Rapid and accurate identification of human isolates of Pasteurella and related species by sequencing the sodA gene

Pasteurella canis soft tissue infection after a cat bite - A case report

Pasteurella canis is a Gram-negative facultative anaerobic bacterium that is a typical commensal of the oral cavity and enteric tract of domestic animals. Human infections caused by this species are most often associated with dog bites and rarely with other animal bites. In this report, we present a case of a 34-year-old man who developed P. canis soft tissue infection of the left hand after a cat bite. The patient was successfully treated by a surgical intervention and antibiotics. The species identification of the isolate was performed by a conventional automatic system and nucleic acid-based methods. The nucleic acid-based methods provide a powerful alternative to the conventional microbiological diagnostic of these bacteria.

Biotypic and genotypic diversity in Pasteurella canis isolated from host animals and humans: differences in trehalose fermentation and nucleotide sequences encoding trehalose-6-phosphate hydrolase (treC)

The biotypic and genotypic features of Pasteurella canis isolated from dogs, cats, and humans were clarified by repetitive sequence-based fingerprinting and nucleotide sequences encoding trehalose-6-phosphate hydrolase (treC). Thirty P. canis and 48 P. multocida isolates were collected from dogs, cats, and humans to perform biotyping. The genotyping of P. canis by fingerprinting was followed by dendrogram construction. The whole-genome sequences (WGSs) were searched for the enzyme-coding nucleotide sequences around the main and adjacent loci constituting the operon. Full-length nucleotide sequences encoding the enzyme were determined using polymerase chain reaction and direct sequencing. Biotypic results were compared to the dendrogram and nucleotide sequence data. We observed a difference in trehalose fermentation with a positivity rate of 46.7%. Two (A-1/A-2) and three (B-1/B-2/B-3) clades were located on the dendrograms generated based on two repetitive sequence-based fingerprinting techniques, showing no association between trehalose fermentation and the clades. Based on the WGSs, two variants of the gene, namely, a 1,641 bp gene treC and a pseudogene (1,335 bp) of treC with its first 306 nucleotides deleted, were observed. Trehalose-positive isolates harbored treC, whereas trehalose-negative isolates lacked treC with or without the pseudogene. Our observations suggest biotypic and genotypic diversity among the P. canis isolates from animal and human hosts, with respect to trehalose fermentation and treC nucleotide sequences. This is the first report on the diversity of treC nucleotide sequences among these isolates.

Phenotypic and Genotypic Traits of Pasteurella multocida subsp. septica Isolates From the Wounds of Two Patients Due to Dog or Cat Biting, 2023

We describe the phenotypic and genotypic traits of Pasteurella multocida subsp. septica isolates from the dog/cat bite wounds of two patients in 2023. A 79-year-old man with diabetes mellitus and cerebral infarction who was bitten by a dog on his left hand developed deep inflammation under the tendon between his left fourth and fifth fingers. The patient's condition was resolved with antimicrobial treatment and surgical intervention. Another patient, a healthy 49-year-old woman who was bitten by a cat on her left hand, developed superficial inflammation of the left thumb and index finger. The patient's condition improved with antimicrobial treatment without surgical intervention. The isolates from the two patients had similar biochemical properties, and the antimicrobial susceptibility data for both isolates indicated erythromycin resistance. Genotypic analyses revealed clade 2 on the dendrogram of repetitive sequence-based fingerprinting, capsule serogroup cap genotype A, and hsf-1-nanH-pmHAS (virulence-associated genes). Our observations show that the two isolates have similar phenotypic and genotypic traits, regardless of differences in patient background, biting pets, wound inflammation, or the necessity of surgical intervention.

