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Zorilla R, Ching LL, Elisara T, Kramer K, Nerurkar VR. Re-Emerging, Under-Recognized Zoonotic, and Neglected Tropical Diseases in Hawai'i. Jpn J Infect Dis 2024; 77:187-200. [PMID: 38825457 DOI: 10.7883/yoken.jjid.2023.476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Hawai'i, the United States' most western geographic state in the Pacific, lies between the North and South American continents and the Indo-Pacific regions, including Japan. The tropical environmental conditions of the Hawaiian Islands provide favorable ecosystems for various infectious pathogens, their vectors, and reservoirs. This creates an environment conducive to the transmission of zoonotic diseases affecting both humans and animals. Hawai'i has experienced an increase in dengue, leptospirosis, and murine typhus outbreaks. Furthermore, toxoplasmosis and neuroangiostrongyliasis cases remain prevalent throughout the state, and the putative presence of autochthonous Zika cases identified in a retrospective study may be of national public health concern. Understanding the factors that affect the transmission and distribution of zoonoses is necessary to identify at-risk locations and populations. The One Health approach seeks to understand, report, and interpret these factors and requires collaboration between private and governmental institutions. One Health should focus on neglected tropical diseases (NTD) and prioritize development of interventions to control and prevent the transmission of diseases that spread between animals and humans. This review focuses on the epidemiological and clinical characteristics of under-recognized zoonotic and NTD affecting Hawai'i, including leptospirosis, murine typhus, neuroangiostrongyliasis, toxoplasmosis, dengue, and Zika.
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Affiliation(s)
- Rodson Zorilla
- Department of Tropical Medicine, Medical Microbiology, and Pharmacology, John A Burns School of Medicine, University of Hawai'i at Mānoa, USA
- Pacific Center for Emerging Infectious Diseases, John A Burns School of Medicine, University of Hawai'i at Mānoa, USA
- Minority Health Research Training Program, John A Burns School of Medicine, University of Hawai'i at Mānoa, USA
| | - Lauren Lei Ching
- Department of Tropical Medicine, Medical Microbiology, and Pharmacology, John A Burns School of Medicine, University of Hawai'i at Mānoa, USA
- Pacific Center for Emerging Infectious Diseases, John A Burns School of Medicine, University of Hawai'i at Mānoa, USA
| | - Tiana Elisara
- Department of Tropical Medicine, Medical Microbiology, and Pharmacology, John A Burns School of Medicine, University of Hawai'i at Mānoa, USA
- Pacific Center for Emerging Infectious Diseases, John A Burns School of Medicine, University of Hawai'i at Mānoa, USA
- Minority Health Research Training Program, John A Burns School of Medicine, University of Hawai'i at Mānoa, USA
| | - Kenton Kramer
- Department of Tropical Medicine, Medical Microbiology, and Pharmacology, John A Burns School of Medicine, University of Hawai'i at Mānoa, USA
| | - Vivek Ramchandra Nerurkar
- Department of Tropical Medicine, Medical Microbiology, and Pharmacology, John A Burns School of Medicine, University of Hawai'i at Mānoa, USA
- Pacific Center for Emerging Infectious Diseases, John A Burns School of Medicine, University of Hawai'i at Mānoa, USA
- Minority Health Research Training Program, John A Burns School of Medicine, University of Hawai'i at Mānoa, USA
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Timsit S, Armand-Lefèvre L, Le Goff J, Salmona M. The clinical and epidemiological impacts of whole genomic sequencing on bacterial and virological agents. Infect Dis Now 2024; 54:104844. [PMID: 38101516 DOI: 10.1016/j.idnow.2023.104844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 12/08/2023] [Indexed: 12/17/2023]
Abstract
Whole Genome Sequencing (WGS) is a molecular biology tool consisting in the sequencing of the entire genome of a given organism. Due to its ability to provide the finest available resolution of bacterial and virological genetics, it is used at several levels in the field of infectiology. On an individual scale and through application of a single technique, it enables the typological identification and characterization of strains, the characterization of plasmids, and enhanced search for resistance genes and virulence factors. On a collective scale, it enables the characterization of strains and the determination of phylogenetic links between different microorganisms during community outbreaks and healthcare-associated epidemics. The information provided by WGS enables real-time monitoring of strain-level epidemiology on a worldwide scale, and facilitates surveillance of the resistance dissemination and the introduction or emergence of pathogenic variants in humans or their environment. There are several possible approaches to completion of an entire genome. The choice of one method rather than another is essentially dictated by the matrix, either a clinical sample or a culture isolate, and the clinical objective. WGS is an advanced technology that remains costly despite a gradual decrease in its expenses, potentially hindering its implementation in certain laboratories and thus its use in routine microbiology. Even though WGS is making steady inroads as a reference method, efforts remain needed in view of so harmonizing its interpretations and decreasing the time to generation of conclusive results.
