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Genome Sequencing Offers Clues to New Species of Leprosy-causing Bacterium

NEW YORK (GenomeWeb) – The pathogen behind a severe form of leprosy called Lucio's leprosy shares extensive genomic conservation with the previously characterized leprosy culprit Mycobacterium leprae, according to a study in the Proceedings of the National Academy of Sciences this week.

Researchers from Switzerland, Germany, and Mexico did deep sequencing on M. lepromatosis isolates in a skin biopsy from an infected patient from Mexico. Through comparisons with the M. leprae genome, they found that the species share extensive sequence conservation, even though each species has experienced gene loss over the nearly 14 million years since they diverged from one another.

The genome sequence offered hints to the new species' enhanced virulence. But it also suggested that M. lepromatosis is more geographically limited than its better known leprosy-causing counterpart, turning up primarily in leprosy cases in Mexico.

"[D]espite their ancient separation, the two leprosy bacilli are remarkably conserved and still cause similar pathogenic conditions," senior author Stewart Cole, a researchers with the Ecole Polytechnique Fédérale de Lausanne's Global Health Institute in Switzerland, and his colleagues wrote.

The alarming symptoms associated with leprosy have traditionally been attributed to a single pathogen, M. leprae. Even so, it's been long realized that the disease sometimes manifests itself differently in parts of Mexico, Cuba, and Costa Rico.

In particular, Lucio's leprosy — also known as diffuse lepromatous leprosy — lacks the skin nodules described in the more common form of leprosy. Instead, afflicted individuals tend to develop extensive patches of spotted or swollen skin that can progress to become blackened and necrotic skin lesions.

It wasn't until 2008 that researchers from the University of Texas MD Anderson Cancer Center described M. lepromatosis — a new species they encountered while analyzing a liver sample from a homeless man from Mexico with diffuse lepromatous leprosy who was found dead in Arizona.

To characterize this newly recognized microbial nuisance genetically, Cole and his colleagues did Illumina sequencing on DNA from an uncultured M. lepromatosis skin biopsy isolate that had or had not been enriched for Mycobacterium sequences using M. leprae sequence-targeting whole-genome array capture or human genomic DNA hybridization and removal.

After generating sufficient sequence to cover the genome to an average depth of 55-fold, the team put together a de novo genome assembly for M. lepromatosis that spanned just over 3.2 million bases. Additional Sanger sequence was generated using DNA from an M. lepromatosis isolate found in another Mexican leprosy case by PCR-based screening.

The original genome housed sequences from four repeat families, as in M. leprae, along with almost 1,500 predicted protein-coding genes and another 1,334 pseudogenes. Just two dozen SNP sites differed between the M. lepromatosis genomes, researchers reported.

Comparisons with the M. leprae genome suggested the M. lepromatosis genome contains orthologs for some 95 percent of the protein-coding sequences in the original leprosy culprit, with extensive nucleotide sequence identity across these genes.

While Lucio's leprosy cases typically lack symptoms associated with Schwann cell infection, for example, M. lepromatosis appears to have retained genes resembling those that M. leprae uses to achieve this invasion.

The team's phylogenetic analysis indicated that the two species diverged an estimated 13.9 million years ago, with M. lepromatosis potentially emerging in Central America.

Although they noted that M. lepromatosis infection was recently detected in red squirrels in the UK, the researchers' differential PCR-based tests on samples from leprosy cases in Mexico, Venezuela, Mali, Brazil, and elsewhere uncovered M. lepromatosis in Mexico alone.

Further work will be needed to uncover the natural reservoir for M. lepromatosis, the study's authors explained, though there are anecdotal reports of field rat meat consumption by several infected individuals in Mexico.

"Availability of the M. lepromatosis genome sequence will enable us to search systematically for its presence in other potential animal reservoirs as well as in extant cases of leprosy," they concluded.