High-Quality Genome Sequence Assembly of R.A73 Enterococcus faecium Isolated from Freshwater fish mucus Exhibiting high Probiotic Potential

Abstract Background: Whole-genome sequencing using high throughput technologies has revolutionized and speeded up the scientific investigation of bacterial genetics, biochemistry, and molecular biology. Lactic acid bacteria (LABs) have been extensively used in fermentation and more recently as probiotics in food products that promote health. Genome sequencing and functional genomics investigations of LABs varieties provide rapid and important information about their diversity and their evolution, revealing a significant molecular basis.This study investigates the whole genome sequences of the Enterococcus faecium genome (HG937697), isolated from the mucus of freshwater fish in Tunisian dams. Genomic DNA was extracted using the Quick-GDNA kit (Zymoresearch) and sequenced using the Illumina HiSeq2500 system. Sequences quality assessment was performed using FastQC software. The complete genome annotation was carried out with the RAST web server then NCBI PGAAP. Results: The Enterococcus faecium R.A73 assembled in 28 contigs consisting of 2,935,283 bps. The genome annotation revealed 2,884 genes in total including 2,834 coding sequences and 50 RNAs containing 3 rRNAs (one rRNA 16s, one rRNA 23s and one rRNA 5s) and 47 tRNAs. Twenty-two genes implicated in bacteriocin production are identified within the Enterococcus faecium R.A73 genome.Conclusions: Data obtained provide insights to further investigate the effective strategy for testing this Enterococcus faecium R.A73 strain in the industrial manufacturing process. Studying their metabolism with bioinformatics tools represents the future challenge and contribution to improving the utilization of the multi-purpose bacteria in food.

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High-Quality Genome Sequence Assembly of R.A73 Enterococcus faecium Isolated from Freshwater fish mucus

10.21203/rs.3.rs-25205/v4 ◽

2020 ◽

Author(s):

Rim El Jeni ◽

Kais Ghedira ◽

Monia El Bour ◽

Sonia Abdelhak ◽

Alia Ben Kahla ◽

...

Keyword(s):

Freshwater Fish ◽

Genome Sequencing ◽

Enterococcus Faecium ◽

Genome Annotation ◽

Whole Genome ◽

Bacterial Genetics ◽

Industrial Manufacturing ◽

Genome Sequence Assembly ◽

Fish Mucus ◽

High Quality Genome

Abstract Background: Whole-genome sequencing using high throughput technologies has revolutionized and speeded up the scientific investigation of bacterial genetics, biochemistry, and molecular biology. Lactic acid bacteria (LABs) have been extensively used in fermentation and more recently as probiotics in food products that promote health. Genome sequencing and functional genomics investigations of LABs varieties provide rapid and important information about their diversity and their evolution, revealing a significant molecular basis.This study investigated the whole genome sequences of the Enterococcus faecium strain (HG937697), isolated from the mucus of freshwater fish in Tunisian dams. Genomic DNA was extracted using the Quick-GDNA kit and sequenced using the Illumina HiSeq2500 system. Sequences quality assessment was performed using FastQC software. The complete genome annotation was carried out with the Rapid Annotation using Subsystem Technology (RAST) web server then NCBI PGAAP. Results: The Enterococcus faecium R.A73 assembled in 28 contigs consisting of 2,935,283 bps. The genome annotation revealed 2,884 genes in total including 2,834 coding sequences and 50 RNAs containing 3 rRNAs (one rRNA 16s, one rRNA 23s and one rRNA 5s) and 47 tRNAs. Twenty-two genes implicated in bacteriocin production are identified within the Enterococcus faecium R.A73 strain. Conclusion: Data obtained provide insights to further investigate the effective strategy for testing this Enterococcus faecium R.A73 strain in the industrial manufacturing process. Studying their metabolism with bioinformatics tools represents the future challenge and contribution to improving the utilization of the multi-purpose bacteria in food.

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High-quality genome sequence assembly of R.A73 Enterococcus faecium isolated from freshwater fish mucus

BMC Microbiology ◽

10.1186/s12866-020-01980-8 ◽

2020 ◽

Vol 20 (1) ◽

Author(s):

Rim El Jeni ◽

Kais Ghedira ◽

Monia El Bour ◽

Sonia Abdelhak ◽

Alia Benkahla ◽

...

