Characterization of Genetically Modified Microorganisms Using Short- and Long-Read Whole-Genome Sequencing Reveals Contaminations of Related Origin in Multiple Commercial Food Enzyme Products

Despite their presence being unauthorized on the European market, contaminations with genetically modified (GM) microorganisms have repeatedly been reported in diverse commercial microbial fermentation produce types. Several of these contaminations are related to a GM Bacillus velezensis used to synthesize a food enzyme protease, for which genomic characterization remains currently incomplete, and it is unknown whether these contaminations have a common origin. In this study, GM B. velezensis isolates from multiple food enzyme products were characterized by short- and long-read whole-genome sequencing (WGS), demonstrating that they harbor a free recombinant pUB110-derived plasmid carrying antimicrobial resistance genes. Additionally, single-nucleotide polymorphism (SNP) and whole-genome based comparative analyses showed that the isolates likely originate from the same parental GM strain. This study highlights the added value of a hybrid WGS approach for accurate genomic characterization of GMM (e.g., genomic location of the transgenic construct), and of SNP-based phylogenomic analysis for source-tracking of GMM.

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Genomic characterization of vancomycin-resistant Enterococcus faecium transmission in hospital by whole genome sequencing

International Journal of Antimicrobial Agents ◽

10.1016/j.ijantimicag.2021.106421.131 ◽

2021 ◽

Vol 58 ◽

pp. 21004027

Author(s):

Hye Mee Kim ◽

Doo Ryeon Chung ◽

Kyungmin Huh ◽

Cheol-In Kang ◽

Kyong Ran Peck

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Enterococcus Faecium ◽

Whole Genome ◽

Vancomycin Resistant Enterococcus ◽

Genomic Characterization ◽

Vancomycin Resistant

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Genomic investigation reveals contaminated detergent as the source of an ESBL-producing Klebsiella michiganensis outbreak in a neonatal unit

10.1101/568154 ◽

2019 ◽

Author(s):

Paul Chapman ◽

Brian M. Forde ◽

Leah W. Roberts ◽

Haakon Bergh ◽

Debra Vesey ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Klebsiella Oxytoca ◽

Hospital Environment ◽

List Type ◽

Whole Genome ◽

Environmental Isolates ◽

Taxonomic Assignment ◽

Antimicrobial Resistance Genes ◽

Long Read

AbstractBackgroundKlebsiella species are problematic pathogens in neonatal units and may cause outbreaks, for which sources of transmission can be challenging to elucidate. We describe the use of whole genome sequencing (WGS) to investigate environmental sources of transmission during an outbreak of extended-spectrum-β-lactamase (ESBL)-producing Klebsiella michiganensis colonizing neonates.MethodsCeftriaxone-resistant Klebsiella spp. isolated from neonates (or their mothers) and the hospital environment were included. Short-read (Illumina) and long-read (MinION, Oxford Nanopore Technologies) sequencing was used to confirm species taxonomy, define antimicrobial resistance genes and determine phylogenetic relationships using single nucleotide polymorphism (SNP) profiling.ResultsA total of 21 organisms (10 patient-derived and 11 environmental isolates) were sequenced. Standard laboratory methods identified the outbreak strain as an ESBL-producing Klebsiella oxytoca, but taxonomic assignment from WGS data suggested closer identity to Klebsiella michiganensis. Strains isolated from baby bath drains and multiple detergent dispensing bottles were either identical or closely related by SNP comparison. Detergent bottles contaminated by K. michiganensis had been used for washing milk-expressing equipment. No new cases were identified once the detergent bottles were removed and the baby baths decommissioned.ConclusionsEnvironmental reservoirs may be an important source in outbreaks of multi-drug resistant organisms. WGS, in conjunction with traditional epidemiological investigation, can be instrumental in revealing routes of transmission and guiding infection control responses.Key pointsK. michiganensis can be misidentified as K. oxytoca and is probably under-recognized as a nosocomial pathogenWhole genome sequencing of neonatal and environmental isolates during an outbreak of ESBL-producing K. michiganensis confirmed contaminated detergent and sinks to be the source

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Preliminary Genomic Characterization of Ten Hardwood Tree Species from Multiplexed Low Coverage Whole Genome Sequencing

PLoS ONE ◽

10.1371/journal.pone.0145031 ◽

2015 ◽

Vol 10 (12) ◽

pp. e0145031 ◽

Cited By ~ 14

Author(s):

Margaret Staton ◽

Teodora Best ◽

Sudhir Khodwekar ◽

Sandra Owusu ◽

Tao Xu ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Tree Species ◽

Whole Genome ◽

Genomic Characterization ◽

Hardwood Tree ◽

Low Coverage

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Faculty Opinions recommendation of Characterization of uterine leiomyomas by whole-genome sequencing.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.718021966.793479049 ◽

2013 ◽

Author(s):

Hiroshi Ishikawa

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Uterine Leiomyomas ◽

Whole Genome

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Characterization of Shiga Toxin‐Producing Escherichia coli Isolated From Cattle and Sheep in Xinjiang Province, China, Using Whole‐Genome Sequencing

Transboundary and Emerging Diseases ◽

10.1111/tbed.13999 ◽

2021 ◽

Author(s):

Yingyu Liu ◽

Huoming Li ◽

Xuhua Chen ◽

Panpan Tong ◽

Yan Zhang ◽

...

