Differentiation of intestinal spirochaetes by multilocus enzyme electrophoresis analysis and 16S rRNA sequence comparisons

Evidence of homologous recombination as a driver of diversity in Brachyspira pilosicoli

The enteric, pathogenic spirochaete Brachyspira pilosicoli colonizes and infects a variety of birds and mammals, including humans. However, there is a paucity of genomic data available for this organism. This study introduces 12 newly sequenced draft genome assemblies, boosting the cohort of examined isolates by fourfold and cataloguing the intraspecific genomic diversity of the organism more comprehensively. We used several in silico techniques to define a core genome of 1751 genes and qualitatively and quantitatively examined the intraspecific species boundary using phylogenetic analysis and average nucleotide identity, before contextualizing this diversity against other members of the genus Brachyspira. Our study revealed that an additional isolate that was unable to be species typed against any other Brachyspira lacked putative virulence factors present in all other isolates. Finally, we quantified that homologous recombination has as great an effect on the evolution of the core genome of the B. pilosicoli as random mutation (r/m=1.02). Comparative genomics has informed Brachyspira diversity, population structure, host specificity and virulence. The data presented here can be used to contribute to developing advanced screening methods, diagnostic assays and prophylactic vaccines against this zoonotic pathogen.

Identification of Brachyspira species by cpn60 universal target sequencing is superior to NADH oxidase gene sequencing

The pig colon is the habitat of diverse Brachyspira species, of which only a few are of clinical importance. Methods for identification have shifted from phenotypic to molecular testing over the last two decades. Following the emergence of B. hampsonii it became evident that relying on species-specific PCRs carries the risk of overlooking important new species. Consequently, sequencing was proposed as an unbiased alternative for identification of isolates. So far, the main target for identification across species has been the NADH oxidase gene (nox). However, multiple copies of this gene in the genome and potential lateral gene transfer reduce confidence when using this gene. This study compared identification and phylogentic relationship inferred from nox sequencing to that inferred from sequencing of the cpn60 universal target using a collection of 168 isolates from different Brachyspira species. The majority of isolates had an identical identification with both methods. There were a few outliers in the trees with uncertain assignment to a species by BLAST analysis. A few major discrepancies pertained to the pathogenic species B. hampsonii (2), B. pilosicoli (1) and B. suanatina (1). Weakly haemolytic variants of B. hyodysenteriae were assigned to the correct species by both methods. Some of the isolates identified as B. hampsonii also had a weakly haemolytic phenotype.

Differentiation of Brachyspira spp. isolated from laying hens using PCR-based methods and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

Avian intestinal spirochetosis (AIS), an important but neglected disease in laying hens, is caused by Brachyspira pilosicoli, B. intermedia, and B. alvinipulli. Poultry are also frequently colonized by putatively nonpathogenic species such as B. murdochii and B. innocens. We evaluated the differentiation of Brachyspira species by 3 methods: sequencing of the reduced nicotinamide adenine dinucleotide (NADH) oxidase gene ( nox), matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), and a new multiplex (m)PCR targeting genes such as the tryptophanase A gene ( tnaA) and the p-aminobenzoyl-glutamate hydrolase subunit B gene ( abgB). Sequencing of 414 bp of the nox PCR amplification products generated from 41 pure cultures of avian Brachyspira isolates allowed presumptive species identification in 33 isolates with at least 99% identity in basic local alignment search tool analysis, including B. pilosicoli, B. intermedia, B. murdochii, B. innocens, and " B. pulli". MALDI-TOF MS analysis was found to be a reliable tool for differentiation after extension of the manufacturer's database. In the mPCR, all isolates identified as B. pilosicoli and B. intermedia were positive for abgB and tnaA, respectively. The mPCR might be very useful in detecting Brachyspira species in mixed cultures including not only nonpathogenic species, such as B. innocens, but also one of the AIS pathogens. We found that MALDI-TOF MS analysis combined with the mPCR targeting tnaA and abgB was suitable for the identification of avian isolates of B. pilosicoli and B. intermedia, 2 important agents of AIS.

The Spirochete Brachyspira pilosicoli, Enteric Pathogen of Animals and Humans

Brachyspira pilosicoli is a slow-growing anaerobic spirochete that colonizes the large intestine. Colonization occurs commonly in pigs and adult chickens, causing colitis/typhlitis, diarrhea, poor growth rates, and reduced production. Colonization of humans also is common in some populations (individuals living in village and peri-urban settings in developing countries, recent immigrants from developing countries, homosexual males, and HIV-positive patients), but the spirochete rarely is investigated as a potential human enteric pathogen. In part this is due to its slow growth and specialized growth requirements, meaning that it is not detectable in human fecal samples using routine diagnostic methods. Nevertheless, it has been identified histologically attached to the colon and rectum in patients with conditions such as chronic diarrhea, rectal bleeding, and/or nonspecific abdominal discomfort, and one survey of Australian Aboriginal children showed that colonization was significantly associated with failure to thrive. B. pilosicoli has been detected in the bloodstream of elderly patients or individuals with chronic conditions such as alcoholism and malignancies. This review describes the spirochete and associated diseases. It aims to encourage clinicians and clinical microbiologists to consider B. pilosicoli in their differential diagnoses and to develop and use appropriate diagnostic protocols to identify the spirochete in clinical specimens.

