British squirrels infected with leprosy: With the exception of armadillos in the Americas, leprosy infections are considered almost exclusively restricted to humans. Avanzi et al. examined warty growths on the faces and extremities of red squirrels in the British Isles and found that two species of leprosy-causing organisms were to blame (see the Perspective by Stinear and Brosch). Mycobacterium leprae in the southern population of Brownsea Island squirrels originated from a medieval human strain. M. lepromatosis was found in red squirrels from elsewhere in the United Kingdom and Ireland. Human leprosy is proving hard to eradicate, despite available drugs. Perhaps other wildlife species are also reservoirs for this stubborn disease. Science , this issue p. 744 ; see also p. 702

Significance: Leprosy was thought to be exclusively caused by infection of humans by Mycobacterium leprae . In 2008, Han et al. proposed that Mycobacterium lepromatosis , a separate unculturable species, might be responsible for a rare yet severe form of the disease called diffuse lepromatous leprosy. Here, by using comparative genomics, we show that the two species are very closely related and derived from a common ancestor that underwent genome downsizing and gene decay. Since their separation 13.9 Mya, the two species have continued to lose genes, but from different regions of the genome, and M. leprae appears to be more recent. In a phylogeographic survey, by using differential PCR, we found that M. lepromatosis was scarce and restricted to patients from Mexico.

Studying ancient DNA allows us to retrace the evolutionary history of human pathogens, such as Mycobacterium leprae, the main causative agent of leprosy. Leprosy is one of the oldest recorded and most stigmatizing diseases in human history. The disease was prevalent in Europe until the 16^th century and is still endemic in many countries with over 200,000 new cases reported annually. Previous worldwide studies on modern and European medieval M. leprae genomes revealed that they cluster into several distinct branches of which two were present in medieval Northwestern Europe. In this study, we analyzed 10 new medieval M. leprae genomes including the so far oldest M. leprae genome from one of the earliest known cases of leprosy in the United Kingdom—a skeleton from the Great Chesterford cemetery with a calibrated age of 415–545 C.E. This dataset provides a genetic time transect of M. leprae diversity in Europe over the past 1500 years. We find M. leprae strains from four distinct branches to be present in the Early Medieval Period, and strains from three different branches were detected within a single cemetery from the High Medieval Period. Altogether these findings suggest a higher genetic diversity of M. leprae strains in medieval Europe at various time points than previously assumed. The resulting more complex picture of the past phylogeography of leprosy in Europe impacts current phylogeographical models of M. leprae dissemination. It suggests alternative models for the past spread of leprosy such as a wide spread prevalence of strains from different branches in Eurasia already in Antiquity or maybe even an origin in Western Eurasia. Furthermore, these results highlight how studying ancient M. leprae strains improves understanding the history of leprosy worldwide. Many controversies surround leprosy, which is one of the oldest recorded diseases of humankind. The origin and past spread of its main causative agent, Mycobacterium leprae, remain unknown although many attempts have been made to reconstruct its past from historical and archeological sources. Analysis of ancient M. leprae genomes reconstructed from archaeological remains can contribute greatly to reconstructing the origin and evolution of this pathogen. With a new set of ancient M. leprae genomes from Europe, we traced back a so far unrecognized past diversity, which places Europe as a key region for the early spread and worldwide dissemination of leprosy. Our results hint to the potential dynamic changes in the prevalence of different M. leprae strains in Europe during Antiquity, and highlight the need to study ancient pathogen genomes in order to better understand our past.

Leprosy is a chronic human disease caused by the yet-uncultured pathogenMycobacterium leprae. Although readily curable with multidrug therapy (MDT), over 200,000 new cases are still reported annually. Here, we obtainM. lepraegenome sequences from DNA extracted directly from patients’ skin biopsies using a customized protocol. Comparative and phylogenetic analysis of 154 genomes from 25 countries provides insight into evolution and antimicrobial resistance, uncovering lineages and phylogeographic trends, with the most ancestral strains linked to the Far East. In addition to known MDT-resistance mutations, we detect other mutations associated with antibiotic resistance, and retrace a potential stepwise emergence of extensive drug resistance in the pre-MDT era. Some of the previously undescribed mutations occur in genes that are apparently subject to positive selection, and two of these (ribD,fadD9) are restricted to drug-resistant strains. Finally, nonsense mutations in thenthexcision repair gene are associated with greater sequence diversity and drug resistance.

