scholarly journals Rule-Out Outbreak: 24-Hour Metagenomic Next-Generation Sequencing for Characterizing Respiratory Virus Source for Infection Prevention

2017 ◽  
Vol 6 (2) ◽  
pp. 168-172 ◽  
Author(s):  
Alexander L. Greninger ◽  
Alpana Waghmare ◽  
Amanda Adler ◽  
Xuan Qin ◽  
Janet L. Crowley ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Infection Prevention ◽  
Respiratory Virus ◽  
Next Generation ◽  
Virus Source ◽  
Generation Sequencing ◽  
Rule Out

scholarly journals Application of next generation sequencing in clinical microbiology and infection prevention

2017 ◽  
Vol 243 ◽  
pp. 16-24 ◽  
Author(s):  
Ruud H. Deurenberg ◽  
Erik Bathoorn ◽  
Monika A. Chlebowicz ◽  
Natacha Couto ◽  
Mithila Ferdous ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Clinical Microbiology ◽  
Infection Prevention ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals Rapid Metagenomic Next-Generation Sequencing during an Investigation of Hospital-Acquired Human Parainfluenza Virus 3 Infections

2016 ◽  
Vol 55 (1) ◽  
pp. 177-182 ◽  
Author(s):  
Alexander L. Greninger ◽  
Danielle M. Zerr ◽  
Xuan Qin ◽  
Amanda L. Adler ◽  
Reigran Sampoleo ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Infection Prevention ◽  
Genomic Sequence ◽  
Clinical Samples ◽  
Whole Genome ◽  
Next Generation ◽  
Sequence Coverage ◽  
Medical Unit ◽  
Hospital Acquired ◽  
Generation Sequencing

ABSTRACT Metagenomic next-generation sequencing (mNGS) is increasingly used for the unbiased detection of viruses, bacteria, fungi, and eukaryotic parasites in clinical samples. Whole-genome sequencing (WGS) of clinical bacterial isolates has been shown to inform hospital infection prevention practices, but this technology has not been utilized during potential respiratory virus outbreaks. Here, we report on the use of mNGS to inform the real-time infection prevention response to a cluster of hospital-acquired human parainfluenza 3 virus (HPIV3) infections at a children's hospital. Samples from 3 patients with hospital-acquired HPIV3 identified over a 12-day period on a general medical unit and 10 temporally associated samples from patients with community-acquired HPIV3 were analyzed. Our sample-to-sequencer time was <24 h, while our sample-to-answer turnaround time was <60 h with a hands-on time of approximately 6 h. Eight (2 cases and 6 controls) of 13 samples had sufficient sequencing coverage to yield the whole genome for HPIV3, while 10 (2 cases and 8 controls) of 13 samples gave partial genomes and all 13 samples had >1 read for HPIV3. Phylogenetic clustering revealed the presence of identical HPIV3 genomic sequence in the two of the cases with hospital-acquired infection, consistent with the concern for recent transmission within the medical unit. Adequate sequence coverage was not recovered for the third case. This work demonstrates the promise of mNGS for providing rapid information for infection prevention in addition to microbial detection.

scholarly journals Reprint of “Application of next generation sequencing in clinical microbiology and infection prevention”

2017 ◽  
Vol 250 ◽  
pp. 2-10 ◽  
Author(s):  
Ruud H. Deurenberg ◽  
Erik Bathoorn ◽  
Monika A. Chlebowicz ◽  
Natacha Couto ◽  
Mithila Ferdous ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Clinical Microbiology ◽  
Infection Prevention ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals Chronic Neurobrucellosis Investigated via Metagenomic Next-Generation Sequencing

2020 ◽  
Vol 1 (1) ◽  
Author(s):  
Yun Zhang ◽  
Xiaodan Shi ◽  
Xiaofei Fei ◽  
Guodong Feng ◽  
Gang Zhao*
Keyword(s):  
Next Generation Sequencing ◽  
Next Generation ◽  
Brucella Infection ◽  
Clinical Resistance ◽  
Epidemic Area ◽  
Generation Sequencing ◽  
Rule Out

We found that NGS technology has great significance for the diagnosis of brucellosis in non-epidemic area and can rule out other infections. The number of Brucella gene fragments detected by NGS may be affected by clinical resistance to Brucella treatment and Brucella infection. The sensitivity of SAT to detect Brucella may is limited.

scholarly journals Comprehensive viral enrichment enables sensitive respiratory virus genomic identification and analysis by next generation sequencing

2018 ◽  
Vol 28 (6) ◽  
pp. 869-877 ◽  
Author(s):  
Brigid M. O'Flaherty ◽  
Yan Li ◽  
Ying Tao ◽  
Clinton R. Paden ◽  
Krista Queen ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Respiratory Virus ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals Rapid metagenomic next-generation sequencing during an investigation of hospital-acquired human parainfluenza virus 3 infections

2016 ◽  
Author(s):  
Alexander L. Greninger ◽  
Danielle M Zerr ◽  
Xuan Qin ◽  
Amanda L. Adler ◽  
Janet A. Englund ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Infection Prevention ◽  
Genomic Sequence ◽  
Clinical Samples ◽  
Next Generation ◽  
Sequence Coverage ◽  
Medical Unit ◽  
Recent Transmission ◽  
Hospital Acquired ◽  
Generation Sequencing

AbstractMetagenomic next-generation sequencing (mNGS) is increasingly used for the unbiased detection of viruses, bacteria, fungi, and eukaryotic parasites in clinical samples. Whole genome sequencing (WGS) of clinical bacterial isolates has been shown to inform hospital infection prevention practices, but the use of this technology during potential respiratory virus outbreaks has not been taken advantage of. Here, we report on the use of mNGS to inform the real-time infection prevention response to a cluster of hospital-acquired human parainfluenza 3 virus (HPIV3) infections at a children’s hospital. Isolates from 3 patients with hospital-acquired HPIV3 identified over a 12-day period on a general medical unit and 10 temporally-associated isolates from patients with community-acquired of HPIV3 were analyzed. Our sample-to-sequencer time was <24 hours while our sample-to-answer turn-around time was <60 hours with a hands-on time of approximately 6 hours. Eight (2 case isolates and 6 control isolates) of 13 samples had sufficient sequencing coverage to yield whole genomes for HPIV3, while 10 (2 cases and 8 controls) of 13 samples gave partial genomes and all 13 samples had >1 read to HPIV3. Phylogenetic clustering revealed the presence of identical HPIV3 genomic sequence in the two of the cases with hospital-acquired infection, consistent with the concern for recent transmission within the medical unit. Adequate sequence coverage was not recovered for the third case. This work demonstrates the promise of mNGS to provide actionable information for infection control in addition to microbial detection.

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