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Article ; Online: Associations of Early COVID-19 Cases in San Francisco With Domestic and International Travel.

Gu, Wei / Deng, Xianding / Reyes, Kevin / Hsu, Elaine / Wang, Candace / Sotomayor-Gonzalez, Alicia / Federman, Scot / Bushnell, Brian / Miller, Steve / Chiu, Charles Y

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

2020 Volume 71, Issue 11, Page(s) 2976–2980

Abstract: In early-to-mid March 2020, 20 of 46 (43%) COVID-19 cases at a tertiary care hospital in San Francisco, California were travel related. Cases were significantly associated with travel to either Europe (odds ratio, 6.1) or New York (odds ratio, 32.9). ... ...

Abstract	In early-to-mid March 2020, 20 of 46 (43%) COVID-19 cases at a tertiary care hospital in San Francisco, California were travel related. Cases were significantly associated with travel to either Europe (odds ratio, 6.1) or New York (odds ratio, 32.9). Viral genomes recovered from 9 of 12 (75%) cases co-clustered with lineages circulating in Europe.
MeSH term(s)	COVID-19 ; Europe ; Humans ; New York ; SARS-CoV-2 ; San Francisco/epidemiology ; Travel ; Travel-Related Illness
Keywords	covid19
Language	English
Publishing date	2020-05-19
Publishing country	United States
Document type	Journal Article
ZDB-ID	1099781-7
ISSN	1537-6591 ; 1058-4838
ISSN (online)	1537-6591
ISSN	1058-4838
DOI	10.1093/cid/ciaa599
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Article ; Online: New Genomes from the Congo Basin Expand History of CRF01_AE Origin and Dissemination.

Junqueira, Dennis Maletich / Wilkinson, Eduan / Vallari, Ana / Deng, Xianding / Achari, Asmeeta / Yu, Guixia / McArthur, Carole / Kaptue, Lazare / Mbanya, Dora / Chiu, Charles / Cloherty, Gavin A / de Oliveira, Tulio / Rodgers, Mary A

AIDS research and human retroviruses

2020 Volume 36, Issue 7, Page(s) 574–582

Abstract: Although the first HIV circulating recombinant form (CRF01_AE) is the predominant strain in many Asian countries, it is uncommonly found in the Congo Basin from where it first originated. To fill the gap in the evolutionary history of this important ... ...

Abstract	Although the first HIV circulating recombinant form (CRF01_AE) is the predominant strain in many Asian countries, it is uncommonly found in the Congo Basin from where it first originated. To fill the gap in the evolutionary history of this important strain, we sequenced near complete genomes from HIV samples with subgenomic CRF01_AE regions collected in Cameroon and the Democratic Republic of the Congo from 2001 to 2006. HIV genomes were generated from
MeSH term(s)	Democratic Republic of the Congo/epidemiology ; Genetic Variation ; Genome, Viral ; Genotype ; HIV Infections/blood ; HIV Infections/epidemiology ; HIV Infections/virology ; HIV-1/genetics ; HIV-1/isolation & purification ; Humans ; Phylogeny ; Phylogeography ; Recombination, Genetic
Language	English
Publishing date	2020-05-18
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	639130-8
ISSN	1931-8405 ; 0889-2229
ISSN (online)	1931-8405
ISSN	0889-2229
DOI	10.1089/AID.2020.0031
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Article ; Online: Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections.

Serpa, Paula Hayakawa / Deng, Xianding / Abdelghany, Mazin / Crawford, Emily / Malcolm, Katherine / Caldera, Saharai / Fung, Monica / McGeever, Aaron / Kalantar, Katrina L / Lyden, Amy / Ghale, Rajani / Deiss, Thomas / Neff, Norma / Miller, Steven A / Doernberg, Sarah B / Chiu, Charles Y / DeRisi, Joseph L / Calfee, Carolyn S / Langelier, Charles R

Genome medicine

2022 Volume 14, Issue 1, Page(s) 74

Abstract: Background: Antimicrobial resistance (AMR) is rising at an alarming rate and complicating the management of infectious diseases including lower respiratory tract infections (LRTI). Metagenomic next-generation sequencing (mNGS) is a recently established ... ...

