Tuberculosis: from prehistory to Robert Koch, as revealed by ancient DNA

Evolution of orthopaedic diseases through four thousand three hundred years: from ancient Egypt with virtual examinations of mummies to the twenty-first century

PURPOSE

This study conducts a comprehensive comparative analysis of bone pathologies between ancient Egypt and today. We aim to elucidate the prevalence, types, and potential aetiological factors influencing skeletal disorders in these two distinct temporal and cultural contexts.

METHODS

The research employs a multidisciplinary approach, integrating osteological, paleopathological, and historical data to understand bone pathologies in mummies and the actual world. Applying radiographs and CT scans as noninvasive techniques has shed new light on past diseases such as fractures, dysplasia, osteoarthritis, surgery, and tuberculosis. Virtual inspection has almost replaced classical autopsy and is essential, especially when dealing with museum specimens.

RESULTS

Findings indicate no significant disparities in the prevalence and types of bone pathologies through 4300 years of evolution. Moreover, this study sheds light on the impact of sociocultural factors on bone health. Examination of ancient Egypt's burial practices and associated cultural beliefs provides insights into potential behavioral and ritualistic influences on bone pathologies and the prevalence of specific pathologies in the past and present.

CONCLUSION

This comparative analysis illuminates the dynamic of bone pathologies, highlighting the interplay of biological, cultural, and environmental factors. By synthesizing archeological and clinical data, this research contributes to a more nuanced understanding of skeletal health's complexities in ancient and modern societies, offering valuable insights for anthropological and clinical disciplines.

The Evolution of Diagnostic Techniques in the Paleopathology of Tuberculosis: A Scoping Review

Tuberculosis (TB) is an ancient chronic infectious disease that remains a global health concern. In human remains, the most common and characteristic clinical signs are the skeletal modifications involving the spine, such as in Pott's disease. Diagnosing TB in ancient human remains is challenging. Therefore, in this systematic review, the authors investigated the studies assessing molecular diagnosis of Pott's disease in ancient human remains with the intention to survey the literature, map the evidence, and identify gaps and future perspectives on TB in paleopathology. Our systematic review offers a full contextualization of the history of Pott's disease in ancient times. Our search strategy was performed between August 2022 and March 2023. The authors initially identified 340 records, and 74 studies were finally included and assessed for qualitative analysis. Due to non-specific clinical signs associated with TB, how best to diagnose tuberculosis in human remains still represents a central point. Nevertheless, ancient DNA (aDNA) analysis, lipid biomarkers, and spoligotyping might be extremely useful tools in the study of TB in human remains. Moreover, we propose the extraction and study of immune response genes involved in innate and adaptive immunity versus Mycobacterium spp. as an innovative and vastly overlooked approach in TB paleopathology. Complementary methodologies should be integrated to provide the best approach to the study of TB in human remains.

Advancements and Challenges in Ancient DNA Research: Bridging the Global North-South Divide

Ancient DNA (aDNA) research first began in 1984 and ever since has greatly expanded our understanding of evolution and migration. Today, aDNA analysis is used to solve various puzzles about the origin of mankind, migration patterns, and the spread of infectious diseases. The incredible findings ranging from identifying the new branches within the human family to studying the genomes of extinct flora and fauna have caught the world by surprise in recent times. However, a closer look at these published results points out a clear Global North and Global South divide. Therefore, through this research, we aim to emphasize encouraging better collaborative opportunities and technology transfer to support researchers in the Global South. Further, the present research also focuses on expanding the scope of the ongoing conversation in the field of aDNA by reporting relevant literature published around the world and discussing the advancements and challenges in the field.

Structural and Functional Characterization of Rv0792c from Mycobacterium tuberculosis: Identifying Small Molecule Inhibitor against HutC Protein

In order to adapt in host tissues, microbial pathogens regulate their gene expression through a variety of transcription factors. Here, we have functionally characterized Rv0792c, a HutC homolog from Mycobacterium tuberculosis. In comparison to the parental strain, a strain of M. tuberculosis with a Rv0792c mutant was compromised for survival upon exposure to oxidative stress and infection in guinea pigs. RNA sequencing analysis revealed that Rv0792c regulates the expression of genes involved in stress adaptation and virulence of M. tuberculosis. Solution small-angle X-ray scattering (SAXS) data-steered model building confirmed that the C-terminal region plays a pivotal role in dimer formation. Systematic evolution of ligands by exponential enrichment (SELEX) resulted in the identification of single-strand DNA (ssDNA) aptamers that can be used as a tool to identify small-molecule inhibitors targeting Rv0792c. Using SELEX and SAXS data-based modeling, we identified residues essential for Rv0792c's aptamer binding activity. In this study, we also identified I-OMe-Tyrphostin as an inhibitor of Rv0792c's aptamer and DNA binding activity. The identified small molecule reduced the growth of intracellular M. tuberculosis in macrophages. The present study thus provides a detailed shape-function characterization of a HutC family of transcription factor from M. tuberculosis. IMPORTANCE Prokaryotes encode a large number of GntR family transcription factors that are involved in various fundamental biological processes, including stress adaptation and pathogenesis. Here, we investigated the structural and functional role of Rv0792c, a HutC homolog from M. tuberculosis. We demonstrated that Rv0792c is essential for M. tuberculosis to adapt to oxidative stress and establish disease in guinea pigs. Using a systematic evolution of ligands by exponential enrichment (SELEX) approach, we identified ssDNA aptamers from a random ssDNA library that bound to Rv0792c protein. These aptamers were thoroughly characterized using biochemical and biophysical assays. Using SAXS, we determined the structural model of Rv0792c in both the presence and absence of the aptamers. Further, using a combination of SELEX and SAXS methodologies, we identified I-OMe-Tyrphostin as a potential inhibitor of Rv0792c. Here we provide a detailed functional characterization of a transcription factor belonging to the HutC family from M. tuberculosis.

