Genotypic relationships among strains classified under the (Pasteurella) haemolytica-complex as indicated by ribotyping and multilocus enzyme electrophoresis

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.

Prevalence of Mannheimia haemolytica in Syrian Awassi sheep

The aim of the present study was to evaluate the prevalence of Mannheimia haemolytica in Syrian Awassi sheep. Between 2008 and 2012, 1520 nasal swabs from pneumonic and apparently healthy sheep, and 110 pneumonic lungs samples were collected and subjected to bacteriological, biochemical and PCR assays. A total of 191 isolates (11.7%) were identified as M. haemolytica, 44 (2.7%) were M. ruminalis and 18 (1.1%) were M. glucosida. All 191 isolates of M. haemolytica gave an amplified product of 1146 bp size by PCR when lktaA primer was applied. The highest rate of M. haemolytica isolation was from pneumonic lungs tissue (21.8%) and pneumonic sheep (14.1%), and the lowest was from apparently healthy sheep (8.5%). Geographical and seasonal distribution of M. haemolytica showed that the majority of the isolates originated from sheep reared in the Syrian Desert (30%) and Euphrates basin (26.7%), and a significant increase (P≤0.05) in the rate of positive isolates in summer and winter as compared to spring. These findings indicate that M. haemolytica may play an important role in development of pneumonia in Syrian Awassi sheep, especially in eastern parts of Syria, where drought and shortage of rain hit these zones periodically.

Analysis of gene order data supports vertical inheritance of the leukotoxin operon and genome rearrangements in the 5' flanking region in genus Mannheimia

Background

The Mannheimia subclades belong to the same bacterial genus, but have taken divergent paths toward their distinct lifestyles. For example, M. haemolytica + M. glucosida are potential pathogens of the respiratory tract in the mammalian suborder Ruminantia, whereas M. ruminalis, the supposed sister group, lives as a commensal in the ovine rumen. We have tested the hypothesis that vertical inheritance of the leukotoxin (lktCABD) operon has occurred from the last common ancestor of genus Mannheimia to any ancestor of the diverging subclades by exploring gene order data.

Results

We examined the gene order in the 5' flanking region of the leukotoxin operon and found that the 5' flanking gene strings, hslVU-lapB-artJ-lktC and xylAB-lktC, are peculiar to M. haemolytica + M. glucosida and M. granulomatis, respectively, whereas the gene string hslVU-lapB-lktC is present in M. ruminalis, the supposed sister group of M. haemolytica + M. glucosida, and in the most ancient subclade M. varigena. In M. granulomatis, we found remnants of the gene string hslVU-lapB-lktC in the xylB-lktC intergenic region.

Conclusion

These observations indicate that the gene string hslVU-lapB-lktC is more ancient than the hslVU-lapB-artJ-lktC and xylAB-lktC gene strings. The presence of (remnants of) the ancient gene string hslVU-lapB-lktC among any subclades within genus Mannheimia supports that it has been vertically inherited from the last common ancestor of genus Mannheimia to any ancestor of the diverging subclades, thus reaffirming the hypothesis of vertical inheritance of the leukotoxin operon. The presence of individual 5' flanking regions in M. haemolytica + M. glucosida and M. granulomatis reflects later genome rearrangements within each subclade. The evolution of the novel 5' flanking region in M. haemolytica + M. glucosida resulted in transcriptional coupling between the divergently arranged artJ and lkt promoters. We propose that the chimeric promoter have led to high level expression of the leukotoxin operon which could explain the increased potential of certain M. haemolytica + M. glucosida strains to cause a particular type of infection.

Evidence for Vertical Inheritance and Loss of the Leukotoxin Operon in Genus Mannheimia

The Mannheimia subclades belong to the same bacterial genus but have taken divergent paths toward their distinct lifestyles. M. haemolytica + M. glucosida are potential pathogens of the respiratory tract in the mammalian suborder Ruminantia, whereas M. ruminalis, the supposed sister group, lives as a commensal in the ovine rumen. We have tested the hypothesis that horizontal gene transfer of the leukotoxin operon has catalyzed pathogenic adaptation and speciation of M. haemolytica + M. glucosida, or other major subclades, by using a strategy that combines compositional and phylogenetic methods. We show that it has been vertically inherited from the last common ancestor of the diverging Mannheimia subclades, although several strains belonging to M. ruminalis have lost the operon. Our analyses support that divergence within M. ruminalis following colonization of the ovine rumen was very rapid and that functional decay of most of the leukotoxin operons occurred early when the adaptation to the rumen was fastest, suggesting that antagonistic pleiotropy was the main contributor to losses in the radiating lineages of M. ruminalis. To sum up, the scenario derived from these analyses reflects two aspects. On one hand, it opposes the hypothesis of horizontal gene transfer as a catalyst of pathogenic adaptation and speciation. On the other hand, it indicates that losses of the leukotoxin operons in the radiating lineages of M. ruminalis have catalyzed their adaptation to a commensal environment and reproductive isolation (speciation).

