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Articles by Joshua Quick
Phylogenetic analysis of the 2025 Ebola outbreak in the Democratic Republic of the Congo
Abstract On 4 September 2025, the Ministry of Public Health, Hygiene and Social Welfare officially declared the 16th Ebola disease outbreak in the Democratic Republic of the Congo (DRC). This outbreak ended on 1 December 2025 and occurred in Bulape Health Zone, Kasaï Province, an area with limited access to appropriate healthcare facilities and resources.
A Simple, Low-Cost, and Efficient Protocol for Rapid Isolation of Pathogenic Bacteria from Human Blood
Abstract Bacteremia is a serious clinical condition in which pathogenic bacteria enter the bloodstream, putting patients at risk of septic shock and necessitating antibiotic treatment. Choosing the most effective antibiotic is crucial not only for resolving the infection but also for minimizing side effects, such as dysbiosis in the healthy microbiome and reducing the selection pressure for antibiotic resistance.
Year after yoga shooting, I think most about Nancy and Maura and wish I could have helped them
Joshua Quick, Guest columnist Published 1:56 p.m. ET Nov. 1, 2019 On Nov. 2, 2018, 2 women were killed by a shooter at a yoga studio in Tallahassee. Others escaped when one person took action. Nate Chute, USA Today Network It’s hard to believe it’s only been one year. Much has happened since the shooting at Tallahassee Hot Yoga, yet I still have vivid recollections from inside that studio.
An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar
Nathan D. Grubaugh1, 2Email author, Karthik Gangavarapu1Email author, Joshua Quick3, Nathaniel L. Matteson1, Jaqueline Goes De Jesus3, 4, Bradley J. Main5, Amanda L. Tan6, Lauren M. Paul6, Doug E. Brackney7, Saran Grewal8, Nikos Gurfield8, Koen K. A. Van Rompay9, Sharon Isern6, Scott F. Michael6, Lark L. Coffey5, Nicholas J. Loman3 and Kristian G. Andersen1, 10View ORCID ID profile Genome Biology201920:8 https://doi.org/10.1186/s13059-018-1618-7 © The Author(s).
Ultra-deep, long-read nanopore sequencing of mock microbial community standards
Ultra-deep, long-read nanopore sequencing of mock microbial community standards Samuel M Nicholls, Joshua C Quick, Shuiquan Tang, Nicholas J Loman bioRxiv 487033; doi: https://doi.org/10.1101/487033
Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples
Genome sequencing of viruses has been used to study the spread of disease in outbreaks1. Real-time genomic surveillance is important in managing viral outbreaks, as it can provide insights into how viruses transmit, spread and evolve1, 2, 3, 4. Such work depends on rapid sequencing of viral material directly from clinical samples—i.e., without the need to isolate the virus in pure culture.
Seeking the source of Pseudomonas aeruginosa infections in a recently opened hospital: an observational study using whole-genome sequencing
Results WGS for 141 P. aeruginosa isolates were obtained from patients, hospital water and the ward environment. Phylogenetic analysis revealed eight distinct clades, with a single clade representing the majority of environmental isolates in the burns unit. Isolates from three patients had identical genotypes compared with water isolates from the same room. There was clear clustering of water isolates by room and outlet, allowing the source of acquisitions to be unambiguously identified.
Real-time, portable genome sequencing for Ebola surveillance
The National Committee of Ethics in Medical Research of Guinea (permit no. 11/CNERS/14) approved the use of diagnostic leftover samples and corresponding patient data for this study. As the samples had been collected as part of the public health response to control the outbreak in West Africa, informed consent was not obtained from patients.
Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of
Background Foodborne outbreaks of Salmonella remain a pressing public health concern. We recently detected a large outbreak of Salmonella enterica serovar Enteritidis phage type 14b affecting more than 30 patients in our hospital. This outbreak was linked to community, national and European-wide cases. Hospital patients with Salmonella are at high risk, and require a rapid response.
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