A review of methods used for studying the molecular epidemiology of Brachyspira hyodysenteriae

Brachyspira (B.) spp. are intestinal spirochaetes isolated from pigs, other mammals, birds and humans. In pigs, seven Brachyspira spp. have been described, i.e. B. hyodysenteriae, B. pilosicoli, B. intermedia, B. murdochii, B. innocens, B. suanatina and B. hampsonii. Brachyspira hyodysenteriae is especially relevant in pigs as it causes swine dysentery and hence considerable economic losses to the pig industry. Furthermore, reduced susceptibility of B. hyodysenteriae to antimicrobials is of increasing concern. The epidemiology of B. hyodysenteriae infections is only partially understood, but different methods for detection, identification and typing have supported recent improvements in knowledge and understanding. In the last years, molecular methods have been increasingly used. Molecular epidemiology links molecular biology with epidemiology, offering unique opportunities to advance the study of diseases. This review is based on papers published in the field of epidemiology and molecular epidemiology of B. hyodysenteriae in pigs. Electronic databases were screened for potentially relevant papers using title and abstract and finally, Barcellos et al. papers were systemically selected and assessed. The review summarises briefly the current knowledge on B. hyodysenteriae epidemiology and elaborates on molecular typing techniques available. Results of the studies are compared and gaps in the knowledge are addressed. Finally, potential areas for future research are proposed.

Emergence of Brachyspira species and strains: reinforcing the need for surveillance

This short review discusses the increasing complexity that has developed around the understanding of Brachyspira species that infect pigs, and their ability to cause disease. It describes the recognition of new weakly haemolytic Brachyspira species, and the growing appreciation that Brachyspira pilosicoli and some other weakly haemolytic species may be pathogenic in pigs. It discusses swine dysentery (SD) caused by the strongly haemolytic Brachyspira hyodysenteriae, particularly the cyclical nature of the disease whereby it can largely disappear as a clinical problem from a farm or region, and re-emerge years later. The review then describes the recent emergence of two newly described strongly haemolytic pathogenic species, “Brachyspira suanatina” and “Brachyspira hampsonii” both of which appear to have reservoirs in migratory waterbirds, and which may be transmitted to and between pigs. “B. suanatina” seems to be confined to Scandinavia, whereas “B. hampsonii” has been reported in North America and Europe, causes a disease indistinguishable from SD, and has required the development of new routine diagnostic tests. Besides the emergence of new species, strains of known Brachyspira species have emerged that vary in important biological properties, including antimicrobial susceptibility and virulence. Strains can be tracked locally and at the national and international levels by identifying them using multilocus sequence typing (MLST) and comparing them against sequence data for strains in the PubMLST databases. Using MLST in conjunction with data on antimicrobial susceptibility can form the basis for surveillance programs to track the movement of resistant clones. In addition some strains of B. hyodysenteriae have low virulence potential, and some of these have been found to lack the B. hyodysenteriae 36 kB plasmid or certain genes on the plasmid whose activity may be associated with colonization. Lack of the plasmid or the genes can be identified using PCR testing, and this information can be added to the MLST and resistance data to undertake detailed surveillance. Strains of low virulence are particularly important where they occur in high health status breeding herds without causing obvious disease: potentially they could be transmitted to production herds where they may colonize more effectively and cause disease under stressful commercial conditions.

Brachyspira and its role in avian intestinal spirochaetosis

The fastidious, anaerobic spirochaete Brachyspira is capable of causing enteric disease in avian, porcine and human hosts, amongst others, with a potential for zoonotic transmission. Avian intestinal spirochaetosis (AIS), the resulting disease from colonisation of the caeca and colon of poultry by Brachyspira leads to production losses, with an estimated annual cost of circa £ 18 million to the commercial layer industry in the United Kingdom. Of seven known and several proposed species of Brachyspira, three are currently considered pathogenic to poultry; B. alvinipulli, B. intermedia and B. pilosicoli. Currently, AIS is primarily prevented by strict biosecurity controls and is treated using antimicrobials, including tiamulin. Other treatment strategies have been explored, including vaccination and probiotics, but such developments have been hindered by a limited understanding of the pathobiology of Brachyspira. A lack of knowledge of the metabolic capabilities and little genomic information for Brachyspira has resulted in a limited understanding of the pathobiology. In addition to an emergence of antibiotic resistance amongst Brachyspira, bans on the prophylactic use of antimicrobials in livestock are driving an urgent requirement for alternative treatment strategies for Brachyspira-related diseases, such as AIS. Advances in the molecular biology and genomics of Brachyspira heralds the potential for the development of tools for genetic manipulation to gain an improved understanding of the pathogenesis of Brachyspira.

Development of a real-time PCR for identification of brachyspira species in human colonic biopsies

BACKGROUND

Brachyspira species are fastidious anaerobic microorganisms, that infect the colon of various animals. The genus contains both important pathogens of livestock as well as commensals. Two species are known to infect humans: B. aalborgi and B. pilosicoli. There is some evidence suggesting that the veterinary pathogenic B. pilosicoli is a potential zoonotic agent, however, since diagnosis in humans is based on histopathology of colon biopsies, species identification is not routinely performed in human materials.