Proposed minimal standards for the description of genera, species and subspecies of the Pasteurellaceae

Principles and guidelines are presented to ensure a solid scientific standard of papers dealing with the taxonomy of taxa of Pasteurellaceae Pohl 1981. The classification of the Pasteurellaceae is in principle based on a polyphasic approach. DNA sequencing of certain genes is very important for defining the borders of a taxon. However, the characteristics that are common to all members of the taxon and which might be helpful for separating it from related taxa must also be identified. Descriptions have to be based on as many strains as possible (inclusion of at least five strains is highly desirable), representing different sources with respect to geography and ecology, to allow proper characterization both phenotypically and genotypically, to establish the extent of diversity of the cluster to be named. A genus must be monophyletic based on 16S rRNA gene sequence-based phylogenetic analysis. Only in very rare cases is it acceptable that monophyly can not be achieved by 16S rRNA gene sequence comparison. Recently, the monophyly of genera has been confirmed by sequence comparison of housekeeping genes. In principle, a new genus should be recognized by a distinct phenotype, and characters that separate the new genus from its neighbours should be given clearly. Due to the overall importance of accurate classification of species, at least two genotypic methods are needed to show coherence and for separation at the species level. The main criterion for the classification of a novel species is that it forms a monophyletic group based on 16S rRNA gene sequence-based phylogenetic analysis. However, some groups might also include closely related species. In these cases, more sensitive tools for genetic recognition of species should be applied, such as DNA-DNA hybridizations. The comparison of housekeeping gene sequences has recently been used for genotypic definition of species. In order to separate species, phenotypic characters must also be identified to recognize them, and at least two phenotypic differences from existing species should be identified if possible. We recommend the use of the subspecies category only for subgroups associated with disease or similar biological characteristics. At the subspecies level, the genotypic groups must always be nested within the boundaries of an existing species. Phenotypic cohesion must be documented at the subspecies level and separation between subspecies and related species must be fully documented, as well as association with particular disease and host. An overview of methods previously used to characterize isolates of the Pasteurellaceae has been given. Genotypic and phenotypic methods are separated in relation to tests for investigating diversity and cohesion and to separate taxa at the level of genus as well as species and subspecies.

Serological and molecular comparison of Mannheimia haemolytica and Pasteurella trehalosi strains isolated from wild and domestic ruminants in the French Alps

Over a period of 17 years, 84 bacterial isolates identified as Mannheimia haemolytica or M. glucosida, and 52 isolates identified as Pasteurella trehalosi were detected in the lungs of domestic and wild ruminants in the French Alps. The isolates were serotyped according to their surface capsular antigens, and those sharing common antigens were further characterized by pulsed field gel electrophoresis. The results showed that the bacterial isolates included in the study clustered according to the host species from which they were isolated. These findings indicate that the transmission of serotypes of M. haemolytica, M. glucosida or P. trehalosi from an animal host in which they are common to another species sharing the same geographical space may be a rare epidemiological event.

Phenotypic and genotypic characterization of Mannheimia (Pasteurella) haemolytica-like strains isolated from diseased animals in Denmark

Trehalose-negative strains of the Pasteurella haemolytica complex have recently been transferred to a new genus, Mannheimia. This genus presently consists of five named species: M. haemolytica, M. glucosida, M. granulomatis, M. ruminalis and M. varigena. The purpose of this study was to investigate the occurrence of these species and lesions associated with these isolates in Denmark. In all 106 M. haemolytica-like strains isolated from pathological material from cattle, sheep, pigs and hares submitted to the Danish Veterinary Laboratory between 1994 and 1998 were investigated. Phenotypic characterization and ribotyping were used for identification in addition to sequencing of the 16S rRNA genes for selected strains. The species allocation was determined by comparison to results from a previous polyphasic taxonomic study. Seventy-one percent of the strains belonged to M. haemolytica, 18% to M. varigena and 8% to unnamed groups within the genus Mannheimia. Single isolates identified as M. glucosida and P. trehalosi, respectively, were detected. Two isolates belonged to M. granulomatis. Forty-three percent of the strains belonged to serotype 1, 41% were untypeable, while the rest belonged to serotypes 2, 7, 9, and 16. The present investigation also showed that a simplified phenotypic characterization using Diatabs Diagnostic Tablets (Rosco, Denmark) represents a useful method for obtaining a quick and reliable species identification. Finally, the investigation confirmed that serotyping does not represent a reliable method for species identification. The heterogeneity of species associated with bovine "pasteurellosis" should be considered in future studies to improve our understanding of the pathogenesis of pneumonic disease.

