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Research article
Quasimetagenomic source tracking of Listeria monocytogenes from naturally contaminated ice cream
Andrea Ottesen
Corresponding Author
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published version at BMC Infectious Diseases.
Background
The more quickly bacterial pathogens can be linked to a vehicle of transmission or a source, the more illnesses can be prevented. Whole genome sequencing (WGS) based approaches to source tracking have greatly increased the speed and resolution with which public health response can pinpoint the vehicle and source of outbreaks. Traditionally, WGS approaches have focused on the culture of an individual isolate before proceeding to DNA extraction and sequencing. For Listeria monocytogenes (Lm), generation of an individual isolate for sequencing typically takes about 6 days. Here we demonstrate that a hybrid, “quasimetagenomic” approach ie; direct sequencing of microbiological enrichments (first step in pathogen detection and recovery) can provide high resolution source tracking sequence data, five days earlier than response that focuses on culture and sequencing of an individual isolate. This expedited approach could save lives, prevent illnesses and potentially minimize unnecessary destruction of food.
Methods
Naturally contaminated ice cream (from a 2015 outbreak) was enriched to recover Listeria monocytogenes following protocols outlined in the Bacteriological Analytic Manual (BAM). DNA from enriching microbiota was extracted and sequenced at incremental time-points during the first 48 hours of pre-enrichment using the Illumina MiSeq platform (2 by 250), to evaluate genomic coverage of target pathogen, Listeria monocytogenes .
Results
Quasimetagenomic sequence data acquired from hour 20 were sufficient to discern whether or not Lm strain/s were part of the ongoing outbreak or not. Genomic data from hours 24, 28, 32, 36, 40, 44, and 48 of pre-enrichments all provided identical phylogenetic source tracking utility to the WGS of individual isolates (which require an additional 5 days to culture).
Conclusions
The speed of this approach (more than twice as fast as current methods) has the potential to reduce the number of illnesses associated with any given outbreak by as many as 75% percent of total cases and potentially with continued optimization of the entire chain of response, contribute to minimized food waste.
Keywords
Quasimetagenomic, (qMGS), quasimetagenome, metagenomic, metagenome, source tracking, Listeria monocytogenes, ice cream, microbiological enrichment
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CURRENT STATUS: Published
Version 3
Posted 03 Jan, 2020
Published
On 29 Jan, 2020
No community comments so far
Submission checks complete
On 04 Jan, 2020
Editorial decision: Accept
On 26 Dec, 2019
Editor assigned
On 25 Dec, 2019
Editor invited
On 24 Dec, 2019
No comments provided
Editorial decision: Minor revision
On 21 Dec, 2019
Editor assigned
On 20 Dec, 2019
Submission checks complete
On 19 Dec, 2019
Editor invited
On 19 Dec, 2019
No comments provided
Editorial decision: Major revision
On 12 Dec, 2019
Review #1 received
Received 04 Nov, 2019
Reviewer #2 agreed
On 21 Oct, 2019
Reviewer #1 agreed
On 21 Oct, 2019
Editor assigned
On 10 Oct, 2019
Reviewers invited
Invitations sent on 10 Oct, 2019
Submission checks complete
On 09 Oct, 2019
Editor invited
On 09 Oct, 2019
First submitted
On 05 Oct, 2019
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Infectious Diseases
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This preprint is under consideration at BMC Infectious Diseases. A preprint is a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research article
Quasimetagenomic source tracking of Listeria monocytogenes from naturally contaminated ice cream
Andrea Ottesen
Corresponding Author
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Published
Version 3
Posted 03 Jan, 2020
Published
On 29 Jan, 2020
No community comments so far
Submission checks complete
On 04 Jan, 2020
Editorial decision: Accept
On 26 Dec, 2019
Editor assigned
On 25 Dec, 2019
Editor invited
On 24 Dec, 2019
No comments provided
Editorial decision: Minor revision
On 21 Dec, 2019
Editor assigned
On 20 Dec, 2019
Submission checks complete
On 19 Dec, 2019
Editor invited
On 19 Dec, 2019
No comments provided
Editorial decision: Major revision
On 12 Dec, 2019
Review #1 received
Received 04 Nov, 2019
Reviewer #2 agreed
On 21 Oct, 2019
Reviewer #1 agreed
On 21 Oct, 2019
Editor assigned
On 10 Oct, 2019
Reviewers invited
Invitations sent on 10 Oct, 2019
Submission checks complete
On 09 Oct, 2019
Editor invited
On 09 Oct, 2019
First submitted
On 05 Oct, 2019
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Infectious Diseases
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published version at BMC Infectious Diseases.
Background
The more quickly bacterial pathogens can be linked to a vehicle of transmission or a source, the more illnesses can be prevented. Whole genome sequencing (WGS) based approaches to source tracking have greatly increased the speed and resolution with which public health response can pinpoint the vehicle and source of outbreaks. Traditionally, WGS approaches have focused on the culture of an individual isolate before proceeding to DNA extraction and sequencing. For Listeria monocytogenes (Lm), generation of an individual isolate for sequencing typically takes about 6 days. Here we demonstrate that a hybrid, “quasimetagenomic” approach ie; direct sequencing of microbiological enrichments (first step in pathogen detection and recovery) can provide high resolution source tracking sequence data, five days earlier than response that focuses on culture and sequencing of an individual isolate. This expedited approach could save lives, prevent illnesses and potentially minimize unnecessary destruction of food.
Methods
Naturally contaminated ice cream (from a 2015 outbreak) was enriched to recover Listeria monocytogenes following protocols outlined in the Bacteriological Analytic Manual (BAM). DNA from enriching microbiota was extracted and sequenced at incremental time-points during the first 48 hours of pre-enrichment using the Illumina MiSeq platform (2 by 250), to evaluate genomic coverage of target pathogen, Listeria monocytogenes .
Results
Quasimetagenomic sequence data acquired from hour 20 were sufficient to discern whether or not Lm strain/s were part of the ongoing outbreak or not. Genomic data from hours 24, 28, 32, 36, 40, 44, and 48 of pre-enrichments all provided identical phylogenetic source tracking utility to the WGS of individual isolates (which require an additional 5 days to culture).
Conclusions
The speed of this approach (more than twice as fast as current methods) has the potential to reduce the number of illnesses associated with any given outbreak by as many as 75% percent of total cases and potentially with continued optimization of the entire chain of response, contribute to minimized food waste.
Figure 1
Figure 2