METHODS

The study population comprised 57 patients with microscopic evidence of Brachyspira infection and 26 patients with no histopathological evidence of Brachyspira infection. Concomitant faecal samples were available from three infected patients. Based on publically available 16S rDNA gene sequences of all Brachyspira species, species-specific primer sets were designed. DNA was extracted and tested by real-time PCR and 16S rDNA was sequenced.

RESULTS

Sensitivity and specificity for identification of Brachyspira species in colon biopsies was 100% and 87.7% respectively. Sequencing revealed B. pilosicoli in 15.4% of patients, B. aalborgi in 76.9% and a third species, tentatively named "Brachyspira hominis", in 26.2%. Ten patients (12.3%) had a double and two (3.1%) a triple infection. The presence of Brachyspira pilosicoli was significantly associated with inflammatory changes in the colon-biopsy (p=0.028).

CONCLUSIONS

This newly designed PCR allows for sub-differentiation of Brachyspira species in patient material and thus allows large-scaled surveillance studies to elucidate the pathogenicity of human Brachyspira infections. One-third of affected patients appeared to be infected with a novel species.

Rapid and accurate diagnosis of human intestinal spirochetosis by fluorescence in situ hybridization

Human intestinal spirochetosis (HIS) is associated with overgrowth of the large intestine by spirochetes of the genus Brachyspira. The microbiological diagnosis of HIS is hampered by the fastidious nature and slow growth of Brachyspira spp. In clinical practice, HIS is diagnosed histopathologically, and a significant portion of cases may be missed. Fluorescence in situ hybridization (FISH) is a molecular method that allows the visualization and identification of single bacteria within tissue sections. In this study, we analyzed intestinal biopsy samples from five patients with possible HIS. All specimens yielded positive results by histopathological techniques. PCR amplification and sequencing of the 16S rRNA gene were performed. Sequences of two isolates clustered in the group of Brachyspira aalborgi, whereas in three cases, the sequences were highly similar to that of Brachyspira pilosicoli. Three phylotypes showed mismatches at distinct nucleotide positions with Brachyspira sp. sequences published previously. In addition, culture for Brachyspira was successful in three cases. On the basis of these data, we designed and evaluated a Brachyspira genus-specific 16S rRNA-directed FISH probe that detects all of the Brachyspira spp. published to date. FISH of biopsy samples resulted in strong, unequivocal signals of brush-like formations at the crypt surfaces. This technique allowed simultaneous visualization of single spirochetes and their identification as Brachyspira spp. In conclusion, FISH provides a fast and accurate technique for the visualization and identification of intestinal spirochetes in tissue sections. It therefore represents a valuable tool for routine diagnosis of HIS.

Intestinal spirochetes isolated from wild-living jackdaws, hooded crows and rooks (genus Corvus): provisionally designated "Brachyspira corvi" sp. nov

Intestinal spirochetes of genus Brachyspira are commonly isolated from mammalian and avian hosts, and several species have been reported to cause enteric disease in pigs and birds. Except for a previous publication on three isolates from corvid birds (order Passeriformes, family Corvidae, genus Corvus), of which two are further studied in this paper, no other reports exist on Brachyspira spp. of passerine birds. In this study, cloacal and intestinal swabs of small and large intestines were collected from 116 corvid birds of three species, i.e. jackdaws (Corvus monedula), hooded crows (Corvus corone cornix) and rooks (Corvus frugilegus), from four separate geographical locations in Sweden. Isolates were obtained by selective culture from 43 of 116 birds. All isolates were weakly hemolytic, indole-negative and lacked hippurate cleavage capacity. Examination by light microscopy did not indicate association with enteric disease in necropsied birds. Pure spirochete cultures were obtained by serial dilution and subculture, and selected isolates were analyzed by PCR (n=14), randomly amplified polymorphic DNA (RAPD) (n=14), and sequencing of the almost complete 16S rRNA (n=14), and partial nox genes (n=4). Positive reactions were noticed by PCR targeting a hexa-T segment of the 16S rRNA gene, which has been previously reported as a signature characteristic of Brachyspira pilosicoli. By 16S rRNA gene sequencing, the isolates formed a separate cluster related to genus Brachyspira, but not consistent with any presently recognized or proposed Brachyspira sp. The sequence similarity of the 16S rRNA gene among the isolates from corvid birds was 99.7-100%. Compared to 16S rRNA gene sequence data from all presently recognized and several proposed Brachyspira spp. the sequence similarity of the isolates from corvid birds varied between 94.1 and 96.5%. In a radial tree based on nox gene sequences, all four analyzed isolates from corvid birds formed a separate cluster. By RAPD analysis, the banding patterns of the isolates differed from all type strains of Brachyspira spp. Based on the results presented in this paper, we propose that the described isolates from corvid birds belong to a novel species within genus Brachyspira, with the provisional name "Brachyspira corvi" (cor'vi. L gen. n. corvi, of a crow).

Human intestinal spirochetosis:Brachyspira aalborgiand/orBrachyspira pilosicoli?

