Molecular studies on ancient M. tuberculosis and M. leprae: methods of pathogen and host DNA analysis.

Humans have evolved alongside infectious diseases for millennia. Despite the efforts to reduce their incidence, infectious diseases still pose a tremendous threat to the world population. Fast development of molecular techniques and increasing risk of new epidemics have resulted in several studies that look to the past in order to investigate the origin and evolution of infectious diseases. Tuberculosis and leprosy have become frequent targets of such studies, owing to the persistence of their molecular biomarkers in ancient material and the characteristic skeletal lesions each disease may cause. This review examines the molecular methods used to screen for the presence of M. tuberculosis and M. leprae ancient DNA (aDNA) and their differentiation in ancient human remains. Examples of recent studies, mainly from Europe, that employ the newest techniques of molecular analysis are also described. Moreover, we present a specific approach based on assessing the likely immunological profile of historic populations, in order to further elucidate the influence of M. tuberculosis and M. leprae on historical human populations.

Insights gained from palaeomicrobiology into ancient and modern tuberculosis.

The direct detection of ancient Mycobacterium tuberculosis molecular biomarkers has profoundly changed our understanding of the disease in ancient and historical times. Initially, diagnosis was based on visual changes to skeletal human remains, supplemented by radiological examination. The introduction of biomolecular methods has enabled the specific identification of tuberculosis in human tissues, and has expanded our knowledge of the palaeopathological changes associated with the disease. We now realize that the incidence of past tuberculosis was greater than previously estimated, as M. tuberculosis biomarkers can be found in calcified and non-calcified tissues with non-specific or no visible pathological changes. Modern concepts of the origin and evolution of M. tuberculosis are informed by the detection of lineages of known location and date.

New skeletal tuberculosis cases in past populations from Western Hungary (Transdanubia).

The distribution, antiquity and epidemiology of tuberculosis (TB) have previously been studied in osteoarchaeological material in the eastern part of Hungary, mainly on the Great Plain. The purpose of this study is to map the occurrence of skeletal TB in different centuries in the western part of Hungary, Transdanubia, and to present new cases we have found. Palaeopathological analysis was carried out using macroscopic observation supported by radiographic and molecular methods. A large human osteoarchaeological sample (n=5684) from Transdanubian archaeological sites ranging from the 2nd to the 18th centuries served as a source of material. Spinal TB was observed in seven individuals (in three specimens with Pott's disease two of which also had cold abscess) and hip TB was assumed in one case. The results of DNA for Mycobacterium tuberculosis were positive in seven of the eight cases identified by paleopathology, and negative in the assumed case of hip TB. However, the molecular results are consistent with highly fragmented DNA, which limited further analysis. Based on the present study and previously published cases, osteotuberculosis was found in Transdanubia mainly during the 9th-13th centuries. However, there are no signs of TB in many other 9th-13th century sites, even in those that lie geographically close to those where osteotuberculous cases were found. This may be due to a true absence of TB caused by the different living conditions, way of life, or origin of these populations. An alternative explanation is that TB was present in some individuals with no typical paleopathology, but that death occurred before skeletal morphological features could develop.

PCR primers that can detect low levels of Mycobacterium leprae DNA.

There are several specific PCR-based methods to detect Mycobacterium leprae DNA, but the amplicons are quite large. For example, primers that target the 36-kDa antigen gene and are in common diagnostic use yield a 530-bp product. This may be a disadvantage when examining samples in which the DNA is likely to be damaged and fragmented. Therefore, two sets of M. leprae-specific nested primers were designed, based on existing primer pairs which have been shown to be specific for M. leprae. Primers that targeted the 18-kDa antigen gene gave an outer product of 136 bp and inner product of 110 bp. The primers based on the RLEP repetitive sequence yielded a 129-bp outer product and 99-bp nested product. With dilutions of a standard M. leprae killed whole-cell preparation as the source of DNA, both single-stage and nested PCR were performed after optimisation of the experimental conditions. Compared with the 36-kDa antigen gene primers, the 18-kDa antigen gene outer primers were 100-fold more sensitive and the RLEP outer primers were 1000-fold more sensitive. As an illustration of two possible applications of these new primers, positive results were obtained from three skin slit samples from treated lepromatous leprosy patients and three archaeological samples from human remains showing typical leprosy palaeopathology. It was concluded that these new primers are a useful means of detecting M. leprae DNA which is damaged or present at a very low level.

Tropheryma whippelii DNA in saliva of healthy people.

In a random sample of 40 healthy people, 35% showed evidence of Tropheryma whippelii DNA in their saliva. Consistent detection of T. whippelii DNA on repeated sampling suggests that this organism can be an oral commensal.

Mycobacterium tuberculosis complex DNA in calcified pleura from remains 1400 years old.