Mycobacterium leprae (M. leprae) is a human pathogen and the causative agent for leprosy, a chronic disease characterized by lesions of the skin and peripheral nerve damage. Zoonotic transmission of M. leprae to humans by nine-banded armadillos (Dasypus novemcinctus) has been shown to occur in the southern United States, mainly in Texas, Louisiana, and Florida. Nine-banded armadillos are also common in South America, and residents living in some areas in Brazil hunt and kill armadillos as a dietary source of protein. This study examines the extent of M. leprae infection in wild armadillos and whether these New World mammals may be a natural reservoir for leprosy transmission in Brazil, similar to the situation in the southern states of the U.S. The presence of the M. leprae-specific repetitive sequence RLEP was detected by PCR amplification in purified DNA extracted from armadillo spleen and liver tissue samples. A positive RLEP signal was confirmed in 62% of the armadillos (10/16), indicating high rates of infection with M. leprae. Immunohistochemistry of sections of infected armadillo spleens revealed mycobacterial DNA and cell wall constituents in situ detected by SYBR Gold and auramine/rhodamine staining techniques, respectively. The M. leprae-specific antigen, phenolic glycolipid I (PGL-I) was detected in spleen sections using a rabbit polyclonal antibody specific for PGL-I. Anti-PGL-I titers were assessed by ELISA in sera from 146 inhabitants of Belterra, a hyperendemic city located in western Pará state in Brazil. A positive anti-PGL-I titer is a known biomarker for M. leprae infection in both humans and armadillos. Individuals who consumed armadillo meat most frequently (more than once per month) showed a significantly higher anti-PGL-I titer than those who did not eat or ate less frequently than once per month. Armadillos infected with M. leprae represent a potential environmental reservoir. Consequently, people who hunt, kill, or process or eat armadillo meat are at a higher risk for infection with M. leprae from these animals. Armadillos have been shown to be a natural reservoir of Mycobacterium leprae infection in the southern states of the U.S. and have been implicated in the zoonotic transmission of leprosy to humans. To investigate this in Brazil, we conducted surveys of armadillos in western Pará state in the Brazilian Amazon region where leprosy is hyperendemic in humans. Individuals living in the small town of Belterra were surveyed for the extent and frequency of interaction with armadillos (hunting, preparing the meat for cooking, or eating the meat for food). We also took samples of liver and spleen from armadillos to look for M. leprae infection in the tissues. We found that a majority of residents had some contact with armadillos (~65%) and that infection by M. leprae in armadillos in this area was also very high (62%). Those individuals who ate armadillo meat more than once a month had a significantly higher antibody titer to the M. leprae-specific antigen, PGL-I. Understanding the dynamics of leprosy transmission in different geographic regions and knowing the behavioral risks of humans interacting with potentially infected animals will help clarify the relative risk of zoonotic transmission of leprosy in this region.

Humans are considered as the main host forMycobacterium leprae¹, the aetiological agent of leprosy, but spillover has occurred to other mammals that are now maintenance hosts, such as nine-banded armadillos and red squirrels^2,3. Although naturally acquired leprosy has also been described in captive nonhuman primates^4–7, the exact origins of infection remain unclear. Here we describe leprosy-like lesions in two wild populations of western chimpanzees (Pan troglodytes verus) in Cantanhez National Park, Guinea-Bissau and Taï National Park, Côte d’Ivoire, West Africa. Longitudinal monitoring of both populations revealed the progression of disease symptoms compatible with advanced leprosy. Screening of faecal and necropsy samples confirmed the presence ofM. lepraeas the causative agent at each site and phylogenomic comparisons with other strains from humans and other animals show that the chimpanzee strains belong to different and rare genotypes (4N/O and 2F). These findings suggest thatM. lepraemay be circulating in more wild animals than suspected, either as a result of exposure to humans or other unknown environmental sources.