Keyword(s):

Freshwater Fish ◽

Genome Sequencing ◽

Enterococcus Faecium ◽

Genome Annotation ◽

Whole Genome ◽

Bacterial Genetics ◽

Industrial Manufacturing ◽

Genome Sequence Assembly ◽

Fish Mucus ◽

High Quality Genome

Abstract Background Whole-genome sequencing using high throughput technologies has revolutionized and speeded up the scientific investigation of bacterial genetics, biochemistry, and molecular biology. Lactic acid bacteria (LABs) have been extensively used in fermentation and more recently as probiotics in food products that promote health. Genome sequencing and functional genomics investigations of LABs varieties provide rapid and important information about their diversity and their evolution, revealing a significant molecular basis. This study investigated the whole genome sequences of the Enterococcus faecium strain (HG937697), isolated from the mucus of freshwater fish in Tunisian dams. Genomic DNA was extracted using the Quick-GDNA kit and sequenced using the Illumina HiSeq2500 system. Sequences quality assessment was performed using FastQC software. The complete genome annotation was carried out with the Rapid Annotation using Subsystem Technology (RAST) web server then NCBI PGAAP. Results The Enterococcus faecium R.A73 assembled in 28 contigs consisting of 2,935,283 bps. The genome annotation revealed 2884 genes in total including 2834 coding sequences and 50 RNAs containing 3 rRNAs (one rRNA 16 s, one rRNA 23 s and one rRNA 5 s) and 47 tRNAs. Twenty-two genes implicated in bacteriocin production are identified within the Enterococcus faecium R.A73 strain. Conclusion Data obtained provide insights to further investigate the effective strategy for testing this Enterococcus faecium R.A73 strain in the industrial manufacturing process. Studying their metabolism with bioinformatics tools represents the future challenge and contribution to improving the utilization of the multi-purpose bacteria in food.

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High-Quality Genome Sequence Assembly of R.A73 Enterococcus faecium Isolated from Freshwater fish mucus

10.21203/rs.3.rs-25205/v3 ◽

2020 ◽

Author(s):

Rim El Jeni ◽

Kais Ghedira ◽

Monia El Bour ◽

Sonia Abdelhak ◽

Alia Ben Kahla ◽

...

Keyword(s):

Freshwater Fish ◽

Genome Sequencing ◽

Enterococcus Faecium ◽

Genome Annotation ◽

Whole Genome ◽

Bacterial Genetics ◽

Industrial Manufacturing ◽

Genome Sequence Assembly ◽

Fish Mucus ◽

High Quality Genome

Abstract Background: Whole-genome sequencing using high throughput technologies has revolutionized and speeded up the scientific investigation of bacterial genetics, biochemistry, and molecular biology. Lactic acid bacteria (LABs) have been extensively used in fermentation and more recently as probiotics in food products that promote health. Genome sequencing and functional genomics investigations of LABs varieties provide rapid and important information about their diversity and their evolution, revealing a significant molecular basis.This study investigated the whole genome sequences of the Enterococcus faecium strain (HG937697), isolated from the mucus of freshwater fish in Tunisian dams. Genomic DNA was extracted using the Quick-GDNA kit and sequenced using the Illumina HiSeq2500 system. Sequences quality assessment was performed using FastQC software. The complete genome annotation was carried out with the RAST web server then NCBI PGAAP. Results: The Enterococcus faecium R.A73 assembled in 28 contigs consisting of 2,935,283 bps. The genome annotation revealed 2,884 genes in total including 2,834 coding sequences and 50 RNAs containing 3 rRNAs (one rRNA 16s, one rRNA 23s and one rRNA 5s) and 47 tRNAs. Twenty-two genes implicated in bacteriocin production are identified within the Enterococcus faecium R.A73 strain. Conclusion: Data obtained provide insights to further investigate the effective strategy for testing this Enterococcus faecium R.A73 strain in the industrial manufacturing process. Studying their metabolism with bioinformatics tools represents the future challenge and contribution to improving the utilization of the multi-purpose bacteria in food.

