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The ability to sequence genomes from ancient biological material has provided a rich source of information for evolutionary biology and engaged considerable public interest. Although most studies of ancient genomes have focused on vertebrates, particularly archaic humans, newer technologies allow the capture of microbial pathogens and microbiomes from ancient and historical human and non-human remains. This coming of age has been made possible by techniques that allow the preferential capture and amplification of discrete genomes from a background of predominantly host and environmental DNA. There are now near-complete ancient genome sequences for three pathogens of considerable historical interest - pre-modern bubonic plague (Yersinia pestis), smallpox (Variola virus) and cholera (Vibrio cholerae) - and for three equally important endemic human disease agents - Mycobacterium tuberculosis (tuberculosis), Mycobacterium leprae (leprosy) and Treponema pallidum pallidum (syphilis). Genomic data from these pathogens have extended earlier work by paleopathologists. There have been efforts to sequence the genomes of additional ancient pathogens, with the potential to broaden our understanding of the infectious disease burden common to past populations from the Bronze Age to the early 20 th century. In this review we describe the state-of-the-art of this rapidly developing field, highlight the contributions of ancient pathogen genomics to multidisciplinary endeavors and describe some of the limitations in resolving questions about the emergence and long-term evolution of pathogens., (Crown Copyright © 2020. Published by Elsevier Inc. All rights reserved.)

Background: Recently, the World Health Organization launched a campaign to eradicate the tropical disease yaws, caused by the bacterium Treponema pallidum subsp. pertenue; however, for decades researchers have questioned whether flies act as a vector for the pathogen that could facilitate transmission., Methods: A total of 207 fly specimens were trapped in areas of Africa in which T. pallidum-induced skin ulcerations are common in wild baboons; 88 flies from Tarangire National Park and 119 from Lake Manyara National Park in Tanzania were analyzed by PCR for the presence of T. pallidum DNA., Findings: We report that in the two study areas, T. pallidum DNA was found in 17-24% of wild-caught flies of the order Diptera. Treponemal DNA sequences obtained from many of the flies match sequences derived from nearby baboon T. pallidum strains, and one of the fly species with an especially high prevalence of T. pallidum DNA, Musca sorbens, has previously been shown to transmit yaws in an experimental setting., Interpretation: Our results raise the possibility that flies play a role in yaws transmission; further research is warranted, given how important understanding transmission is for the eradication of this disfiguring disease., (Copyright © 2016 Forschungsgesellschaft für Arbeitsphysiologie und Arbeitschutz e.V. Published by Elsevier B.V. All rights reserved.)

Reasons for Performing Study: Equine hoof canker is a chronic pododermatitis of still unknown aetiology. Recent findings reported for 3 canker-bearing individuals are suggestive for Treponema spp. having a role in disease pathogenesis., Objectives: Based on this hypothesised association, we assessed a larger number of DNA samples from hooves with canker and normal hooves for the presence of treponemal DNA., Study Design: Retrospective survey of archived material., Methods: The study involved 71 archival, PCR-compatible DNA extractions purified from 59 canker samples obtained from 26 equine cases and from 12 hoof biopsies taken from 9 canker-free control horses. Presence of treponemal DNA was assessed by qualitative PCR using 4 different primer pairs recognising in sum a broad range of Treponema ssp. Obtained amplification products were identified by bidirectional sequencing and BLAST alignment., Results: Treponemal DNA was detected in 37 of 59 canker DNA samples from 19 of 26 cases and in 9 of 12 hoof DNA samples from 7 of 9 healthy individuals. Canine oral Treponema sp. and Treponema medium ssp. bovis were the most frequently detected treponemal sequences in hoof canker, while control tissues were mainly shown to harbour Treponema refringens-like or canine oral Treponema-like DNA. All control samples tested negative for T. medium ssp. bovis DNA., Conclusions: Treponema DNA was detectable in the majority of hoof canker and control samples. The sample groups differed to some extent regarding identified Treponema phylotypes; however, this finding may be explained by the methodology used. Treponemes that are highly similar to bovine digital dermatitis treponemes are present in canker lesions. However, further work is needed to clarify the specific contribution of the identified Treponema phylotypes to the pathogenesis of disease., (© 2014 EVJ Ltd.)

Morphologically and biochemically diverse members of the Treponema genus are present in the gastrointestinal tract of ruminants, yet very little is understood about their functional importance to this microbiome. Here we describe the annotated draft genome sequence of Treponema sp. strain JC4, a novel spirochete isolated from a bovine rumen sample.