Actinobacillus utilizes a binding protein-dependent ABC transporter to acquire the active form of vitamin B6

Bacteria require high-efficiency uptake systems to survive and proliferate in nutrient-limiting environments, such as those found in host organisms. ABC transporters in the bacterial plasma membrane provide a mechanism for transport of many substrates. In this study, we examine an operon containing a periplasmic binding protein in Actinobacillus for its potential role in nutrient acquisition. The electron density map of 1.76 Å resolution obtained from the crystal structure of the periplasmic binding protein was best fit with a molecular model containing a pyridoxal-5'-phosphate (P5P/pyridoxal phosphate/the active form of vitamin B6) ligand within the protein's binding site. The identity of the P5P bound to this periplasmic binding protein was verified by isothermal titration calorimetry, microscale thermophoresis, and mass spectrometry, leading us to name the protein P5PA and the operon P5PAB. To illustrate the functional utility of this uptake system, we introduced the P5PAB operon from Actinobacillus pleuropneumoniae into an Escherichia coli K-12 strain that was devoid of a key enzyme required for P5P synthesis. The growth of this strain at low levels of P5P supports the functional role of this operon in P5P uptake. This is the first report of a dedicated P5P bacterial uptake system, but through bioinformatics, we discovered homologs mainly within pathogenic representatives of the Pasteurellaceae family, suggesting that this operon exists more widely outside the Actinobacillus genus.

Isolation of Drug-Resistant Gallibacterium anatis from Calves with Unresponsive Bronchopneumonia, Belgium

Gallibacterium anatis is an opportunistic pathogen, previously associated with deaths in poultry, domestic birds, and occasionally humans. We obtained G. anatis isolates from bronchoalveolar lavage samples of 10 calves with bronchopneumonia unresponsive to antimicrobial therapy. Collected isolates were multidrug-resistant to extensively drug-resistant, exhibiting resistance against 5–7 classes of antimicrobial drugs. Whole-genome sequencing revealed 24 different antimicrobial-resistance determinants, including genes not previously described in the Gallibacterium genus or even the Pasteurellaceae family, such as aadA23, bla_CARB-8, tet(Y), and qnrD1. Some resistance genes were closely linked in resistance gene cassettes with either transposases in close proximity or situated on putative mobile elements or predicted plasmids. Single-nucleotide polymorphism genotyping revealed large genetic variation between the G. anatis isolates, including isolates retrieved from the same farm. G. anatis might play a hitherto unrecognized role as a respiratory pathogen and resistance gene reservoir in cattle and has unknown zoonotic potential.

MOLECULAR IDENTIFICATION OF MEMBERS OF THE FAMILY PASTEURELLACEAE FROM THE ORAL CAVITY OF KOALAS (PHASCOLARCTOS CINEREUS) AND THEIR RELATIONSHIP WITH ISOLATES FROM KOALA BITE WOUNDS IN HUMANS

A total of 22 Pasteurellaceae isolates obtained from the oral cavity of koalas (Phascolarctos cinereus) at different wildlife centers in Australia were investigated using amplification and sequencing of two housekeeping genes, rpoA and recN. The available sequences from the Lonepinella koalarum type strain (ACM3666^T) and the recent isolates of Lonepinella-like bacteria obtained from human infected wounds associated with koala bites were also included. Phylogenetic analysis was performed on the concatenated rpoA-recN genes and genome relatedness was calculated based on the recN sequences. The oral cavity isolates, the koala bite wound isolates, and L. koalarum ACM3666T resulted in four clusters (Clusters 1-4). Clusters 1-3 were clearly not members of the genus Lonepinella. Cluster 1 was closely related to the genus Fredericksenia, and Clusters 2 and 3 appeared to be novel genera. Cluster 4 consisted of three subclusters: Cluster 4a with one koala bite wound isolate and L. koalarum ACM3666^T, Cluster 4b with three oral cavity isolates and two Lonepinella-like wound isolates, and Cluster 4c with three nearly identical oral cavity isolates that may represent a different species within the genus Lonepinella. The rich Pasteurellaceae population, including potential novel taxa in the oral cavity of koalas supports an important role of these highly adapted microorganisms in the physiology of koalas. Moreover, the pathogenic potential of Lonepinella-like species is an important consideration when investigating infected koala bites in humans.