Postoperative clinicoradiological outcome of pott's spine

Introduction:

Tuberculosis (TB) is one of the main diseases impacting humanity. Fifty percent of all the cases of skeletal TB belong to spinal TB (STB), and it is also the most common form of TB. In India, patients usually present late after the onset of neurological symptoms, for which surgical management is essential for recovery. In our study, we have evaluated the outcome of forty patients of STB who underwent posterior decompression and instrumentation.

Methods:

Forty patients with STB who underwent posterior decompression and instrumentation were reviewed. All cases were followed up for 18 months. The groups were compared by parameters such as improvement in pain, improvement in kyphosis, and neurological recovery. Visual Analog Scale (VAS) score and american spinal cord injury assosciation (ASIA) score are used for the assessment.

Results:

VAS score was significantly decreased postoperatively (mean: 1.28) as compared to preoperative values (mean: 7.25). Erythrocyte sedimentation rate (ESR) was significantly decreased postoperatively (mean: 30.95) as compared to preoperative values (76.15). Cobb's angle was significantly decreased immediate postoperatively (mean: 7.8) as compared to preoperative values (mean: 24.8). There was no deterioration of neurological symptoms in any of the patients.

Conclusion:

Surgical intervention in Pott's spine with posterior decompression and stabilization, whenever indicated, gives good improvement in pain, decreases kyphotic deformity, and in most cases, also improves neurology.

An investigation of tuberculosis progression revealing the role of macrophages apoptosis via sensitivity and bifurcation analysis

Mycobacterium tuberculosis infection features various disease outcomes: clearance, latency, active disease, and latent tuberculosis infection (LTBI) reactivation. Identifying the decisive factors for disease outcomes and progression is crucial to elucidate the macrophages-tuberculosis interaction and provide insights into therapeutic strategies. To achieve this goal, we first model the disease progression as a dynamical shift among different disease outcomes, which are characterized by various steady states of bacterial concentration. The causal mechanisms of steady-state transitions can be the occurrence of transcritical and saddle-node bifurcations, which are induced by slowly changing parameters. Transcritical bifurcation, occurring when the basic reproduction number equals to one, determines whether the infection clears or spreads. Saddle-node bifurcation is the key mechanism to create and destroy steady states. Based on these two steady-state transition mechanisms, we carry out two sample-based sensitivity analyses on transcritical bifurcation conditions and saddle-node bifurcation conditions. The sensitivity analysis results suggest that the macrophage apoptosis rate is the most significant factor affecting the transition in disease outcomes. This result agrees with the discovery that the programmed cell death (apoptosis) plays a unique role in the complex microorganism-host interplay. Sensitivity analysis narrows down the parameters of interest, but cannot answer how these parameters influence the model outcomes. To do this, we employ bifurcation analysis and numerical simulation to unfold various disease outcomes induced by the variation of macrophage apoptosis rate. Our findings support the hypothesis that the regulation mechanism of macrophage apoptosis affects the host immunity against tuberculosis infection and tuberculosis virulence. Moreover, our mathematical results suggest that new treatments and/or vaccines that regulate macrophage apoptosis in combination with weakening bacillary viability and/or promoting adaptive immunity could have therapeutic value.

The past, present and future of ancient bacterial DNA

Groundbreaking studies conducted in the mid-1980s demonstrated the possibility of sequencing ancient DNA (aDNA), which has allowed us to answer fundamental questions about the human past. Microbiologists were thus given a powerful tool to glimpse directly into inscrutable bacterial history, hitherto inaccessible due to a poor fossil record. Initially plagued by concerns regarding contamination, the field has grown alongside technical progress, with the advent of high-throughput sequencing being a breakthrough in sequence output and authentication. Albeit burdened with challenges unique to the analysis of bacteria, a growing number of viable sources for aDNA has opened multiple avenues of microbial research. Ancient pathogens have been extracted from bones, dental pulp, mummies and historical medical specimens and have answered focal historical questions such as identifying the aetiological agent of the black death as Yersinia pestis. Furthermore, ancient human microbiomes from fossilized faeces, mummies and dental plaque have shown shifts in human commensals through the Neolithic demographic transition and industrial revolution, whereas environmental isolates stemming from permafrost samples have revealed signs of ancient antimicrobial resistance. Culminating in an ever-growing repertoire of ancient genomes, the quickly expanding body of bacterial aDNA studies has also enabled comparisons of ancient genomes to their extant counterparts, illuminating the evolutionary history of bacteria. In this review we summarize the present avenues of research and contextualize them in the past of the field whilst also pointing towards questions still to be answered.

