoides. Phenotypic characterization showed that the strains are typical marine halophiles, Gram negative, aerobic chemoorganotrophs, and allowed their differentiation from the closely related taxa. The G+C content of the novel strains was 52.2 ± 1 mol% and the predominant fatty acids were C16:0, C16:1 ω7c/C16:1 ω6c and C18:1 ω7c. The value for DNA-DNA relatedness between strain 3CM4(T) and the S. caligoides type strain LMG 25705(T) was 46  %. Hybridization values between strain 3CM4(T) and the other scallop isolates ranged from 82 to 93.6 %. Based on all data collected, the six scallop strains represent a novel species of the genus Sinobacterium, for which the name Sinobacterium norvegicum sp. nov., is proposed with strain 3CM4(T) (=CECT 8267(T); =CAIM 1884(T)) as type strain.

Phylogenomic and molecular demarcation of the core members of the polyphyletic pasteurellaceae genera actinobacillus, haemophilus, and pasteurella

The genera Actinobacillus, Haemophilus, and Pasteurella exhibit extensive polyphyletic branching in phylogenetic trees and do not represent coherent clusters of species. In this study, we have utilized molecular signatures identified through comparative genomic analyses in conjunction with genome based and multilocus sequence based phylogenetic analyses to clarify the phylogenetic and taxonomic boundary of these genera. We have identified large clusters of Actinobacillus, Haemophilus, and Pasteurella species which represent the “sensu stricto” members of these genera. We have identified 3, 7, and 6 conserved signature indels (CSIs), which are specifically shared by sensu stricto members of Actinobacillus, Haemophilus, and Pasteurella, respectively. We have also identified two different sets of CSIs that are unique characteristics of the pathogen containing genera Aggregatibacter and Mannheimia, respectively. It is now possible to demarcate the genera Actinobacillus sensu stricto, Haemophilus sensu stricto, and Pasteurella sensu stricto on the basis of discrete molecular signatures. The other members of the genera Actinobacillus, Haemophilus, and Pasteurella that do not fall within the “sensu stricto” clades and do not contain these molecular signatures should be reclassified as other genera. The CSIs identified here also provide useful diagnostic targets for the identification of current and novel members of the indicated genera.

Comparison of MALDI-TOF MS, housekeeping gene sequencing, and 16S rRNA gene sequencing for identification of Aeromonas clinical isolates

PURPOSE

The genus Aeromonas is a pathogen that is well known to cause severe clinical illnesses, ranging from gastroenteritis to sepsis. Accurate identification of A. hydrophila, A. caviae, and A. veronii is important for the care of patients. However, species identification remains difficult using conventional methods. The aim of this study was to compare the accuracy of different methods of identifying Aeromonas at the species level: a biochemical method, matrix-assisted laser desorption ionization mass spectrometry-time of flight (MALDI-TOF MS), 16S rRNA sequencing, and housekeeping gene sequencing (gyrB, rpoB).

MATERIALS AND METHODS

We analyzed 65 Aeromonas isolates recovered from patients at a university hospital in Korea between 1996 and 2012. The isolates were recovered from frozen states and tested using the following four methods: a conventional biochemical method, 16S rRNA sequencing, housekeeping gene sequencing with phylogenetic analysis, and MALDI-TOF MS.

RESULTS

The conventional biochemical method and 16S rRNA sequencing identified Aeromonas at the genus level very accurately, although species level identification was unsatisfactory. MALDI-TOF MS system correctly identified 60 (92.3%) isolates at the species level and an additional four (6.2%) at the genus level. Overall, housekeeping gene sequencing with phylogenetic analysis was found to be the most accurate in identifying Aeromonas at the species level.

CONCLUSION

The most accurate method of identification of Aeromonas to species level is by housekeeping gene sequencing, although high cost and technical difficulty hinder its usage in clinical settings. An easy-to-use identification method is needed for clinical laboratories, for which MALDI-TOF MS could be a strong candidate.

Bisgaardia miroungae sp. nov., a new member of the family Pasteurellaceae isolated from the oral cavity of northern elephant seals (Mirounga angustirostris), and emended description of the genus Bisgaardia