Keyword(s):

Escherichia Coli ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Shiga Toxin ◽

Whole Genome ◽

Cattle And Sheep

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Long-read whole-genome sequencing identified a partial MBD5 deletion in an exome-negative patient with neurodevelopmental disorder

Journal of Human Genetics ◽

10.1038/s10038-020-00893-8 ◽

2021 ◽

Author(s):

Sachiko Ohori ◽

Rie S. Tsuburaya ◽

Masako Kinoshita ◽

Etsuko Miyagi ◽

Takeshi Mizuguchi ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Neurodevelopmental Disorder ◽

Whole Genome ◽

Negative Patient ◽

Long Read

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SureSelect targeted enrichment, a new cost effective method for the whole genome sequencing of Candidatus Liberibacter asiaticus

Scientific Reports ◽

10.1038/s41598-019-55144-4 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 2

Author(s):

Weili Cai ◽

Schyler Nunziata ◽

John Rascoe ◽

Michael J. Stulberg

Keyword(s):

Whole Genome Sequencing ◽

Molecular Characterization ◽

Genome Sequencing ◽

Whole Genome Sequence ◽

Whole Genome ◽

Genome Coverage ◽

Metagenomic Sample ◽

Liberibacter Asiaticus

AbstractHuanglongbing (HLB) is a worldwide deadly citrus disease caused by the phloem-limited bacteria ‘Candidatus Liberibacter asiaticus’ (CLas) vectored by Asian citrus psyllids. In order to effectively manage this disease, it is crucial to understand the relationship among the bacterial isolates from different geographical locations. Whole genome sequencing approaches will provide more precise molecular characterization of the diversity among populations. Due to the lack of in vitro culture, obtaining the whole genome sequence of CLas is still a challenge, especially for medium to low titer samples. Hundreds of millions of sequencing reads are needed to get good coverage of CLas from an HLB positive citrus sample. In order to overcome this limitation, we present here a new method, Agilent SureSelect XT HS target enrichment, which can specifically enrich CLas from a metagenomic sample while greatly reducing cost and increasing whole genome coverage of the pathogen. In this study, the CLas genome was successfully sequenced with 99.3% genome coverage and over 72X sequencing coverage from low titer tissue samples (equivalent to 28.52 Cq using Li 16 S qPCR). More importantly, this method also effectively captures regions of diversity in the CLas genome, which provides precise molecular characterization of different strains.

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Detecting a long insertion variant in SAMD12 by SMRT sequencing: implications of long-read whole-genome sequencing for repeat expansion diseases

Journal of Human Genetics ◽

10.1038/s10038-018-0551-7 ◽

2018 ◽

Vol 64 (3) ◽

pp. 191-197 ◽

Cited By ~ 12

Author(s):

Takeshi Mizuguchi ◽

Tomoko Toyota ◽

Hiroaki Adachi ◽

Noriko Miyake ◽

Naomichi Matsumoto ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Repeat Expansion ◽

Whole Genome ◽

Smrt Sequencing ◽

Long Read

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Improving tuberculosis surveillance by detecting international transmission using publicly available whole-genome sequencing data

10.1101/834150 ◽

2019 ◽

Author(s):

Andrea Sanchini ◽

Christine Jandrasits ◽

Julius Tembrockhaus ◽

Thomas Andreas Kohl ◽

Christian Utpatel ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Large Scale ◽

Added Value ◽

Whole Genome Sequencing Data ◽

Whole Genome ◽

International Transmission ◽

The Public ◽

Public Dataset ◽

Public Repositories

AbstractIntroductionImproving the surveillance of tuberculosis (TB) is especially important for multidrug-resistant (MDR) and extensively drug-resistant (XDR)-TB. The large amount of publicly available whole-genome sequencing (WGS) data for TB gives us the chance to re-use data and to perform additional analysis at a large scale.AimWe assessed the usefulness of raw WGS data of global MDR/XDR-TB isolates available from public repositories to improve TB surveillance.MethodsWe extracted raw WGS data and the related metadata of Mycobacterium tuberculosis isolates available from the Sequence Read Archive. We compared this public dataset with WGS data and metadata of 131 MDR- and XDR-TB isolates from Germany in 2012-2013.ResultsWe aggregated a dataset that includes 1,081 MDR and 250 XDR isolates among which we identified 133 molecular clusters. In 16 clusters, the isolates were from at least two different countries. For example, cluster2 included 56 MDR/XDR isolates from Moldova, Georgia, and Germany. By comparing the WGS data from Germany and the public dataset, we found that 11 clusters contained at least one isolate from Germany and at least one isolate from another country. We could, therefore, connect TB cases despite missing epidemiological information.ConclusionWe demonstrated the added value of using WGS raw data from public repositories to contribute to TB surveillance. By comparing the German and the public dataset, we identified potential international transmission events. Thus, using this approach might support the interpretation of national surveillance results in an international context.

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