Abstract	Background: Antimicrobial resistance (AMR) is rising at an alarming rate and complicating the management of infectious diseases including lower respiratory tract infections (LRTI). Metagenomic next-generation sequencing (mNGS) is a recently established method for culture-independent LRTI diagnosis, but its utility for predicting AMR has remained unclear. We aimed to assess the performance of mNGS for AMR prediction in bacterial LRTI and demonstrate proof of concept for epidemiological AMR surveillance and rapid AMR gene detection using Cas9 enrichment and nanopore sequencing. Methods: We studied 88 patients with acute respiratory failure between 07/2013 and 9/2018, enrolled through a previous observational study of LRTI. Inclusion criteria were age ≥ 18, need for mechanical ventilation, and respiratory specimen collection within 72 h of intubation. Exclusion criteria were decline of study participation, unclear LRTI status, or no matched RNA and DNA mNGS data from a respiratory specimen. Patients with LRTI were identified by clinical adjudication. mNGS was performed on lower respiratory tract specimens. The primary outcome was mNGS performance for predicting phenotypic antimicrobial susceptibility and was assessed in patients with LRTI from culture-confirmed bacterial pathogens with clinical antimicrobial susceptibility testing (n = 27 patients, n = 32 pathogens). Secondary outcomes included the association between hospital exposure and AMR gene burden in the respiratory microbiome (n = 88 patients), and AMR gene detection using Cas9 targeted enrichment and nanopore sequencing (n = 10 patients). Results: Compared to clinical antimicrobial susceptibility testing, the performance of respiratory mNGS for predicting AMR varied by pathogen, antimicrobial, and nucleic acid type sequenced. For gram-positive bacteria, a combination of RNA + DNA mNGS achieved a sensitivity of 70% (95% confidence interval (CI) 47-87%) and specificity of 95% (CI 85-99%). For gram-negative bacteria, sensitivity was 100% (CI 87-100%) and specificity 64% (CI 48-78%). Patients with hospital-onset LRTI had a greater AMR gene burden in their respiratory microbiome versus those with community-onset LRTI (p = 0.00030), or those without LRTI (p = 0.0024). We found that Cas9 targeted sequencing could enrich for low abundance AMR genes by > 2500-fold and enabled their rapid detection using a nanopore platform. Conclusions: mNGS has utility for the detection and surveillance of resistant bacterial LRTI pathogens.
MeSH term(s)	Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/therapeutic use ; Bacterial Infections ; Critical Illness ; Drug Resistance, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/methods ; RNA ; Respiratory Tract Infections/diagnosis ; Respiratory Tract Infections/drug therapy ; Respiratory Tract Infections/microbiology ; Sensitivity and Specificity
Chemical Substances	Anti-Bacterial Agents ; RNA (63231-63-0)
Language	English
Publishing date	2022-07-12
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2484394-5
ISSN	1756-994X ; 1756-994X
ISSN (online)	1756-994X
ISSN	1756-994X
DOI	10.1186/s13073-022-01072-4
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Rapid Detection of 2019 Novel Coronavirus SARS-CoV-2 Using a CRISPR-based DETECTR Lateral Flow Assay.

Broughton, James P / Deng, Xianding / Yu, Guixia / Fasching, Clare L / Singh, Jasmeet / Streithorst, Jessica / Granados, Andrea / Sotomayor-Gonzalez, Alicia / Zorn, Kelsey / Gopez, Allan / Hsu, Elaine / Gu, Wei / Miller, Steve / Pan, Chao-Yang / Guevara, Hugo / Wadford, Debra A / Chen, Janice S / Chiu, Charles Y

medRxiv : the preprint server for health sciences

2020

Abstract: An outbreak of novel betacoronavirus, SARS-CoV-2 (formerly named 2019-nCoV), began in Wuhan, China in December 2019 and the COVID-19 disease associated with infection has since spread rapidly to multiple countries. Here we report the development of SARS- ... ...

Abstract	An outbreak of novel betacoronavirus, SARS-CoV-2 (formerly named 2019-nCoV), began in Wuhan, China in December 2019 and the COVID-19 disease associated with infection has since spread rapidly to multiple countries. Here we report the development of SARS-CoV-2 DETECTR, a rapid (~30 min), low-cost, and accurate CRISPR-Cas12 based lateral flow assay for detection of SARS-CoV-2 from respiratory swab RNA extracts. We validated this method using contrived reference samples and clinical samples from infected US patients and demonstrated comparable performance to the US CDC SARS-CoV-2 real-time RT-PCR assay.
Keywords	covid19
Language	English
Publishing date	2020-03-27
Publishing country	United States
Document type	Preprint
DOI	10.1101/2020.03.06.20032334
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Article: Whole-genome Sequencing for Surveillance of Invasive Pneumococcal Diseases in Ontario, Canada: Rapid Prediction of Genotype, Antibiotic Resistance and Characterization of Emerging Serotype 22F.

Deng, Xianding / Memari, Nader / Teatero, Sarah / Athey, Taryn / Isabel, Marc / Mazzulli, Tony / Fittipaldi, Nahuel / Gubbay, Jonathan B

Frontiers in microbiology

2016 Volume 7, Page(s) 2099

Abstract: Background: ...