A total of 17 bacterial isolates from northern elephant seals, tentatively classified within the family Pasteurellaceae, were further characterized by genotypic and phenotypic tests. Phylogenetic analysis of partial 16S rRNA and rpoB gene sequences showed that the isolates investigated formed a monophyletic group, closely related to the genus Bisgaardia within the family Pasteurellaceae . The rpoB gene sequence similarity was 97.2–100 % within the group and 16S rRNA gene sequence comparisons showed 99.2–99.8 % similarity within the group. According to 16S rRNA gene sequence analysis, the most closely related species with a validly published name was Bisgaardia hudsonensis with 96.9 % similarity and the most closely related species based on rpoB sequence comparison was Bisgaardia genomospecies 1 with an rpoB sequence similarity of 90.9 %. All the isolates investigated exhibited the phenotypic characteristics of the family Pasteurellaceae . However, these isolates could be separated from existing species of the genus Bisgaardia by the following characteristics: ability to grow at 42 °C, and acid production from lactose, melibiose, raffinose and l-rhamnose, but not from d-mannitol or trehalose. On the basis of both phylogenetic and phenotypic evidence, it is proposed that the strains should be classified as representatives of a novel species within the genus Bisgaardia : Bisgaardia miroungae sp. nov. The type strain, WildatricT ( = CCUG 65148T = DSM 28141T), was isolated from the oral cavity of a wild northern elephant seal at The Marine Mammal Center, California, USA in 2011. To include the novel species, the description of the genus Bisgaardia has been emended.

Uruburuella testudinis sp. nov., isolated from tortoise (Testudo)

A polyphasic taxonomic analysis was carried out on 11 uncommon Gram-stain-negative, non-motile, catalase- and oxidase-positive, but indole-negative, bacterial strains isolated from tortoises. Phenotypically and genetically they represented a homogeneous group of organisms most closely related to, but distinct from, Uruburuella suis. In a reconstructed 16S rRNA gene tree they clustered on a monophyletic branch next to U. suis with gene similarities between strains of 99.5-100%, and of up to 98.2% with U. suis . DNA-DNA hybridization indicated the organisms represented a novel species with only 40% DNA-DNA similarity with U. suis . Partial sequencing of rpoB resulted in two subclusters confirming the 16S rRNA gene phylogeny; both genes allowed clear separation and identification of the novel species. Furthermore, they could be unambiguously identified by matrix-assisted laser desorption ionization time-of-flight MS, where, again, they formed a highly homogeneous cluster separate from U. suis and other members of the family Neisseriaceae . The major fatty acids were C(16 : 0) and summed feature C(16 : 1)ω7c/iso-C(15 : 0) 2-OH. The DNA G+C content was 54.4 mol%. Based on phenotypic and genetic data we propose classifying these organisms as representatives of a novel species named Uruburuella testudinis sp. nov. The type strain is 07_OD624(T) ( = DSM 26510(T) = CCUG 63373(T)).

Taxonomy of Histophilus somni

Histophilus somni was proposed in 2003 as a common name for bacteria that earlier had been called "Haemophilus somni", "Haemophilus agni", "Haemophilus somnifer", and "Histophilus ovis". The species is clearly separated from other species and genera within the family Pasteurellaceae. The species is phenotypically variable, but highly uniform regarding the 16S rDNA sequence. Whole-genome sequencing has revealed distinct genetic differences between a commensal and a pathogenic strain, particularly in regard to putative virulence factors. However, broad generalizations regarding the genetics of H. somni cannot be applied to the entire species until the genomes of additional strains are sequenced.

Evaluating the occurrence of Escherichia albertii in chicken carcass rinses by PCR, Vitek analysis, and sequencing of the rpoB gene

Escherichia albertii is a recently described species that has been associated with gastroenteritis in humans and with healthy and ill birds. Most recently, it has been identified as the causative agent in a food-borne outbreak in Japan. The distribution and clinical importance of E. albertii are not well studied because its importance is unclear. Culture methods for clinical isolation frequently miss E. albertii or incorrectly identify it as Shigella spp., Escherichia coli, or Hafnia alvei. This study was designed to determine if E. albertii could be recovered from chicken carcass rinses collected at slaughter during a 1-year period from November 2009 until October 2010. Colonies were isolated from chicken carcass rinses and tested by PCR for the presence or absence of clpX, lysP, mdh, intimin (eae), Shiga toxins 1 and 2 (stx1, stx2, and stx2f), heat-stable enterotoxin A (staA), and cytolethal distending toxins 1 and 2 (cdtB) genes. Sixty-five isolates were analyzed by sequencing a section of the rpoB gene. Analysis of the rpoB gene sequences revealed 14 fixed differences between E. albertii and other, closely related organisms. The fixed differences found in the rpoB gene could aid in future discrimination of E. albertii from closely related bacteria.

Identification of clinical aeromonas species by rpoB and gyrB sequencing and development of a multiplex PCR method for detection of Aeromonas hydrophila, A. caviae, A. veronii, and A. media

Conventional identification of Aeromonas species based on biochemical methods is challenged by the heterogeneous nature of the species. Here, we present a new multiplex PCR method directed toward the gyrB and rpoB genes that identifies four Aeromonas species, A. hydrophila, A. media, A. veronii, and A. caviae, and we describe the application of this method on a Danish strain collection.