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Whole genome sequencing and genome annotation of Dermacoccus abyssi strain HZAU 226 isolated from spoiled eggs

Genomics ◽

10.1016/j.ygeno.2020.12.005 ◽

2020 ◽

Author(s):

Xinshuai Zhang ◽

Yao Ruan ◽

Wukang Liu ◽

Qian Chen ◽

Lihong Gu ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genome Annotation ◽

Whole Genome

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Whole-genome sequencing revealed independent emergence of vancomycin-resistant Enterococcus faecium causing sequential outbreaks over 3 years in a tertiary care hospital

European Journal of Clinical Microbiology & Infectious Diseases ◽

10.1007/s10096-019-03524-z ◽

2019 ◽

Vol 38 (6) ◽

pp. 1163-1170 ◽

Cited By ~ 8

Author(s):

Mohamed H. H. Abdelbary ◽

Laurence Senn ◽

Gilbert Greub ◽

Gregory Chaillou ◽

Estelle Moulin ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Enterococcus Faecium ◽

Tertiary Care Hospital ◽

Tertiary Care ◽

Whole Genome ◽

Care Hospital ◽

Vancomycin Resistant Enterococcus ◽

Vancomycin Resistant

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Outbreak of Vancomycin-resistant Enterococcus faecium in Interventional Radiology: Detection Through Whole-genome Sequencing-based Surveillance

Clinical Infectious Diseases ◽

10.1093/cid/ciz666 ◽

2019 ◽

Vol 70 (11) ◽

pp. 2336-2343 ◽

Cited By ~ 7

Author(s):

Alexander J Sundermann ◽

Ahmed Babiker ◽

Jane W Marsh ◽

Kathleen A Shutt ◽

Mustapha M Mustapha ◽

...

Keyword(s):

Interventional Radiology ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Enterococcus Faecium ◽

Whole Genome ◽

Training Video ◽

Prevention Interventions ◽

Vancomycin Resistant ◽

Record Review ◽

Hospital Acquired

Abstract Background Vancomycin-resistant enterococci (VRE) are a major cause of hospital-acquired infections. The risk of infection from interventional radiology (IR) procedures is not well documented. Whole-genome sequencing (WGS) surveillance of clinical bacterial isolates among hospitalized patients can identify previously unrecognized outbreaks. Methods We analyzed WGS surveillance data from November 2016 to November 2017 for evidence of VRE transmission. A previously unrecognized cluster of 10 genetically related VRE (Enterococcus faecium) infections was discovered. Electronic health record review identified IR procedures as a potential source. An outbreak investigation was conducted. Results Of the 10 outbreak patients, 9 had undergone an IR procedure with intravenous (IV) contrast ≤22 days before infection. In a matched case-control study, preceding IR procedure and IR procedure with contrast were associated with VRE infection (matched odds ratio [MOR], 16.72; 95% confidence interval [CI], 2.01 to 138.73; P = .009 and MOR, 39.35; 95% CI, 7.85 to infinity; P < .001, respectively). Investigation of IR practices and review of the manufacturer’s training video revealed sterility breaches in contrast preparation. Our investigation also supported possible transmission from an IR technician. Infection prevention interventions were implemented, and no further IR-associated VRE transmissions have been observed. Conclusions A prolonged outbreak of VRE infections related to IR procedures with IV contrast resulted from nonsterile preparation of injectable contrast. The fact that our VRE outbreak was discovered through WGS surveillance and the manufacturer’s training video that demonstrated nonsterile technique raise the possibility that infections following invasive IR procedures may be more common than previously recognized.

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Successful containment of two vancomycin-resistant Enterococcus faecium (VRE) outbreaks in a Dutch teaching hospital using environmental sampling and whole genome sequencing

Journal of Hospital Infection ◽

10.1016/j.jhin.2021.02.007 ◽

2021 ◽

Author(s):

K.B. Gast ◽

A.J.G. van Oudheusden ◽

J.L. Murk ◽

J.J.J.M. Stohr ◽

A.G. Buiting ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Teaching Hospital ◽

Enterococcus Faecium ◽

Environmental Sampling ◽

Whole Genome ◽

Vancomycin Resistant Enterococcus ◽

Vancomycin Resistant

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Complete Genome Sequence of the Gut Commensal and Laboratory Strain Enterococcus faecium 64/3

Genome Announcements ◽

10.1128/genomea.01275-15 ◽

2015 ◽

Vol 3 (6) ◽

Cited By ~ 5

Author(s):

Jennifer K. Bender ◽

Stefan Fiedler ◽

Ingo Klare ◽

Guido Werner

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genome Sequence ◽

Complete Genome Sequence ◽

Enterococcus Faecium ◽

Complete Genome ◽

Laboratory Strain ◽

Whole Genome ◽

Coding Sequences

The genome sequence of the commensal and widely used laboratory strain Enterococcus faecium 64/3 was resolved by means of PacificBioscience and Illumina whole-genome sequencing. The genome comprises 2,575,333 bp with 2,382 coding sequences as assigned by NCBI.

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