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Dr. Hamza Mbareche
Sunnybrook Research Institute

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Research Keywords & Expertise

0 Environmental Microbiology
0 infectious disease
0 Bioinfomatics
0 bioaerosols
0 Genomic analyses

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Short Biography

Postdoctoral Fellow at the Sunnybrook Translational Research Group for Emerging Respiratory Viruses (SERV) - Laboratory of Medicine and Pathobiology, University of Toronto. I'm Interested in airborne microorganisms & viruses, genomics and bioinformatics

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Research article
Published: 15 August 2021 in American Journal of Respiratory and Critical Care Medicine
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ACS Style

Ryan J. Hiebert; Hamza Mbareche; Hamed Avari; Robert A. Fowler; Samira Mubareka. Reply to Tandjaoui-Lambiotte et al.: Viral Dispersion in the ICU: The Wind Effect. American Journal of Respiratory and Critical Care Medicine 2021, 204, 489 -489.

AMA Style

Ryan J. Hiebert, Hamza Mbareche, Hamed Avari, Robert A. Fowler, Samira Mubareka. Reply to Tandjaoui-Lambiotte et al.: Viral Dispersion in the ICU: The Wind Effect. American Journal of Respiratory and Critical Care Medicine. 2021; 204 (4):489-489.

Chicago/Turabian Style

Ryan J. Hiebert; Hamza Mbareche; Hamed Avari; Robert A. Fowler; Samira Mubareka. 2021. "Reply to Tandjaoui-Lambiotte et al.: Viral Dispersion in the ICU: The Wind Effect." American Journal of Respiratory and Critical Care Medicine 204, no. 4: 489-489.

Preprint content
Published: 20 May 2021
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Background The aim of this prospective cohort study was to determine the burden of SARS-CoV-2 in air and on surfaces in rooms of patients hospitalized with COVID-19, and to identify patient characteristics associated with SARS-CoV-2 environmental contamination. Methods Nasopharyngeal swabs, surface, and air samples were collected from the rooms of 78 inpatients with COVID-19 at six acute care hospitals in Toronto from March to May 2020. Samples were tested for SARS-CoV-2 viral RNA and cultured to determine potential infectivity. Whole viral genomes were sequenced from nasopharyngeal and surface samples. Association between patient factors and detection of SARS-CoV-2 RNA in surface samples were investigated using a mixed-effects logistic regression model. Findings SARS-CoV-2 RNA was detected from surfaces (125/474 samples; 42/78 patients) and air (3/146 samples; 3/45 patients) in COVID-19 patient rooms; 14% (6/42) of surface samples from three patients yielded viable virus. Viral sequences from nasopharyngeal and surface samples clustered by patient. Multivariable analysis indicated hypoxia at admission, a PCR-positive nasopharyngeal swab with a cycle threshold of ≤30 on or after surface sampling date, higher Charlson co-morbidity score, and shorter time from onset of illness to sample date were significantly associated with detection of SARS-CoV-2 RNA in surface samples. Interpretation The infrequent recovery of infectious SARS-CoV-2 virus from the environment suggests that the risk to healthcare workers from air and near-patient surfaces in acute care hospital wards is likely limited. Surface contamination was greater when patients were earlier in their course of illness and in those with hypoxia, multiple co-morbidities, and higher SARS-CoV-2 RNA concentration in NP swabs. Our results suggest that, while early detection and isolation of COVID-19 patients is important, air and surfaces may pose limited risk a few days after admission to acute care hospitals.

ACS Style

Jonathon D. Kotwa; Alainna J. Jamal; Hamza Mbareche; Lily Yip; Patryk Aftanas; Shiva Barati; Natalie G. Bell; Elizabeth Bryce; Eric D Coomes; Gloria Crowl; Caroline Duchaine; Amna Faheem; Lubna Farooqi; Ryan Hiebert; Kevin Katz; Saman Khan; Robert Kozak; Angel X. Li; Henna P. Mistry; Mohammad Mozafarihashjin; Jalees A. Nasir; Kuganya Nirmalarajah; Emily M. Panousis; Aimee Paterson; Simon Plenderleith; Jeff Powis; Karren Prost; Renee Schryer; Maureen Taylor; Marc Veillette; Titus Wong; Xi Zoe Zhong; Andrew G. McArthur; Allison J. McGeer; Samira Mubareka. Surface and air contamination with SARS-CoV-2 from hospitalized COVID-19 patients in Toronto, Canada. 2021, 1 .