Investigation of taxa of the family Pasteurellaceae isolated from Syrian and European hamsters and proposal of Mesocricetibacter intestinalis gen. nov., sp. nov. and Cricetibacter osteomyelitidis gen. nov., sp. nov

Eleven strains from hamster of Bisgaard taxa 23 and 24, also referred to as Krause’s groups 2 and 1, respectively, were investigated by a polyphasic approach including data published previously. Strains showed small, regular and circular colonies with smooth and shiny appearance, typical of members of the family Pasteurellaceae . The strains formed two monophyletic groups based on 16S rRNA gene sequence comparison to other members of the family Pasteurellaceae . Partial rpoB sequencing as well as published data on DNA–DNA hybridization showed high genotypic relationships within both groups. Menaquinone 7 (MK7) was found in strains of both groups as well as an unknown ubiquinone with shorter chain length than previously reported for any other member of the family Pasteurellaceae . A new genus with one species, Mesocricetibacter intestinalis gen. nov., sp. nov., is proposed to accommodate members of taxon 24 of Bisgaard whereas members of taxon 23 of Bisgaard are proposed to represent Cricetibacter osteomyelitidis gen. nov., sp. nov. Major fatty acids of type strains of type species of both genera are C14 : 0, C14 : 0 3-OH/iso-C16 : 1 I, C16 : 1ω7c and C16 : 0. The two genera are clearly separated by phenotype from each other and from existing genera of the family Pasteurellaceae . The type strain of Mesocricetibacter intestinalis is HIM 933/7T ( = Kunstyr 246/85T = CCUG 28030T = DSM 28403T) while the type strain of Cricetibacter osteomyelitidis is HIM943/7T ( = Kunstyr 507/85T = CCUG 36451T = DSM 28404T).

Proposal of Vespertiliibacter pulmonis gen. nov., sp. nov. and two genomospecies as new members of the family Pasteurellaceae isolated from European bats

Five bacterial strains isolated from bats of the family Vespertilionidae were characterized by phenotypic tests and multilocus sequence analysis (MLSA) using the 16S rRNA gene and four housekeeping genes (rpoA, rpoB, infB, recN). Phylogenetic analyses of individual and combined datasets indicated that the five strains represent a monophyletic cluster within the family Pasteurellaceae. Comparison of 16S rRNA gene sequences demonstrated a high degree of similarity (98.3-99.9%) among the group of bat-derived strains, while searches in nucleotide databases indicated less than 96% sequence similarity to known members of the Pasteurellaceae. The housekeeping genes rpoA, rpoB, infB and recN provided higher resolution compared with the 16S rRNA gene and subdivided the group according to the bat species from which the strains were isolated. Three strains derived from noctule bats shared 98.6-100% sequence similarity in all four genes investigated, whereas, based on rpoB, infB and recN gene sequences, 91.8-96% similarity was observed with and between the remaining two strains isolated from a serotine bat and a pipistrelle bat, respectively. Genome relatedness as deduced from recN gene sequences correlated well with the results of MLSA and indicated that the five strains represent a new genus. Based on these results, it is proposed to classify the five strains derived from bats within Vespertiliibacter pulmonis gen. nov., sp. nov. (the type species), Vespertiliibacter genomospecies 1 and Vespertiliibacter genomospecies 2. The genus can be distinguished phenotypically from recognized genera of the Pasteurellaceae by at least three characteristics. All strains are nutritionally fastidious and require a chemically defined supplement with NAD for growth. The DNA G+C content of strain E127/08(T) is 38.2 mol%. The type strain of Vespertiliibacter pulmonis gen. nov., sp. nov. is E127/08(T) ( = CCUG 64585(T) = DSM 27238(T)). The reference strains of Vespertiliibacter genomospecies 1 and 2 are E145/08 and E157/08, respectively.

Molecular Typing ofPasteurella pneumotropicaIsolated from Rodents by Amplified 16S Ribosomal DNA Restriction Analysis and Pulsed-Field Gel Electrophoresis

A total of 52 isolates of Pasteurella pneumotropica obtained from rodents were examined for their genetic heterogeneity. On the basis of DNA restriction analysis, including amplified 16S ribosomal DNA restriction analysis (ARDRA) and pulsed-field gel electrophoresis (PFGE), differences were identified among the isolates. ARDRA typing with Hae III revealed 4 different banding patterns of the P. pneumotropica isolates. Eighty-two percent of the 23 isolates identified as a-1 were derived from mice, whereas all the isolates identified as a-3 were derived from rats. Most of the isolates, which showed hemolytic activity on blood agar, obtained from mice and rats, were identified as a-2 and a-4, respectively. By restriction analysis of genomic DNA, Apa I and Not I digestion differentiated 9 variants and an undiscriminating group. However, no close relation with regard to the phenotypic characteristics was observed among the variants. The isolates identified as a-2 and a-4 could not be distinguished by PFGE analysis. DNA restriction analysis revealed that the genetic diversity of the P. pneumotropica isolates was more complex than the phenotypic characteristics among the species, and that at least the P. pneumotropica isolates were clearly differentiated into 4 groups by ARDRA typing with Hae III.