Isolation and Characterization of Live Yeast Cells from Ancient Clay Vessels

Ancient fermented food has been studied mainly based on residue analysis and recipes and reconstruction attempts were performed using modern domesticated yeast. Furthermore, microorganisms which participated in fermentation were studied using ancient-DNA techniques. In a recent paper, we presented a novel approach based on the hypothesis that enriched yeast populations in fermented beverages could have become the dominant species in storage vessels and their descendants could be isolated and studied today. Here we present a pipeline for isolation of yeast from clay vessels uncovered in archeological sites and transferred to the microbiology lab where they can be isolated and characterized. This method opens new avenues for experimental archeology and enables attempts to recreate ancient food and beverages using the original microorganisms.

The association between skeletal lesions and tuberculosis diagnosis using a probabilistic approach

Sensitivity and specificity estimates for 18 skeletal lesions were generated from modern skeletons for future paleoepidemiological analyses of tuberculosis prevalence in archaeological samples. A case-control study was conducted using 480 skeletons from 20^th century American skeletal collections. One-half of the skeletons were documented tuberculosis cases (Terry Collection). The remaining age and sex-matched skeletons were controls (Bass Collection). The association between 18 candidate skeletal lesions and tuberculosis was established by comparing lesion distributions in case and control groups. Lesion indicators at six locations - visceral surface of ribs, ventral vertebral bodies, lateral part of ilium, acetabular fossa, iliac auricular surface, and ulna olecranon process - occurred significantly more often among cases than in controls, and were associated with one another. The most useful indicator proved to be a bony reaction on ventral thoracic and lumbar vertebral bodies. Its presence means a 53.3% probability of a true tuberculosis diagnosis. Because of the nature of the reference sample - 20th century American cases - sensitivity and specificity estimates will better estimate disease prevalence in archaeological samples from cultural settings where pulmonary tuberculosis predominated. The general approach of this proof-of-concept study is applicable to other diseases that occur commonly and affect bone.

Tuberculosis and leprosy associated with historical human population movements in Europe and beyond - an overview based on mycobacterial ancient DNA

Context: Tuberculosis and leprosy are readily recognised in human remains due to their typical palaeopathology. Both Mycobacterium tuberculosis (MTB) and Mycobacterium leprae (ML) are obligate pathogens and have been detected in ancient human populations. Objective: To demonstrate historical tuberculosis and leprosy cases in Europe and beyond using molecular methods, as human populations are associated with different mycobacterial genotypes. Methods: MTB and ML ancient DNA (aDNA) has been detected by DNA amplification using PCR, or by whole genome sequencing. Mycobacterial cell wall lipids also provide specific markers for identification. Results: In 18th century Hungary, the European indigenous MTB genotype 4 strains have been found. However, many individuals were co-infected with up to three MTB sub-genotypes. In 8th-14th century Europe significant differences in ML genotypes were found between northwest Europe compared with central, southern, or eastern Europe. In addition, several co-infections of MTB and ML were detected in historical samples. Conclusion: Both MTB and ML strain types differ between geographically separate populations. This is associated with ancient human migration after an evolutionary bottleneck and clonal expansion. The absence of indigenous leprosy in Europe today may be due to the greater mortality of tuberculosis in individuals who are co-infected with both organisms.

Isolation and Characterization of Live Yeast Cells from Ancient Vessels as a Tool in Bio-Archaeology

So far, most of the study of ancient organisms has been based mainly on the analysis of ancient DNA. Here we show that it is possible to isolate and study microorganisms—yeast in this case—from ancient pottery vessels used for fermentation. We demonstrate that it is highly likely that these cells are descendants of the original yeast strains that participated in the fermentation process and were absorbed into the clay matrix of the pottery vessels. Moreover, we characterized the isolated yeast strains, their genomes, and the beer they produced. These results open new and exciting avenues in the study of domesticated microorganisms and contribute significantly to the fields of bio- and experimental archaeology that aim to reconstruct ancient artifacts and products.

Ancient fermented food has been studied based on recipes, residue analysis, and ancient-DNA techniques and reconstructed using modern domesticated yeast. Here, we present a novel approach based on our hypothesis that enriched yeast populations in fermented beverages could have become the dominant species in storage vessels and their descendants could be isolated and studied today. We developed a pipeline of yeast isolation from clay vessels and screened for yeast cells in beverage-related and non-beverage-related ancient vessels and sediments from several archaeological sites. We found that yeast cells could be successfully isolated specifically from clay containers of fermented beverages. The findings that genotypically the isolated yeasts are similar to those found in traditional African beverages and phenotypically they grow similar to modern beer-producing yeast strongly suggest that they are descendants of the original fermenting yeast. These results demonstrate that modern microorganisms can serve as a new tool in bio-archaeology research.

