Positive Diagnosis of Ancient Leprosy and Tuberculosis Using Ancient DNA and Lipid Biomarkers

Sensitive lipid biomarker detection for tuberculosis in late Neanderthal skeletons from Subalyuk Cave, Hungary

Skeletal remains of two Neanderthal individuals, a 25-35 year-old woman and a 3-4 year-old child, were discovered in a Subalyuk Cave in North-Eastern Hungary. Radiocarbon dating of the female and child remains revealed an age of 39,732-39,076 and 36,117-35,387 cal BP, respectively. Paleopathological studies of these Neanderthal remains revealed probable evidence of skeletal mycobacterial infection, including in the sacrum of the adult specimen and the endocranial surface of the child's skull. Application of PCR amplification to the juvenile cranium and a vertebra gave a positive result (IS6110) for tuberculosis, backed up by spoligotyping. Lipid biomarker analyses of the same two specimens revealed definitive signals for C32 mycoserosates, a very characteristic component of the Mycobacterium tuberculosis complex (MTBC). A vertebra from the adult provided weak evidence for mycocerosate biomarkers. The correlation of probable skeletal lesions with characteristic amplified DNA fragments and a proven lipid biomarker points to the presence of tuberculosis in these Neanderthals. In particular, the closely similar biomarker profiles, for two distinct juvenile cranial and vertebral bones, strengthen this diagnosis.

Re-examination of the Subalyuk Neanderthal remains uncovers signs of probable TB infection (Subalyuk Cave, Hungary)

In 1932, skeletal remains of two Neanderthal individuals, a young adult female and a 3-4-year-old child, were discovered in Subalyuk Cave in Northern Hungary [1,2]. Results of the anthropological examination were published some years after this important discovery. Methodological progress encouraged re-examination of the material during the last few years. Radiocarbon dating revealed a chronological age of 39,732-39,076 cal. BP for the adult female and 36,117-35,387 cal. BP for the child [3]. Morphological paleopathological studies of these Neanderthal remains uncovered distinct evidence of skeletal infections. Alterations of the adult individual's sacrum suggest probable early-stage sacroiliitis, while several vertebral bodies indicate superficial osseous remodelling of infectious origin. Traces of pathological lesions were observed on the endocranial surface of the child's skull, reflecting a reaction of meningeal tissues, a consequence of a probable TB-related meningeal infectious process. Results of recent paleomicrobiological examinations - lipid biomarker and aDNA studies - support the morphological diagnosis of probable TB infections [4].

Professor David Minnikin Memorial Lecture: An era of the mycobacterial cell wall lipid biomarkers

This paper is dedicated to the memory of Professor David Ernest Minnikin (1939-2021). David was one of the key scientists who pioneered the field of Mycobacterium tuberculosis cell envelope research for over half a century. From the classification, identification, and extraction of the unusual lipids of the mycobacterial cell wall, to exploiting them as characteristic lipid biomarkers for sensitive detection, his ideas enlightened a whole world of possibilities within the tuberculosis (TB) field. In addition, his definition of the intricate models now forms a key milestone in our understanding of the M. tuberculosis cell envelope and has resolved many unanswered questions on the evolution of M. tuberculosis.

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.

Developing an archaeology of malaria. A critical review of current approaches and a discussion on ways forward

OBJECTIVE

This paper presents the current state of the art in the investigation of past malaria by providing an extensive review of previous studies and identifying research possibilities for the future.

MATERIALS

All previous research on the detection of malaria in human skeletal material using macroscopic and biomolecular approaches is considered.

METHODS

The approaches and methods used by scholars and the results they obtained are evaluated and the limitations discussed.

RESULTS

There is a link between malaria and porous lesions with significantly higher prevalence in malaria-endemic areas, however, they are not pathognomonic or specific for malaria. Malaria can be identified using biomolecular techniques, yet, to date there is no completely satisfactory method that is able to consistently diagnose the disease.

CONCLUSIONS

Using macroscopic and biomolecular techniques, malaria can be investigated in past populations and the impact of the disease studied. Yet, this is not a straightforward process and the use of multiple lines of evidence is necessary to obtain the best results.