AMA Style

Jonathon D. Kotwa, Alainna J. Jamal, Hamza Mbareche, Lily Yip, Patryk Aftanas, Shiva Barati, Natalie G. Bell, Elizabeth Bryce, Eric D Coomes, Gloria Crowl, Caroline Duchaine, Amna Faheem, Lubna Farooqi, Ryan Hiebert, Kevin Katz, Saman Khan, Robert Kozak, Angel X. Li, Henna P. Mistry, Mohammad Mozafarihashjin, Jalees A. Nasir, Kuganya Nirmalarajah, Emily M. Panousis, Aimee Paterson, Simon Plenderleith, Jeff Powis, Karren Prost, Renee Schryer, Maureen Taylor, Marc Veillette, Titus Wong, Xi Zoe Zhong, Andrew G. McArthur, Allison J. McGeer, Samira Mubareka. Surface and air contamination with SARS-CoV-2 from hospitalized COVID-19 patients in Toronto, Canada. . 2021; ():1.

Chicago/Turabian Style

Jonathon D. Kotwa; Alainna J. Jamal; Hamza Mbareche; Lily Yip; Patryk Aftanas; Shiva Barati; Natalie G. Bell; Elizabeth Bryce; Eric D Coomes; Gloria Crowl; Caroline Duchaine; Amna Faheem; Lubna Farooqi; Ryan Hiebert; Kevin Katz; Saman Khan; Robert Kozak; Angel X. Li; Henna P. Mistry; Mohammad Mozafarihashjin; Jalees A. Nasir; Kuganya Nirmalarajah; Emily M. Panousis; Aimee Paterson; Simon Plenderleith; Jeff Powis; Karren Prost; Renee Schryer; Maureen Taylor; Marc Veillette; Titus Wong; Xi Zoe Zhong; Andrew G. McArthur; Allison J. McGeer; Samira Mubareka. 2021. "Surface and air contamination with SARS-CoV-2 from hospitalized COVID-19 patients in Toronto, Canada." , no. : 1.

Journal article
Published: 01 May 2021 in American Journal of Respiratory and Critical Care Medicine
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RATIONALE: Patients with severe COVID-19 require supplemental oxygen and ventilatory support. It is unclear whether some respiratory support devices may increase the dispersion of infectious bioaerosols and thereby place healthcare workers at increased risk of infection with SARS-CoV-2. OBJECTIVES: To quantitatively compare viral dispersion from invasive and non-invasive respiratory support modalities. METHODS: A simulated intensive care unit room with a breathing patient simulator exhaling nebulized bacteriophage from the lower respiratory tract with various respiratory support modalities: invasive ventilation (through an endotracheal tube with inflated cuff connected to a mechanical ventilator); helmet ventilation with PEEP valve; non-invasive bilevel positive pressure ventilation; non-rebreather face mask; high-flow nasal oxygen; and nasal prongs. MEASUREMENTS AND MAIN RESULTS: Invasive ventilation and helmet ventilation with a PEEP valve were associated with the lowest bacteriophage concentrations in the air, and high-flow nasal oxygen and nasal prongs the highest. At the intubating position, bacteriophage concentrations associated with high-flow nasal oxygen (2.66 × 104 PFU/L of air sampled), nasal prongs (1.60 × 104 PFU/L of air sampled), non-rebreather facemask (7.87 × 102 PFU/L of air sampled), and BiPAP (1.91 × 102 PFU/L of air sampled) were significantly higher when compared to invasive ventilation (each P < 0.05). The difference between bacteriophage concentrations associated with helmet ventilation with a PEEP valve (4.29 × 10-1 PFU/L of air sampled) and invasive ventilation was not statistically significant. This article is open access and distributed under the terms of the Creative Commons Attribution Non-Commercial No Derivatives License 4.0 (http://creativecommons.org/licenses/by-nc-nd/4.0/).