Effect of High Glucose on Human Alveolar Macrophage Phenotype and Phagocytosis of Mycobacteria

PURPOSE

Diabetes mellitus (DBM) reduces immunological activity and increases susceptibility to various infections, including tuberculosis (TB). Human alveolar macrophage (hAM) functions are altered in DBM.

METHODS

To mimic hyperglycemic conditions in the lung alveolus, we co-cultured a hAM cell line (Daisy cell line) with human umbilical vein endothelial cells for 48 h in the presence of culture media alone, normal glucose (5 mM), and high glucose (22 mM). Using flow cytometry, immunophenotype characterization included cell surface markers CD 11c, CD14, CD16, CD86, CD163, CD169, CD206, CX3CR-1, CSF-1R, and matrix metalloproteinase-9 (MMP9). Phagocytic function was measured by immunofluorescence microscopy at 24 h after inoculation of cells with GFP-expressing Mycobacterium smegmatis.

RESULTS

Direct exposure of AMs to high glucose and exposure in the co-culture system yield different results for the same phenotypic markers. MMP9 expression was increased under both conditions. CD169 and CX3CR1 expressions were decreased when AMs were exposed directly to high glucose but increased under co-culture. Immunofluorescence assay revealed that phagocytosis decreased in AMs when directly exposed to increased glucose levels from 2.5 mM to normal glucose (5 mM), yet AMs under co-culture did not show decreased phagocytosis until concentrations were raised to 25 mM.

CONCLUSION

Alteration in the expression of certain receptors may contribute to defective sentinel function of AMs, promoting susceptibility to TB in a diabetic host. Variability in cell surface marker expression under direct glucose exposure compared to exposure via co-culture reveals that cell signaling between endothelial cells and AMs may play a crucial role in the phenotypic expression of AMs.

The History of In Vivo Tuberculin Testing in Bovines: Tuberculosis, a "One Health" Issue

Tuberculosis (TB) is more than 3 million years old thriving in multiple species. Ancestral Mycobacterium tuberculosis gave rise to multiple strains including Mycobacterium bovis now distributed worldwide with zoonotic transmission happening in both directions between animals and humans. M. bovis in milk caused problems with a significant number of deaths in children under 5 years of age due largely to extrapulmonary TB. This risk was effectively mitigated with widespread milk pasteurization during the twentieth century, and fewer young children were lost to TB. Koch developed tuberculin in 1890 and recognizing the possibility of using tuberculin to detect infected animals the first tests were quickly developed. Bovine TB (bTB) control/eradication programmes followed in the late nineteenth century/early twentieth century. Many scientists collaborated and contributed to the development of tuberculin tests, to refining and optimizing the production and standardization of tuberculin and to determining test sensitivity and specificity using various methodologies and injection sites. The WHO, OIE, and EU have set legal standards for tuberculin production, potency assay performance, and intradermal tests for bovines. Now, those using tuberculin tests for bTB control/eradication programmes rarely, see TB as a disease. Notwithstanding the launch of the first-ever roadmap to combat zoonotic TB, many wonder if bTB is actually a problem? Is there a better way of dealing with bTB? Might alternative skin test sites make the test “better” and easier to perform? Are all tuberculins used for testing equally good? Why have alternative “better” tests not been developed? This review was prompted by these types of questions. This article attempts to succinctly summarize the data in the literature from the late nineteenth century to date to show why TB, and zoonotic TB specifically, was and still is important as a “One Health” concern, and that the necessity to reduce the burden of zoonotic TB, to save lives and secure livelihoods is far too important to await the possible future development of novel diagnostic assays for livestock before renewing efforts to eliminate it. Consequently, it is highly probable that the tuberculin skin test will remain the screening test of choice for farmed livestock for the considerable future.

The emergence of latent infection in the early evolution of Mycobacterium tuberculosis

Mycobacterium tuberculosis has an unusual natural history in that the vast majority of its human hosts enter a latent state that is both non-infectious and devoid of any symptoms of disease. From the pathogen perspective, it seems counterproductive to relinquish reproductive opportunities to achieve a détente with the host immune response. However, a small fraction of latent infections reactivate to the disease state. Thus, latency has been argued to provide a safe harbour for future infections which optimizes the persistence of M. tuberculosis in human populations. Yet, if a pathogen begins interactions with humans as an active disease without latency, how could it begin to evolve latency properties without incurring an immediate reproductive disadvantage? We address this question with a mathematical model. Results suggest that the emergence of tuberculosis latency may have been enabled by a mechanism akin to cryptic genetic variation in that detrimental latency properties were hidden from natural selection until their expression became evolutionarily favoured.