A simple and novel method for retrieval of Pasteurellaceae from swab samples collected in the field

Traditionally it has been difficult or impossible to collect and preserve bacterial samples of especially fastidious bacteria in mixed primary cultures, unless the samples could be transported to a laboratory within approximately 24 h. Therefore, a simple novel method for preserving swab samples until bacterial isolation can be completed in the laboratory was developed and evaluated. Pasteurellaceae bacteria were used as a representative for fastidious bacteria. A 7.5% glucose serum medium was used as freeze medium. Swab samples were soaked in the medium a maximum of 2 h after collection and stored at −20°C. As a control study, 15 samples were collected from the oral cavity of a captive brown bear. One was immediately plated, while the remaining 12 swabs were stored at −20°C for 7 days and multiples of 30 days up to 330 days prior to plating. Two samples were stored without the medium for 7 and 30 days prior to plating. From a field setting in Greenland, eight polar bear samples were collected and subsequently stored for 240 to 259 days at −20°C before incubation. Pasteurellaceae bacteria were isolated and genotyped from all samples stored in the freeze medium, indicating that the medium enabled the bacteria to survive for at least 330 days at −20°C. The 100% recovery of target organisms in the polar bear samples even following lengthy storage and transport demonstrates that the method is very useful under remote field conditions.

The uneven rate of the molecular evolution of gene sequences of DNA-Dependent RNA polymerase I of the Genus Lamium L

RNA polymerase type I (plastid-encoded polymerase, PEP) is one of the key chloroplast enzymes. However, the rpo genes that encode its subunits (rpoA, rpoB, rpoC1 and rpoC2) are relatively rapidly evolving sequences. The aim of this study was to investigate the rate of the molecular evolution of rpo genes and to evaluate them as phylogenetic markers on the example of the genus Lamium L. (Lamiaceae). The analyzed genes were shown to differ in the level of variation, rate of intragenic mutations, phylogenetic informativeness, and in the impact of these mutations on the properties of encoded peptides. Destabilizing effects of the positive pressure were observed in all genes examined coding for PEP enzyme. We have demonstrated the relationship between mutations fixed by positive selection and the separation of phylogenetic lines within the genus Lamium. The study showed also that the rpo genes were reliable phylogenetic markers, useful in the reconstruction of interconnections of species belonging to the same genus. Of the four tested genes, the most promising phylogenetic marker was rpoA gene, while the least useful gene appeared to be rpoC1.

Protective anti-outer membrane protein immunity against Pasteurella pneumotropica infection of mice

The ability of recombinant outer membrane proteins of Pasteurella pneumotropica to vaccinate against the infections of mice was studied. The proteins examined were the homologues of the P4, P6, P26, and D15 proteins of Haemophilus influenzae. Intranasal vaccination with P4 and P6 produced protection against pneumonia. P6 vaccination, which was most studied, reduced the peak bacteria load in lungs by 50-fold and caused a rapid resolution of an infection that lasted for at least 5 days in unvaccinated animals. Protection could be partially transferred with CD4(+) T cells and pulmonary challenge with the P6 antigen induced interferon-γ and the Th17 cytokine IL-21. This is the first demonstration of the ability of a recombinant P6 to mediate protective immunity to a pathogen in its natural host and it is proposed that it would not only have utility for mouse breeding but also for investigating how to improve the efficacy of vaccination with homologous proteins for related species.

Pasteurella multocida carriage in red-necked wallabies (Macropus rufogriseus)

The isolation of Pasteurella multocida from several red-necked wallabies (Macropus rufogriseus) with purulent to necrotizing gingivitis, mandibular osteomyelitis, and conjunctivitis in a private zoological park prompted a cross-sectional prevalence study in two zoological collections. The study demonstrated a high prevalence of P. multocida carriage in clinically healthy red-necked wallabies. In one collection (n= 7), P. multocida was isolated from the gingival mucosa of two animals (28.6%) and the conjunctiva of one animal (14.3%). In another collection (n = 29), P. multocida was isolated from the buccal mucosa in two animals (6.9%) and the pharyngeal mucosa of eight animals (27.6%). Multilocus sequence typing showed that sequence types varied among, but were identical within, collections.