ACS Style

Hamed Avari; Ryan J. Hiebert; Agnes A. Ryzynski; Ariela Levy; Julie Nardi; Hasina Kanji-Jaffer; Peter Kiiza; Ruxandra Pinto; Simon W. Plenderleith; Robert A. Fowler; Hamza Mbareche; Samira Mubareka. Quantitative Assessment of Viral Dispersion Associated with Respiratory Support Devices in a Simulated Critical Care Environment. American Journal of Respiratory and Critical Care Medicine 2021, 203, 1112 -1118.

AMA Style

Hamed Avari, Ryan J. Hiebert, Agnes A. Ryzynski, Ariela Levy, Julie Nardi, Hasina Kanji-Jaffer, Peter Kiiza, Ruxandra Pinto, Simon W. Plenderleith, Robert A. Fowler, Hamza Mbareche, Samira Mubareka. Quantitative Assessment of Viral Dispersion Associated with Respiratory Support Devices in a Simulated Critical Care Environment. American Journal of Respiratory and Critical Care Medicine. 2021; 203 (9):1112-1118.

Chicago/Turabian Style

Hamed Avari; Ryan J. Hiebert; Agnes A. Ryzynski; Ariela Levy; Julie Nardi; Hasina Kanji-Jaffer; Peter Kiiza; Ruxandra Pinto; Simon W. Plenderleith; Robert A. Fowler; Hamza Mbareche; Samira Mubareka. 2021. "Quantitative Assessment of Viral Dispersion Associated with Respiratory Support Devices in a Simulated Critical Care Environment." American Journal of Respiratory and Critical Care Medicine 203, no. 9: 1112-1118.

Journal article
Published: 30 January 2021 in Journal of Fungi
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This paper presents an in silico analysis to assess the current state of the fungal UNITE database in terms of the two eukaryote nuclear ribosomal regions, Internal Transcribed Spacers 1 and 2 (ITS1 and ITS2), used in describing fungal diversity. Microbial diversity is often evaluated with amplicon-based high-throughput sequencing approaches, which is a target enrichment method that relies on the amplification of a specific target using particular primers before sequencing. Thus, the results are highly dependent on the quality of the primers used for amplification. The goal of this study is to validate if the mismatches of the primers on the binding sites of the targeted taxa could explain the differences observed when using either ITS1 or ITS2 in describing airborne fungal diversity. Hence, the choice of the pairs of primers for each barcode concur with a study comparing the performance of ITS1 and ITS2 in three occupational environments. The sequence length varied between the amplicons retrieved from the UNITE database using the pair of primers targeting ITS1 and ITS2. However, the database contains an equal number of unidentified taxa from ITS1 and ITS2 regions in the six taxonomic levels employed (phylum, class, order, family, genus, species). The chosen ITS primers showed differences in their ability to amplify fungal sequences from the UNITE database. Eleven taxa consisting of Trichocomaceae, Dothioraceae, Botryosphaeriaceae, Mucorales, Saccharomycetes, Pucciniomycetes, Ophiocordyceps, Microsporidia, Archaeorhizomycetes, Mycenaceae, and Tulasnellaceae showed large variations between the two regions. Note that members of the latter taxa are not all typical fungi found in the air. As no universal method is currently available to cover all the fungal kingdom, continuous work in designing primers, and particularly combining multiple primers targeting the ITS region is the best way to compensate for the biases of each one to get a larger view of the fungal diversity.

ACS Style

Hamza Mbareche; Marc Veillette; Guillaume Bilodeau. In Silico Study Suggesting the Bias of Primers Choice in the Molecular Identification of Fungal Aerosols. Journal of Fungi 2021, 7, 99 .

