PMID- 29374775
OWN - NLM
STAT- MEDLINE
DCOM- 20180911
LR  - 20180911
IS  - 1618-2650 (Electronic)
IS  - 1618-2642 (Linking)
VI  - 410
IP  - 22
DP  - 2018 Sep
TI  - Serogroup-level resolution of the "Super-7" Shiga toxin-producing Escherichia 
      coli using nanopore single-molecule DNA sequencing.
PG  - 5439-5444
LID - 10.1007/s00216-018-0877-1 [doi]
AB  - DNA sequencing and other DNA-based methods are now broadly used for detection and 
      identification of bacterial foodborne pathogens. For the identification of 
      foodborne bacterial pathogens, taxonomic assignments must be made to the species 
      or even subspecies level. Long-read DNA sequencing provides finer taxonomic 
      resolution than short-read sequencing. Here, we demonstrate the potential of 
      long-read shotgun sequencing obtained from the Oxford Nanopore Technologies (ONT) 
      MinION single-molecule sequencer, in combination with the Basic Local Alignment 
      Search Tool (BLAST) with custom sequence databases, for foodborne pathogen 
      identification. A library of mixed DNA from strains of the "Super-7" Shiga 
      toxin-producing Escherichia coli (STEC) serogroups (O26, O45, O103, O111, O121, 
      O145, and O157[:H7]) was sequenced using the ONT MinION resulting in 44,245 
      long-read sequences. The ONT MinION sequences were compared to a custom database 
      composed of the E. coli O-antigen gene clusters. A vast majority of the sequence 
      reads were from outside of the O-antigen cluster and did not align to any 
      sequences in the O-antigen database. However, 58 sequences (0.13% of the total 
      sequence reads) did align to a specific Super-7 O-antigen gene cluster, with each 
      O-antigen cluster aligning to at least four sequence reads. BLAST analysis 
      against a custom whole-genome database revealed that 5096 (11.5%) of the MinION 
      sequence reads aligned to one and only one sequence in the database, of which 
      99.6% aligned to a sequence from a "Super-7" STEC. These results demonstrate the 
      ability of the method to resolve STEC to the serogroup level and the potential 
      general utility of the MinION for the detection and typing of foodborne 
      pathogens.
FAU - Peritz, Adam
AU  - Peritz A
AD  - Molecular Characterization of Foodborne Pathogens Research Unit, Eastern Regional 
      Research Center, Agricultural Research Service, U. S. Department of Agriculture, 
      600 East Mermaid Lane, Wyndmoor, PA, 19038, USA. adam_peritz@yahoo.com.
FAU - Paoli, George C
AU  - Paoli GC
AD  - Molecular Characterization of Foodborne Pathogens Research Unit, Eastern Regional 
      Research Center, Agricultural Research Service, U. S. Department of Agriculture, 
      600 East Mermaid Lane, Wyndmoor, PA, 19038, USA. George.Paoli@ars.usda.gov.
FAU - Chen, Chin-Yi
AU  - Chen CY
AD  - Molecular Characterization of Foodborne Pathogens Research Unit, Eastern Regional 
      Research Center, Agricultural Research Service, U. S. Department of Agriculture, 
      600 East Mermaid Lane, Wyndmoor, PA, 19038, USA.
FAU - Gehring, Andrew G
AU  - Gehring AG
AD  - Molecular Characterization of Foodborne Pathogens Research Unit, Eastern Regional 
      Research Center, Agricultural Research Service, U. S. Department of Agriculture, 
      600 East Mermaid Lane, Wyndmoor, PA, 19038, USA.
LA  - eng
PT  - Journal Article
DEP - 20180127
PL  - Germany
TA  - Anal Bioanal Chem
JT  - Analytical and bioanalytical chemistry
JID - 101134327
RN  - 0 (DNA, Bacterial)
SB  - IM
MH  - DNA, Bacterial/*genetics/isolation & purification
MH  - Escherichia coli Infections/*microbiology
MH  - Foodborne Diseases/*microbiology
MH  - Genomics/methods
MH  - Humans
MH  - Nanopores/ultrastructure
MH  - Sequence Analysis, DNA/*methods
MH  - Serogroup
MH  - Serotyping/methods
MH  - Shiga-Toxigenic Escherichia coli/*genetics/isolation & purification
OTO - NOTNLM
OT  - Foodborne pathogen detection
OT  - MinION
OT  - Nanopore DNA sequencing
OT  - Shiga toxin-producing E. coli, STEC
EDAT- 2018/01/29 06:00
MHDA- 2018/09/12 06:00
CRDT- 2018/01/29 06:00
PHST- 2017/09/29 00:00 [received]
PHST- 2018/01/12 00:00 [accepted]
PHST- 2018/01/04 00:00 [revised]
PHST- 2018/01/29 06:00 [pubmed]
PHST- 2018/09/12 06:00 [medline]
PHST- 2018/01/29 06:00 [entrez]
AID - 10.1007/s00216-018-0877-1 [pii]
AID - 10.1007/s00216-018-0877-1 [doi]
PST - ppublish
SO  - Anal Bioanal Chem. 2018 Sep;410(22):5439-5444. doi: 10.1007/s00216-018-0877-1. 
      Epub 2018 Jan 27.