Multilocus sequence analysis of Pasteurella multocida demonstrates a type species under development

The aim of the present study was to use multilocus sequence typing (MLST) of a diverse collection of Pasteurella multocida with regard to animal source, place and date of collection, including all available serovars of Carter, Heddleston, Little & Lyon, Namioka, Cornelius and Roberts, to further investigate the evolution of this species with a focus on two lineages, A (P. multocida subsp. multocida and P. multocida subsp. gallicida) and B (P. multocida subsp. septica), previously reported. Isolates of P. multocida (n = 116) including reference strains of major serotyping systems were investigated by MLST based on partial sequences of the genes adk, est, gdh, mdh, pgi, pmi and zwf, and 67 sequence types (STs) were observed. Phylogenetic analysis of these concatenated sequences confirmed the separation of groups A (41 STs, 71 isolates) and B (22 STs, 38 isolates) out of the 67 STs. All Carter serovars, 12 Heddleston serovars, all three Little-Lyon types, six out of seven Namioka serovars, all five Roberts types and all four Cornelius serovars were allocated to the A group, while group B included the remaining four Heddleston serovars, 6, 7, 8 and 13, in addition to Namioka type 8 : A. The overrepresentation of reference strains of serotyping systems in the A group contrasts with the high number of isolates obtained from diseased birds in the B group, the effect of which should be addressed in future vaccine development. Isolates from birds (25) dominated the B group, which also included four isolates from Felidae, whereas group A included isolates from all types of hosts. The evolutionary implications of the lack of capsular type D, pig and bovine isolates in group B, as well as its association with Aves and Felidae that also applied to the whole Rural Industries Research and Development Corporation (RIRDC) MLST database, need further investigation. The combination of rpoB and 16S rRNA gene sequence comparison as well as the developed PCR test assigned isolates to lineage A, represented by the type strain of P. multocida subsp. Multocida, or lineage B represented by the type strain of P. multocida subsp. septica. It was not possible to circumscribe either the A or B lineages with a set of conserved phenotypic characters, calling into question the validity of subspecies within P. multocida. Phylogenetic analysis carried out on individual MLST genes showed deviations as to single or multiple genes for 17 % of group A and 43 % of group B, indicating that lineage A probably developed from lineage B, and that major changes are ongoing. From a genotypical point of view, we conclude that P. multocida subsp. gallicida represents an artificial unit.

A major outbreak of Streptococcus equi subsp. zooepidemicus infections in free-range chickens is linked to horses

Infections of poultry due to Streptococcus equi subsp. zooepidemicus have been rare during the past decades and dissimilarities have been reported as to symptoms and lesions; likewise, the source of serious outbreaks has remained speculative. An outbreak affecting 11,000 free-range chickens at the age of 47 wk is reported. The outbreak manifested itself as acute at the onset and was followed by a chronic stage, resulting in some 80% mortality within 21 wk. Small-colony variants (SCVs) of S. equi subsp. zooepidemicus associated with the chronic phase are reported for the first time, and it is discussed whether SCVs might explain the change in lesions observed. Comparison of partial sequences of rpoB, multilocus sequence typing, and pulsed-field gel electrophoresis of isolates from chickens and horses kept at the farm showed the isolates to be identical and horses a likely source of infection. The present findings underline the importance of protecting free-range chickens from contact with other animals and birds known to host pathogens of importance to poultry.

Otariodibacter oris gen. nov., sp. nov., a member of the family Pasteurellaceae isolated from the oral cavity of pinnipeds

A total of 27 bacterial isolates from California sea lions and a walrus tentatively classified within the family Pasteurellaceae was further characterized by genotypic and phenotypic tests. Phylogenetic analysis of partial 16S rRNA and rpoB gene sequences showed that the isolates investigated formed a monophyletic group, tentatively designated Bisgaard taxon 57. According to 16S rRNA gene sequences, the most closely related species with a validly published name was Bisgaardia hudsonensis and the most closely related species based on rpoB sequence comparison was Pasteurella multocida subsp. multocida; highest similarities between the isolates and the type strains of B. hudsonensis and P. multocida subsp. multocida were 95.0 and 88.2%. respectively. All isolates of Bisgaard taxon 57 exhibit the phenotypic characters of the family Pasteurellaceae . Members of Bisgaard taxon 57 can be separated from existing genera of the Pasteurellaceae by the following tests: positive reactions for catalase, oxidase, Voges–Proskauer and indole; no X- or V-factor dependency; and acid production from l-arabinose (slow), l-fucose, maltose and trehalose, but not from dulcitol, d-mannitol, d-mannose or sucrose. The main fatty acids of Bisgaard taxon 57 (CCUG 59994T) are C14 : 0, C16 : 0, C16 : 1ω7c and the summed feature C14 : 0 3-OH/iso-C16 : 1 I. This fatty acid profile is characteristic of members of the Pasteurellaceae . The quinone profile of Bisgaard taxon 57 (DSM 23800T) was similar to that of other genera in the Pasteurellaceae . The DNA G+C content of strain Baika1T is 36.2 mol%, which is at the lower end of the range for members of the family Pasteurellaceae . On the basis of both phylogenetic and phenotypic evidence, it is proposed that members of Bisgaard taxon 57 should be classified as representatives of a novel species in a new genus, Otariodibacter oris gen. nov., sp. nov. The type strain of Otariodibacter oris is Baika1T ( = CCUG 59994T = DSM 23800T), which was isolated from the oral cavity of a healthy California sea lion in Copenhagen Zoo, Denmark, in 2007.