Mycobacterium tuberculosis complex DNA was isolated and identified in calcified pleura from remains 1400 years old, with the polymerase chain reaction. This is the first demonstration of tuberculosis in non-mummified archaeological tissue other than bone; the presence of mycobacterial mycolic acids in the sample supports this conclusion. The study of ancient DNA from microbial pathogens is of interest as it enables verification of traditional diagnoses, may answer long-standing questions in the history of disease, and provides ancient DNA sequences that can be compared with those of modern isolates.

A longitudinal study of environmental mycobacteria on a farm in south-west England.

Soil, stream beds and cattle drinking troughs were sampled every 3 months over 3 years. More than 750 putative mycobacteria were isolated and grouped into more than 50 biotypes pending full identification. Samples from woodland and farmed land yielded fewer isolates per site compared with other terrains (P < 0.05). Some seasonal effects were noted but the greatest difference was between years 1 and 3. This appeared not to be due to differences in temperature, rainfall or experimental procedure, but coincided with the introduction of organic farming practices. In year 3 there was a significant increase in nitrate-reducing slow growers, both pigmented (P < or = 0.006) and non-pigmented strains (P < or = 0.002), and a shift in biotypes was noted. In contrast, all fast growers declined with time, as did those slow growers unable to reduce nitrate. Changing farming practice may alter the profile of environmental mycobacteria, which has important implications for the immunological priming of humans and animals.

Variation within Mycobacterium scrofulaceum.

The purpose of this study was to identify Mycobacterium scrofulaceum reliably and rapidly and investigate diversity within the species. Fifty-four cultures were identified as Myco. scrofulaceum by preliminary cultural and biochemical tests, thin-layer chromatography and double diffusion. These strains were examined by PCR based on the 65 kDa heat stress protein gene, followed by restriction enzyme analysis of the product with BstEII and HaeIII. This produced seven groups, most with fewer fragments than had been reported previously. The technique was a rapid and reliable method for studying variation within Myco. scrofulaceum but alone, was unable to discriminate between some of these variants and other genetically similar species. When PCR-RFLP results were combined with biochemical tests, the major groups appeared to relate to different disease situations and thus, may have some epidemiological value.

Application of polymerase chain reaction for the detection of Mycobacterium leprae DNA in specimens from treated leprosy patients.

In this study of leprosy patients apparently cured by dapsone monotherapy, the polymerase chain reaction (PCR), one of the most reliable and sensitive DNA-based assays, was used for the specific detection of Mycobacterium leprae DNA. Sputum and slit-skin samples from 44 such patients at Baba Baghi Leprosy Sanatorium in Iran were examined. Primers for a 530-base-pair fragment of the gene encoding the 36-kDa antigen of M. leprae were used for the study. The PCR results were compared with microscopy for acid-fast bacilli. Of the 44 sputum samples, 2 were positive by PCR (4.5%) and of the 44 slit-skin swabs taken from the same patients, 10 were PCR positive (22.7%). Only one patient was PCR positive for both sputum and slit-skin specimens (2.3%). No positive results were found by acid-fast microscopy. In total, 11 of 44 (25%) patients in this study were found to be PCR positive for M. leprae, and it was thought probable that this indicated the presence of live organisms. Particularly interesting was the statistically significant association of positive results from slit-skin swabs with paucibacillary rather than multibacillary leprosy. It is suggested that whereas relapse or immunological reaction in paucibacillary disease may result from surviving organisms, in multibacillary leprosy this may be due to re-infection.

Effect of nutrients on defined bacterial plaques and Streptococcus mutans C67-1 implantation in a model mouth.

Actinomyces viscosus WVU 627, Streptococcus oralis LPA-1 and Veillonella dispar OMZ 193 were cocultured on teeth in a model mouth for 66 h. Synthetic saliva containing bovine salivary glycoprotein supported bacterial growth, although the delivery of an intermittent nutrient supplement, containing 1% (w/v) glucose or sucrose, gave greater bacterial cell and viable counts. When Streptococcus mutans C67-1 was super-inoculated onto 24-hour mixed plaques, it became established under all regimens, but there was pronounced colonization resistance. With saliva only, the proportion of S. mutans at 66 h was less than 0.5% of the total cultivable microflora. When a glucose supplement was delivered for 1 h every 6 h, S. mutans attained a final proportion of 2.4%. With sucrose, both S. mutans C67-1 and its non-cariogenic glucan-deficient mutant, C67-25, attained similar proportions of 15-20%. These experiments indicate how this model can be used to study the factors influencing colonizing ability and microbial interactions in biofilms under controlled conditions.

Colonization resistance of defined bacterial plaques to Streptococcus mutans implantation on teeth in a model mouth.