SIGNIFICANCE

The extensive discussion on ways malaria can and cannot be identified in past populations and the suggestions for new approaches provide a steppingstone for future research into this debilitating, global disease.

LIMITATIONS

Malaria is a difficult disease to study archaeologically and successful identification depends on many intrinsic and extrinsic factors.

SUGGESTIONS FOR FURTHER RESEARCH

More large-scale spatial analyses of porous lesions as well as targeting different tissues or molecules for biomolecular identification may improve the archaeological understanding of malaria.

Spotlight on mycobacterial lipid exploitation using nanotechnology for diagnosis, vaccines, and treatments

Tuberculosis (TB), historically the most significant cause of human morbidity and mortality, has returned as the top infectious disease worldwide, under circumstances worsened by the COVID-19 pandemic's devastating effects on public health. Although Mycobacterium tuberculosis, the causal agent, has been known of for more than a century, the development of tools to control it has been largely neglected. With the advancement of nanotechnology, the possibility of engineering tools at the nanoscale creates unique opportunities to exploit any molecular type. However, little attention has been paid to one of the major attributes of the pathogen, represented by the atypical coat and its abundant lipids. In this review, an overview of the lipids encountered in M. tuberculosis and interest in exploiting them for the development of TB control tools are presented. Then, the amalgamation of nanotechnology with mycobacterial lipids from both reported and future works are discussed.

The two extremes of Hansen’s disease—Different manifestations of leprosy and their biological consequences in an Avar Age (late 7th century CE) osteoarchaeological series of the Duna-Tisza Interfluve (Kiskundorozsma–Daruhalom-dűlő II, Hungary)

To give an insight into the different manifestations of leprosy and their biological consequences in the Avar Age of the Hungarian Duna-Tisza Interfluve, two cases from the 7^th-century-CE osteoarchaeological series of Kiskundorozsma–Daruhalom-dűlő II (Hungary; n = 94) were investigated. Based on the macromorphology of the bony changes indicative of Hansen’s disease, KD271 (a middle-aged male) and KD520 (a middle-aged female) represent the two extremes of leprosy. KD271 appears to have an advanced-stage, long-standing near-lepromatous or lepromatous form of the disease, affecting not only the rhinomaxillary region but also both upper and lower limbs. This has led to severe deformation and disfigurement of the involved anatomical areas of the skeleton, resulting in his inability to perform the basic activities of daily living, such as eating, drinking, grasping, standing or walking. The skeleton of KD520 shows no rhinomaxillary lesions and indicates the other extreme of leprosy, a near-tuberculoid or tuberculoid form of the disease. As in KD271, Hansen’s disease has resulted in disfigurement and disability of both of the lower limbs of KD520; and thus, the middle-aged female would have experienced difficulties in standing, walking, and conducting occupational physical activities. KD271 and KD520 are amongst the very few published cases with leprosy from the Avar Age of the Hungarian Duna-Tisza Interfluve, and the only examples with detailed macromorphological description and differential diagnoses of the observed leprous bony changes. The cases of these two severely disabled individuals, especially of KD271 –who would have required regular and substantial care from others to survive–imply that in the Avar Age community of Kiskundorozsma–Daruhalom-dűlő II there was a willingness to care for people in need.

Mycobacterial Adhesion: From Hydrophobic to Receptor-Ligand Interactions

Adhesion is crucial for the infective lifestyles of bacterial pathogens. Adhesion to non-living surfaces, other microbial cells, and components of the biofilm extracellular matrix are crucial for biofilm formation and integrity, plus adherence to host factors constitutes a first step leading to an infection. Adhesion is, therefore, at the core of pathogens’ ability to contaminate, transmit, establish residency within a host, and cause an infection. Several mycobacterial species cause diseases in humans and animals with diverse clinical manifestations. Mycobacterium tuberculosis, which enters through the respiratory tract, first adheres to alveolar macrophages and epithelial cells leading up to transmigration across the alveolar epithelium and containment within granulomas. Later, when dissemination occurs, the bacilli need to adhere to extracellular matrix components to infect extrapulmonary sites. Mycobacteria causing zoonotic infections and emerging nontuberculous mycobacterial pathogens follow divergent routes of infection that probably require adapted adhesion mechanisms. New evidence also points to the occurrence of mycobacterial biofilms during infection, emphasizing a need to better understand the adhesive factors required for their formation. Herein, we review the literature on tuberculous and nontuberculous mycobacterial adhesion to living and non-living surfaces, to themselves, to host cells, and to components of the extracellular matrix.