Abstract	Background:
Language	English
Publishing date	2016-12-27
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2016.02099
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Article ; Online: Population structure and drug resistance patterns of emerging non-PCV-13 Streptococcus pneumoniae serotypes 22F, 15A, and 8 isolated from adults in Ontario, Canada.

Duvvuri, Venkata R / Deng, Xianding / Teatero, Sarah / Memari, Nader / Athey, Taryn / Fittipaldi, Nahuel / Gubbay, Jonathan B

Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases

2016 Volume 42, Page(s) 1–8

Abstract: The introduction of pneumococcal conjugate vaccines has led to the emergence of non-vaccine serotypes, which contributed to invasive pneumococcal disease in Canada and worldwide. A significant increase in the prevalence of non-13-valent pneumococcal ... ...

Abstract	The introduction of pneumococcal conjugate vaccines has led to the emergence of non-vaccine serotypes, which contributed to invasive pneumococcal disease in Canada and worldwide. A significant increase in the prevalence of non-13-valent pneumococcal conjugate vaccine (PCV-13)-included serotypes 22F, 15A, and 8 was observed from 2009 to 2013 in Ontario (all p values<0.01). In this study, whole genome sequencing was conducted on the 25 isolates of serotype 22F, seven of 15A and 10 of 8 to investigate the population structure and antibiotic resistance. All seven serotype 15A isolates were found to be multidrug resistant. From whole genome analysis, we observed recombination events among serotypes 22F, 15A and 8 populations. Serotype 22F (ST433) has emerged into two sub-populations, with 28% (7/25) exhibiting recombination events, and five also acquiring macrolide resistance as a result of recombination. This study enhances the knowledge on the molecular evolution of emerging non-PCV-13 vaccine serotype 22F, including acquisition of resistance genes through recombination events. It underpins the importance of whole genome sequencing in studying Streptococcus pneumoniae population structures and dynamics, and its utility in molecular surveillance.
MeSH term(s)	Adult ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Evolution, Molecular ; Genome, Bacterial ; Humans ; Macrolides/pharmacology ; Microbial Sensitivity Tests ; Ontario/epidemiology ; Phylogeny ; Pneumococcal Infections/drug therapy ; Pneumococcal Infections/epidemiology ; Pneumococcal Infections/immunology ; Pneumococcal Infections/microbiology ; Pneumococcal Vaccines/genetics ; Pneumococcal Vaccines/immunology ; Prevalence ; Recombination, Genetic ; Serogroup ; Serotyping ; Streptococcus pneumoniae/classification ; Streptococcus pneumoniae/drug effects ; Streptococcus pneumoniae/genetics ; Streptococcus pneumoniae/isolation & purification
Chemical Substances	13-valent pneumococcal vaccine ; Anti-Bacterial Agents ; Macrolides ; Pneumococcal Vaccines
Language	English
Publishing date	2016
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2037068-4
ISSN	1567-7257 ; 1567-1348
ISSN (online)	1567-7257
ISSN	1567-1348
DOI	10.1016/j.meegid.2016.04.007
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Article ; Online: Streptococcus pneumoniae infection: a Canadian perspective.

Deng, Xianding / Church, Deirdre / Vanderkooi, Otto G / Low, Donald E / Pillai, Dylan R

Expert review of anti-infective therapy

2013 Volume 11, Issue 8, Page(s) 781–791

Abstract: Streptococcus pneumoniae infections have resulted in significant morbidity and mortality worldwide in children and adults. In Canada, Streptococcus pneumoniae remains one of the leading causes of infectious disease including pneumonia, meningitis, ... ...

Abstract	Streptococcus pneumoniae infections have resulted in significant morbidity and mortality worldwide in children and adults. In Canada, Streptococcus pneumoniae remains one of the leading causes of infectious disease including pneumonia, meningitis, bacteremia and otitis media. Although the widespread use of pneumococcal conjugate vaccines (PCVs) in Canadian children has reduced the incidence of pneumococcal diseases associated with vaccine-serotypes, rapid increase of non-vaccine serotypes in carriage and pneumococcal infections is of great concern to clinicians. The main goal of this review is to provide an overall picture of invasive pneumococcal diseases (IPD) in Canada for the past few decades, including serotype changes and shifts in antibiotic resistance patterns. The effects of PCV vaccines on incidence, serotype distribution, antibiotic resistance of pneumococcal infections and nasopharyngeal (NP) carriage are discussed. We also examined historical outbreaks of Streptococcus pneumoniae and their public health impact. Recent developments in universal protein vaccines against pneumococcus show promise.
MeSH term(s)	Canada/epidemiology ; Disease Outbreaks ; Drug Resistance, Bacterial ; Humans ; Incidence ; Pneumococcal Infections/epidemiology ; Pneumococcal Infections/prevention & control ; Pneumococcal Infections/transmission ; Pneumococcal Vaccines/therapeutic use ; Serotyping ; Streptococcus pneumoniae/classification ; Streptococcus pneumoniae/drug effects ; Streptococcus pneumoniae/isolation & purification
Chemical Substances	Pneumococcal Vaccines
Language	English
Publishing date	2013-08
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	2181279-2
ISSN	1744-8336 ; 1478-7210
ISSN (online)	1744-8336
ISSN	1478-7210
DOI	10.1586/14787210.2013.814831
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Article ; Online: Introduction, Transmission Dynamics, and Fate of Early Severe Acute Respiratory Syndrome Coronavirus 2 Lineages in Santa Clara County, California.

