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Metagenomic Analysis Uncovers Contemporary Outbreak-related TB Strains in Hungarian Mummy

NEW YORK (GenomeWeb News) – A research team from the UK, Hungary, and Israel has used metagenomic sequencing to uncover a pair of co-infecting Mycobacterium tuberculosis strains in lung tissue from a 215-year-old mummy found in a Hungarian crypt more than a decade ago.

As they reported in a correspondence article in the New England Journal of Medicine this week, the researchers characterized M. tuberculosis sequences from lung tissue in the mummified remains of a 28-year-old woman who died on Christmas Day in 1797.

Results of the analysis indicate that the woman was infected with two different M. tuberculosis strains, each showing genetic similarities to an M. tuberculosis strain involved in a tuberculosis outbreak that began about a decade-and-a-half ago in Germany.

"It was fascinating to see the similarities between the [tuberculosis] genome sequences we recovered and the genome of a recent outbreak strain in Germany," corresponding author Mark Pallen, a microbial genomics researcher at the University of Warwick, said in a statement.

"It shows once more that using metagenomics can be remarkably effective in tracking the evolution and spread of microbes without the need for culture — in this case, metagenomes revealed that some strain lineages have been circulating in Europe for more than two centuries," he added.

The mummy in question was one of 242 bodies discovered in a crypt in a Hungarian town called Vác in 1994.

Despite the fact that investigators could not see tuberculosis-related signs of lung damage in the woman using chest radiograph imaging, the wasting and muscle loss initially observed in the her body hinted that she may have had tuberculosis.

Indeed, prior molecular and genotyping-based tests on the remains indicated that the young woman had been infected with M. tuberculosis. And the well-preserved condition of the M. tuberculosis DNA detected in the mummified sample hinted that more extensive analyses of the tuberculosis-causing pathogens might be possible.

For the latest study, Pallen and colleagues from the University of Warwick, University College London, the University of Birmingham, the Hungarian Natural History Museum, and Tel Aviv University turned to metagenomic sequencing to get a closer look at the M. tuberculosis bacteria involved in the mummy's infection.

"Most other attempts to recover DNA sequences from historical or ancient samples have suffered from the risk of contamination," Pallen noted, "because they rely on amplification of DNA in the laboratory, plus they have required onerous optimization of target-specific assays."

"The beauty of metagenomics is that it provides a simple but highly informative, assumption-free, one-size-fits-all approach that works in a wide variety of contexts," he said.

After isolating total DNA from mummy lung tissue, the team used Illumina's MiSeq instrument to generate roughly 5.5 million sequence reads from the genetic material. Of those, roughly 8 percent could be successfully mapped to the M. tuberculosis reference genome.

Through comparisons with that reference genome — and with sequences from additional M. tuberculosis strains — the researchers discovered that the mummified woman's tuberculosis stemmed from two different strains of the bacteria.

Both of the strains resembled an M. tuberculosis strain detected during a German tuberculosis outbreak that occurred between 1998 and 2010, the study authors noted. But one of the mummy strains shared especially close genetic ties to the strain found in that contemporary outbreak.

"One strain from the mummy, M2, was more similar to the outbreak strain than was the other strain, M1," they wrote, adding that "[t]his study shows the power of metagenomic analysis in providing information from historical and perhaps even contemporary specimens."