Intestinal spirochetosis in humans (HIS) is a condition defined by the presence of a layer of spirochetes attached by one cell end to the colorectal epithelium. The pathologic significance of HIS is uncertain, but it has been linked to chronic diarrhea and other abdominal complaints. Two anaerobic intestinal spirochete species have been associated with HIS, namelyBrachyspira pilosicoliandBrachyspira aalborgi.Brachyspira pilosicoli, which colonizes many animal species, is common (~30%) in the feces of people from developing countries, including Australian Aborigines, and in HIV+ patients and male homosexuals in Western societies. It is also commonly seen attached to the rectal mucosa of homosexual males. In other groups in Western societies both the presence of B.pilosicoliin feces and histologic HIS are uncommon (~1.5%).Brachyspira aalborgiis an extremely slow growing and fastidious spirochete, which previously had been isolated from an HIS patient in Denmark. Recent studies using polymerase chain reaction amplification of DNA from intestinal biopsies from a series of cases of HIS in the general Western population demonstrated thatB. aalborgi, rather thanB. pilosicoli, was the main spirochete species involved in these patients. This review outlines recent developments in the study of HIS and the two spirochete species, and identifies priorities for future research.

Classification ofBrachyspiraspp. isolated from Swedish dogs

Brachyspira spp.were isolated from 21 of 32 sampled dogs (66%) in a colony of Swedish beagle dogs with a history of diarrhea and from 3 of 17 Swedish pet dogs (17%) with diarrhea. All Swedish isolates were weakly β-hemolytic and gave a negative indole reaction. Eighty-eight percent showed negative α-galactosidase and hippurate reactions, but a positive β-glucosidase reaction. Two isolates were hippurate positive with a negative β-glucosidase reaction. One additional German isolate diverged by showing a positive indole reaction in combination with a positive hippurate reaction. Sequencing of 16S rDNA indicated that the hippurate-positive isolates belonged to the speciesBrachyspira pilosicoli. Four representative isolates were examined using pulsed-field gel electrophoresis (PFGE) and compared with six reference strains and five porcine isolates ofBrachyspiraspp. The canine isolates clustered together in the PFGE analysis. Necropsy examination of a culture-positiveB. pilosicolicolony-raised beagle dog revealed macro- and microscopical lesions of colitis with numerous spiral-shaped bacteria in the lumens of the crypts, in goblet cells and within the colonic epithelium.

Brachyspiraspp. (Serpulinaspp.) in birds: a review and results from a study of Swedish game birds

Only limited data concerning the prevalence of intestinal spirochetes are available in game birds. This paper describes the prevalence and biochemical reactions of spirochetes isolated from 25 common partridges, 7 pheasants and 16 mallards originating from nine Swedish game-bird farms. The birds, which had been submitted for post-mortem examination due to various problems, showed a variety of underlying diseases. Additionally, fecal droppings from 22 common partridges, 20 pheasants and 20 mallards obtained at one of the farms were included in the study. Intestinal spirochetes were isolated from 85.4% of the game birds and from 71% of the fecal droppings. Seven biochemical types were identified. Seventeen per cent of all isolates were classified as Brachyspira pilosicoli and 3% as B. intermedia. One isolate showed strong -hemolysis and a positive indole reaction that is consistent with B. hyodysenteriae. In addition, three previously unknown biochemical types were found. Unclassified spirochetes in presumed mixed cultures were observed in 21% of all samples of fecal droppings. Histologic examination of spirochete-positive birds revealed numerous spirochetes in the lumen and crypts of the cecum, in some cases densely adhered by one end to the luminal surface. The significance of the findings is discussed.

Reclassification of Serpulina intermedia and Serpulina murdochii in the genus Brachyspira as Brachyspira intermedia comb. nov. and Brachyspira murdochii comb. nov

A reassessment was undertaken of published characteristics of the five species of anaerobic intestinal spirochaetes in the genus Brachyspira (Brachyspira aalborgi, Brachyspira alvinipulli, Brachyspira hyodysenteriae, Brachyspira innocens and Brachyspira pilosicoli) and the two species in the genus Serpulina (Serpulina intermedia and Serpulina murdochii). Comparisons were made of published descriptions, including phenotypic properties, grouping by multilocus enzyme electrophoresis, DNA base composition, DNA-DNA relative reassociation values and 16S rRNA gene sequence similarity. On the basis of extensive similarities between all the species, it is proposed to reclassify Serpulina intermedia Stanton et al. 1997 and Serpulina murdochii Stanton et al. 1997 in the genus Brachyspira, as Brachyspira intermedia comb. nov. (type strain ATCC 51140T) and Brachyspira murdochii comb. nov. (type strain ATCC 51284T).

Application of nox-restriction fragment length polymorphism for the differentiation of Brachyspira intestinal spirochetes isolated from pigs and poultry in Australia

Sixty-nine intestinal spirochetes isolated from pigs and poultry in eastern Australia were selected to evaluate the effectiveness of a species-specific PCR-based restriction fragment length polymorphism (RFLP) analysis of the Brachyspira nox gene. For comparative purposes, all isolates were subjected to species-specific PCRs for the pathogenic species Brachyspira hyodysenteriae and Brachyspira pilosicoli, and selected isolates were examined further by sequence analysis of the nox and 16S ribosomal RNA genes. Modifications to the original nox-RFLP method included direct inoculation of bacterial cells into the amplification mixture and purification of the PCR product, which further optimized the nox-RFLP for use in a veterinary diagnostic laboratory, producing sufficient product for both species identification and future comparisons. Although some novel profiles that prevented definitive identification were observed, the nox-RFLP method successfully classified 45 of 51 (88%) porcine and 15 of 18 (83%) avian isolates into 5 of the 6 recognized species of Brachyspira. This protocol represents a significant improvement over conventional methods currently used in veterinary diagnostic laboratories for rapid specific identification of Brachyspira spp. isolated from both pigs and poultry.