Advances in bacterial genetics came with the discovery of the genetic code, followed by the development of recombinant DNA technologies. Now the field is undergoing a new revolution because of investigators' ability to sequence and assemble complete bacterial genomes. Over 200 genome projects have been completed or are in progress, and the oral microbiology research community has benefited through projects for oral bacteria and their non-oral-pathogen relatives. This review describes features of several oral bacterial genomes, and emphasizes the themes of species relationships, comparative genomics, and lateral gene transfer. Genomics is having a broad impact on basic research in microbial pathogenesis, and will lead to new approaches in clinical research and therapeutics. The oral microbiota is a unique community especially suited for new challenges to sequence the metagenomes of microbial consortia, and the genomes of uncultivable bacteria.

Molecular methods have been used recently to investigate the bacteria encountered in human endodontic infections. The aim of the present study was to compare the ability of a 16S rDNA-based PCR assay and checkerboard DNA-DNA hybridisation in detecting Actinobacillus actinomycetemcomitans, Bacteroides forsythus, Peptostreptococcus micros, Porphyromonas endodontalis, Por. gingivalis and Treponema denticola directly from clinical samples. Specimens were obtained from 50 cases of endodontic infections and the presence of the target species was investigated by whole genomic DNA probes and checkerboard DNA-DNA hybridisation or taxon-specific oligonucleotides with PCR assay. Prevalence of the target species was based on data obtained by each method. The sensitivity and specificity of each molecular method was compared with the data generated by the other method as the reference--a value of 1.0 representing total agreement with the chosen standard. The methods were also compared with regard to the prevalence values for each target species. Regardless of the detection method used, T. denticola, Por. gingivalis, Por. endodontalis and B. forsythus were the most prevalent species. If the checkerboard data for these four species were used as the reference, PCR detection sensitivities ranged from 0.53 to 1.0, and specificities from 0.5 to 0.88, depending on the target bacterial species. When PCR data for the same species were used as the reference, the detection sensitivities for the checkerboard method ranged from 0.17 to 0.73, and specificities from 0.75 to 1.0. Accuracy values ranged from 0.6 to 0.74. On the whole, matching results between the two molecular methods ranged from 60% to 97.5%, depending on the target species. The major discrepancies between the methods comprised a number of PCR-positive but checkerboard-negative results. Significantly higher prevalence figures for Por. endodontalis and T. denticola were observed after PCR assessment. There was no further significant difference between the methods with regard to detection of the other target species.

We examined 26 atherosclerotic lesions and 14 nondiseased aorta specimens to detect the periodontopathogenic part of the bacterial 16S rRNA locus by PCR. Treponema denticola sequence of the 16S rRNA locus was found in 6 out of 26 DNA samples (23.1%) from the formalin-fixed, paraffin-embeded atherosclerotic lesions obtained during surgery but not in any of the 14 nondiseased aorta samples from deceased persons. Utilizing immunofluorescence microscopy, we observed aggregated antigenic particles reacting with rabbit antiserum against T. denticola in thin sections of the PCR-positive samples, but we could not detect any reacting particles in the PCR-negative thin sections.

The species Treponema pallidum includes three subspecies (pallidum, pertenue, and endemicum) that cause syphilis, yaws, and bejel, respectively. A closely related species, Treponema paraluiscuniculi, is the etiologic agent of venereal syphilis in rabbits but does not infect humans. Although these treponemes cause distinct diseases, no laboratory method for differentiation has been reported. Genetic signatures were defined in the 5' and 3' flanking regions of the 15-kDa lipoprotein gene (tpp15) that distinguish the human pathogens and T. paraluiscuniculi, as well as distinguishing T. pallidum subsp. pallidum from the causes of human nonvenereal treponematoses. A single Eco47III restriction site in the 5' flanking region differentiates T. pallidum subsp. pallidum from the other subspecies and species, and an XcmI site in the 3' flanking region differentiates T. paraluiscuniculi from the human pathogens. Polymerase chain reaction methods and restriction polymorphism were used to analyze 27 strains of pathogenic Treponema species.