We investigated the ability of Streptococcus mutans C67-1 to colonize simple bacterial plaques and the effects of age and stability of the pre-formed plaque on colonization resistance. Mixed-plaques of Actinomyces viscosus WVU627, 'Streptococcus mitior' LPA-1, and Veillonella dispar OMZ193 were grown on tooth segments, mounted back to back for simulation of approximal sites in a model mouth for 66 h. S. mutans C67-1 was either included in the original inoculum or super-inoculated onto the developing plaque. Inclusion of S. mutans C67-1 did not alter the total viable counts, but the proportional composition changed due to inter-species interactions. Colonization resistance of the mixed-plaque samples developed within 24 h, although S. mutans C67-1 was always able to colonize these stagnation sites. Colonization resistance of 24-hour plaque against a fresh isolate, S. mutans CP3, was also studied. There was greater colonization resistance by the basic plaque to this organism, compared with S. mutans C67-1, although the reasons for this were not clear. These initial experiments demonstrate the way in which the factors involved in bacterial colonization resistance in microbial films on teeth can be studied under controlled conditions.

A laboratory microcosm (artificial mouth) for the culture and continuous pH measurement of oral bacteria on surfaces.

A laboratory microcosm has been designed for the cultivation of bacteria on surfaces subjected to an adjustable supply of fluids. Bacteria are grown as a microbial film on halved premolar teeth, mounted back to back. Synthetic saliva is dropped slowly over the teeth throughout experiments. A nutrient supplement is provided at regular intervals. The drops of fluid retained by the teeth can be sampled for metabolic end-products. Alternatively, a miniature glass electrode may be set into one half of a tooth assembly to monitor the pH continuously at the stagnation site between tooth segments. Up to six replicate culture flasks and six electrodes can be accommodated in a single experiment. Satisfactory electrode performance was maintained during 66 h experiments. In initial 48 h experiments, teeth were inoculated with Streptococcus rattus BHT or 'Streptococcus mitior' LPA-1 in pure culture and provided with 1% (w/v) glucose for 1 h every 6 h. Bacteria produced typical responses to glucose feeds leading to the formation of 'Stephan'-like curves of pH-fall. Under these conditions, 'Strep. mitior' was more acidogenic than Strep. rattus and the pattern of acid production was distinct for each organism.

The role of H2O2 and the lactoperoxidase-SCN(-)-H2O2 system on the interaction between two bacteria originating from human dental plaque, Streptococcus rattus (mutans) BHT and Streptococcus mitior LPA-1, grown on human teeth in an artificial mouth.

Teeth were inoculated with either the organisms separately or with a freshly-prepared mixture of both. The apparatus was swept with 5 per cent (v/v) CO2 in either air or N2, and incubated for 90 h. A nutrient supplement containing 1 per cent (w/v) glucose was supplied for 1 h in every 6 h. Both organisms achieved similar numbers when grown aerobically in pure culture, yet in mixed culture there was pronounced inhibition of BHT (p less than 0.001). When the synthetic saliva was supplemented with catalase the strain BHT count in mixed culture was much higher (p less than 0.001). It was concluded, therefore, that the strain LPA-1 produced inhibitory levels of hydrogen peroxide (H2O2) on the tooth surface under aerobic conditions. This was supported by finding that a lower viable count of LPA-1 in pure culture was attained when lactoperoxidase (LPO) was included in the saliva (p less than 0.005), as all components of the LPO-SCN-H2O2 system were presumably present. With the N2-CO2 mixture, conditions were not strictly anaerobic and both catalase and LPO increased all viable counts. Under these conditions, therefore, when H2O2 was limiting, LPO protected bacteria against its bactericidal effect.

Effect of inoculation sequence and nutrients upon Streptococcus mutans BHT and Streptococcus mitior LPA-1 growing on human teeth in an artificial mouth.

Human teeth in an artificial mouth were inoculated with Streptococcus mutans BHT, Streptococcus mitior LPA-1, or sequentially with both organisms. Incubation was continued for 90 h. Mixed populations were largest when a nutrient supplement containing 5.0% (w/v) sucrose was supplied. Fewer organisms were recovered from experiments with synthetic saliva only, or when a supplement containing 0.05% (w/v) glucose was available. The inoculation sequence determined the total viable count and a larger population resulted when Strep. mutans was the initial colonizer (P less than 0.01). Strep. mutans was always able to become established even when super-infected on to a 24 h plaque of Strep. mitior. The final proportion of Strep mutans was lower when it was the superinfecting organism and the sucrose (P less than 0.01) or glucose (P less than 0.05) nutrient supplement was provided. This work confirms the importance of inoculation sequence and presence of sugars in plaque accumulation and demonstrates the fundamental role of microbial interactions in this process.

Discrimination between oral streptococci by pyrolysis gas-liquid chromatography.

Washed organisms, including strains of Streptococcus mitior, S. mutans, and S. sanguis, were examined by curie-point pyrolysis gas-liquid chromatography. A linear discriminant function based upon three items from the output data was adequate for segregating the strains according to species. Strains with intermediate properties were also encountered. Sources of variability in cultures were evaluated, chromatographic performance was maintained throughout the investigation, and matching performance from a duplicate pair of chromatographic columns was demonstrated.