Paleomicrobiology of Human Tuberculosis

Tuberculosis is a significant global disease today, so understanding its origins and history is important. It is primarily a lung infection and is transmitted by infectious aerosols from person to person, so a high population density encourages its spread. The causative organism is Mycobacterium tuberculosis, an obligate pathogen in the M. tuberculosis complex that also contains closely related species, such as Mycobacterium bovis, that primarily infect animals. Typical bone lesions occur in about 5% of untreated infections. These can be recognized in historical and archaeological material, along with nonspecific paleopathology such as new bone formation (periostitis), especially on ribs. Based on such lesions, tuberculosis has been found in ancient Egypt, pre-Columbian America, and Neolithic Europe. The detection of M. tuberculosis ancient DNA (aDNA) by using PCR led to the development of the new field of paleomicrobiology. As a result, a large number of tuberculosis cases were recognized in mummified tissue and bones with nonspecific or no lesions. In parallel with these developments, M. tuberculosis cell wall lipid biomarkers have detected tuberculosis suggested by paleopathology and confirmed aDNA findings. In well-preserved cases, molecular typing has identified M. tuberculosis lineages and genotypes. The current interest in targeted enrichment, shotgun sequencing, and metagenomic analysis reveals ancient mixed infections with different M. tuberculosis strains and other pathogens. Identification of M. tuberculosis lineages from samples of known age enables the date of the emergence of strains and lineages to be calculated directly rather than by making assumptions on the rate of evolutionary change.

Evidence of tuberculosis among children in medieval (13th–15th century) Wrocław: A case study of hip joint tuberculosis in a juvenile skeleton excavated from the crypt of the St. Elizabeth church

Paleopathological examinations of the skeletal remains of people who died centuries ago are material source of knowledge about health and diseases in the past. In this article, a case of skeletal tuberculosis from historical (13th-15th c.) Wrocław, Poland has been presented. The juvenile skeleton excavated from grave No 93, from the crypt located under the church of St. Elizabeth, displayed pathological lesions within the right hip joint resulting from a chronic inflammation, which might have been assigned to signs typical for skeletal tuberculosis. The results of macroscopic and radiological analyses appeared to be consistent, and allowed to determine a reliable diagnosis of this paleopathological case.

Musculoskeletal Tuberculosis

Musculoskeletal tuberculosis (TB) accounts for approximately 10% of all extrapulmonary TB cases in the United States and is the third most common site of extrapulmonary TB after pleural and lymphatic disease. Vertebral involvement (tuberculous spondylitis, or Pott's disease) is the most common type of skeletal TB, accounting for about half of all cases of musculoskeletal TB. The presentation of musculoskeletal TB may be insidious over a long period and the diagnosis may be elusive and delayed, as TB may not be the initial consideration in the differential diagnosis. Concomitant pulmonary involvement may not be present, thus confusing the diagnosis even further. Early diagnosis of bone and joint disease is important to minimize the risk of deformity and enhance outcome. The introduction of newer imaging modalities, including MRI (imaging procedure of choice) and CT, has enhanced the diagnostic evaluation of patients with musculoskeletal TB and for directed biopsies of affected areas of the musculoskeletal system. Obtaining appropriate specimens for culture and other diagnostic tests is essential to establish a definitive diagnosis and recover M. tuberculosis for susceptibility testing. A total of 6 to 9 months of a rifampin-based regimen, like treatment of pulmonary TB, is recommended for the treatment of drug susceptible musculoskeletal disease. Randomized trials of tuberculous spondylitis have demonstrated that such regimens are efficacious. These data and those from the treatment of pulmonary TB have been extrapolated to form the basis of treatment regimen recommendations for other forms of musculoskeletal TB.

Tuberculosis. Digging deep in the soul of humanity

Tuberculosis (TB) is one of the oldest infectious diseases that affected humankind. A quintessential social disease, TB remains one of the world's deadliest communicable diseases, with still a high mortality and burden of disease. Social representations of TB focus on aspects associated to feelings and manifestations awakened by the disease, sometimes reinforcing stigmas and prejudices about the way of perceiving TB. TB is a historic disease now reborn with a deeper social stigma. Despite the modest reduction in TB incidence worldwide, its incidence is still rising in certain crisis-affected populations like refugees, and in those bearing high prevalence of HIV, persisting poverty, especially in the developing world. Fear and stigma may appear justified with the increasing rates of multi-drug resistant (MDR) TB, and now extremely drug resistant (XDR) TB. However, stigmatization of TB poses serious obstacles to current TB control efforts, as socio-cultural aspects can influence adherence to TB treatment.

Paleomicrobiology: a Snapshot of Ancient Microbes and Approaches to Forensic Microbiology

Paleomicrobiology, or the study of ancient microorganisms, has raised both fascination and skepticism for many years. While paleomicrobiology is not a recent field, the application of emerging techniques, such as DNA sequencing, is proving essential and has provided novel information regarding the evolution of viruses, antibiotic resistance, saprophytes, and pathogens, as well as ancient health and disease status, cultural customs, ethnic diets, and historical events. In this review, we highlight the importance of studying ancient microbial DNA, its contributions to current knowledge, and the role that forensic paleomicrobiology has played in deciphering historical enigmas. We also discuss the emerging techniques used to study the microbial composition of ancient samples as well as major concerns that accompany ancient DNA analyses.