Fifteen oral spirochete strains belonging to the species Treponema denticola, Treponema vencentii and Treponema socranskii as well as 9 fresh clinical isolates were screened for the presence of extrachromosomal plasmid DNA by a modified alkaline lysis procedure. A 2.6-kb plasmid was detected in both T. denticola ATCC 33520 and T. denticola e'. The 2.6-kb plasmid from T. denticola e' was shown to be similar to pTD1, previously reported by Ivic et al. in T. denticola ATCC 33520 on the basis of molecular weight, restriction endonuclease profile and DNA:DNA hybridization. T. denticola ATCC 33520 and T. denticola e' share 65% DNA homology and belong to different serological groups. This dissimilarity has been reconfirmed by specific immunofluorescence using polyclonal and monoclonal antibodies. A plasmid-free T. denticola ATCC 33520 was identified. Comparative studies have shown no antigenic, morphological, or genetic differences between the plasmid-bearing and the plasmid-free strain. In addition, screening of fresh clinical isolates of spirochetes revealed the presence of a 4.2-kb plasmid in 4 of these strains.

In the present study DNA restriction patterns and corresponding ribotypes of 17 subgingival small-sized spirochetes (1:2:1 and 2:4:2 isolates), 2 Treponema socranskii strains and two Treponema denticola strains were examined. Purified chromosomal DNA was digested by BamHI, HindIII, PstI and ClaI. The DNA fragments were separated in a horizontal slab of 0.7% agarose containing ethidium bromide and transferred by nylon membranes. Hybridization was carried out with digoxigenin-labelled copy DNA of 16S and 23S ribosomal RNA from Escherichia coli. Depending on the restriction endonuclease used, up to 4 distinct bands were observed for the 2:4:2 isolates and the T. denticola strains. For each of the endonucleases used, identical band patterns were always observed for this group of isolates, and these patterns differed persistently from the T. denticola strains. For the 1:2:1 strains, up to 11 distinct bands were observed after digestion with HindIII, whereas a maximum of 6 bands were observed when PstI or ClaI was used. By using ClaI, the examined 1:2:1 isolates were separated into 8 groups, whereas PstI and HindIII separated these isolates into 5 groups. The ribotyping showed that the tested 1:2:1 spirochetes were more heterogeneous than the 2:4:2 spirochetes examined.

Three of 16 isolates of Treponema denticola were found to contain small (2.0-2.7 kb) cryptic plasmids. These were pTD1 from T. denticola ATCC 33520, pTD2 from strain T32A, and pTD3 from strain D3A1. These plasmids were characterized by restriction mapping and cloned into E. coli plasmid pUC19. Extensive homology between these plasmids was revealed by Southern blot, and single-stranded DNA regions were found by neutral Southern blots and S1 nuclease mapping. These plasmids were not found in serovars usually associated with human periodontal disease nor are they universal in all T. denticola strains and serovars.

The purposes of this study were two-fold: to compare the DNA probe and enzyme linked immunosorbent assay (ELISA) microbial identification tests and correlate the levels of microorganisms with adult periodontitis. A single plaque sample were taken from each of 2 sites in 52 patients. Twelve of these patients were also sampled during and after treatment. The experimental site had clinical indicators of disease (bleeding on probing, probing and attachment loss of > or = 6 mm) and the contralateral site (control) was clinically healthy. A total of 176 plaque samples were collected, divided, processed, and sent for both types of quantitative microbial analyses. All of these samples were used to compare the DNA probe and ELISA methods while only the initial 104 pretreatment sites were used to correlate microorganisms/method with clinical indicators of adult periodontitis. DNA probes were used to assay for A. actinomycetemcomitans, P. gingivalis, P. intermedia, E. corrodens, F. nucleatum, T. denticola, and C. rectus. An ELISA utilizing monoclonal antibodies was used to assay for P. gingivalis, E. corrodens, T. denticola, and C. rectus. Comparison of the two methods revealed that the ELISA test identified P. gingivalis and C. rectus significantly more often than the DNA probe method and that T. denticola was detected more frequently with the DNA probe. The sensitivities and specificities varied widely among organisms and by test. P. gingivalis, as identified by ELISA, had the highest degree of sensitivity and specificity (0.90 and 0.82 respectively) to clinical indicators of adult periodontitis.