AMA Style

Hamza Mbareche, Marc Veillette, Guillaume Bilodeau. In Silico Study Suggesting the Bias of Primers Choice in the Molecular Identification of Fungal Aerosols. Journal of Fungi. 2021; 7 (2):99.

Chicago/Turabian Style

Hamza Mbareche; Marc Veillette; Guillaume Bilodeau. 2021. "In Silico Study Suggesting the Bias of Primers Choice in the Molecular Identification of Fungal Aerosols." Journal of Fungi 7, no. 2: 99.

Review
Published: 08 September 2020 in Life
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High-throughput DNA sequencing (HTS) has changed our understanding of the microbial composition present in a wide range of environments. Applying HTS methods to air samples from different environments allows the identification and quantification (relative abundance) of the microorganisms present and gives a better understanding of human exposure to indoor and outdoor bioaerosols. To make full use of the avalanche of information made available by these sequences, repeated measurements must be taken, community composition described, error estimates made, correlations of microbiota with covariates (variables) must be examined, and increasingly sophisticated statistical tests must be conducted, all by using bioinformatics tools. Knowing which analysis to conduct and which tools to apply remains confusing for bioaerosol scientists, as a litany of tools and data resources are now available for characterizing microbial communities. The goal of this review paper is to offer a guided tour through the bioinformatics tools that are useful in studying the microbial ecology of bioaerosols. This work explains microbial ecology features like alpha and beta diversity, multivariate analyses, differential abundances, taxonomic analyses, visualization tools and statistical tests using bioinformatics tools for bioaerosol scientists new to the field. It illustrates and promotes the use of selected bioinformatic tools in the study of bioaerosols and serves as a good source for learning the “dos and don’ts” involved in conducting a precise microbial ecology study.

ACS Style

Hamza Mbareche; Nathan Dumont-Leblond; Guillaume J. Bilodeau; Caroline Duchaine. An Overview of Bioinformatics Tools for DNA Meta-Barcoding Analysis of Microbial Communities of Bioaerosols: Digest for Microbiologists. Life 2020, 10, 185 .

AMA Style

Hamza Mbareche, Nathan Dumont-Leblond, Guillaume J. Bilodeau, Caroline Duchaine. An Overview of Bioinformatics Tools for DNA Meta-Barcoding Analysis of Microbial Communities of Bioaerosols: Digest for Microbiologists. Life. 2020; 10 (9):185.

Chicago/Turabian Style

Hamza Mbareche; Nathan Dumont-Leblond; Guillaume J. Bilodeau; Caroline Duchaine. 2020. "An Overview of Bioinformatics Tools for DNA Meta-Barcoding Analysis of Microbial Communities of Bioaerosols: Digest for Microbiologists." Life 10, no. 9: 185.

Journal article
Published: 15 August 2020 in Viruses
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Genome sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is increasingly important to monitor the transmission and adaptive evolution of the virus. The accessibility of high-throughput methods and polymerase chain reaction (PCR) has facilitated a growing ecosystem of protocols. Two differing protocols are tiling multiplex PCR and bait capture enrichment. Each method has advantages and disadvantages but a direct comparison with different viral RNA concentrations has not been performed to assess the performance of these approaches. Here we compare Liverpool amplification, ARTIC amplification, and bait capture using clinical diagnostics samples. All libraries were sequenced using an Illumina MiniSeq with data analyzed using a standardized bioinformatics workflow (SARS-CoV-2 Illumina GeNome Assembly Line; SIGNAL). One sample showed poor SARS-CoV-2 genome coverage and consensus, reflective of low viral RNA concentration. In contrast, the second sample had a higher viral RNA concentration, which yielded good genome coverage and consensus. ARTIC amplification showed the highest depth of coverage results for both samples, suggesting this protocol is effective for low concentrations. Liverpool amplification provided a more even read coverage of the SARS-CoV-2 genome, but at a lower depth of coverage. Bait capture enrichment of SARS-CoV-2 cDNA provided results on par with amplification. While only two clinical samples were examined in this comparative analysis, both the Liverpool and ARTIC amplification methods showed differing efficacy for high and low concentration samples. In addition, amplification-free bait capture enriched sequencing of cDNA is a viable method for generating a SARS-CoV-2 genome sequence and for identification of amplification artifacts.