A loop-mediated isothermal amplification procedure targeting the sodA gene for rapid and specific identification of Gallibacterium anatis

This paper reports on the development and validation of a real-time loop-mediated isothermal amplification assay (LAMP) for rapid and specific identification of Gallibacterium anatis. To design a set of 6 primers using the LAMP technique, the conserved region of the G. anatis sodA gene was selected as a target. To evaluate primer specificity we used 120 field strains, the reference strain G. anatis ATCC 43329, and 9 non-G. anatis bacteria. The results confirmed positive reactions for all G. anatis strains tested by LAMP at 63°C for 60 min, with no cross-reactivity observed for the negative control bacteria, i.e., Haemophilus parainfluenzae (ATCC 51505 and ATCC 33392), Aggregatibacter aphrophilus ATCC 7901, Avibacterium endocarditis, Pasteurella multocida, Actinobacillus pleuropneumoniae, Avibacterium paragallinarum, Ornithobacterium rhinotracheale, and Escherichia coli. The lowest detectable amount of DNA for the LAMP reaction was 0.2561 pg, which was detected in about 34 min, while the highest available concentration of the G. anatis reference strain was detected in about 10 min. The lowest detectable amount of DNA for the real-time PCR reaction was 21.24 pg, which was detected in about 20 min, while the highest available concentration of the G. anatis reference strain was detected in about 7 min. Moreover, using the real-time LAMP assay the reaction could be effectively carried out in a volume of just 13 μL, about half the officially recommended reaction volume (25 μL). The aim of this study was to develop a highly sensitive and specific G. anatis real-time LAMP assay that is less time-consuming and less costly than quantitative PCR.

Quantification of Pasteurella multocida in experimentally infected pigs using a real-time PCR assay

The aim of the study was to quantify Pasteurella multocida in experimentally infected pigs using a new qPCR assay based on the sodA gene and validated with 35 P. multocida strains, including strains isolated from pigs with pneumonia, clinically healthy pigs (nasal cavities), and human infections. The specificity of the test was verified with a collection of 60 strains of bacterial species other than P. multocida. The estimated detection threshold was 10 genome equivalents per microliter. The amplification efficiency and value of the correlation coefficients were 95.5% (±3.5%) and 0.995 (±0.005), respectively. Analysis of P. multocida suspensions in Buffered Peptone Water Broth and of samples prepared from lungs experimentally spiked with P. multocida revealed detection thresholds of 1.4CFU/μl and 8.4CFU/μl, respectively. In live pigs, experimentally-infected, approximately 10⁵, 10⁷ and 10⁸genomeequivalents/ml of P. multocida DNA was detected on Day 8 post-infection in the nasal cavities, tonsils and trachea samples, respectively. In dead pigs, approximatively 10⁷genomeequivalents/ml of P. multocida DNA was detected in the lung tissue with pneumonia. The qPCR assay's diagnostic specificity and sensitivity were 100% and 96%, respectively. This new qPCR assay should be a very useful tool for controlling enzootic pneumonia and studying the dynamics of infections in pig herds.

Validation of Reference Genes for Real-Time Quantitative PCR (qPCR) Analysis of Avibacterium paragallinarum

Real-time quantitative reverse transcription PCR (qRT-PCR) offers a robust method for measurement of gene expression levels. Selection of reliable reference gene(s) for gene expression study is conducive to reduce variations derived from different amounts of RNA and cDNA, the efficiency of the reverse transcriptase or polymerase enzymes. Until now reference genes identified for other members of the family Pasteurellaceae have not been validated for Avibacterium paragallinarum. The aim of this study was to validate nine reference genes of serovars A, B, and C strains of A. paragallinarum in different growth phase by qRT-PCR. Three of the most widely used statistical algorithms, geNorm, NormFinder and ΔCT method were used to evaluate the expression stability of reference genes. Data analyzed by overall rankings showed that in exponential and stationary phase of serovar A, the most stable reference genes were gyrA and atpD respectively; in exponential and stationary phase of serovar B, the most stable reference genes were atpD and recN respectively; in exponential and stationary phase of serovar C, the most stable reference genes were rpoB and recN respectively. This study provides recommendations for stable endogenous control genes for use in further studies involving measurement of gene expression levels.

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.

Bacterial determinants of importance in the virulence of Gallibacterium anatis in poultry