Species-specific DNA probes were used to determine the presence of Actinobacillus actinomycetemcomitans (A.a.), Porphyromonas (Bacteroides) gingivalis, Prevotella intermedia, Treponema denticola, Eikenella corrodens, Fusobacterium nucleatum, and Wolinella recta in subgingival plaque from deep pockets/sites of patients with advanced periodontitis. The subjects were 20 patients with severe adult periodontitis, 13 men and 7 women (mean age 45.6 +/- 6.7 yr). For each subject, 9-10 subgingival sites with the deepest probing depths from each quadrant were sampled by the paper point method, a total of 198 sites, with mean probing depth 7.2 +/- 1.6 mm and clinical attachment level 9.5 +/- 2.7 mm. A.a. was present in at least one site in 75% of the subjects; P. gingivalis was found in 95%; P. intermedia and W. recta were found in 90%, respectively; and T. denticola, E. corrodens, and F. nucleatum were found in all subjects. In the 198 samples, A.a. was detected in 25.8%, P. gingivalis in 51.5%, P. intermedia in 64.1%, T. denticola in 60.6%, E. corrodens in 72.9%, F. nucleatum in 74.7%, and W. recta in 65.7%. The predominant combination was the simultaneous presence of P. intermedia, T. denticola, E. corrodens, F. nucleatum, and W. recta in 89.5% of the subjects and 46.8% of the sites. Of these sites, 51.1% showed the combined presence of P. gingivalis and 28.4% that of both A.a. and P. gingivalis. None of the seven bacteria could be detected in 14.4% of the total sites sampled. The present study indicates that severe destructive adult periodontitis is a multibacterial infection and that certain combinations of periodontopathogens seem to be important in the pathogenesis of the disease.

Serpulina (Treponema) hyodysenteriae strain A-1 partially purified rRNA, labelled with photobiotin, was used as a non-radioactive probe to identify the rRNA gene restriction patterns of S. hyodysenteriae strains and other spirochetes. Sau3A restriction enzyme digests resulted in similar rRNA gene restriction patterns in S. hyodysenteriae strains from five different countries. Some S. hyodysenteriae strains could be differentiated by variations in their rRNA gene restriction patterns after cleavage of DNA by restriction enzymes SspI or BglII. S. innocens and Treponema succinifaciens, non-pathogenic pig intestinal spirochetes, had rRNA gene restriction patterns that differed markedly from the S. hyodysenteriae patterns, and from each other.

A total of 91 isolates of Treponema hyodysenteriae which were obtained from 62 piggeries located around Australia were typed by serology and by DNA restriction endonuclease analysis (REA). The isolates fell into eight serogroups, of which groups B and D were the most common. Isolates with different REA patterns were recognised within serogroups, whilst a few isolates with the same REA pattern were placed into different serogroups. Some of the latter isolates were either from the same piggery or from farms with epidemiological links, thus indicating the bacteria may have altered their antigenic properties. A total of 31 different REA patterns were recognised amongst the Australian isolates. These comprised eight major patterns, with four of these being subdivided on the basis of minor differences in banding. Where a number of isolates were obtained from individual piggeries these all had the same REA pattern, and in one piggery isolates with the same pattern were recovered over a five year period. Plasmid bands were observed in 70 of the Australian isolates (77%), and in six of the seven overseas isolates included in the study for comparison. These plasmids did not affect the REA pattern. Of the States from which substantial numbers of isolates were examined, the greatest number of different strains (12 amongst 19 piggeries) were found from Victoria, and there were 10 REA patterns in strains from 24 piggeries in Queensland. Despite the large total number of different strains of T. hyodysenteriae in Australia, only three were found in more than one State.

A whole chromosomal DNA probe labelled with photobiotin was used in a dot blot hybridisation to identify DNA from isolates of Treponema hyodysenteriae, the aetiological agent of swine dysentery. The probe was evaluated using DNA from 13 isolates of T hyodysenteriae and 13 isolates of non-T hyodysenteriae spirochaetes recovered from pigs. The initial test had both a sensitivity and specificity of 92.3 per cent, although when it was repeated the specificity fell to 84.6 per cent. The test was helpful in distinguishing between T hyodysenteriae and other morphologically similar treponemes that are part of the normal flora in the large intestine of pigs. The probe could also be used to detect as little as 10 ng of purified DNA from T hyodysenteriae, or DNA from 2 x 10(6) bacterial cells lysed directly onto nitrocellulose.

Restriction endonuclease analysis (REA) was used to type eight well-characterised strains of Treponema hyodysenteriae originating from the U.K., Canada and the U.S.A., and 16 isolates from cases of swine dysentery in Western Australia (W.A.). Several of the W.A. isolates were also serotyped by the method of Baum and Joens (1979), and the two typing techniques were compared. REA typing was more discriminatory than serotyping, being able to distinguish strains within serotypes. The new technique was neither more difficult nor more time-consuming to perform than serotyping. Within the 16 W.A. isolates, three different REA patterns were identified, with common patterns found on different farms. The eight overseas strains had seven different REA patterns, all of which could be distinguished from the patterns of the W.A. isolates.