Network Analysis of Human Genes Influencing Susceptibility to Mycobacterial Infections

Tuberculosis and nontuberculous mycobacterial infections constitute a high burden of pulmonary disease in humans, resulting in over 1.5 million deaths per year. Building on the premise that genetic factors influence the instance, progression, and defense of infectious disease, we undertook a systems biology approach to investigate relationships among genetic factors that may play a role in increased susceptibility or control of mycobacterial infections. We combined literature and database mining with network analysis and pathway enrichment analysis to examine genes, pathways, and networks, involved in the human response to Mycobacterium tuberculosis and nontuberculous mycobacterial infections. This approach allowed us to examine functional relationships among reported genes, and to identify novel genes and enriched pathways that may play a role in mycobacterial susceptibility or control. Our findings suggest that the primary pathways and genes influencing mycobacterial infection control involve an interplay between innate and adaptive immune proteins and pathways. Signaling pathways involved in autoimmune disease were significantly enriched as revealed in our networks. Mycobacterial disease susceptibility networks were also examined within the context of gene-chemical relationships, in order to identify putative drugs and nutrients with potential beneficial immunomodulatory or anti-mycobacterial effects.

Calcified Pulmonary Nodules Identified in a 350-Year-Old-Joseon Mummy: the First Report on Ancient Pulmonary Tuberculosis from Archaeologically Obtained Pre-modern Korean Samples

We found calcified pulmonary nodules in a middle-aged female mummy discovered from 350-yr-old Joseon tomb of Korea. In the CT scan, we found six radiopaque nodules in right lung, through the levels of thoracic vertebrae 1 to 6. We also found presumptive pleural adhesions in right thoracic cavity of CT images. We re-confirmed radiological findings by our post-factum dissection on the same mummy. By the differential diagnosis, we speculate that the radiopaque calcification nodules and associated pleural adhesion could have been caused by tuberculosis. This is the first-ever report on the pulmonary tuberculosis identified in archaeologically obtained, pre-modern Korean samples.

Mycobacterial Pathogenomics and Evolution

Most mycobacterial species are harmless saprophytes, often found in aquatic environments. A few species seem to have evolved from this pool of environmental mycobacteria into major human pathogens, such as Mycobacterium tuberculosis, the agent of tuberculosis, Mycobacterium leprae, the leprosy bacillus, and Mycobacterium ulcerans, the agent of Buruli ulcer. While the pathogenicity of M. ulcerans relates to the acquisition of a large plasmid encoding a polyketide-derived toxin, the molecular mechanisms by which M. leprae or M. tuberculosis have evolved to cause disease are complex and involve the interaction between the pathogen and the host. Here we focus on M. tuberculosis and closely related mycobacteria and discuss insights gained from recent genomic and functional studies. Comparison of M. tuberculosis genome data with sequences from nontuberculous mycobacteria, such as Mycobacterium marinum or Mycobacterium kansasii, provides a perception of the more distant evolution of M. tuberculosis, while the recently accomplished genome sequences of multiple tubercle bacilli with smooth colony morphology, named Mycobacterium canettii, have allowed the ancestral gene pool of tubercle bacilli to be estimated. The resulting findings are instrumental for our understanding of the pathogenomic evolution of tuberculosis-causing mycobacteria. Comparison of virulent and attenuated members of the M. tuberculosis complex has further contributed to identification of a specific secretion pathway, named ESX or Type VII secretion. The molecular machines involved are key elements for mycobacterial pathogenicity, strongly influencing the ability of M. tuberculosis to cope with the immune defense mounted by the host.

Co-evolution of Mycobacterium tuberculosis and Homo sapiens

The causative agent of human tuberculosis (TB), Mycobacterium tuberculosis, is an obligate pathogen that evolved to exclusively persist in human populations. For M. tuberculosis to transmit from person to person, it has to cause pulmonary disease. Therefore, M. tuberculosis virulence has likely been a significant determinant of the association between M. tuberculosis and humans. Indeed, the evolutionary success of some M. tuberculosis genotypes seems at least partially attributable to their increased virulence. The latter possibly evolved as a consequence of human demographic expansions. If co-evolution occurred, humans would have counteracted to minimize the deleterious effects of M. tuberculosis virulence. The fact that human resistance to infection has a strong genetic basis is a likely consequence of such a counter-response. The genetic architecture underlying human resistance to M. tuberculosis remains largely elusive. However, interactions between human genetic polymorphisms and M. tuberculosis genotypes have been reported. Such interactions are consistent with local adaptation and allow for a better understanding of protective immunity in TB. Future 'genome-to-genome' studies, in which locally associated human and M. tuberculosis genotypes are interrogated in conjunction, will help identify new protective antigens for the development of better TB vaccines.

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.