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Affiliation(s)
- Sarah Timsit
- Service de Virologie, Hôpital Saint-Louis, APHP, Paris, France; Service de Bactériologie, Hôpital Bichat-Claude Bernard, APHP, Paris, France
| | - Laurence Armand-Lefèvre
- Service de Bactériologie, Hôpital Bichat-Claude Bernard, APHP, Paris, France; IAME UMR 1137, INSERM, Université Paris Cité, Paris, France
| | - Jérôme Le Goff
- Service de Virologie, Hôpital Saint-Louis, APHP, Paris, France; INSERM U976, Insight Team, Université Paris Cité, Paris, France
| | - Maud Salmona
- Service de Virologie, Hôpital Saint-Louis, APHP, Paris, France; INSERM U976, Insight Team, Université Paris Cité, Paris, France.
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Song Y, Zhong S, Li Y, Jiang M, Wei Q. Constructing an Interactive and Integrated Analysis and Identification Platform for Pathogenic Microorganisms to Support Surveillance Capacity. Genes (Basel) 2023; 14:2156. [PMID: 38136978 PMCID: PMC10742832 DOI: 10.3390/genes14122156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/09/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023] Open
Abstract
INTRODUCTION Whole genome sequencing (WGS) holds significant promise for epidemiological inquiries, as it enables the identification and tracking of pathogenic origins and dissemination through comprehensive genome analysis. This method is widely preferred for investigating outbreaks and monitoring pathogen activity. However, the effective utilization of microbiome sequencing data remains a challenge for clinical and public health experts. Through the National Pathogen Resource Center, we have constructed a dynamic and interactive online analysis platform to facilitate the in-depth analysis and use of pathogen genomic data, by public health and associated professionals, to support infectious disease surveillance framework building and capacity warnings. METHOD The platform was implemented using the Java programming language, and the front-end pages were developed using the VUE framework, following the MVC (Model-View-Controller) pattern to enable interactive service functionalities for front-end data collection and back-end data computation. Cloud computing services were employed to integrate biological information analysis tools for conducting fundamental analysis on sequencing data. RESULT The platform achieved the goal of non-programming analysis, providing an interactive visual interface that allows users to visually obtain results by setting parameters in web pages. Moreover, the platform allows users to export results in various formats to further support their research. DISCUSSION We have established a dynamic and interactive online platform for bioinformatics analysis. By encapsulating the complex background experiments and analysis processes in a cloud-based service platform, the complex background experiments and analysis processes are presented to the end-user in a simple and interactive manner. It facilitates real-time data mining and analysis by allowing users to independently select parameters and generate analysis results at the click of a button, based on their needs, without the need for a programming foundation.
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Affiliation(s)
- Yang Song
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, Beijing 102206, China;
| | - Songchao Zhong
- National Pathogen Resource Center, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (S.Z.); (Y.L.); (M.J.)
| | - Yixiao Li
- National Pathogen Resource Center, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (S.Z.); (Y.L.); (M.J.)
| | - Mengnan Jiang
- National Pathogen Resource Center, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (S.Z.); (Y.L.); (M.J.)
| | - Qiang Wei
- National Pathogen Resource Center, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (S.Z.); (Y.L.); (M.J.)