Analysis of genetic variation in Brachyspira aalborgi and related spirochaetes determined by partial sequencing of the 16S rRNA and NADH oxidase genes

The purpose of this study was to investigate genetic variation in the anaerobic intestinal spirochaete Brachyspira aalborgi by partial sequencing of the 16S rRNA and NADH oxidase genes. The spirochaete is poorly cultivable; hence, only six isolates were available for analysis. Additional sequences were amplified from DNA extracted from fixed colorectal biopsies from 26 patients with histological evidence of intestinal spirochaetosis, and from the faeces of six non-human primates (NHP). Multiple biopsies from sites along the large intestine were tested from three of the 26 patients. Sequences from two biopsies were closely related to those of the spirochaete Brachyspira pilosicoli. Eight B. aalborgi-like 16S rDNA sequences were generated from the biopsies from the other 24 patients, and four from the NHP faeces. The B. aalborgi 16S rDNA sequences were divided into three clusters, 1, 2 and 4, with individual sequence similarities to the type strain ranging from 97.49 to 100 %. All human isolates of B. aalborgi were located in cluster 1, as was the sequence of the so-called 'Brachyspira ibaraki'. All four 16S rDNA sequences from the NHP faeces and the two NHP isolates of B. aalborgi were located in cluster 4, which was distinct. Cluster 4 may represent a novel Brachyspira species. Evidence for multiple strains of B. aalborgi or other Brachyspira species was found in biopsies from two patients. In the three individuals from whom multiple biopsies were amplified, the sequences at each intestinal site were the same, indicating the presence of one dominant strain.

Characterization of Treponema phagedenis-like spirochetes isolated from papillomatous digital dermatitis lesions in dairy cattle

Four spirochete strains were isolated from papillomatous digital dermatitis (PDD) lesions in Iowa dairy cattle and compared with two previously described spirochete strains isolated from dairy cattle in California. These six strains shared an identical 16S ribosomal DNA sequence that was 98% similar to Treponema phagedenis and 99% similar to the uncultivated PDD spirochete sequence DDLK-4. The whole-cell protein profiles resolved by sodium dodecyl sulfate-polyacrylamide gel electrophoresis of these six strains were similar. However, these strains showed differences in the antigenic diversity of lipopolysaccharide (LPS). Genetic diversity was also detected by pulsed-field gel electrophoresis of genomic DNA digests, revealing differences among five of the six strains. Serum immunoglobulin G antibodies from dairy cattle with active PDD lesions reacted with the LPS of all but one PDD spirochete strain. Likewise, peripheral blood mononuclear cells from cattle with active PDD lesions produced blastogenic responses to one of the two California isolates. Both antibody and lymphocyte blastogenic responses were reduced in convalescent dairy cattle, suggesting the immune response to these spirochetes has short duration. These results demonstrate genetic and antigenic diversity among T. phagedenis-like treponemes and provide further evidence for the involvement of these spirochetes in the pathogenesis of PDD.

Phylogenetic evidence for novel and genetically different intestinal spirochetes resembling Brachyspira aalborgi in the mucosa of the human colon as revealed by 16S rDNA analysis

Intestinal spirochetes (Brachyspira spp.) are causative agents of intestinal disorders in animals and humans. Phylogenetic analysis of cloned 16S rRNA genes from biopsies of the intestinal mucosa of the colon from two Swedish 60-years old adults without clinical symptoms revealed the presence of intestinal spirochetes. Seventeen clones from two individuals and 11 reference strains were analyzed and the intestinal spirochetes could be divided into two lineages, the Brachyspira aalborgi and the Brachyspira hyodysenteriae lineages. All of the clones grouped in the B. aalborgi lineage. Moreover, the B. aalborgi lineage could be divided into three distinct phylogenetic clusters as confirmed by bootstrap and signature nucleotide analysis. The first cluster comprised 6 clones and the type strain B. aalborgi NCTC 11492T. The cluster 1 showed a 16S rRNA gene similarity of 99.4-99.9%. This cluster also harbored the only other strain of B. aalborgi isolated so far, namely strain W1, which was subjected to phylogenetic analysis in this work. The second cluster harbored 9 clones with a 98.7 to 99.5% range of 16S rDNA similarity to the B. aalborgi cluster 1. Two clones branched distinct and early of the B. aalborgi line forming the third cluster and was found to be 98.7% similar to cluster 1 and 98.3-99.1% to cluster 2. Interestingly, this shows that considerable variation of intestinal spirochetes can be found as constituents of the colonic microbiota in humans, genetically resembling B. aalborgi. The presented data aid significantly to the diagnostic and taxonomic work on these organisms.

