Evolutionary history of Mycobacterium leprae in the Pacific Islands

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.

MiR-1290: a potential therapeutic target for regenerative medicine or diagnosis and treatment of non-malignant diseases

MicroRNAs are a set of small non-coding RNAs that could change gene expression with post-transcriptional regulation. MiRNAs have a significant role in regulating molecular signaling pathways and innate and adaptive immune system activity. Moreover, miRNAs can be utilized as a powerful instrument for tissue engineers and regenerative medicine by altering the expression of genes and growth factors. MiR-1290, which was first discovered in human embryonic stem cells, is one of those miRNAs that play an essential role in developing the fetal nervous system. This review aims to discuss current findings on miR-1290 in different human pathologies and determine whether manipulation of miR-1290 could be considered a possible therapeutic strategy to treat different non-malignant diseases. The results of these studies suggest that the regulation of miR-1290 may be helpful in the treatment of some bacterial (leprosy) and viral infections (HIV, influenza A, and Borna disease virus). Also, adjusting the expression of miR-1290 in non-infectious diseases such as celiac disease, necrotizing enterocolitis, polycystic ovary syndrome, pulmonary fibrosis, ankylosing spondylitis, muscle atrophy, sarcopenia, and ischemic heart disease can help to treat these diseases better. In addition to acting as a biomarker for the diagnosis of non-malignant diseases (such as NAFLD, fetal growth, preeclampsia, down syndrome, chronic rhinosinusitis, and oral lichen planus), the miR-1290 can also be used as a valuable instrument in tissue engineering and reconstructive medicine. Consequently, it is suggested that the regulation of miR-1290 could be considered a possible therapeutic target in the treatment of non-malignant diseases in the future.

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.

Metagenomic Research of Infectious Diseases in Archaeological Contexts: Evidence from the Hospital Real de Todos-os-Santos (Portugal)

Syphilis is one of the most exciting diseases explored in paleopathology and, therefore, tracing back its origin and development has provided a prolific debate. The combination of paleopathological data with historical sources, iconography, and archaeological contexts were the primary sources used to reconstruct its historical path. However, there are some limitations to paleopathological diagnosis due to the nature of bone reaction to stimuli. In addition, historical sources are subjected to a bias of social and cultural nature and the knowledge of those who wrote them. Hence, ancient DNA analysis offers the possibility of acquiring proof of cause by identifying pathogens in an organism. We undertook a metagenomic study of a skeleton exhumed from the Royal Hospital of All Saints (Portugal), renowned for treating syphilis from the 16th century onwards. The skeleton had previously been diagnosed with syphilis according to paleopathological analysis. However, the metagenomics analysis showed no presence of the pathogen associated with syphilis (i.e., Treponema pallidum) but revealed pathogenic microorganisms related to respiratory diseases (pneumonia), nonspecific bone infections (osteomyelitis), and oral bacterial pathologies as well as Hansen’s disease (also known as leprosy). The results are exciting and demand a reappraisal of the observed bone changes, recontextualizing their characterization as syphilis related. They prove that past reconstruction of health and disease diagnoses based on assessing human osteological remains of known context (such as a syphilitic hospital) may bias interpretations and, therefore, caution is recommended, not forgetting that the absence of evidence is not evidence of absence (in this case of syphilis) in life.

Genomics of Ancient Pathogens: First Advances and Prospects

Paleogenomics is one of the urgent and promising areas of interdisciplinary research in the today's world science. New genomic methods of ancient DNA (aDNA) analysis, such as next generation sequencing (NGS) technologies, make it possible not only to obtain detailed genetic information about historical and prehistoric human populations, but also to study individual microbial and viral pathogens and microbiomes from different ancient and historical objects. Studies of aDNA of pathogens by reconstructing their genomes have so far yielded complete sequences of the ancient pathogens that played significant role in the history of the world: Yersinia pestis (plague), Variola virus (smallpox), Vibrio cholerae (cholera), HBV (hepatitis B virus), as well as the equally important endemic human infectious agents: Mycobacterium tuberculosis (tuberculosis), Mycobacterium leprae (leprosy), and Treponema pallidum (syphilis). Genomic data from these pathogens complemented the information previously obtained by paleopathologists and allowed not only to identify pathogens from the past pandemics, but also to recognize the pathogen lineages that are now extinct, to refine chronology of the pathogen appearance in human populations, and to reconstruct evolutionary history of the pathogens that are still relevant to public health today. In this review, we describe state-of-the-art genomic research of the origins and evolution of many ancient pathogens and viruses and examine mechanisms of the emergence and spread of the ancient infections in the mankind history.