The Journal of infectious diseases

2021 Volume 224, Issue 2, Page(s) 207–217

Abstract: We combined viral genome sequencing with contact tracing to investigate introduction and evolution of severe acute respiratory syndrome coronavirus 2 lineages in Santa Clara County, California, from 27 January to 21 March 2020. From 558 persons with ... ...

Abstract	We combined viral genome sequencing with contact tracing to investigate introduction and evolution of severe acute respiratory syndrome coronavirus 2 lineages in Santa Clara County, California, from 27 January to 21 March 2020. From 558 persons with coronavirus disease 2019, 101 genomes from 143 available clinical samples comprised 17 lineages, including SCC1 (n = 41), WA1 (n = 9; including the first 2 reported deaths in the United States, with postmortem diagnosis), D614G (n = 4), ancestral Wuhan Hu-1 (n = 21), and 13 others (n = 26). Public health intervention may have curtailed the persistence of lineages that appeared transiently during February and March. By August, only D614G lineages introduced after 21 March were circulating in Santa Clara County.
MeSH term(s)	Adult ; Aged ; COVID-19/epidemiology ; COVID-19/prevention & control ; COVID-19/transmission ; California/epidemiology ; Contact Tracing ; Female ; Genetic Variation ; Genome, Viral/genetics ; Genotype ; Humans ; Male ; Middle Aged ; Phylogeny ; Risk Factors ; SARS-CoV-2/classification ; SARS-CoV-2/genetics ; Travel ; Young Adult
Language	English
Publishing date	2021-04-23
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	3019-3
ISSN	1537-6613 ; 0022-1899
ISSN (online)	1537-6613
ISSN	0022-1899
DOI	10.1093/infdis/jiab199
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Article: Associations of Early COVID-19 Cases in San Francisco with Domestic and International Travel

Gu, Wei / Deng, Xianding / Reyes, Kevin / Hsu, Elaine / Wang, Candace / Sotomayor-Gonzalez, Alicia / Federman, Scot / Bushnell, Brian / Miller, Steve / Chiu, Charles

Clin. infect. dis

Abstract: In early-to-mid March 2020, 20 of 46 (43%) COVID-19 cases at a tertiary care hospital in San Francisco, California were travel-related. Cases were significantly associated with travel to Europe or New York (odds ratio 32.9). Viral genomes recovered from ... ...

Abstract	In early-to-mid March 2020, 20 of 46 (43%) COVID-19 cases at a tertiary care hospital in San Francisco, California were travel-related. Cases were significantly associated with travel to Europe or New York (odds ratio 32.9). Viral genomes recovered from 9 of 12 (75%) cases co-clustered with lineages circulating in Europe.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #327175
Database	COVID19

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Article ; Online: Associations of Early COVID-19 Cases in San Francisco With Domestic and International Travel

Gu, Wei / Deng, Xianding / Reyes, Kevin / Hsu, Elaine / Wang, Candace / Sotomayor-Gonzalez, Alicia / Federman, Scot / Bushnell, Brian / Miller, Steve / Chiu, Charles Y

Clinical Infectious Diseases ; ISSN 1058-4838 1537-6591

2020

Abstract: Abstract In early-to-mid March 2020, 20 of 46 (43%) COVID-19 cases at a tertiary care hospital in San Francisco, California were travel related. Cases were significantly associated with travel to either Europe (odds ratio, 6.1) or New York (odds ratio, ... ...

Abstract	Abstract In early-to-mid March 2020, 20 of 46 (43%) COVID-19 cases at a tertiary care hospital in San Francisco, California were travel related. Cases were significantly associated with travel to either Europe (odds ratio, 6.1) or New York (odds ratio, 32.9). Viral genomes recovered from 9 of 12 (75%) cases co-clustered with lineages circulating in Europe.
Keywords	Microbiology (medical) ; Infectious Diseases ; covid19
Language	English
Publisher	Oxford University Press (OUP)
Publishing country	uk
Document type	Article ; Online
DOI	10.1093/cid/ciaa599
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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