Gallibacterium anatis, a member of the Pasteurellaceae family, constitute a part of the normal micro-flora of the upper respiratory tract and the lower genital tract in chickens. However, increasing evidence indicate that G. anatis is also associated with a wide range of pathological changes, particularly in the reproductive organs, which leads to decreased egg production, lowered animal welfare and increased mortality. As a recently defined opportunistic pathogen limited focus has been placed on the pathogenesis and putative virulence factors permitting G. anatis to cause disease. One of the most studied virulence determinants is a large RTX-like toxin (GtxA), which has been demonstrated to induce a strong leukotoxic effect on avian macrophages. A number of fimbria of different sizes and shapes has been described. Particularly fimbriae belonging to the F17-like family appears to be common in a diverse selection of G. anatis strains. Mutants lacking the FlfA fimbria were severely attenuated in experimentally infected chickens. Additional characteristics including the ability to express capsular material possibly involved in serum resistance; secretion of metalloproteases capable of degrading immunoglobulins, and hemagglutinins, which may promote biofilm formation are all factors likely linked to the virulence of G. anatis. A major advantage for the study of how G. anatis interact with its host is the ability to perform biologically relevant experimental infections where natural routes of exposure allows reproduction of lesions observed during spontaneous infections. This review summarizes the current understanding of the G. anatis pathogenesis and discusses the contribution of the established and putative virulence factors described for this bacterium to date.

Proposed reclassification of Pasteurella lymphangitidis Sneath & Stevens 1990 as Yersinia pseudotuberculosis

The 16S rRNA gene sequences of Pasteurella lymphangitidis , Yersinia pseudotuberculosis and Yersinia pestis were found to be identical and multilocus sequence analysis could not discriminate between the three species. The susceptibility to a Y. pseudotuberculosis phage and the presence of the Y. pseudotuberculosis -specific invasin gene in P. lymphangitidis indicate that the latter should be reclassified as Y. pseudotuberculosis .

Identification of clinical Pasteurella isolates by MALDI-TOF -- a comparison with VITEK 2 and conventional microbiological methods

The aim of this study was to compare the performance of four methods that are widely used in the clinical microbiology laboratory for identification of Pasteurella species. The 4 methods evaluated were VITEK2, VITEK MS (BioMerieux), and Bruker Biotyper MS (Bruker) as well as traditional biochemical tests. Sequencing of the sodA gene was used as the reference method. Sixty-five isolates of Pasteurella spp. from 65 patients were analyzed. One Pasteurella multocida isolate from American Type Culture Collection (Manassas, VA, USA) was used as a reference. Traditional biochemical tests accurately identified 62/66 (94%) isolates. Both Bruker and Vitek matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) identified 59/66 (89%) strains, but VITEK2 could only identify 32/66 (48.5%) isolates correctly. The mean time to identification using biochemical tests was 20 hours; VITEK2 took 6 hours and MALDI-TOF approximately 10 minutes. In conclusion, MALDI-TOF is a quick method, which accurately identified most isolates of Pasteurella to the species level. Thus, MALDI-TOF constitutes a valuable diagnostic tool in the clinical laboratory.

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.

[Manganese in atherogenesis: detection, origin, and role]

The role of transition metal ions in atherogenesis is controversial; they can participate in the hydroxyl radical generation and catalyze the reactive oxygen species neutralization reaction as cofactors of antioxidant enzymes. Using EPR spectroscopy, we revealed that 70% of the samples of aorta with atherosclerotic lesions possessed superoxide dismutase activity, 100% of the samples initiated Fenton reaction and demonstrated the presence of manganese paramagnetic centers. The sodA gene encoding manganese-dependent bacterial superoxide dismutase was not found in the samples of atherosclerotic plaques by PCR using degenerate primers. The data obtained indicates the perspectives of manganese analysis as a marker element in the express diagnostics of atherosclerosis.

Pasteurella canis Isolation following Penetrating Eye Injury: A Case Report

A 3-year-old boy presented with history of trauma to the left eye after he accidentally injured his eye with a broom stick made up from coconut skewers. There was history of cats as their pets but not dogs. Ocular examination revealed left superonasal conjunctival laceration and scleral perforation with prolapsed vitreous. Fundus examination showed minimal vitreous haemorrhage and flat retina. Conjunctiva swab at the wound site was sent for gram staining, culture, and sensitivity. He underwent scleral suturing, vitreous tap, and intravitreal injection of Ceftazidime and Amikacin. Vitreous tap was sent for gram stained, culture and sensitivity. Postoperatively, he was started empirically on IV Ciprofloxacin 160 mg BD, Guttae Ciprofloxacin, and Guttae Ceftazidime. Conjunctiva swab grew Pasteurella canis which was sensitive to all Beta lactams, Ciprofloxacin, Chloramphenicol, and Aminoglycoside. Post-operative was uneventful, absent signs of endophthalmitis or orbital cellulitis.