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Cristina Diaconu C, Madalina Pitica I, Chivu-Economescu M, Georgiana Necula L, Botezatu A, Virginia Iancu I, Iulia Neagu A, L. Radu E, Matei L, Maria Ruta S, Bleotu C. SARS-CoV-2 Variant Surveillance in Genomic Medicine Era. Infect Dis (Lond) 2023. [DOI: 10.5772/intechopen.107137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/26/2024] Open
Abstract
In the genomic medicine era, the emergence of SARS-CoV-2 was immediately followed by viral genome sequencing and world-wide sequences sharing. Almost in real-time, based on these sequences, resources were developed and applied around the world, such as molecular diagnostic tests, informed public health decisions, and vaccines. Molecular SARS-CoV-2 variant surveillance was a normal approach in this context yet, considering that the viral genome modification occurs commonly in viral replication process, the challenge is to identify the modifications that significantly affect virulence, transmissibility, reduced effectiveness of vaccines and therapeutics or failure of diagnostic tests. However, assessing the importance of the emergence of new mutations and linking them to epidemiological trend, is still a laborious process and faster phenotypic evaluation approaches, in conjunction with genomic data, are required in order to release timely and efficient control measures.
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Chiara M, D’Erchia AM, Gissi C, Manzari C, Parisi A, Resta N, Zambelli F, Picardi E, Pavesi G, Horner DS, Pesole G. Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities. Brief Bioinform 2021; 22:616-630. [PMID: 33279989 PMCID: PMC7799330 DOI: 10.1093/bib/bbaa297] [Citation(s) in RCA: 125] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 09/27/2020] [Accepted: 10/07/2020] [Indexed: 12/31/2022] Open
Abstract
Various next generation sequencing (NGS) based strategies have been successfully used in the recent past for tracing origins and understanding the evolution of infectious agents, investigating the spread and transmission chains of outbreaks, as well as facilitating the development of effective and rapid molecular diagnostic tests and contributing to the hunt for treatments and vaccines. The ongoing COVID-19 pandemic poses one of the greatest global threats in modern history and has already caused severe social and economic costs. The development of efficient and rapid sequencing methods to reconstruct the genomic sequence of SARS-CoV-2, the etiological agent of COVID-19, has been fundamental for the design of diagnostic molecular tests and to devise effective measures and strategies to mitigate the diffusion of the pandemic. Diverse approaches and sequencing methods can, as testified by the number of available sequences, be applied to SARS-CoV-2 genomes. However, each technology and sequencing approach has its own advantages and limitations. In the current review, we will provide a brief, but hopefully comprehensive, account of currently available platforms and methodological approaches for the sequencing of SARS-CoV-2 genomes. We also present an outline of current repositories and databases that provide access to SARS-CoV-2 genomic data and associated metadata. Finally, we offer general advice and guidelines for the appropriate sharing and deposition of SARS-CoV-2 data and metadata, and suggest that more efficient and standardized integration of current and future SARS-CoV-2-related data would greatly facilitate the struggle against this new pathogen. We hope that our 'vademecum' for the production and handling of SARS-CoV-2-related sequencing data, will contribute to this objective.
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Affiliation(s)
- Matteo Chiara
- molecular biology and bioinformatics at the University of Milan
| | - Anna Maria D’Erchia
- molecular biology at the University of Bari and research associate at the Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies of the National Research Council in Bari
| | - Carmela Gissi
- molecular biology at the University of Bari and research associate at the Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies of the National Research Council in Bari
| | - Caterina Manzari
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies of the National Research Council in Bari
| | - Antonio Parisi
- Genetic and Molecular Epidemiology Laboratory at the Experimental Zooprophylactic Institute of Apulia and Basilicata
| | - Nicoletta Resta
- Medical Genetics at the University of Bari. She heads the Laboratory Unit of Medical Genetics and the School of Specialization in Medical Genetics
| | | | - Ernesto Picardi
- molecular biology and bioinformatics at the University of Bari and research associate at the Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies of the National Research Council in Bari
| | - Giulio Pavesi
- Associate Professor of bioinformatics at the University of Milan (Italy)
| | - David S Horner
- molecular biology and bioinformatics at the University of Milan
| | - Graziano Pesole
- molecular biology at the University of Bari and Research Associate at the Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies of the National Research Council in Bari
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