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Pyroprinting: novel pyrosequencing‐based method for studying E. coli diversity and microbial source tracking (779.8)
Author(s) -
Kent Jason,
Alvarado Maria,
VanderKelen Jennifer,
Montana Aldrin,
Soliman Jan,
Dekhtyar Alex,
Goodman Anya,
Kitts Christopher,
Black Michael
Publication year - 2014
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.28.1_supplement.779.8
Subject(s) - pyrosequencing , biology , escherichia coli , ribosomal rna , internal transcribed spacer , computational biology , source tracking , typing , operon , microbiology and biotechnology , genetics , gene , computer science , world wide web
We have developed a novel genotypic fingerprinting method for typing Escherichia coli strains via simultaneous, multi‐locus pyrosequencing of the internal transcribed spacer (ITS) regions in ribosomal RNA operons. The data generated, called pyroprints, are unique to the polymorphic ITS alleles and their relative frequency among the seven rRNA operons in each E. coli isolate. Pyroprinting is a rapid, inexpensive, and highly reproducible method that produces readily digitized data for computational analysis and effectively discriminates closely related strains. A pyroprint database ( www.cplop.org ) and analytical tools for environmental forensics and microbial source tracking (MST) applications have been developed. Our pyroprint library currently contains over 5,000 E. coli isolates from avian and mammalian hosts. Pyroprinted isolates have been clustered into strains, some of which are shared by multiple hosts, while others appear host‐specific. To validate this method for MST, we have simulated environmental water samples by spiking them with fecal material from known hosts in pre‐determined ratios. Pyroprinting E. coli isolates from the simulated samples has allowed us to identify the origin of the isolates and ratios of different hosts that contributed to the mixed samples. This new MST method has been employed to identify sources of fecal contamination in San Luis Obispo Creek. Grant Funding Source : Supported by NSF TUES # 1140828.