Polymerase chain reaction-based identification of clinically relevant Pasteurellaceae isolated from cats and dogs in Poland

A set of polymerase chain reaction (PCR) assays for identification of the most important Pasteurellaceae species encountered in cats and dogs were developed. Primers for Pasteurella multocida were designed to detect a fragment of the kmt, a gene encoding the outer-membrane protein. Primers specific to Pasteurella canis, Pasteurella dagmatis, and Pasteurella stomatis were based on the manganese-dependent superoxide dismutase gene (sodA) and those specific to [Haemophilus] haemoglobinophilus on species-specific sequences of the 16S ribosomal RNA gene. All the primers were tested on respective reference and control strains and applied to the identification of 47 canine and feline field isolates of Pasteurellaceae. The PCR assays were shown to be species specific, providing a valuable supplement to phenotypic identification of species within this group of bacteria.

Pasteurella multocida involved in respiratory disease of wild chimpanzees

Pasteurella multocida can cause a variety of diseases in various species of mammals and birds throughout the world but nothing is known about its importance for wild great apes. In this study we isolated P. multocida from wild living, habituated chimpanzees from Taï National Park, Côte d'Ivoire. Isolates originated from two chimpanzees that died during a respiratory disease outbreak in 2004 as well as from one individual that developed chronic air-sacculitis following this outbreak. Four isolates were subjected to a full phenotypic and molecular characterisation. Two different clones were identified using pulsed field gel electrophoresis. Multi Locus Sequence Typing (MLST) enabled the identification of previous unknown alleles and two new sequence types, ST68 and ST69, were assigned. Phylogenetic analysis of the superoxide dismutase (sodA) gene and concatenated sequences from seven MLST-housekeeping genes showed close clustering within known P. multocida isolated from various hosts and geographic locations. Due to the clinical relevance of the strains described here, these results make an important contribution to our knowledge of pathogens involved in lethal disease outbreaks among endangered great apes.

Vertebral osteomyelitis and meningomyelitis caused by Pasteurella canis in a dog--clinicopathological case report

A clinicopathological case study of vertebral osteomyelitis caused by Pasteurella canis in a 2.5-year-old male Jack Russell Terrier is presented. The case was characterised by a chronic course with signs of spinal pain and acute paraplegia. The diagnosis was established by radiography, myelography, post-myelographic CT examination, and laboratory tests including routine blood work and cerebrospinal fluid (CSF) cytology, and confirmed by postmortem pathological and microbiological examinations. Diagnostic imaging showed severe osteolysis, ventral spondylosis and spinal cord compression at the 4th and 5th lumbar vertebrae. The blood tests revealed mild leukocytosis and anaemia, while CSF cytology showed lymphocytic and mononuclear pleocytosis. Necropsy demonstrated severe osteomyelitis and meningomyelitis, but the source of infection could not be established. To the authors' knowledge, this is the first description of canine vertebral osteomyelitis caused by this organism.

Diagnostic and typing options for investigating diseases associated with Pasteurella multocida

Pasteurella multocida is responsible for major animal diseases of economic significance in both developed and developing countries whereas human infections related to this bacterium are infrequent. Significantly, development of a carrier status or latent infections plays a critical role in the epidemiology of these diseases. Aiming at increased knowledge of these infections, we examine potential diagnostic and selected typing systems for investigating diseases caused by P. multocida. Detection of P. multocida from clinical specimen by; (i) isolation and identification, (ii) polymerase chain reaction (PCR), iii) specific hybridisation probes, (iv) serological tests and (v) other alternative methods is critically evaluated. These detection systems provide a wide spectrum of options for rapid diagnosis and for detecting and understanding of latent infections in herd/flock health control programmes, though PCR methods for detecting P. multocida in clinical specimen appear increasingly preferred. For establishing the clonality of outbreak strains, we select to discuss macromolecular profiling, serotyping, biotyping, restriction enzyme analysis, ribotyping and multiplex PCR typing. Although P. multocida infections can be rapidly diagnosed with molecular and serological tests, isolation and accurate species identification are central to epidemiological tracing of outbreak strains. Our review brings together comprehensive and essential information that may be adapted for confirming diagnosis and determining the molecular epidemiology of diseases associated with P. multocida.