Human macrophage polarization in the response to Mycobacterium leprae genomic DNA

Infection with Mycobacterium leprae, the causative organism of leprosy, is still endemic in numerous parts of the world including the southwestern United States. The broad variation of symptoms in the leprosy disease spectrum range from the milder tuberculoid leprosy (paucibacillary) to the more severe and disfiguring lepromatous leprosy (multibacillary). The established thinking in the health community is that host response, rather than M. leprae strain variation, is the reason for the range of disease severity. More recent discoveries suggest that macrophage polarization also plays a significant role in the spectrum of leprosy disease but to what degree it contributes is not fully established. In this study, we aimed to analyze if different strains of M. leprae elicit different transcription responses in human macrophages, and to examine the role of macrophage polarization in these responses. Genomic DNA from three different strains of M. leprae DNA (Strains NHDP, Br4923, and Thai-53) were used to stimulate human macrophages under three polarization conditions (M1, M1-activated, and M2). Transcriptome analysis revealed a large number of differentially expressed (DE) genes upon stimulation with DNA from M. leprae strain Thai-53 compared to strains NHDP and Br4923, independent of the macrophage polarization condition. We also found that macrophage polarization affects the responses to M. leprae DNA, with up-regulation of numerous interferon stimulated genes. These findings provide a deeper understanding of the role of macrophage polarization in the recognition of M. leprae DNA, with the potential to improve leprosy treatment strategies.

Mycobacterium leprae diversity and population dynamics in medieval Europe from novel ancient genomes

BACKGROUND

Hansen's disease (leprosy), widespread in medieval Europe, is today mainly prevalent in tropical and subtropical regions with around 200,000 new cases reported annually. Despite its long history and appearance in historical records, its origins and past dissemination patterns are still widely unknown. Applying ancient DNA approaches to its major causative agent, Mycobacterium leprae, can significantly improve our understanding of the disease's complex history. Previous studies have identified a high genetic continuity of the pathogen over the last 1500 years and the existence of at least four M. leprae lineages in some parts of Europe since the Early Medieval period.

RESULTS

Here, we reconstructed 19 ancient M. leprae genomes to further investigate M. leprae's genetic variation in Europe, with a dedicated focus on bacterial genomes from previously unstudied regions (Belarus, Iberia, Russia, Scotland), from multiple sites in a single region (Cambridgeshire, England), and from two Iberian leprosaria. Overall, our data confirm the existence of similar phylogeographic patterns across Europe, including high diversity in leprosaria. Further, we identified a new genotype in Belarus. By doubling the number of complete ancient M. leprae genomes, our results improve our knowledge of the past phylogeography of M. leprae and reveal a particularly high M. leprae diversity in European medieval leprosaria.

CONCLUSIONS

Our findings allow us to detect similar patterns of strain diversity across Europe with branch 3 as the most common branch and the leprosaria as centers for high diversity. The higher resolution of our phylogeny tree also refined our understanding of the interspecies transfer between red squirrels and humans pointing to a late antique/early medieval transmission. Furthermore, with our new estimates on the past population diversity of M. leprae, we gained first insights into the disease's global history in relation to major historic events such as the Roman expansion or the beginning of the regular transatlantic long distance trade. In summary, our findings highlight how studying ancient M. leprae genomes worldwide improves our understanding of leprosy's global history and can contribute to current models of M. leprae's worldwide dissemination, including interspecies transmissions.

Simultaneous Determination of Mycobacterium leprae Drug Resistance and Single-Nucleotide Polymorphism Genotype by Use of Nested Multiplex PCR with Amplicon Sequencing

Mycobacterium leprae is the predominant cause of leprosy worldwide, and its genotypes can be classified into four single-nucleotide polymorphism (SNP) types and 16 subtypes. Determining M. leprae drug resistance and genotype is typically done by PCR and Sanger DNA sequencing, which require substantial effort. Here, we describe a rapid method involving multiplex PCR in combination with nested amplification and next-generation sequence analysis that allows simultaneous determination of M. leprae drug resistance and SNP genotype directly from clinical specimens. We used this method to analyze clinical samples from two paucibacillary, nine multibacillary, and six type-undetermined leprosy patients. Regions in folP1, rpoB, gyrA, and gyrB that determine drug resistance and those for 84 SNP-InDels in the M. leprae genome were amplified from clinical samples and their sequences determined. The results showed that seven samples were subtype 1A, three were 1D, and seven were 3K. Three samples of the subtype 3K had folp1 mutation. The method may allow more rapid genetic analyses of M. leprae in clinical samples.