Occurrence and characteristics of extended-spectrum β-lactamase (ESBL) producing Enterobacteriaceae in food producing animals, minced meat and raw milk

Background

The impact of food animals as a possible reservoir for extended-spectrum beta-lactamase (ESBL) producing Enterobacteriaceae, and the dissemination of such strains into the food production chain need to be assessed. In this study 334 fecal samples from pigs, cattle, chicken and sheep were investigated at slaughter. Additionally, 100 raw milk samples, representing bulk tank milk of 100 different dairy farms, 104 minced meat (pork and beef) samples and 67 E. coli isolates from cattle E. coli mastitis were analyzed.

Results

As many as 15.3% of the porcine, 13.7% of the bovine, 8.6% of the sheep and 63.4% of the chicken fecal samples yielded ESBL producers after an enrichment step. In contrast, none of the minced meat, none of the bulk tank milk samples and only one of the mastitis milk samples contained ESBL producing strains. Of the total of 91 isolates, 89 were E. coli, one was Citrobacter youngae and one was Enterobacter cloacae. PCR analysis revealed that 78 isolates (85.7%) produced CTX-M group 1 ESBLs while six isolates (6.6%) produced CTX-M group 9 enzymes. Five detected ESBLs (5.5%) belonged to the SHV group and 2 isolates (2.2%) contained a TEM-type enzyme. A total of 27 CTX-M producers were additionally PCR-positive for TEM-beta-lactamase. The ESBL-encoding genes of 53 isolates were sequenced of which 34 produced CTX-M-1, 6 produced CTX-M-14, 5 produced CTX-M-15 and also 5 produced SHV-12. Two isolates produced TEM-52 and one isolate expressed a novel CTX-M group 1 ESBL, CTX-M-117. One isolate--aside from a CTX-M ESBL-- contained an additional novel TEM-type broad-spectrum beta-lactamase, TEM-186.

Conclusions

The relatively high rates of ESBL producers in food animals and the high genetic diversity among these isolates are worrisome and indicate an established reservoir in farm animals.

Identification of animal Pasteurellaceae by MALDI-TOF mass spectrometry

Species of the family Pasteurellaceae play an important role as primary or opportunistic animal pathogens. In veterinary diagnostic laboratories identification of this group of bacteria is mainly done by phenotypic assays while genetic identification based on housekeeping genes is mostly used for research and particularly important diagnostic samples. MALDI-TOF MS seems to represent a promising alternative to the currently practiced cumbersome, phenotypic diagnostics carried out in many veterinary diagnostic laboratories. We therefore assessed its application for animal associated members of the family Pasteurellaceae. The Bruker Biotyper 3.0 database was complemented with reference spectra of clinically relevant as well as commensal animal Pasteurellaceae species using generally five strains per species or subspecies and tested for its diagnostic potential with additional, well characterized field isolates. About 250 strains comprising 15 genera and more than 40 species and subspecies were included in the study, covering most representatives of the family. A high discrimination at the genus and species level was observed. Problematic discrimination was only observed with some closely related species and subspecies. MALDI-TOF MS was shown to represent a highly potent method for the diagnosis of this group of animal pathogens, combining speed, precision and low running costs.

Classification of avian haemolytic Actinobacillus-like organisms (Bisgaard taxon 26) associated with anseriforme birds as Actinobacillus anseriformium sp. nov