The sodA gene as a target for phylogenetic dissection of the genus Haemophilus and accurate identification of human clinical isolates

The genus Haemophilus constitutes a heterogeneous group of Pasteurellaceae species, and conventional identification of isolates other than Haemophilus influenzae and Haemophilus parainfluenzae is often challenging. Here, simple colony-PCR and sequencing assays with the same pair of degenerate primers were used to characterize a 449- to 458-bp fragment (sodA(int)) internal to the sodA gene encoding the manganese-dependent superoxide dismutase in type strains of all 15 Haemophilus species and Actinobacillus actinomycetemcomitans. The topology of a sodA(int)-based phylogenetic tree was in general agreement with that inferred from the analysis of 16S rRNA and other housekeeping gene sequences, but allowed more confident delineation of the main clusters of species. The sodA(int) sequences showed a markedly higher divergence than those of the corresponding 16S rRNA genes, and 38 independent human clinical isolates were identified by comparing their sodA(int) sequence to those of the type species. Except for one Haemophilus aphrophilus strain, all isolates were unambiguously characterized in spite of a high intraspecific sodA(int) sequence diversity. This study provides a comprehensive sequence-based phylogenetic analysis of the entire genus Haemophilus, and confirms that sodA is a potent target for the identification of clinical isolates of Pasteurellaceae. This approach might contribute to the taxonomic reappraisal of this family, and to the development of diagnostic tools.

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.

Application of SmartGene IDNS software to partial 16S rRNA gene sequences for a diverse group of bacteria in a clinical laboratory

Laboratories often receive clinical isolates for bacterial identification that have ambiguous biochemical profiles by conventional testing. With the emergence of 16S rRNA gene sequencing as an identification tool, we evaluated the usefulness of SmartGene IDNS, a 16S rRNA sequence database and software program for microbial identification. Identification by conventional methods of a diverse group of bacterial clinical isolates was compared with gene sequences interrogated by the SmartGene and MicroSeq databases. Of 300 isolates, SmartGene identified 295 (98%) to the genus level and 262 (87%) to the species level, with 5 (2%) being inconclusive. MicroSeq identified 271 (90%) to the genus level and 223 (74%) to the species level, with 29 (10%) being inconclusive. SmartGene and MicroSeq agreed on the genus for 233 (78%) isolates and the species for 212 (71%) isolates. Conventional methods identified 291 (97%) isolates to the genus level and 208 (69%) to the species level, with 9 (3%) being inconclusive. SmartGene, MicroSeq, and conventional identifications agreed for 193 (64%) of the results. Twenty-seven microorganisms were not represented in MicroSeq, compared to only 2 not represented in SmartGene. Overall, SmartGene IDNS provides comprehensive and accurate identification of a diverse group of bacteria and has the added benefit of being a user-friendly program that can be modified to meet the unique needs of clinical laboratories.

Prediction of whole-genome DNA–DNA similarity, determination of G+C content and phylogenetic analysis within the family Pasteurellaceae by multilocus sequence analysis (MLSA)

Genome predictions based on selected genes would be a very welcome approach for taxonomic studies, including DNA–DNA similarity, G+C content and representative phylogeny of bacteria. At present, DNA–DNA hybridizations are still considered the gold standard in species descriptions. However, this method is time-consuming and troublesome, and datasets can vary significantly between experiments as well as between laboratories. For the same reasons, full matrix hybridizations are rarely performed, weakening the significance of the results obtained. The authors established a universal sequencing approach for the three genes recN, rpoA and thdF for the Pasteurellaceae, and determined if the sequences could be used for predicting DNA–DNA relatedness within the family. The sequence-based similarity values calculated using a previously published formula proved most useful for species and genus separation, indicating that this method provides better resolution and no experimental variation compared to hybridization. By this method, cross-comparisons within the family over species and genus borders easily become possible. The three genes also serve as an indicator of the genome G+C content of a species. A mean divergence of around 1 % was observed from the classical method, which in itself has poor reproducibility. Finally, the three genes can be used alone or in combination with already-established 16S rRNA, rpoB and infB gene-sequencing strategies in a multisequence-based phylogeny for the family Pasteurellaceae. It is proposed to use the three sequences as a taxonomic tool, replacing DNA–DNA hybridization.