Steps towards the discovery of Mycobacterium tuberculosis by Robert Koch, 1882

Palaeomicrobiology has detected the tuberculosis agent in animal and human skeletons that are thousands of years old. The German doctor Robert Koch was the first microbiologist to report in 1882 the successful isolation of the causative agent of tuberculosis, named 1 year later as Mycobacterium tuberculosis. This immense discovery, however, was not made from scratch, but involved the combining of previous scientific knowledge, chiefly the previous demonstration by the French doctor Jean-Antoine Villemin that tuberculosis was a transmissible disease, and two innovations--a new staining procedure that allowed R. Koch to consistently observe the new organism in tuberculous lesions, and use of a solidified, serum-based medium instead of broths for the culture. These innovations allowed R. Koch not only to isolate M. tuberculosis from animal and patient specimens for the first time, but also to reproduce the disease in experimentally inoculated guinea pigs. It is thanks to R. Koch that one of the most lethal diseases in human history could be diagnosed, could be treated and cured after the discovery of streptomycin 65 years later, and could be efficiently prevented by isolation of cases. His microbiological innovations are now being renewed with molecular and improved culture-based detection being the twenty-first century weapons in the fight against this disease, which remains a major killer.

Mycobacterium tuberculosis: ecology and evolution of a human bacterium

Some species of the Mycobacterium tuberculosis complex (MTBC), particularly Mycobacterium tuberculosis, which causes human tuberculosis (TB), are the first cause of death linked to a single pathogen worldwide. In the last decades, evolutionary studies have much improved our knowledge on MTBC history and have highlighted its long co-evolution with humans. Its ability to remain latent in humans, the extraordinary proportion of asymptomatic carriers (one-third of the entire human population), the deadly epidemics and the observed increasing level of resistance to antibiotics are proof of its evolutionary success. Many MTBC molecular signatures show not only that these bacteria are a model of adaptation to humans but also that they have influenced human evolution. Owing to the unbalance between the number of asymptomatic carriers and the number of patients with active TB, some authors suggest that infection by MTBC could have a protective role against active TB disease and also against other pathologies. However, it would be inappropriate to consider these infectious pathogens as commensals or symbionts, given the level of morbidity and mortality caused by TB.

Ancient pathogen genomics: insights into timing and adaptation

Disease is a major cause of natural selection affecting human evolution, whether through a sudden pandemic or persistent morbidity and mortality. Recent contributions in the field of ancient pathogen genomics have advanced our understanding of the antiquity and nature of human-pathogen interactions through time. Technical advancements have facilitated the recovery, enrichment, and high-throughput sequencing of pathogen and parasite DNA from archived and archaeological remains. These time-stamped genomes are crucial for calibrating molecular clocks to infer the timing of evolutionary events, while providing finer-grain resolution to phylogenetic reconstructions and complex biogeographical patterns. Additionally, genome scale data allow better identification of substitutions linked to adaptations of the pathogen to their human hosts. As methodology continues to improve, ancient genomes of humans and their diverse microbiomes from a range of eras and archaeological contexts will enable population-level ancient analyses in the near future and a better understanding of their co-evolutionary history.

Modeling the potential impact of host population survival on the evolution of M. tuberculosis latency

Tuberculosis (TB) is an infectious disease with a peculiar feature: Upon infection with the causative agent, Mycobacterium Tuberculosis (MTB), most hosts enter a latent state during which no transmission of MTB to new hosts occurs. Only a fraction of latently infected hosts develop TB disease and can potentially infect new hosts. At first glance, this seems like a waste of transmission potential and therefore an evolutionary suboptimal strategy for MTB. It might be that the human immune response keeps MTB in check in most hosts, thereby preventing it from achieving its evolutionary optimum. Another possible explanation is that long latency and progression to disease in only a fraction of hosts are evolutionary beneficial to MTB by allowing it to persist better in small host populations. Given that MTB has co-evolved with human hosts for millenia or longer, it likely encountered small host populations for a large share of its evolutionary history and had to evolve strategies of persistence. Here, we use a mathematical model to show that indeed, MTB persistence is optimal for an intermediate duration of latency and level of activation. The predicted optimal level of activation is above the observed value, suggesting that human co-evolution has lead to host immunity, which keeps MTB below its evolutionary optimum.

Mycolic Acids as Markers of Osseous Tuberculosis in the Neolithic Skeleton from Kujawy Region (Central Poland)

The subject of analysis is the male skeleton from a double burial of the Globular Amphora Culture, derived from the Neolithic site at Brześć Kujawski in Kujawy region (central Poland). Within the spine of the individual advanced lesions are observed (destruction of the vertebral bodies, symptoms of the periostitis in the thoracic region) which are characteristic of skeletal tuberculosis. To check whether the observed morphological changes resulted from infection with Mycobacterium tuberculosis (M.tb), the bone material was tested positively for the presence of mycolic acids, the specific components of the cell wall of pathogenic M.tb bacilli, by mass spectrometry.

