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An artificial intelligence-assisted low-cost portable device for the rapid detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is presented here. This standalone temperature-controlled device houses tubes designed for conducting reverse transcription loop-mediated isothermal amplification (RT-LAMP) assays. Moreover, the device utilises tubes illuminated by LEDs, an in-built camera, and a small onboard computer with automated image acquisition and processing algorithms. This intelligent device significantly reduces the normal assay run time and removes the subjectivity associated with operator interpretation of colourimetric RT-LAMP results. To further improve this device’s usability, a mobile app has been integrated into the system to control the LAMP assay environment and to visually display the assay results by connecting the device to a smartphone via Bluetooth. This study was undertaken using ~5000 images produced from the ~200 LAMP amplification assays using the prototype device. Synthetic RNA and a small panel of positive and negative SARS-CoV-2 patient samples were assayed for this study. State-of-the-art image processing and artificial intelligence algorithms were applied to these images to analyse them and to select the most efficient algorithm. The template matching algorithm for image extraction and MobileNet CNN architecture for classification results provided 98.0% accuracy with an average run time of 20 min to confirm the endpoint result. Two working points were chosen based on the best compromise between sensitivity and specificity. The high sensitivity point has a sensitivity value of 99.12% and specificity value of 70.8%, while at the high specificity point, the sensitivity is 96.05% and specificity 93.59%. Furthermore, this device provides an efficient and cost-effective platform for non-health professionals to detect not only SARS-CoV-2 but also other pathogens in resource-limited laboratories, factories, airports, schools, universities, and homes.
Mukunthan Tharmakulasingam; Nouman S. Chaudhry; Anil Fernando; Manoharanehru Branavan; Wamadeva Balachandran; Aurore C. Poirier; Mohammed A. Rohaim; Muhammad Munir; Roberto M. La Ragione. An Artificial Intelligence-Assisted Portable Low-Cost Device for the Rapid Detection of SARS-CoV-2. Electronics 2021, 10, 2065 .
AMA StyleMukunthan Tharmakulasingam, Nouman S. Chaudhry, Anil Fernando, Manoharanehru Branavan, Wamadeva Balachandran, Aurore C. Poirier, Mohammed A. Rohaim, Muhammad Munir, Roberto M. La Ragione. An Artificial Intelligence-Assisted Portable Low-Cost Device for the Rapid Detection of SARS-CoV-2. Electronics. 2021; 10 (17):2065.
Chicago/Turabian StyleMukunthan Tharmakulasingam; Nouman S. Chaudhry; Anil Fernando; Manoharanehru Branavan; Wamadeva Balachandran; Aurore C. Poirier; Mohammed A. Rohaim; Muhammad Munir; Roberto M. La Ragione. 2021. "An Artificial Intelligence-Assisted Portable Low-Cost Device for the Rapid Detection of SARS-CoV-2." Electronics 10, no. 17: 2065.
Until vaccines and effective therapeutics become available, the practical solution to transit safely out of the current coronavirus disease 19 (CoVID-19) lockdown may include the implementation of an effective testing, tracing and tracking system. However, this requires a reliable and clinically validated diagnostic platform for the sensitive and specific identification of SARS-CoV-2. Here, we report on the development of a de novo, high-resolution and comparative genomics guided reverse-transcribed loop-mediated isothermal amplification (LAMP) assay. To further enhance the assay performance and to remove any subjectivity associated with operator interpretation of results, we engineered a novel hand-held smart diagnostic device. The robust diagnostic device was further furnished with automated image acquisition and processing algorithms and the collated data was processed through artificial intelligence (AI) pipelines to further reduce the assay run time and the subjectivity of the colorimetric LAMP detection. This advanced AI algorithm-implemented LAMP (ai-LAMP) assay, targeting the RNA-dependent RNA polymerase gene, showed high analytical sensitivity and specificity for SARS-CoV-2. A total of ~200 coronavirus disease (CoVID-19)-suspected NHS patient samples were tested using the platform and it was shown to be reliable, highly specific and significantly more sensitive than the current gold standard qRT-PCR. Therefore, this system could provide an efficient and cost-effective platform to detect SARS-CoV-2 in resource-limited laboratories.