ACS Style

Jalees A. Nasir; Robert A. Kozak; Patryk Aftanas; Amogelang R. Raphenya; Kendrick M. Smith; Finlay Maguire; Hassaan Maan; Muhannad Alruwaili; Arinjay Banerjee; Hamza Mbareche; Brian P. Alcock; Natalie C. Knox; Karen Mossman; Bo Wang; Julian A. Hiscox; Andrew G. McArthur; Samira Mubareka. A Comparison of Whole Genome Sequencing of SARS-CoV-2 Using Amplicon-Based Sequencing, Random Hexamers, and Bait Capture. Viruses 2020, 12, 895 .

AMA Style

Jalees A. Nasir, Robert A. Kozak, Patryk Aftanas, Amogelang R. Raphenya, Kendrick M. Smith, Finlay Maguire, Hassaan Maan, Muhannad Alruwaili, Arinjay Banerjee, Hamza Mbareche, Brian P. Alcock, Natalie C. Knox, Karen Mossman, Bo Wang, Julian A. Hiscox, Andrew G. McArthur, Samira Mubareka. A Comparison of Whole Genome Sequencing of SARS-CoV-2 Using Amplicon-Based Sequencing, Random Hexamers, and Bait Capture. Viruses. 2020; 12 (8):895.

Chicago/Turabian Style

Jalees A. Nasir; Robert A. Kozak; Patryk Aftanas; Amogelang R. Raphenya; Kendrick M. Smith; Finlay Maguire; Hassaan Maan; Muhannad Alruwaili; Arinjay Banerjee; Hamza Mbareche; Brian P. Alcock; Natalie C. Knox; Karen Mossman; Bo Wang; Julian A. Hiscox; Andrew G. McArthur; Samira Mubareka. 2020. "A Comparison of Whole Genome Sequencing of SARS-CoV-2 Using Amplicon-Based Sequencing, Random Hexamers, and Bait Capture." Viruses 12, no. 8: 895.

Review article
Published: 21 November 2019 in Aerosol Science and Technology
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Because bioaerosols are related to adverse health effects in exposed humans and indoor environments represent a unique framework of exposure, concerns about indoor bioaerosols have risen over recent years. One of the major issues in indoor bioaerosol research is the lack of standardization in the methodology, from air sampling strategies and sample treatment to the analytical methods applied. The main characteristics to consider in the choice of indoor sampling methods for bioaerosols are the sampler performance, the representativeness of the sampling, and the concordance with the analytical methods to be used. The selection of bioaerosol collection methods is directly dependent on the analytical methods, which are chosen to answer specific questions raised while designing a study for exposure assessment. In this review, the authors present current practices in the analytical methods and the sampling strategies, with specificity for each type of microbe (fungi, bacteria, archaea and viruses). In addition, common problems and errors to be avoided are discussed. Based on this work, recommendations are made for future efforts towards the development of viable bioaerosol samplers, standards for bioaerosol exposure limits, and making association studies to optimize the use of the big data provided by high-throughput sequencing methods.

ACS Style

Jennie Cox; Hamza Mbareche; William G. Lindsley; Caroline Duchaine. Field sampling of indoor bioaerosols. Aerosol Science and Technology 2019, 54, 572 -584.

AMA Style

Jennie Cox, Hamza Mbareche, William G. Lindsley, Caroline Duchaine. Field sampling of indoor bioaerosols. Aerosol Science and Technology. 2019; 54 (5):572-584.

Chicago/Turabian Style

Jennie Cox; Hamza Mbareche; William G. Lindsley; Caroline Duchaine. 2019. "Field sampling of indoor bioaerosols." Aerosol Science and Technology 54, no. 5: 572-584.

