When did Mycobacterium tuberculosis infection first occur in the New World? An important question with public health implications

Looking Backward To Move Forward: the Utility of Sequencing Historical Bacterial Genomes

Many pathogens that caused devastating disease throughout human history, such as Yersinia pestis, Mycobacterium tuberculosis, and Mycobacterium leprae, remain problematic today. Historical bacterial genomes represent a unique source of genetic information and advancements in sequencing technologies have allowed unprecedented insights from this previously understudied resource. This minireview brings together example studies which have utilized ancient DNA, individual historical isolates (both extant and dead) and collections of historical isolates. The studies span human history and highlight the contribution that sequencing and analysis of historical bacterial genomes have made to a wide variety of fields. From providing retrospective diagnosis, to uncovering epidemiological pathways and characterizing genetic diversity, there is clear evidence for the utility of historical isolate studies in understanding disease today. Studies utilizing historical isolate collections, such as those from the National Collection of Type Cultures, the American Type Culture Collection, and the Institut Pasteur, offer enhanced insight since they typically span a wide time period encompassing important historical events and are useful for the investigating the phylodynamics of pathogens. Furthermore, historical sequencing studies are particularly useful for looking into the evolution of antimicrobial resistance, a major public health concern. In summary, although there are limitations to working with historical bacterial isolates, especially when utilizing ancient DNA, continued improvement in molecular and sequencing technologies and the resourcefulness of investigators mean this area of study will continue to expand and contribute to the understanding of pathogens.

Evidence of neurofibromatosis type 1 in a multi-morbid Inca child mummy: A paleoradiological investigation using computed tomography

Objective

In this study, an Inca bundle was examined using computed tomography (CT). The primary aim was to determine the preservation status of bony and soft tissues, the sex, the age at the time of death, possible indicators for disease or even the cause of death, as well as the kind of mummification. A secondary aim was to obtain a brief overview of the wrapping in order to gain additional information on the cultural background.

Materials and methods

The bundle belongs to the Museum of Cultures in Basel, Switzerland, and was bought in Munich, Germany, in 1921. Radiocarbon dating of the superficial textile yielded a calibrated age between 1480 and 1650 AD. The mummy was investigated using multi-slice CT with slice thickness of 0.75 mm and 110 kilovolt. For standardized assessment of soft tissue preservation, a recently developed checklist was applied.

Results

CT revealed the mummy of a seven to nine year old boy with superior preservation of bony and soft tissues allowing detailed assessment. Indicators of neurofibromatosis type 1 (paravertebral and cutaneous neurofibromas, a breast neurofibroma, sphenoid wing dysplasia), Chagas disease (dilatation of the esophagus, stomach, rectum, and large amounts of feces), and lung infection (pleural adherence, calcifications), probably due to tuberculosis, were found. Furthermore, signs of peri-mortem violence (transection of the chest and a defect in the abdominal wall) were detected. CT images revealed a carefully performed wrapping.

Conclusion

CT examination of the Inca bundle proved to be an important non-destructive examination method. Standardized assessment, especially of the soft tissue structures, allowed for diagnoses of several diseases, indicating a multi-morbid child at the time of death. The careful wrapping pointed to a ceremonial burial. Within the cultural background, the signs of fatal violence were discussed as a possible result of war, murder, accident, or human sacrifice.

From Evolutionary Advantage to Disease Agents: Forensic Reevaluation of Host-Microbe Interactions and Pathogenicity

As the "human microbiome era" continues, there is an increasing awareness of our resident microbiota and its indispensable role in our fitness as holobionts. However, the host-microbe relationship is not so clearly defined for some human symbionts. Here we discuss examples of "accidental pathogens," meaning previously nonpathogenic and/or environmental microbes thought to have inadvertently experienced an evolutionary shift toward pathogenicity. For instance, symbionts such as Helicobacter pylori and JC polyomavirus have been shown to have accompanied humans since prehistoric times and are still abundant in extant populations as part of the microbiome. And yet, the relationship between a subgroup of these microbes and their human hosts seems to have changed with time, and they have recently gained notoriety as gastrointestinal and neuropathogens, respectively. On the other hand, environmental microbes such as Legionella spp. have recently experienced a shift in host range and are now a major problem in industrialized countries as a result of artificial ecosystems. Other variables involved in this accidental phenomenon could be the apparent change or reduction in the diversity of human-associated microbiota because of modern medicine and lifestyles. All of this could result in an increased prevalence of accidental pathogens in the form of emerging pathogens.