Genetic relationships among two strains of Treponema pallidum (Nichols and KKJ) and a strain of T. pertenue were determined by measuring the degree of deoxyribonucleic acid sequence homology. The results in indicated that these three virulent, noncultivable treponemes were genetically indistinguishable. Like T. pallidum (Nichols), T. pertenue (Gauthier) had no detectable deoxyribonucleic acid sequence homology with T. phagedenis (biotype Reiter), T. refringens (biotype Noguchi), or with salmon sperm.

Lyme disease, a tick-borne disease long recognized in Europe but only recently recognized in the United States, was shown in 1982-1983 to be caused by a spirochete, the Lyme disease spirochete. Whether one or more species of the spirochete exists is unknown, as is its taxonomic status. To answer these questions, we determined (i) the DNA base (guanidine-plus-cytosine) content for five strains; (ii) the DNA relatedness of 10 strains from Europe or the United States (isolated from ticks, humans, and a mouse) by DNA hybridization (hydroxyapatite assay at 50 and 65 degrees C); and (iii) the DNA relatedness to other pathogenic spirochetes. The guanine-plus-cytosine content of the Lyme disease spirochete strains was 27.5 to 29.0 mol%, most similar to those of Borrelia hermsii (30.6 mol%) and Treponema hyodysenteriae (25.6 mol%) among the other spirochetes tested. DNA hybridization studies with 32P-labeled DNA from Lyme disease spirochete strain TLO-005, a human blood isolate, revealed divergence (unpaired bases) within related nucleotide sequences of only 0.0 to 1.0% for all nine Lyme disease spirochete strains tested for relatedness to TLO-005. Relatedness values of seven strains to TLO-005 were 58 to 98% (mean, 71%) in 50 degrees C reactions and 50 to 93% (mean, 69%) in 65 degrees C reactions. Two other strains, from which very low yields of DNA were obtained, showed less relatedness (36 to 50 degrees C, 38 to 47% at 65 degrees C). These were nonetheless considered to belong to the same species because of the low amount of divergence in the sequences related to TLO-005 and the absence of decreased relatedness in reactions done at 65 degrees Celsius compared with those done at 50 degrees Celsius. DNA from strain TLO-005 showed relatedness of 1% to DNAs of two leptospires and 16% relatedness to DNA from T. hyodysenteriae. B. hermsii DNA was 30 to 40% related to three Lyme disease spirochete strains in 50 degrees Celsius reactions. Divergence in these reactions was 16.5 to 18.5%, and relatedness in 65 degree Celsius reactions was 8 to 10%. On the bases of phenotypic similarity, guanine-plus-cytosine content, and DNA relatedness to B. hermsii, we conclude the Lyme disease spirochete is single previously undescribed species which belongs in the genus Borrelia.

Chromosomal deoxyribonucleic acids (DNAs) of five strains formally assigned to Treponema hyodysenteriae and Treponema innocens have been compared. The results of DNA-DNA-hybridization indicate that all the strains belong to the same species. The very low guanine-plus-cytosine values between 24.7 and 29.7 mol% are regarded as further evidence in favour of the reclassification of the swine dysentery agent as Borrelia hyodysenteriae (comb. nov. Blaha).

Genetic studies were performed on the following spirochetes: three Lyme disease spirochetes isolated from Ixodes ticks and from human spinal fluid; three species of North American borreliae; four species of Treponema; and two species of Leptospira. The mol% G+C values for Lyme disease spirochetes were 27.3 to 30.5%, similar to values of 28.0 to 30.5% for Borrelia species but different from the values of Leptospira or Treponema species which ranged from 35.3 to 53%. Lyme disease spirochetes represent a new species of Borrelia, with DNA homologies of 31 to 59% with the three North American strains of Borrelia studied. These studies also showed that Lyme disease spirochetes from three sources constituted a single species, with DNA homologies ranging from 76 to 100%. A high degree of relatedness was also seen between the three North American borreliae, with homology varying from 77 to 95%, indicating that these spirochetes represent a single species. Lyme disease spirochetes and Borrelia species exhibited almost no homology with Leptospira and Treponema species (0 to 2%). Plasmids were detected in the three Lyme disease spirochetes and in the three North American borreliae.

Saturation reassociation assays with 125I-labeled treponemal DNAs show that Treponema hyodysenteriae is genetically unrelated to T. pallidum (Nichols), T. phagedenis biotype Reiter, and T. refringens biotype Noguchi. Pathogenic and nonpathogenic isolates of T. hyodysenteriae exhibited 28% sequence homology and had an extremely low guanine-plus-cytosine content (25.8%).