Subspecies characterization of porcine Campylobacter coli and Campylobacter jejuni by multilocus enzyme electrophoresis typing

Enteropathogenic Campylobacterjejuni, C. coli and C. lari are currently the most common causes of acute infectious diarrhoeal illness in the UK. Many domestic animals, including pigs, act as natural reservoirs of these organisms and infection may occur through the ingestion of contaminated foodstuffs. C jejuni and C. coli, isolated from the livers of bacon pigs, were examined at subspecies level by multilocus enzyme electrophoresis (MEE) typing with seven enzymic loci. Polymorphological variation was highest with indophenol oxidase, isocitrate dehydrogenase and L-phenylalanyl-L-leucine peptidase giving 5. 5 and 4 alleles at these loci, respectively. The 35 Campylobacter isolates examined in this study (12 C. jejuni and 23 C coli) represented 30 unique electrophoretic types (ETs). Of these ETs, 8 unique types were detected for the 12 C jejuni isolates and 19 unique ETs were detected for the 23 C coli isolates. In addition, 3 types (ETs 2, 5, 10) were shared in common among C. jejuni and C coli. The average number of alleles per enzyme locus was 3.28. The mean genetic diversity, i.e. arithmetic average over all loci assayed, including monomorphic values, was 0.5573 and 0.5350 for C jejuni and C coli. respectively. Alleles were shared by C jejuni and C coli, suggesting an exchange of genetic material between the species. MEE analyses of isolates showed that there was a wide range of subspecies types within both C. jejuni and C coli in porcine livers. In certain cases, up to four phenotypically different strains of C coli were isolated from one liver, indicating multiple infections.

Genetic diversity of Pasteurella multocida fowl cholera isolates as demonstrated by ribotyping and 16S rRNA and partial atpD sequence comparisons

The genetic diversity of Pasteurella multocida, the aetiological agent of fowl cholera, was investigated. The strain collection comprised 69 clinical isolates representing a wide spectrum of hosts and geographic origin. The three type strains for the subspecies of P. multocida were also included. Avian isolates of P. multocida subsp. multocida and P. multocida subsp. septica did not represent separate lines by HpaII ribotyping and the two type strains of mammalian origin (porcine and cat bite) seemed to be representative of avian strains of P. multocida subspp. multocida and septica. By ribotyping, all P. multocida subsp. gallicida strains, except one chicken isolate and the type strain, clustered together. This indicated that the bovine type strain was not representative of this subspecies and that most strains of P. multocida subsp. gallicida are genetically related and may be distantly related to other P. multocida isolates, including those of avian origin. By 16S rRNA and atpD sequence comparisons of selected strains, including both P. multocida isolated from birds and mammals and selected distantly related Pasteurella species associated with birds and mammals, it was found that P. multocida is monophyletic. Extended DNA-DNA hybridizations are highly indicated since strains may exist which would connect the existing subspecies at species level. The considerable genetic diversity of P. multocida fowl cholera isolates is probably related to the clonal nature of this organism, resulting in many divergent lines.

Characterisation of a novel Mannheimia sp from Australian feedlot cattle

OBJECTIVE

To characterise eight isolates of a Gram-negative organism obtained from the upper respiratory tract of cattle showing evidence of mild upper respiratory tract disease.

DESIGN

The isolates were compared with the five recognised species within the genus Mannheimia - M haemolytica, M glucosida, M granulomatis, M ruminalis and M varigena--using a range of phenotypic and genotypic methods.