Mohammed Rohaim; Emily Clayton; Irem Sahin; Julianne Vilela; Manar Khalifa; Mohammad Al-Natour; Mahmoud Bayoumi; Aurore Poirier; Manoharanehru Branavan; Mukunthan Tharmakulasingam; Nouman Chaudhry; Ravinder Sodi; Amy Brown; Peter Burkhart; Wendy Hacking; Judy Botham; Joe Boyce; Hayley Wilkinson; Craig Williams; Jayde Whittingham-Dowd; Elisabeth Shaw; Matt Hodges; Lisa Butler; Michelle Bates; Roberto La Ragione; Wamadeva Balachandran; Anil Fernando; Muhammad Munir. Artificial Intelligence-Assisted Loop Mediated Isothermal Amplification (ai-LAMP) for Rapid Detection of SARS-CoV-2. Viruses 2020, 12, 972 .
AMA StyleMohammed Rohaim, Emily Clayton, Irem Sahin, Julianne Vilela, Manar Khalifa, Mohammad Al-Natour, Mahmoud Bayoumi, Aurore Poirier, Manoharanehru Branavan, Mukunthan Tharmakulasingam, Nouman Chaudhry, Ravinder Sodi, Amy Brown, Peter Burkhart, Wendy Hacking, Judy Botham, Joe Boyce, Hayley Wilkinson, Craig Williams, Jayde Whittingham-Dowd, Elisabeth Shaw, Matt Hodges, Lisa Butler, Michelle Bates, Roberto La Ragione, Wamadeva Balachandran, Anil Fernando, Muhammad Munir. Artificial Intelligence-Assisted Loop Mediated Isothermal Amplification (ai-LAMP) for Rapid Detection of SARS-CoV-2. Viruses. 2020; 12 (9):972.
Chicago/Turabian StyleMohammed Rohaim; Emily Clayton; Irem Sahin; Julianne Vilela; Manar Khalifa; Mohammad Al-Natour; Mahmoud Bayoumi; Aurore Poirier; Manoharanehru Branavan; Mukunthan Tharmakulasingam; Nouman Chaudhry; Ravinder Sodi; Amy Brown; Peter Burkhart; Wendy Hacking; Judy Botham; Joe Boyce; Hayley Wilkinson; Craig Williams; Jayde Whittingham-Dowd; Elisabeth Shaw; Matt Hodges; Lisa Butler; Michelle Bates; Roberto La Ragione; Wamadeva Balachandran; Anil Fernando; Muhammad Munir. 2020. "Artificial Intelligence-Assisted Loop Mediated Isothermal Amplification (ai-LAMP) for Rapid Detection of SARS-CoV-2." Viruses 12, no. 9: 972.
Until vaccines and effective therapeutics become available, the practical way to transit safely out of the current lockdown may include the implementation of an effective testing, tracing and tracking system. However, this requires a reliable and clinically validated diagnostic platform for the sensitive and specific identification of SARS-CoV-2. Here, we report on the development of a de novo, high-resolution and comparative genomics guided reverse-transcribed loop-mediated isothermal amplification (LAMP) assay. To further enhance the assay performance and to remove any subjectivity associated with operator interpretation of result, we engineered a novel hand-held smart diagnostic device. The robust diagnostic device was further furnished with automated image acquisition and processing algorithms, and the collated data was processed through artificial intelligence (AI) pipelines to further reduce the assay run time and the subjectivity of the colorimetric LAMP detection. This advanced AI algorithm-implemented LAMP (ai-LAMP) assay, targeting the RNA-dependent RNA polymerase gene, showed high analytical sensitivity and specificity for SARS-CoV-2. A total of ∼200 coronavirus disease (CoVID-19)-suspected patient samples were tested using the platform and it was shown to be reliable, highly specific and significantly more sensitive than the current gold standard qRT-PCR. The system could provide an efficient and cost-effective platform to detect SARS-CoV-2 in resource-limited laboratories.
Mohammed A Rohaim; Emily Clayton; Irem Sahin; Julianne Vilela; Manar E Khalifa; Mohammed Q Al-Natour; Mahmoud Bayoumi; Aurore Poirier; Manoharanehru Branavan; Mukunthan Tharmakulasingam; Nouman S Chaudhry; Ravinder Sodi; Amy Brown; Peter Burkhart; Wendy Hacking; Judy Botham; Joe Boyce; Hayley Wilkinson; Craig Williams; Michelle Bates; Roberto La Ragione; Wamadeva Balachandran; Anil Fernando; Muhammad Munir. Artificial Intelligence-Assisted Loop Mediated Isothermal Amplification (ai-LAMP) for Rapid and Reliable Detection of SARS-CoV-2. 2020, 1 .