Evaluation of a 23S rDNA polymerase chain reaction assay for identification of Serpulina intermedia, and strain typing using pulsed-field gel electrophoresis

A polymerase chain reaction assay, amplifying a 1027 base pair portion of the 23S rDNA gene, was evaluated for identification of the intestinal spirochaete Serpulina intermedia. A total of 34 strains of S. intermedia isolated from pigs and chickens and 195 strains of other related species were tested. The optimised assay correctly identified all the S. intermedia strains, but generated 11 false positive reactions, giving a test sensitivity of 100% and a test specificity of 94.3%. The false positive reactions were generated from strains of four different species of intestinal spirochaetes, and the product was of the original predicted size. This suggests that the primer sites selected on the 23S rRNA gene were not completely specific for S. intermedia. Pulsed-field gel electrophoresis was then developed to investigate diversity amongst the S. intermedia strains. All strains tested had distinct DNA banding patterns using Mlu1, although three isolates from chickens on the same farm appeared closely related. The collection exhibited considerable genetic diversity, and strains from pigs and chickens were distributed in clusters throughout the dendrogram produced. The most closely related porcine and avian strains shared only 62% similarity.

Differentiation of Serpulina species by NADH oxidase gene (nox) sequence comparisons and nox-based polymerase chain reaction tests

The NADH oxidase genes (nox) of 18 strains of intestinal spirochaetes were partially sequenced over 1246 bases. Strains examined included 17 representatives from six species of the genus Serpulina, and the type strain 513A(T) of the human intestinal spirochaete Brachyspira aalborgi. Sequences were aligned and used to investigate phylogenetic relationships between the organisms. Nox sequence identities between strains within the genus Serpulina were within the range 86.3-100%, whilst the nox gene of B. aalborgi shared between 78.8-83.0% sequence identity with the nox sequences of the various Serpulina strains. A phenogram produced based on sequence dissimilarities was in good agreement with the current classification of species in the genus Serpulina, although an atypical strongly beta-haemolytic porcine strain (P280/1), previously thought to be S. innocens, appeared distinct from other members of this species. Primer pairs were developed from the nox sequence alignments for use in polymerase chain reaction (PCR) identification of the pathogenic species S. hyodysenteriae (NOX1), S. intermedia (NOX2), and S. pilosicoli (NOX3), and for the combined non-pathogenic species S. innocens and S. murdochii (NOX4). The PCRs were optimised using 80 strains representing all currently described species in the genus Serpulina, as well as the type strain of B. aalborgi. Tests NOX1 and NOX4 specifically amplified DNA from all members of their respective target species, whilst tests NOX2 and NOX3 were less sensitive. NOX2 amplified DNA from all 10 strains of S. intermedia from pigs but from only 4 of 10 strains from chickens, whilst NOX3 amplified DNA from only 18 of 21 S. pilosicoli strains, even at low stringency. Tests NOX1 and NOX4 should prove useful in veterinary diagnostic laboratories, whilst NOX2 and NOX3 require further refinement.

PCR amplification from fixed tissue indicates frequent involvement of Brachyspira aalborgi in human intestinal spirochetosis

PCR procedures amplifying portions of the 16S rRNA and NADH oxidase genes of Brachyspira aalborgi and Serpulina pilosicoli were applied to DNA extracted from paraffin-embedded human colonic or rectal tissues from 30 Norwegian, Australian, and U.S. patients, 16 of whom had histologic evidence of intestinal spirochetosis (IS). B. aalborgi-specific sequences were identified by PCR in 10 of the IS patients (62.5%) but none of the others, while S. pilosicoli sequences were not detected in tissues from any patient. Direct sequencing of products from three of the positive samples provided further confirmation of the presence of B. aalborgi. B. aalborgi may be a more common cause of intestinal spirochetosis than has been previously thought.

In vitro activity of four antimicrobial agents against North American isolates of porcine Serpulina pilosicoli

Porcine colonic spirochetosis is a nonfatal diarrheal disease that affects pigs during the growing and finishing stages of production. The disease is caused by Serpulina pilosicoli, a newly recognized species of pathogenic intestinal spirochete. Antimicrobial therapy aimed at reducing the infection may be helpful in controlling spirochetal diarrhea. In this study, the in vitro antimicrobial susceptibilities of the reference isolate S. pilosicoli P43/6/78 from the United Kingdom and 19 field isolates obtained from pigs in Canada (n = 5) and the United States (n = 14) were determined against the antimicrobial agents carbadox, gentamicin, lincomycin, and tiamulin, all of which are commonly used for control of the related pathogenic intestinal spirochete S. hyodysenteriae. Additionally, the susceptibility or resistance of each isolate against each antimicrobial agent was estimated on the basis of available data on the in vitro antimicrobial susceptibility breakpoints of S. hyodysenteriae. Each isolate was identified on the basis of phenotypic and genotypic markers, and the minimum inhibitory concentration of each antimicrobial agent was determined by the agar-dilution method. All the isolates were susceptible to carbadox and tiamulin. The percentages of isolates susceptible, intermediate, and resistant to lincomycin were 42.1%, 42.1%, and 15.8%, respectively. Slightly less than half of the isolates (47.4%) were susceptible to gentamicin, and the remainder (52.6%) were resistant. Implementation of rational control measures to reduce infection by S. pilosicoli should improve overall health and productivity in swine herds.