Metabolic Perspectives on Persistence

Accumulating evidence has left little doubt about the importance of persistence or metabolism in the biology and chemotherapy of tuberculosis. However, knowledge of the intersection between these two factors has only recently begun to emerge. Here, we provide a focused review of metabolic characteristics associated with Mycobacterium tuberculosis persistence. We focus on metabolism because it is the biochemical foundation of all physiologic processes and a distinguishing hallmark of M. tuberculosis physiology and pathogenicity. In addition, it serves as the chemical interface between host and pathogen. Existing knowledge, however, derives largely from physiologic contexts in which replication is the primary biochemical objective. The goal of this review is to reframe current knowledge of M. tuberculosis metabolism in the context of persistence, where quiescence is often a key distinguishing characteristic. Such a perspective may help ongoing efforts to develop more efficient cures and inform on novel strategies to break the cycle of transmission sustaining the pandemic.

Origin, spread and demography of the Mycobacterium tuberculosis complex

The evolutionary timing and spread of the Mycobacterium tuberculosis complex (MTBC), one of the most successful groups of bacterial pathogens, remains largely unknown. Here, using mycobacterial tandem repeat sequences as genetic markers, we show that the MTBC consists of two independent clades, one composed exclusively of M. tuberculosis lineages from humans and the other composed of both animal and human isolates. The latter also likely derived from a human pathogenic lineage, supporting the hypothesis of an original human host. Using Bayesian statistics and experimental data on the variability of the mycobacterial markers in infected patients, we estimated the age of the MTBC at 40,000 years, coinciding with the expansion of "modern" human populations out of Africa. Furthermore, coalescence analysis revealed a strong and recent demographic expansion in almost all M. tuberculosis lineages, which coincides with the human population explosion over the last two centuries. These findings thus unveil the dynamic dimension of the association between human host and pathogen populations.

Genomics and the evolution, pathogenesis, and diagnosis of tuberculosis

Tuberculosis kills nearly 2 million people annually, and current approaches to tuberculosis control are expensive, have limited efficacy, and are vulnerable to being overcome by extensively drug-resistant strains of Mycobacterium tuberculosis. Determination of the genome sequence of M. tuberculosis has revolutionized tuberculosis research, contributed to major advances in the understanding of the evolution and pathogenesis of M. tuberculosis, and facilitated development of new diagnostic tests with increased specificity for tuberculosis. In this review, we describe some of the major progress in tuberculosis research that has resulted from knowledge of the genome sequence and note some of the problems that remain unsolved.

Microsatellite polymorphism across the M. tuberculosis and M. bovis genomes: implications on genome evolution and plasticity

Background

Microsatellites are the tandem repeats of nucleotide motifs of size 1–6 bp observed in all known genomes. These repeats show length polymorphism characterized by either insertion or deletion (indels) of the repeat units, which in and around the coding regions affect transcription and translation of genes.

Results

Systematic comparison of all the equivalent microsatellites in the coding regions of the three mycobacterial genomes, viz. Mycobacterium tuberculosis H37Rv, Mycobacterium tuberculosis CDC1551 and Mycobacterium bovis, revealed for the first time the presence of several polymorphic microsatellites. The coding regions affected by frame-shifts owing to microsatellite indels have undergone changes indicative of gene fission/fusion, premature termination and length variation. Interestingly, the genes affected by frame-shift mutations code for membrane proteins, transporters, PPE, PE_PGRS, cell-wall synthesis proteins and hypothetical proteins.

Conclusion

This study has revealed the role of microsatellite indel mutations in imparting novel functions and a certain degree of plasticity to the mycobacterial genomes. There seems to be some correlation between microsatellite polymorphism and the variations in virulence, host-pathogen interactions mediated by surface antigen variations, and adaptation of the pathogens. Several of the polymorphic microsatellites reported in this study can be tested for their polymorphic nature by screening clinical isolates and various mycobacterial strains, for establishing correlations between microsatellite polymorphism and the phenotypic variations among these pathogens.