RESULTS

Phenotypic characterisation indicated that the isolates belonged to the trehalose-negative [Pasteurella] haemolytica complex. This complex has recently been reorganised into five species within the new genus Mannheimia. Ribotyping performed using HindIII and a computerised analysis system indicated that the eight Australian isolates formed a distinct cluster that was related to, but different from, the five recognised species of Mannheimia. The 16S rRNA sequence of one isolate (BNO311) was determined and a phylogenetic analysis performed. Isolate BNO311 was distinct from the five named Mannheimia spp but did join a larger cluster consisting of rRNA cluster IV (M varigena) and the unnamed rRNA cluster V of Mannheimia. DNA:DNA hybridisation between isolate BNO311 and M haemolytica NCTC 9380T, M granulomatis P411 and Actinobacillus ligniersii NCTC 4189T all suggested similarities of approximately 30%.

CONCLUSIONS

These phenotypic and genotypic characterisation studies suggest that the eight Australian isolates represent a new species of Mannheimia. Until further characterisation studies are performed, we are unwilling to propose a name for this taxon, preferring to refer to this possible new species as Bisgaard taxon 39 of cluster V of Mannheimia.

Investigations on the species specificity of Mannheimia (Pasteurella) haemolytica serotyping

Eleven serotypes (1, 2, 5-9, 12-14 and 16) have been demonstrated within Mannheimia haemolytica. Subsequent serotyping of 166 Mannheimia haemolytica-like strains, genetically and phenotyphically distinct from Mannheimia haemolytica, and isolated from ruminants, pigs, hares and rabbits showed that 13.2% were typeable, 19 of which were serotype 11 representing strains now being classified as M. glucosida. In addition, three strains belonged to serotypes 6, 9 and 16, respectively. Additionally, the serotyping results of 98 (P.) haemolytica-like isolates from non-ruminant sources collected by the UK Veterinary Investigation Centres during the period 1982-1996 were investigated. None of these isolates have been kept, making further genetic characterization impossible. Among these isolates, 25.5% were typeable representing serotypes 1, 2, 3, 5, 6, 9, 10, 13 and 15. Substantial evidence has been reported indicating that M. haemolytica-like isolates from non-ruminant sources represent species different from M. haemolytica. The present investigation underlines that serotyping does not represent a reliable method for the identification of M. haemolytica or M. glucosida. These observations emphasize that extended phenotypic and genetic characterization is necessary for the proper identification of these organisms.

Phenotypic and genotypic diversity of organisms previously classified as maltose positive Pasteurella multocida

Fifteen isolates tentatively classified as maltose positive Pasteurella multocida have been characterized in 79 biochemical tests and by ribotyping using HindIII and HpaII for digestion of DNA. Phenotypic and genotypic results were analysed using the computer programmes NTSYS and GelCompar, respectively. Two strains were classified as maltose positive P. multocida ssp. multocida while six strains were classified as maltose positive P. multocida ssp. septica. The remaining strains clustered with P. volantium and P. gallinarum, but remained unclassified. With the exception of a single isolate correlation was observed between phenotypic and genotypic results. The unclassified isolates which represented three different sources were heterogenous according to both phenotypic and genotypic results. The findings obtained support the 16S rRNA sequencing results indicating that the genus Pasteurella sensu stricto might represent two or more genera.

Diversity among isolates of Actinobacillus equuli and related organisms as revealed by ribotyping

OBJECTIVE

The objective of this work was to examine the diversity within Australian isolates of Actinobacillus equuli and related organisms by the genotypic method of ribotyping.

DESIGN

Ribotyping, performed using the enzyme HaeIII, was used to examine the diversity in 12 field isolates of A equuli (five being capable of fermenting L-arabinose), one field isolate of Pasteurella caballi and two unclassifiable field isolates. Isolates were obtained from Australian horses, except for three isolates of A equuli (one L-arabinose positive and two L-arabinose negative) which were obtained from horses and a pig in Africa. In addition, the type strains for A equuli and P caballi and a reference strain for Bisgaard Taxon 9 were included in the study.

RESULTS

The ribotype patterns were analysed by computerised cluster analysis, yielding five clusters (A to E). All five of the L-arabinose positive A equuli were assigned to cluster A, with all the other seven A equuli isolates (all L-arabinose negative) and the type strain being assigned to cluster B. One of the two unclassified isolates formed cluster C along with the reference strain for Bisgaard Taxon 9. The remaining unclassified isolate formed cluster D. Cluster E consisted of the field isolate and reference strain of P caballi.

CONCLUSION

The results of this study indicate that A equuli is a diverse species, with L-arabinose positive isolates of A equuli being quite distinct from typical L-arabinose negative isolates. Ribotyping appears to be a useful tool in confirming the identity of A equuli-like organisms from horses.