Approaches to osteoporosis in paleopathology: How did methodology shape bone loss research?

OBJECTIVE

This paper will review how different methods employed to study bone loss in the past were used to explore different questions and aspects of bone loss, how methodology has changed over time, and how these different approaches have informed our understanding of bone loss in the past.

MATERIALS AND METHODS

A review and discussion is conducted on research protocols and results of 84 paleopathology publications on bone loss in archaeological skeletal collections published between 1969 and 2021.

CONCLUSIONS

The variety in research protocols confounds accurate meta-analysis of previously published research; however, more recent publications incorporate a combination of bone mass and bone quality based methods. Biased sample selection has resulted in a predominance of European and Medieval publications, limiting more general observations on bone loss in the past. Collection of dietary or paleopathological covariables is underemployed in the effort to interpret bone loss patterns.

SIGNIFICANCE

Paleopathology publications have demonstrated differences in bone loss between distinct archaeological populations, between sex and age groups, and have suggested factors underlying observed differences. However, a lack of a gold standard has encouraged the use of a wide range of methods. Understanding how this array of methods effects results is crucial in contextualizing our knowledge of bone loss in the past.

LIMITATIONS

The development of a research protocol is also influenced by available expertise, available equipment, restrictions imposed by the curator, and site-specific taphonomic aspects. These factors will likely continue to cause (minor) biases even if a best practice can be established.

SUGGESTIONS FOR FUTURE RESEARCH

Greater effort to develop uniform terminology and operational definitions of osteoporosis in skeletal remains, as well as the expansion of time scale and geographical areas studied. The Next-Generation Sequencing revolution has also opened up the possibility of ancient DNA analyses to study genetic predisposition to bone loss in the past.

Verification of tuberculosis infection among Vác mummies (18th century CE, Hungary) based on lipid biomarker profiling with a new HPLC-HESI-MS approach

Tuberculosis (TB) was a large burden of infections that peaked during the 19th century in Europe. Mummies from the 18th century CE, discovered in the crypt of a church at Vác, Hungary, had high TB prevalence, as revealed by amplification of key fragments of TB DNA and genome-wide TB analysis. Complementary methods are needed to confirm these diagnoses and one approach uses the identification of specific lipid biomarkers, such as TB mycocerosic acids (MCs). Previously, MC derivatives were profiled by specialised gas chromatography-mass spectrometry (GC-MS), so an alternative more direct approach has been developed. Underivatized MCs are extracted and analysed by high-performance liquid chromatography linked to a mass spectrometer, in heated electrospray ionisation mode (HPLC-HESI-MS). The method was validated using representatives of the Mycobacterium tuberculosis complex and other mycobacteria and tested on six Vác mummy cases, previously considered positive for TB infection. Analysing both rib and soft tissue samples, four out of six cases gave profiles of main C32 and major C29 and C39 mycocerosates correlating well with those of M. tuberculosis. Multidisciplinary methods are needed in the diagnosis of ancient tuberculosis; this new protocol accesses important confirmatory evidence, as demonstrated by the confirmation of TB in the Vác mummies.

Oldest evidence of tuberculosis in Argentina: A multidisciplinary investigation in an adult male skeleton from Saujil, Tinogasta, Catamarca (905-1030 CE)

The Mycobacterium tuberculosis complex (MTC) has affected South American populations since ca. 200 years BCE. In Argentina, possible cases date from ca. 1000-1400 Common Era (CE). This paper describes the oldest (905-1030 CE) confirmed case of tuberculosis (TB) in a young adult male from Lomitas de Saujil (Tinogasta, Catamarca, Argentina). Osteolytic lesions on the bodies of the lower spine were macroscopically and radiographically identified. Bilateral new bone formation was seen on the visceral vertebral third of several ribs and in long bones, compatible with hypertrophic osteoarthropathy. Representative rib and hand bones gave profiles for MTC-specific C₂₇-C₃₂ mycocerosic acid lipid biomarkers; these were strongest in one heavily-lesioned lower rib, which also had MTC-diagnostic C₇₆-C₈₉ mycolic acids and positive amplification of MTC-typical IS6110 aDNA fragments. During the first millennium CE, the intense social interaction, the spatial circumscription of villages among the pre-Hispanic societies in the mesothermal valleys of Catamarca and the fluid contacts with the Eastern lowlands, valleys and puna, were factors likely to favor disease transmission. It is proposed that TB arrived from northern Chile and dispersed towards the northeast into the Yocavil valley, where several cases of TB infection were macroscopically identified for a later chronology.