Avian haemolytic Actinobacillus-like organisms have tentatively been named Bisgaard taxon 26. Phenotypic information has been published on 65 strains of this taxon. In the current study, 31 isolates were selected for genotypic characterization. Thirty strains had the same rpoB sequence and only one strain diverged in 1 nt. The highest rpoB similarity to members of other taxa was 89.7 % to the type strain of Actinobacillus equuli subsp. haemolyticus and the similarity to the type strain of the type species, Actinobacillus lignieresii, was 88.2 %. The lowest 16S rRNA gene sequence similarity between strains of the group was determined in previous investigations to be 99.6 % and the highest similarities of 96.4 and 96.2 % outside the group were obtained to the reference strain of Actinobacillus genomospecies 2 and to the type strain of A. equuli subsp. equuli, respectively; 95.8–95.3 % similarity was obtained with the type strain of A. lignieresii. recN gene sequence similarities within the group were from 99.5 % (strains F66T and F64) to 99.8 % (strains F66T and F67) corresponding to genome similarities of 93.9–94.6 %, which are near the upper limit for species compared with other members of the Pasteurellaceae. The highest recN similarity outside the group (83.4 %) was observed to the type strain of Actinobacillus capsulatus, whereas the similarity to the type strain of A. lignieresii was 80.9 %, corresponding to genome similarities of 57.7 and 52.0 %, respectively. All isolates meet the phenotypic characters outlined for Actinobacillus (urease-, phosphatase- and porphyrin-positive, indole-negative, acid production from fructose, sucrose, maltose and dextrin). β-Haemolysis of bovine blood is observed and isolates may demonstrate in vitro satellitic growth, referred to as V-factor or NAD requirement. Isolates have been obtained from the upper respiratory tract of web-footed birds in which they may cause sinusitis, conjunctivitis and septicaemia. Based on the characterization reported, it is proposed that the isolates belong to a novel species, Actinobacillus anseriformium sp. nov., which includes taxon 26 and a V-factor-dependent strain. The major fatty acids of the type strain are C16 : 1ω7c, C14 : 0, C16 : 0 and C14 : 0 3-OH and/or iso-C16 : 1 I, corresponding to the profile observed for the type strain of A. lignieresii. Five to 12 characters separate A. anseriformium from other taxa of Actinobacillus, with Actinobacillus ureae being most closely related; A. anseriformium can be differentiated from A. ureae based on haemolysis, β-glucosidase, and production of acid from (−)-d-sorbitol, trehalose and glycosides. The type strain of A. anseriformium is F66T ( = CCUG 60324T = CCM 7846T), which was isolated from conjunctivitis in a White Pekin duck.

A new variant of Actinobacillus pleuropneumoniae serotype 3 lacking the entire apxII operon

Actinobacillus pleuropneumoniae is an important respiratory pathogen causing pleuropneumonia in pig. The species is genetically characterized by the presence of 4 RTX (Repeats in the Structural ToXin) toxin genes: apxI, apxII, and apxIII genes are differentially present in various combinations among the different serotypes, thereby defining pathogenicity; the apxIV gene is present in all serotypes. Polymerase chain reaction (PCR)-based apx gene typing is done in many veterinary diagnostic laboratories, especially reference laboratories. The present report describes the isolation of atypical A. pleuropneumoniae from 4 independent cases from 2 countries. All isolates were beta-nicotinamide adenine dinucleotide (β-NAD) dependent and nonhemolytic but showed strong co-hemolysis with the sphingomyelinase of Staphylococcus aureus on sheep blood agar. Classical biochemical tests as well as Matrix-assisted laser desorption ionization time-of-flight mass spectrometry and sequence-based analysis (16S ribosomal RNA [rRNA] and rpoB genes) identified them as A. pleuropneumoniae. Apx-toxin gene typing using 2 different PCR systems showed the presence of apxIV and only the apxIII operon (apxIIICABD). None of the apxI or apxII genes were present as confirmed by Southern blot analysis. The 16S rRNA and rpoB gene analyses as well as serotype-specific PCR indicate that the isolates are variants of serotype 3. Strains harboring only apxIV and the apxIII operon are possibly emerging types of A. pleuropneumoniae and should therefore be carefully monitored for epidemiological reasons.

Proposal of Bisgaardia hudsonensis gen. nov., sp. nov. and an additional genomospecies, isolated from seals, as new members of the family Pasteurellaceae

Phenotypic and phylogenetic studies were performed on eight Gram-negative-staining, rod-shaped bacteria isolated from seals. Biochemical and physiological studies showed identical profiles for all of the isolates and indicated that they were related to the family Pasteurellaceae. 16S rRNA gene sequencing demonstrated that the organism represented a distinct cluster with two sublines within the family Pasteurellaceae with <96 % sequence similarity to any recognized species. Multilocus sequence analysis (MLSA) including rpoB, infB and recN genes further confirmed these findings with the eight isolates forming a genus-like cluster with two branches. Genome relatedness as deduced from recN gene sequences suggested that the isolates represented a new genus with two species. On the basis of the results of the phylogenetic analysis and phenotypic criteria, it is proposed that these bacteria from seals are classified as Bisgaardia hudsonensis gen. nov., sp. nov. (the type species) and Bisgaardia genomospecies 1. The G+C content of the DNA was 39.5 mol%. The type strain of Bisgaardia hudsonensis gen. nov., sp. nov. is M327/99/2T ( = CCUG 43067T = NCTC 13475T = 98-D-690BT) and the reference strain of Bisgaardia genomospecies 1 is M1765/96/5 ( = CCUG 59551 = NCTC 13474).

