DetectionMicrobial detection array detects plague in ancient human remains

Scientists who study past pandemics, such as the fourteenth century Black Death which devastated much of Europe, might soon be turning to an innovative biological detection technology for some extra help.

The apparent first use of this technology, known as a microarray, for studying pathogens from ancient DNA, was reported today by a team of scientists in Scientific Reports.

An LLNL release reports that researchers at McMaster University, led by Hendrik Poinar, an associate professor of evolutionary genetics, and Lawrence Livermore National Laboratory (LLNL) tested the application of a novel microarray, the Lawrence Livermore Microbial Detection Array (LLMDA), to identify human bacterial pathogens from archaeological remains. The team tested two samples that had been previously verified as containing pathogens through another technology.

One of the samples, an intestinal substance, showed the presence of cholera and was preserved from a patient who died from the disease during an 1849 outbreak in Philadelphia. The specimen was provided by the Philadelphia-based Mütter Museum.

The other sample tested with the LLMDA indicated the presence of Yersinia pestis (or plague) in a medieval tooth from 1348 from the East Smithfield burial ground in London. An estimated 30 to 50 percent of the European population succumbed to plague from 1347 to 1351.

Both Poinar and LLNL biologist Crystal Jaing believe that the Lab’s LLMDA technology will be tenfold faster and tenfold less expensive than current genomic sequencing as a means of studying pathogens in ancient DNA.

“Microarrays may be a potential alternative solution, as well as a complementary tool, to genomic sequencing for studying ancient DNA,” Jaing said. “It offers a faster and cheaper approach to studying complex samples.”

Poinar, who is an expert on ancient DNA, agreed.

“We know that most bacterial pathogens likely go undetected in ancient remains due to the overwhelmingly strong contaminant signal from molecules that don’t originate in human organs. One way to access this information would be to sequence everything in the sample and analyze it. But this is prohibitively costly and requires a lot of bioinformatics time.

“The LLMDA selectively targets pathogens that are likely to be of interest from an evolutionary standpoint and appears to work well with heavily degraded DNA, typical of most fossil and archival remains, so this is an excellent tool,” Poinar continued.