AMA StyleMohammed A Rohaim, Emily Clayton, Irem Sahin, Julianne Vilela, Manar E Khalifa, Mohammed Q Al-Natour, Mahmoud Bayoumi, Aurore Poirier, Manoharanehru Branavan, Mukunthan Tharmakulasingam, Nouman S Chaudhry, Ravinder Sodi, Amy Brown, Peter Burkhart, Wendy Hacking, Judy Botham, Joe Boyce, Hayley Wilkinson, Craig Williams, Michelle Bates, Roberto La Ragione, Wamadeva Balachandran, Anil Fernando, Muhammad Munir. Artificial Intelligence-Assisted Loop Mediated Isothermal Amplification (ai-LAMP) for Rapid and Reliable Detection of SARS-CoV-2. . 2020; ():1.
Chicago/Turabian StyleMohammed A Rohaim; Emily Clayton; Irem Sahin; Julianne Vilela; Manar E Khalifa; Mohammed Q Al-Natour; Mahmoud Bayoumi; Aurore Poirier; Manoharanehru Branavan; Mukunthan Tharmakulasingam; Nouman S Chaudhry; Ravinder Sodi; Amy Brown; Peter Burkhart; Wendy Hacking; Judy Botham; Joe Boyce; Hayley Wilkinson; Craig Williams; Michelle Bates; Roberto La Ragione; Wamadeva Balachandran; Anil Fernando; Muhammad Munir. 2020. "Artificial Intelligence-Assisted Loop Mediated Isothermal Amplification (ai-LAMP) for Rapid and Reliable Detection of SARS-CoV-2." , no. : 1.
Vibrios are ubiquitous in marine environments and opportunistically colonize a broad range of hosts. Strains of Vibrio tasmaniensis present in oyster farms can thrive in oysters during juvenile mortality events and behave as facultative intracellular pathogen of oyster haemocytes. Herein, we wondered whether V. tasmaniensis LGP32 resistance to phagocytosis is specific to oyster immune cells or contributes to resistance to other phagocytes, like marine amoebae. To address this question, we developed an integrative study, from the first description of amoeba diversity in oyster farms to the characterization of LGP32 interactions with amoebae. An isolate of the Vannella genus, Vannella sp. AP1411, which was collected from oyster farms, is ubiquitous, and belongs to one clade of Vannella that could be found associated with Vibrionaceae. LGP32 was shown to be resistant to grazing by Vannella sp. AP1411 and this phenotype depends on some previously identified virulence factors: secreted metalloprotease Vsm and copper efflux p-ATPase CopA, which act at different steps during amoeba-vibrio interactions, whereas some other virulence factors were not involved. Altogether, our work indicates that some virulence factors can be involved in multi-host interactions of V. tasmaniensis ranging from protozoans to metazoans, potentially favouring their opportunistic behaviour.
Etienne Robino; Aurore Poirier; Hajar Amraoui; Sandra Le Bissonnais; Angélique Perret; Carmen Lopez‐Joven; Jean‐Christophe Auguet; Tristan Rubio; Chantal Cazevieille; Jean‐Luc Rolland; Yann Héchard; Delphine Destoumieux-Garzon; Guillaume M. Charrière. Resistance of the oyster pathogen Vibrio tasmaniensis LGP32 against grazing by Vannella sp. marine amoeba involves Vsm and CopA virulence factors. Environmental Microbiology 2019, 22, 4183 -4197.
AMA StyleEtienne Robino, Aurore Poirier, Hajar Amraoui, Sandra Le Bissonnais, Angélique Perret, Carmen Lopez‐Joven, Jean‐Christophe Auguet, Tristan Rubio, Chantal Cazevieille, Jean‐Luc Rolland, Yann Héchard, Delphine Destoumieux-Garzon, Guillaume M. Charrière. Resistance of the oyster pathogen Vibrio tasmaniensis LGP32 against grazing by Vannella sp. marine amoeba involves Vsm and CopA virulence factors. Environmental Microbiology. 2019; 22 (10):4183-4197.
