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Ancient Peruvian Samples Point to TB Transfer to New World via Marine Mammals

NEW YORK (GenomeWeb) – A new genetic analysis in Nature suggests marine mammals transported a tuberculosis-causing Mycobacterium species from Europe to the New World prior to the arrival of Columbus.

A German-led team used targeted sequencing to test for M. tuberculosis-related DNA in dozens of New World skeletal samples with tuberculosis-like lesions. The analysis pointed to the presence of Mycobacterium in samples from individuals in Peru who died an estimated 734 to 986 years ago — hundreds of years before Columbian contact with the New World.

The researchers' subsequent sequencing and comparative genomic analysis revealed genetic ties between those ancient strains and a Mycobacterium species that currently infects marine mammals, pointing to past transmission from such sea creatures to humans.

"What we found was really surprising," co-corresponding author Anne Stone, a human evolution and social change researcher at Arizona State University, said in a statement. "The ancient strains are distinct from any known human-adapted tuberculosis strain."

The team used in-solution capture of M. tuberculosis genes and Illumina's MiSeq instrument to search for genetic evidence of tuberculosis infection in its initial screen of 68 New World skeletal samples dated both before and after European contact.

When they did more extensive sequencing on three samples that seemed to carry Mycobacterium DNA, the researchers were able to map just a fraction of the resulting reads mapped to the M. tuberculosis reference genome. To get around that problem, they enriched for Mycobacterium DNA with Agilent arrays before sequencing each of the three isolates on the MiSeq.

With the resulting genomes — together with sequences from hundreds of bugs in the M. tuberculosis complex and several more animal-infecting Mycobacterium species — the team reconstructed the sequences for a shared ancestral strain.

From SNP patterns detected in sequenced Mycobacterium strains relative to that ancestor, the researchers determined that the isolates found in the ancient Peruvians clustered most closely with M. pinnipedii, a pathogen known for infecting seals in the Southern Hemisphere.

Based on these and other genetic patterns, the researchers proposed that the tuberculosis pathogen was transmitted from humans in Africa to marine mammals, before making its way to South America to infect humans once again.

"Our results show unequivocal evidence of human infection caused by pinnipeds (sea lions and seals) in pre-Columbian South America," Stone said in a statement. "Within the past 2,500 years, the marine animals likely contracted the disease from an African host species and carried it across the ocean to coastal people in South America."

With the arrival of Europeans, the M. pinnipedii-based form of tuberculosis seems to have been replaced by M. tuberculosis in the Americas, the study authors noted, while M. pinnipedii was apparently re-introduced to Australian seal colonies within the past 700 years or so.

The study's authors cautioned that additional date calibrations and tests on historical samples from North and South America are needed to verify their results and to better understand the extent to which tuberculosis pathogens passed from marine mammals may have spread and changed upon arriving in the New World.

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