Journal article
Published: 16 April 2019 in International Journal of Environmental Research and Public Health
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Background: Bioaerosols are a major concern for public health and sampling for exposure assessment purposes is challenging. The nasopharyngeal region could be a potent carrier of long-term bioaerosol exposure agents. This study aimed to evaluate the correlation between nasopharyngeal bacterial flora of swine workers and the swine barns bioaerosol biodiversity. Methods: Air samples from eight swine barns as well as nasopharyngeal swabs from pig workers (n = 25) and from a non-exposed control group (n = 29) were sequenced using 16S rRNA gene high-throughput sequencing. Wastewater treatment plants were used as the industrial, low-dust, non-agricultural environment control to validate the microbial link between the bioaerosol content (air) and the nasopharynxes of workers. Results: A multivariate analysis showed air samples and nasopharyngeal flora of pig workers cluster together, compared to the non-exposed control group. The significance was confirmed with the PERMANOVA statistical test (p-value of 0.0001). Unlike the farm environment, nasopharynx samples from wastewater workers did not cluster with air samples from wastewater treatment plants. The difference in the microbial community of nasopharynx of swine workers and a control group suggest that swine workers are carriers of germs found in bioaerosols. Conclusion: Nasopharynx sampling and microbiota could be used as a proxy of air sampling for exposure assessment studies or for the determination of exposure markers in highly contaminated agricultural environments.

ACS Style

Hamza Mbareche; Marc Veillette; Jonathan Pilote; Valérie Létourneau; Caroline Duchaine. Bioaerosols Play a Major Role in the Nasopharyngeal Microbiota Content in Agricultural Environment. International Journal of Environmental Research and Public Health 2019, 16, 1375 .

AMA Style

Hamza Mbareche, Marc Veillette, Jonathan Pilote, Valérie Létourneau, Caroline Duchaine. Bioaerosols Play a Major Role in the Nasopharyngeal Microbiota Content in Agricultural Environment. International Journal of Environmental Research and Public Health. 2019; 16 (8):1375.

Chicago/Turabian Style

Hamza Mbareche; Marc Veillette; Jonathan Pilote; Valérie Létourneau; Caroline Duchaine. 2019. "Bioaerosols Play a Major Role in the Nasopharyngeal Microbiota Content in Agricultural Environment." International Journal of Environmental Research and Public Health 16, no. 8: 1375.

Review
Published: 01 December 2017 in Science of The Total Environment
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Bioaerosols are among the less studied particles in the environment. The lack of standardization in sampling procedures, difficulties related to the effect of sampling processes on the integrity of microorganisms, and challenges associated with the application of environmental microbiology analyses and molecular and culture methods frighten many young scientists. Every microorganism has its own particularities and acts differently when aerosolized in various conditions. Because the air is an extremely biologically diluted environment, it is necessary to concentrate its content before any analysis is performed. Challenges faced when applying molecular methods to air samples reveal the need for a better standardization of approaches for cell and nucleic acid recovery, the choice of genetic markers, and interpretation of data. This paper presents a few of the limits and difficulties tackled when molecular methods are applied to bioaerosols, suggests some improvements by specifying the critical stages that should be considered when studying the microbial ecology of bioaerosols, and provides thoughtful insights on how to overcome the challenges encountered.

ACS Style

Hamza Mbareche; Evelyne Brisebois; Marc Veillette; Caroline Duchaine. Bioaerosol sampling and detection methods based on molecular approaches: No pain no gain. Science of The Total Environment 2017, 599-600, 2095 -2104.

AMA Style

Hamza Mbareche, Evelyne Brisebois, Marc Veillette, Caroline Duchaine. Bioaerosol sampling and detection methods based on molecular approaches: No pain no gain. Science of The Total Environment. 2017; 599-600 ():2095-2104.

Chicago/Turabian Style

Hamza Mbareche; Evelyne Brisebois; Marc Veillette; Caroline Duchaine. 2017. "Bioaerosol sampling and detection methods based on molecular approaches: No pain no gain." Science of The Total Environment 599-600, no. : 2095-2104.