Chicago/Turabian StyleEtienne Robino; Aurore Poirier; Hajar Amraoui; Sandra Le Bissonnais; Angélique Perret; Carmen Lopez‐Joven; Jean‐Christophe Auguet; Tristan Rubio; Chantal Cazevieille; Jean‐Luc Rolland; Yann Héchard; Delphine Destoumieux-Garzon; Guillaume M. Charrière. 2019. "Resistance of the oyster pathogen Vibrio tasmaniensis LGP32 against grazing by Vannella sp. marine amoeba involves Vsm and CopA virulence factors." Environmental Microbiology 22, no. 10: 4183-4197.
Barry Fuller; Jordi Gonzalez-Molina; Eloy Erro; Joana De Mendonca; Sheri Chalmers; Maooz Awan; Aurore Poirier; Clare Selden. Applications and optimization of cryopreservation technologies to cellular therapeutics. Cell and Gene Therapy Insights 2017, 3, 359 -378.
AMA StyleBarry Fuller, Jordi Gonzalez-Molina, Eloy Erro, Joana De Mendonca, Sheri Chalmers, Maooz Awan, Aurore Poirier, Clare Selden. Applications and optimization of cryopreservation technologies to cellular therapeutics. Cell and Gene Therapy Insights. 2017; 3 (5):359-378.
Chicago/Turabian StyleBarry Fuller; Jordi Gonzalez-Molina; Eloy Erro; Joana De Mendonca; Sheri Chalmers; Maooz Awan; Aurore Poirier; Clare Selden. 2017. "Applications and optimization of cryopreservation technologies to cellular therapeutics." Cell and Gene Therapy Insights 3, no. 5: 359-378.
Recent studies revealed that several vibrio species have evolved the capacity to survive inside host cells. However, it is still often ignored if intracellular stages are required for pathogenicity. Virulence of Vibrio tasmaniensis LGP32, a strain pathogenic for Crassostrea gigas oysters, depends on entry into hemocytes, the oyster immune cells. We investigated here the mechanisms of LGP32 intracellular survival and their consequences on the host–pathogen interaction. Entry and survival inside hemocytes were required for LGP32‐driven cytolysis of hemocytes, both in vivo and in vitro. LGP32 intracellular stages showed a profound boost in metabolic activity and a major transcription of antioxidant and copper detoxification genes, as revealed by RNA sequencing. LGP32 isogenic mutants showed that resistance to oxidative stress and copper efflux are two main functions required for vibrio intracellular stages and cytotoxicity to hemocytes. Copper efflux was also essential for host colonization and virulence in vivo. Altogether, our results identify copper resistance as a major mechanism to resist killing by phagocytes, induce cytolysis of immune cells and colonize oysters. Selection of such resistance traits could arise from vibrio interactions with copper‐rich environmental niches including marine invertebrates, which favour the emergence of pathogenic vibrios resistant to intraphagosomal killing across animal species.
Audrey S. Vanhove; Tristan Rubio; An N. Nguyen; Astrid Lemire; David Roche; Julie Nicod; Agnès Vergnes; Aurore Poirier; Elena Disconzi; Evelyne Bachère; Frédérique Le Roux; Annick Jacq; Guillaume Charrière; Delphine Destoumieux-Garzón. Copper homeostasis at the host vibrio interface: lessons from intracellular vibrio transcriptomics. Environmental Microbiology 2015, 18, 875 -888.
AMA StyleAudrey S. Vanhove, Tristan Rubio, An N. Nguyen, Astrid Lemire, David Roche, Julie Nicod, Agnès Vergnes, Aurore Poirier, Elena Disconzi, Evelyne Bachère, Frédérique Le Roux, Annick Jacq, Guillaume Charrière, Delphine Destoumieux-Garzón. Copper homeostasis at the host vibrio interface: lessons from intracellular vibrio transcriptomics. Environmental Microbiology. 2015; 18 (3):875-888.
Chicago/Turabian StyleAudrey S. Vanhove; Tristan Rubio; An N. Nguyen; Astrid Lemire; David Roche; Julie Nicod; Agnès Vergnes; Aurore Poirier; Elena Disconzi; Evelyne Bachère; Frédérique Le Roux; Annick Jacq; Guillaume Charrière; Delphine Destoumieux-Garzón. 2015. "Copper homeostasis at the host vibrio interface: lessons from intracellular vibrio transcriptomics." Environmental Microbiology 18, no. 3: 875-888.
