FEATURE
How much sequencing do you need before you are confident about results ? We need a set of criteria , and the guidelines and recommendations don ’ t exist .” Enoma Omoregie , PhD
“ I don ’ t know of any public health laboratory actively using metagenomics . They either don ’ t have the capacity , or the personnel trained to do it .” Pandori is advancing NSPHL ’ s research and collaboration opportunities throughout Nevada by facilitating partnerships with CDC , the Federal Bureau of Investigation , state and federal agencies , hospitals , state and county health districts and departments .
Omoregie says the biggest barrier to implementing metagenomics in public laboratories is the lack of standards and protocols .
“ How much sequencing do you need before you are confident about results ? We need a set of criteria , and the guidelines and recommendations don ’ t exist .” He also cites a need for bioinformatic knowledge and some public health laboratories may not have the necessary expertise .
“ Although the concept of running one set on a sample — whether human , water or waste — is valuable , it requires advanced bioinformatic analyses and / or significant biochemical modifications to the preparation process ,” said Pandori .
Joel Sevinsky , PhD , founder of
Theiagen Genomics and former member of the Molecular Science Laboratory at the
Colorado Department of Public Health and Environment , said because of their size and limitations , some public health laboratories may be much better off using
metabarcoding metagenomics rather than
shotgun metagenomics . Metabarcoding is the barcoding of DNA or eDNA ( environmental DNA ) that allows for simultaneous identification of many taxa within the same environmental sample , however often within the same organism group .
A CDC microbiologist begins an NGS run of nucleic acid extracted from water samples . Photo : CDC / Laura Bishop
8 LAB MATTERS Summer 2021