Canine intestinal spirochetes consist of Serpulina pilosicoli and a newly identified group provisionally designated "Serpulina canis" sp. nov

The spirochetes inhabiting the large intestines of humans and animals consist of a diverse group of related organisms. Intestinal spirochetosis caused by Serpulina pilosicoli is a newly recognized enteric disease of human beings and animals with potential public health significance. The purpose of this study was to determine the species identity of canine intestinal spirochetes by comparing 30 isolates obtained from dogs in Australia (n = 25) and the United States (n = 5) with reference strains representing Serpulina species and Brachyspira aalborgi, by phenotypic and genetically based typing methods. All of the canine isolates were indole negative and produced a weak beta-hemolysis when cultured anaerobically on agar medium containing blood. Four isolates were identified as S. pilosicoli by 16S rRNA-specific PCR assays, rRNA gene restriction fragment length polymorphism or ribotyping, and multilocus enzyme electrophoresis. The remaining 26 isolates formed a cluster related to porcine Serpulina innocens as determined by multilocus enzyme electrophoresis but had a unique ribotype pattern. The data suggested the existence of a novel Serpulina species, provisionally designated "Serpulina canis," colonizing the intestines of dogs.

Evaluation of day-old specific pathogen-free chicks as an experimental model for pathogenicity testing of intestinal spirochaete species

Specific pathogen-free chicks aged 1 day were challenged per os with strains of five different species of intestinal spirochaete originally isolated from pigs or human beings. A virulent strain of Serpulina hyodysenteriae (WA 15) colonized chicks, causing retarded growth rate and histological changes, including caecal atrophy, epithelial and goblet cell hyperplasia, and crypt elongation. A further strain of S. hyodysenteriae (SA3), which was apparently avirulent for pigs, and a strain of Serpulina intermedia (889) colonized fewer chicks, caused less severe lesions and did not significantly depress growth rate. Strains of Serpulina murdochii and Brachyspira aalborgi failed to colonize or cause histological changes. Four strains of Serpulina pilosicoli (Kar, Rosie-2299 and GAP 401, isolated from human beings, and 3295, isolated from a pig) colonized chicks, and large numbers showed polar attachment to the caecal epithelium; all strains, apart from Rosie-2299, caused watery diarrhoea and wet litter, but did not significantly retard growth. Variation both in the degree of spirochaetal attachment and the resulting development of lesions was observed between S. pilosicoli strains as well as between individual chicks infected with the same strain. The study indicated that chicks may be useful in studying the pathogenicity of strains of S. hyodysenteriae, S. intermedia and S. pilosicoli.

Restriction fragment length polymorphism of the periplasmic flagellar flaA1 gene of Serpulina species

Forty-one reference and field isolates of intestinal spirochetes representing Serpulina hyodysenteriae, Serpulina innocens, Serpulina pilosicoli, Brachyspira aalborgi, and nonclassified weakly beta-hemolytic intestinal spirochetes were compared by restriction fragment length polymorphism (RFLP) of the periplasmic flagellar (PF) flaA1 gene. Six genetically distinct groups (I through VI), each with a unique RFLP fingerprint pattern, were identified by Southern blotting analysis of EcoRV chromosomal DNA digests with a PCR-amplified digoxigenin-labeled 1-kb fragment of the S. hyodysenteriae isolate B78 PF flaA1 gene. The RFLP fingerprint patterns corresponded to known DNA homology differences between Serpulina species and to provisionally designated species described previously by using phenotypic and genotypic classification schemes. RFLP fingerprinting of the PF flaA1 gene provides a relatively simple genotypic method for identification of intestinal spirochetes without the use of radioisotopes.

Evidence for Serpulina hyodysenteriae being recombinant, with an epidemic population structure

The population structure of Serpulina hyodysenteriae was investigated using multilocus enzyme electrophoresis. A total of 231 isolates were divided into 50 electrophoretic types (ETs), with a mean genetic diversity of 0.29 for the number of ETs and 0.23 for the number of isolates. Subsets of isolates from two Australian states (71 isolates from Victoria and 68 isolates from Queensland) exhibited as much genetic variation as the entire collection. The calculated index of association (IA) for the number of ETs (0.29 +/- 0.17) was not significantly different from zero, and hence provided evidence for the occurrence of significant genetic recombination accounting for the observed variation between strains. In contrast, the IA for the number of isolates (3.93 +/- 0.03) was significantly different from zero, with seven of the 50 ETs (ETs 4, 6, 13, 14, 20, 33 and 35) containing 51% of all the isolates. Even when multiple isolates from the same farm were removed from the analysis, the IA value for the number of isolates remained significantly greater than zero (IA 9.87 +/- 0.04), indicating that it was not biased by their inclusion. The results suggest that S. hyodysenteriae has an epidemic population structure.