Oysters are sessile filter feeders that live in close association with abundant and diverse communities of microorganisms that form the oyster microbiota. In such an association, cellular and molecular mechanisms have evolved to maintain oyster homeostasis upon stressful conditions including infection and changing environments. We give here cellular and molecular insights into the Crassostrea gigas antimicrobial defense system with focus on antimicrobial peptides and proteins (AMPs). This review highlights the central role of the hemocytes in the modulation and control of oyster antimicrobial response. As vehicles for AMPs and other antimicrobial effectors, including reactive oxygen species (ROS), and together with epithelia, hemocytes provide the oyster with local defense reactions instead of systemic humoral ones. These reactions are largely based on phagocytosis but also, as recently described, on the extracellular release of antimicrobial histones (ETosis) which is triggered by ROS. Thus, ROS can signal danger and activate cellular responses in the oyster. From the current literature, AMP production/release could serve similar functions. We provide also new lights on the oyster genetic background that underlies a great diversity of AMP sequences but also an extraordinary individual polymorphism of AMP gene expression. We discuss here how this polymorphism could generate new immune functions, new pathogen resistances or support individual adaptation to environmental stresses.
Evelyne Bachère; Rafael Diego Rosa; Paulina Schmitt; Aurore Poirier; Nicolas Merou; Guillaume M. Charrière; Delphine Destoumieux-Garzón. The new insights into the oyster antimicrobial defense: Cellular, molecular and genetic view. Fish & Shellfish Immunology 2015, 46, 50 -64.
AMA StyleEvelyne Bachère, Rafael Diego Rosa, Paulina Schmitt, Aurore Poirier, Nicolas Merou, Guillaume M. Charrière, Delphine Destoumieux-Garzón. The new insights into the oyster antimicrobial defense: Cellular, molecular and genetic view. Fish & Shellfish Immunology. 2015; 46 (1):50-64.
Chicago/Turabian StyleEvelyne Bachère; Rafael Diego Rosa; Paulina Schmitt; Aurore Poirier; Nicolas Merou; Guillaume M. Charrière; Delphine Destoumieux-Garzón. 2015. "The new insights into the oyster antimicrobial defense: Cellular, molecular and genetic view." Fish & Shellfish Immunology 46, no. 1: 50-64.
Although antimicrobial histones have been isolated from multiple metazoan species, their role in host defense has long remained unanswered. We found here that the hemocytes of the oyster Crassostrea gigas release antimicrobial H1-like and H5-like histones in response to tissue damage and infection. These antimicrobial histones were shown to be associated with extracellular DNA networks released by hemocytes, the circulating immune cells of invertebrates, in response to immune challenge. The hemocyte-released DNA was found to surround and entangle vibrios. This defense mechanism is reminiscent of the neutrophil extracellular traps (ETs) recently described in vertebrates. Importantly, oyster ETs were evidenced in vivo in hemocyte-infiltrated interstitial tissues surrounding wounds, whereas they were absent from tissues of unchallenged oysters. Consistently, antimicrobial histones were found to accumulate in oyster tissues following injury or infection with vibrios. Finally, oyster ET formation was highly dependent on the production of reactive oxygen species by hemocytes. This shows that ET formation relies on common cellular and molecular mechanisms from vertebrates to invertebrates. Altogether, our data reveal that ET formation is a defense mechanism triggered by infection and tissue damage, which is shared by relatively distant species suggesting either evolutionary conservation or convergent evolution within Bilateria
Aurore Poirier; Paulina Schmitt; Rafael Diego Rosa; Audrey S. Vanhove; Sylvie Kieffer-Jaquinod; Tristan Rubio; Guillaume M. Charrière; Delphine Destoumieux-Garzon. Antimicrobial Histones and DNA Traps in Invertebrate Immunity. Journal of Biological Chemistry 2014, 289, 24821 -24831.
AMA StyleAurore Poirier, Paulina Schmitt, Rafael Diego Rosa, Audrey S. Vanhove, Sylvie Kieffer-Jaquinod, Tristan Rubio, Guillaume M. Charrière, Delphine Destoumieux-Garzon. Antimicrobial Histones and DNA Traps in Invertebrate Immunity. Journal of Biological Chemistry. 2014; 289 (36):24821-24831.
Chicago/Turabian StyleAurore Poirier; Paulina Schmitt; Rafael Diego Rosa; Audrey S. Vanhove; Sylvie Kieffer-Jaquinod; Tristan Rubio; Guillaume M. Charrière; Delphine Destoumieux-Garzon. 2014. "Antimicrobial Histones and DNA Traps in Invertebrate Immunity." Journal of Biological Chemistry 289, no. 36: 24821-24831.