Tuberculosis in medieval and early modern Denmark: A paleoepidemiological perspective

Millions of people worldwide have sickened and died from tuberculosis in recent centuries. Yet for most of human existence, the impact of tuberculosis on society is largely unknown. It is, indeed, unknowable without methods suitable for estimating disease prevalence in skeletal samples. Here such a procedure is applied to medieval and early modern Danish skeletons, and it shows how disease prevalence varied with differences in socioeconomic conditions. The approach is based on sensitivity and specificity estimates from modern skeletons. To augment our understanding of tuberculosis in Danish history, 713 adult skeletons were examined, all from Ribe. Tuberculosis increased from 17% to 40% in the medieval to early modern periods in Ribe. Low status (29%) people were more likely to contract the disease than those of high status (10%). The general model, derived from the modern expression of tuberculosis, fits the early modern sample better than it does the medieval skeletons. Differences in the model's fit indicate the skeletal expression changed over time. Notably, rib lesions increased in frequency from the medieval to early modern periods. The approach developed here can provide insights into host-pathogen relationships and disease expression in future work with tuberculosis and other diseases that affect the skeleton.

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.

The rapid detection and differentiation of Mycobacterium tuberculosis complex members from cattle and water buffaloes in the delta area of Egypt, using a combination of real-time and conventional PCR

Mycobacterium tuberculosis complex (MTBC) has the potential to cause infections in animals and human beings. The combination of real-time PCR targeting atpE or lpqT and RD1, and conventional PCR targeting regions of difference (RD) was rigorously evaluated as a descriptive molecular epidemiology tool. A total of 2100 cattle and buffaloes from the Menoufia, Sharkia, Gharbia, Dakahlia, Elbuhaira, and Cairo Governorates were tested by single intradermal comparative cervical tuberculin test (SICCT). The frequency was 74/2100 (3.5%); thereafter, on post-mortem examination (PM), 49/74 (66.21%) showed visible lesions, while only 25/74 (33.78%) were non-visible with a significant difference of (p < .0001). Real-time PCR using atpE or lpqT and RD1 similarly detected the frequency of infection, sensitivity, specificity, positive predictive value, negative predictive value, and accuracy, which represented 73/74 (98.65%), 98.65, 100, 100, 90.91, and 98.81%, respectively. Multiplex conventional PCR targeting RD1, 4, 9, and 12 confirmed that 49/74 (66.21%) were M.bovis, while the simplex conventional PCR targeting RD4 and RD9 confirmed mycobacteria in 71/74 (95.94%) samples, which included 61/74 (82.4%) M.bovis and 2/74 (2.7%) M.tuberculosis. Additionally, 8/74 (10.8%) exhibited mixed patterns of M.bovis and M.tuberculosis, and 3/74 (4.05%) were negative. There was a significant difference between the results of simplex and multiplex conventional PCR (p < .0001). Moreover, simplex conventional PCR targeting RD4 and RD9 proved higher sensitivity, specificity, positive predictive value, negative predictive value, and accuracy, which were 95.95, 100, 100, 76.92, and 96.43%, respectively, when compared with the values of multiplex conventional PCR targeting RD1,4,9, and 12 which were 66.22, 100, 100, 28.57, and 70.24%, respectively. The repeatability results of real-time PCR using atpE or lpqT and RD1, and simplex conventional PCR targeting RD4 and RD9 were acceptable. In conclusion, a combination of real-time PCR using atpE or lpqT and RD1 as the first step with simplex conventional PCR targeting RD4 and RD9 as the second step was reliable as a diagnostic tool.