Sub-specific differentiation of intestinal spirochaete isolates by macrorestriction fragment profiling

Macrorestriction fragment profile analysis by PFGE was used to distinguish intestinal spirochaetes, some of which were isolated from cases of swine dysentery and intestinal spirochaetosis in humans, pigs, mice, chickens and dogs. Macrorestriction fragment profiles using SmaI and SacII restriction enzymes were produced and used in statistical analysis. This permitted the division of the isolates into two major clusters. One cluster contained isolates which were identified as Serpulina pilosicoli and the second cluster contained isolates identified as Serpulina hyodysenteriae by immunoblotting with species-specific mAbs. Both species contained sub-specific groups, although these rarely correlated with the source of the isolates. We conclude that PFGE is capable of sub-specific differentiation of intestinal spirochaetes, but that the current species contain a large variety of genotypes among which cross-species transmission may be feasible.

Genetic and phenotypic characterization of intestinal spirochetes colonizing chickens and allocation of known pathogenic isolates to three distinct genetic groups

Infection with intestinal spirochetes has recently been recognized as a cause of lost production in the poultry industry. Little is known about these organisms, so a collection of 56 isolates originating from chickens in commercial flocks in Australia, the United States, The Netherlands, and the United Kingdom was examined. Strength of beta-hemolysis on blood agar, indole production, API ZYM enzyme profiles, and cellular morphology were determined, and multilocus enzyme electrophoresis was used to analyze the extent of genetic diversity among the isolates. The results were compared with those previously obtained for well-characterized porcine intestinal spirochetes. The chicken isolates were genetically heterogeneous. They were divided into 40 electrophoretic types distributed among six diverse genetic groups (groups b to g), with a mean genetic diversity of 0.587. Strains in two groups (groups d and e) may represent new species of Serpulina, and the groups contained only strains isolated from chickens. Three genetic groups contained isolates previously shown to be pathogenic for chickens. These corresponded to the proposed species "Serpulina intermedius," to an unnamed group (group e), and to Serpulina pilosicoli. Two of the chicken isolates (one "S. intermedius" and one S. pilosicoli isolate) were strongly beta-hemolytic, two (both "S. intermedius") had an intermediate level of beta-hemolysis, and the rest were weakly beta-hemolytic. Fourteen isolates of "S. intermedius" produced indole, as did one isolate from group d. Isolates identified as S. pilosicoli resembled porcine isolates of this species, having four to six periplasmic flagella inserted subterminally in a single row at each end of the cell, and had tapered cell ends. All other spirochetes were morphologically similar, having seven or more periplasmic flagella and blunt cell ends. The identification of three genetic groups containing pathogenic isolates provides an opportunity for more detailed epidemiologic studies with these pathogens and for the development of improved diagnostic tests.

Genetic relatedness amongst intestinal spirochaetes isolated from rats and birds

Multilocus enzyme electrophoresis was used to determine genetic relationships amongst 32 intestinal spirochaetes (Serpulina spp.) isolated from rats (17), rheas (7), chickens, (4), ducks (2), a swan (1) and a flamingo (1). The strains were divided into 20 electrophoretic types (ETs), with a mean genetic diversity per locus of 0.62. The results were compared with those previously published for porcine intestinal spirochaetes. One strain from a healthy rat, and three rhea strains which were recovered from cases of necrotizing typhlitis, were grouped in the same ETs as certain porcine strains of Serpulina hyodysenteriae. The rhea strains could be differentiated from these by pulsed-field gel electrophoresis. Fifteen of the rat strains were genetically and phenotypically closely related. In contrast the avian strains were genetically more heterogeneous, with pathogenic isolates located in three different genetic groups.

Identification of the swine pathogen Serpulina hyodysenteriae in rheas (Rhea americana)

Recently intestinal spirochetes were isolated from rheas in Ohio and Iowa with a necrotizing typhlocolitis. These intestinal spirochetes, strains R1 and NIV-1, were characterized and compared with other intestinal spirochetes, including strains of S. hyodysenteriae. Both rhea spirochetes were indole positive, strongly beta-hemolytic, grew under a 1% O2:99% N2 atmosphere, and were morphologically similar to spirochetes in the genus Serpulina. Analysis of rRNA gene restriction patterns (ribotypes), and immunoblots of whole cell proteins, indicated both spirochetes were similar to Serpulina hyodysenteriae strains from swine. Comparisons of nearly complete sequences (> 1458 bases) of the 16S rRNA gene of the two rhea spirochetes with S. hyodysenteriae strains confirmed that rhea spirochetes R1 and NIV-1 were strains of S. hyodysenteriae. These results indicate that S. hyodysenteriae has a broader host range than previously recognized.

Phenotypic characteristics of Serpulina pilosicoli the agent of intestinal spirochaetosis

The phenotypic characteristics of three Serpulina pilosicoli strains isolated from humans with diarrhoea (WesB, Kar, Hrm7) and two porcine S. pilosicoli strains isolated from pigs with intestinal spirochaetosis (1648, 3295), were compared with the type strain of the species P43/6/78T (T = type strain) and other intestinal spirochaetes within the genus Serpulina. All S. pilosicoli strains had a characteristic ultrastructural appearance, displayed similar growth rates, hydrolysed hippurate, lacked beta-glucosidase activity, utilised D-ribose as a growth substrate, and had similar sensitivities to rifampicin and spiramycin. The only consistent phenotypic characteristic that differentiated human strains from porcine strains of S. pilosicoli was that the human strains all utilised the pentose sugar D-xylose. These distinguishing phenotypic traits appear useful for identifying S. pilosicoli.