A new evolutionary scenario for the Mycobacterium tuberculosis complex

The distribution of 20 variable regions resulting from insertion-deletion events in the genomes of the tubercle bacilli has been evaluated in a total of 100 strains of Mycobacterium tuberculosis, Mycobacterium africanum, Mycobacterium canettii, Mycobacterium microti, and Mycobacterium bovis. This approach showed that the majority of these polymorphisms did not occur independently in the different strains of the M. tuberculosis complex but, rather, resulted from ancient, irreversible genetic events in common progenitor strains. Based on the presence or absence of an M. tuberculosis specific deletion (TbD1), M. tuberculosis strains can be divided into ancestral and "modern" strains, the latter comprising representatives of major epidemics like the Beijing, Haarlem, and African M. tuberculosis clusters. Furthermore, successive loss of DNA, reflected by region of difference 9 and other subsequent deletions, was identified for an evolutionary lineage represented by M. africanum, M. microti, and M. bovis that diverged from the progenitor of the present M. tuberculosis strains before TbD1 occurred. These findings contradict the often-presented hypothesis that M. tuberculosis, the etiological agent of human tuberculosis evolved from M. bovis, the agent of bovine disease. M. canettii and ancestral M. tuberculosis strains lack none of these deleted regions, and, therefore, seem to be direct descendants of tubercle bacilli that existed before the M. africanum-->M. bovis lineage separated from the M. tuberculosis lineage. This observation suggests that the common ancestor of the tubercle bacilli resembled M. tuberculosis or M. canettii and could well have been a human pathogen already.

Tuberculosis in the Caribbean: using spacer oligonucleotide typing to understand strain origin and transmission

We used direct repeat (DR)-based spacer oligonucleotide typing (spoligotyping) (in association with double-repetitive element polymerase chain reaction, IS6110-restriction fragment length polymorphism [RFLP], and sometimes DR-RFLP and polymorphic GC-rich sequence-RFLP) to detect epidemiologic links and transmission patterns of Mycobacterium tuberculosis on Martinique, Guadeloupe, and French Guiana. In more than a third of the 218 strains we typed from this region, clusters and isolates shared genetic identity, which suggests epidemiologic links. However, because of limited epidemiologic information, only 14.2% of the strains could be directly linked. When spoligotyping patterns shared by two or more isolates were pooled with 392 spoligotypes from other parts of the world, new matches were detected, which suggests imported transmission. Persisting foci of endemic disease and increased active transmission due to high population flux and HIV-coinfection may be linked to the recent reemergence of tuberculosis in the Caribbean. We also found that several distinct families of spoligotypes are overrepresented in this region.

Molecular fingerprinting of Mycobacterium tuberculosis on a Caribbean island with IS6110 and DRr probes

Because of a substantial increase in human immunodeficiency virus (HIV) infection and HIV-linked tuberculosis in the Caribbean, a molecular fingerprinting study of clinical isolates of Mycobacterium tuberculosis isolated at the Pasteur Institute of Guadeloupe from 1994 to 1995 was undertaken with the insertion sequence IS6110 and the direct repeat DRr probes. We present the results for 72 isolates from 51 patients. A major cluster (cluster A) representing isolates from 12 patients (24%) was detected upon PvuII-IS6110 fingerprinting, which revealed a pattern of four bands among these isolates. Homogeneity was retained when the isolates were further analyzed with the DRr probe or further characterized by AluI and SmaI-DRr restriction fragment length polymorphism analysis. The isolates of cluster A, from 10 men and 2 women, was present in people of all ages and of different ethnic and geographical backgrounds, and infection with these isolates was independent of the HIV status of the patients (except for 2 HIV-positive patients from the same ward from whom the tubercle bacilli were isolated at the same time). The percentage of reactivation versus active transmission events could not be precisely determined in this study. These results are discussed on the basis of the genetic advantage of predominant clusters and/or specific characteristics of the settings from which a similar cluster of isolates with four bands has so far been reported, which include South Africa, French Polynesia, and Guadeloupe.