Classification of Pasteurella species B as Pasteurella oralis sp. nov

Pasteurella species B has so far only been reported from the oral cavity of dogs, cats and a ferret. In the present study, information from 15 recent isolates from different sources, including African hedgehogs (Atelerix albiventris), banded mongoose (Mungos mungo), Moholi bushbabies (Galago moholi) and pneumonia of a cat, were compared to five strains investigated previously from bite wounds in humans inflicted by a cat and dog and from gingiva of a cat. rpoB gene sequence comparison showed that 17 isolates, including the reference strain (CCUG 19794(T)), had identical sequences, whereas two were closely related and demonstrated 97.9 and 99.6 % similarity to strain CCUG 19794(T), respectively; the type strain of Pasteurella stomatis was the most closely related strain, with 92.3 % similarity. This is within the mean range (76-100 %) of rpoB gene sequence similarity between species of the same genus within the family Pasteurellaceae. 16S rRNA gene sequencing of four strains selected based on rpoB sequence comparison showed at least 99.7 % similarity between strains of Pasteurella species B, with 96.2 % similarity to the type strain of the closest related species (Pasteurella canis), indicating that Pasteurella species B should have separate species status. Separate species status was also documented when recN sequence comparisons were converted to a genome similarity of 93.7 % within Pasteurella species B and 59.0 % to the type strain of the closest related species (P. canis). Based on analysis of the phylogenetic and phenotypic data, and since most isolates originate from the oral cavities of a diverse group of animals, it is suggested that these bacteria be classified as Pasteurella oralis sp. nov.; the type strain is P683(T) ( = CCUG 19794(T) = CCM 7950(T) = strain 23193(T) = MCCM 00102(T)), obtained from a cat. Previous reports of the type strain have shown ubiquinone-8, demethylmenaquinone-8 and menaquinone-8 as the major quinones. Polyamines in the type strain were reported as diaminopropane, putrescine, cadaverine, sym-norspermidine, spermidine and spermine in a previous investigation, and the major fatty acids of the type strain were reported to be C(16:0), C(16:1)ω7c and C(14:0), with minor amounts of C(18:0) and C(18:1)ω9c. The DNA G+C content of the type strain has been reported to be 40.0 mol%.

Classification of organisms previously reported as the SP and Stewart–Letscher groups, with descriptions of Necropsobacter gen. nov. and of Necropsobacter rosorum sp. nov. for organisms of the SP group

To allow classification of bacteria previously reported as the SP group and the Stewart–Letscher group, 35 isolates from rodents (21), rabbits (eight), a dog and humans (five) were phenotypically and genotypically characterized. Comparison of partial rpoB sequences showed that 34 of the isolates were closely related, demonstrating at least 97.4 % similarity. 16S rRNA gene sequence comparison of 20 selected isolates confirmed the monophyly of the SP group and revealed 98.5 %–100 % similarity between isolates. A blast search using the 16S rRNA gene sequences showed that the highest similarity outside the SP group was 95.5 % to an unclassified rat isolate. The single strain, P625, representing the Stewart–Letscher group showed the highest 16S rRNA gene similarity (94.9–95.5 %) to members of the SP group. recN gene sequence analysis of 11 representative strains resulted in similarities of 97–100 % among the SP group strains, which showed 80 % sequence similarity to the Stewart–Letscher group strain. Sequence similarity values based on the recN gene, indicative for whole genome similarity, showed the SP group being clearly separated from established genera, whereas the Stewart–Letscher group strain was associated with the SP group. A new genus, Necropsobacter gen. nov., with only one species, Necropsobacter rosorum sp. nov., is proposed to include all members of the SP group. The new genus can be separated from existing genera of the family Pasteurellaceae by at least three phenotypic characters. The most characteristic properties of the new genus are that haemolysis is not observed on bovine blood agar, positive reactions are observed in the porphyrin test, acid is produced from (+)-l-arabinose, (+)-d-xylose, dulcitol, (+)-d-galactose, (+)-d-mannose, maltose and melibiose, and negative reactions are observed for symbiotic growth, urease, ornithine decarboxylase and indole. Previous publications have documented that both ubiquinones and demethylmenaquinone were produced by the proposed type strain of the new genus, Michel A/76T, and that the major polyamine of representative strains (type strain not included) of the genus is 1,3-diaminopropane, spermidine is present in moderate amounts and putrescine and spermine are detectable only in minor amounts. The major fatty acids of strain Michel A/76T are C14 : 0, C16 : 0, C16:1ω7c and summed feature C14 : 0 3-OH/iso-C16 : 1 I. This fatty acid profile is typical for members of the family Pasteurellaceae. The G+C content of DNA of strain Michel A/76T was estimated to be 52.5 mol% in a previous investigation. The type strain is P709T ( = Michel A/76T  = CCUG 28028T  = CIP 110147T  = CCM 7802T).