Time-dependent diaryl ether inhibitors of InhA: structure-activity relationship studies of enzyme inhibition, antibacterial activity, and in vivo efficacy

The diaryl ethers are a novel class of antituberculosis drug candidates that inhibit InhA, the enoyl-ACP reductase involved in the fatty acid biosynthesis (FASII) pathway, and have antibacterial activity against both drug-sensitive and drug-resistant strains of Mycobacterium tuberculosis. In the present work, we demonstrate that two time-dependent B-ring modified diaryl ether InhA inhibitors have antibacterial activity in a mouse model of TB infection when delivered by intraperitoneal injection. We propose that the efficacy of these compounds is related to their residence time on the enzyme, and to identify structural features that modulate drug-target residence time in this system, we have explored the inhibition of InhA by a series of B-ring modified analogues. Seven ortho-substituted compounds were found to be time-dependent inhibitors of InhA, where the slow step leading to the final enzyme-inhibitor complex (EI*) is thought to correlate with closure and ordering of the InhA substrate binding loop. A detailed mechanistic understanding of the molecular basis for residence time in this system will facilitate the development of InhA inhibitors with improved in vivo activity.

Osteological and biomolecular evidence of a 7000-year-old case of hypertrophic pulmonary osteopathy secondary to tuberculosis from neolithic hungary

Seventy-one individuals from the late Neolithic population of the 7000-year-old site of Hódmezővásárhely-Gorzsa were examined for their skeletal palaeopathology. This revealed numerous cases of infections and non-specific stress indicators in juveniles and adults, metabolic diseases in juveniles, and evidence of trauma and mechanical changes in adults. Several cases showed potential signs of tuberculosis, particularly the remains of the individual HGO-53. This is an important finding that has significant implications for our understanding of this community. The aim of the present study was to seek biomolecular evidence to confirm this diagnosis. HGO-53 was a young male with a striking case of hypertrophic pulmonary osteopathy (HPO), revealing rib changes and cavitations in the vertebral bodies. The initial macroscopic diagnosis of HPO secondary to tuberculosis was confirmed by analysis of Mycobacterium tuberculosis complex specific cell wall lipid biomarkers and corroborated by ancient DNA (aDNA) analysis. This case is the earliest known classical case of HPO on an adult human skeleton and is one of the oldest palaeopathological and palaeomicrobiological tuberculosis cases to date.

Bone tuberculosis in Roman Period Pannonia (western Hungary)

The purpose of this study was to analyse a skeleton (adult female, 25-30 years) that presented evidence of tuberculous spondylitis. The skeleton, dated from the Roman Period (III-VI centuries), was excavated near the town of Győr, in western Hungary. The skeleton was examined by gross observation supplemented with mycolic acid and proteomic analyses using MALDI-TOF/TOF tandem mass spectrometry. The biomolecular analyses supported the morphological diagnosis.

Palaeopathology and genes: investigating the genetics of infectious diseases in excavated human skeletal remains and mummies from past populations

The aim of this paper is to review the use of genetics in palaeomicrobiology, and to highlight the importance of understanding past diseases. Palaeomicrobiology is the study of disease pathogens in skeletal and mummified remains from archaeological contexts. It has revolutionarised our understanding of health in the past by enabling a deeper knowledge of the origins and evolution of many diseases that have shaped us as a species. Bacterial diseases explored include tuberculosis, leprosy, bubonic plague, typhoid, syphilis, endemic and epidemic typhus, trench fever, and Helicobacter pylori. Viral diseases discussed include influenza, hepatitis B, human papilloma virus (HPV), human T-cell lymphotrophic virus (HTLV-1) and human immunodeficiency virus (HIV). Parasitic diseases investigated include malaria, leishmaniasis, Chagas' disease, roundworm, whipworm, pinworm, Chinese liver fluke, fleas and lice. Through a better understanding of disease origins and their evolution, we can place into context how many infectious diseases are changing over time, and so help us estimate how they may change in the future.

Genome-wide comparison of medieval and modern Mycobacterium leprae

Leprosy was endemic in Europe until the Middle Ages. Using DNA array capture, we have obtained genome sequences of Mycobacterium leprae from skeletons of five medieval leprosy cases from the United Kingdom, Sweden, and Denmark. In one case, the DNA was so well preserved that full de novo assembly of the ancient bacterial genome could be achieved through shotgun sequencing alone. The ancient M. leprae sequences were compared with those of 11 modern strains, representing diverse genotypes and geographic origins. The comparisons revealed remarkable genomic conservation during the past 1000 years, a European origin for leprosy in the Americas, and the presence of an M. leprae genotype in medieval Europe now commonly associated with the Middle East. The exceptional preservation of M. leprae biomarkers, both DNA and mycolic acids, in ancient skeletons has major implications for palaeomicrobiology and human pathogen evolution.

Bacterial epibionts and endolichenic actinobacteria and fungi in the Lower Devonian lichen Chlorolichenomycites salopensis

The charcoalified fragment of the dorsiventrally organized, internally stratified presumed green algal lichen Chlorolichenomycites salopensis from the Lower Devonian Lochkovian strata in the Welsh Borderland carries bacterial colonies on the upper surface, i.e. the cortex, and actinobacterial filaments in the medulla underneath the photobiont layer. Moreover relatively thin hyphae of presumed endolichenic fungi were found. As in extant lichens, which are best regarded as consortia with an unknown number of participants, this internally stratified, fossil thallus fragment of a presumed green algal lichen harbours a diverse microbial community.