Current Uses and Future Perspectives of Genomic Technologies in Clinical Microbiology

Antibiotics, Год журнала: 2023, Номер 12(11), С. 1580 - 1580

Опубликована: Окт. 30, 2023

Recent advancements in sequencing technology and data analytics have led to a transformative era pathogen detection typing. These developments not only expedite the process, but also render it more cost-effective. Genomic analyses of infectious diseases are swiftly becoming standard for analysis control. Additionally, national surveillance systems can derive substantial benefits from genomic data, as they offer profound insights into epidemiology emergence antimicrobial-resistant strains. Antimicrobial resistance (AMR) is pressing global public health issue. While clinical laboratories traditionally relied on culture-based antimicrobial susceptibility testing, integration AMR holds immense promise. Genomic-based furnish swift, consistent, highly accurate predictions phenotypes specific strains or populations, all while contributing invaluable surveillance. Moreover, genome assumes pivotal role investigation hospital outbreaks. It aids identification infection sources, unveils genetic connections among isolates, informs strategies The One Health initiative, with its focus intricate interconnectedness humans, animals, environment, seeks develop comprehensive approaches disease surveillance, control, prevention. When integrated epidemiological systems, forecast expansion bacterial populations species transmissions. Consequently, this provides evolution relationships pathogens, hosts, environment.

Язык: Английский

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ViralFlow v1.0—a computational workflow for streamlining viral genomic surveillance

NAR Genomics and Bioinformatics, Год журнала: 2024, Номер 6(2)

Опубликована: Апрель 4, 2024

Abstract ViralFlow v1.0 is a computational workflow developed for viral genomic surveillance. Several key changes turned into general-purpose reference-based genome assembler all viruses with an available reference genome. New virus-agnostic modules were implemented to further study nucleotide and amino acid mutations. runs on broad range of infrastructures, from laptop computers high-performance computing (HPC) environments, generates standard well-formatted outputs suited both public health reporting scientific problem-solving. at: https://viralflow.github.io/index-en.html.

Язык: Английский

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Whole-Genome Sequencing and Mutation Analyses of SARS-CoV-2 Isolates from Indonesia

Pathogens, Год журнала: 2024, Номер 13(4), С. 279 - 279

Опубликована: Март 25, 2024

The SARS-CoV-2 infection that caused the COVID-19 pandemic has become a significant public health concern. New variants with distinct mutations have emerged, potentially impacting its infectivity, immune evasion capacity, and vaccine response. A whole-genome sequencing study of 292 isolates collected from selected regions Indonesia between January October 2021 was performed to identify distribution common in Indonesia. During January–April 2021, Indonesian lineages B.1.466.2 B.1.470 dominated, but May Delta’s AY.23 lineage outcompeted them. An analysis 7515 published sequences June 2022 revealed decline Delta November followed by emergence Omicron December 2021. We identified C241T (5′UTR), P314L (NSP12b), F106F (NSP3), D614G (Spike) all sequences. other substitutions included P681R (76.4%) T478K (60%) Spike, D377Y Nucleocapsid (61%), I82T Membrane proteins. Breakthrough prolonged viral shedding cases were associated carrying Spike T19R, G142D, L452R, T478K, D614G, P681R, D950N, V1264L mutations. dynamic highlights importance continuous genomic surveillance monitoring identifying potential strains leading disease outbreaks.

Язык: Английский

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Increasing evolution, prevalence, and outbreaks for rift valley fever virus in the process of breaking geographical barriers

The Science of The Total Environment, Год журнала: 2024, Номер 917, С. 170302 - 170302

Опубликована: Янв. 24, 2024

Язык: Английский

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Monitoring and Early Warning System: Regional Monitoring Strategy in Lombardy Region

Epidemiologia, Год журнала: 2025, Номер 6(1), С. 7 - 7

Опубликована: Фев. 11, 2025

This article examines the infectious disease surveillance system in Lombardy region of Italy, with a focus on its response mechanisms to respiratory syndromes. study aims describe alert and organizational procedures place, assessing their effectiveness managing health crises. is based analysis Lombardy's regional resolution No. 1125, developed by public experts. Surveillance levels were categorized incidence thresholds healthcare impacts, establishing specific indicators activation protocols. Information flows are managed through real-time data portals, enabling monitoring COVID-19, influenza, other diseases. A multi-level was established, ranging from ordinary regimes critical epidemic activation. Each level includes actions, such as resource reallocation, emergency department support, suspension elective procedures. The use technological tools, electronic records, streamlined reporting processes, flow management, has strengthened region's capabilities. underscores value structured, for showing that unified approach improves crisis efficiency. It suggests sharing protocols within scientific community can help harmonize national international responses future pandemics. system, while effective current context, may require adaptation challenges.

Язык: Английский

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SARS-CoV-2 genomic surveillance using self-collected saliva specimens during occupational testing programs

Frontiers in Public Health, Год журнала: 2025, Номер 13

Опубликована: Апрель 8, 2025

Continually emerging SARS-CoV-2 variants pose challenges to clinical and public health interventions, necessitating sustainable approaches real-time variant monitoring. This case study describes an innovative screening surveillance program that demonstrates the utility of sequencing-based monitoring using self-collected saliva specimens. We conducted saliva-based in occupational settings Omaha, Nebraska from December 2021 through November 2022. 8,372 specimens collected 1,480 participants were tested for RNA by extraction-free PCR, with 334 positive samples referred whole-genome sequencing analysis. Program utilization, quality metrics, outputs compared across sites. Specimen was high settings, demonstrating suitability PCR genomic testing. Virus successfully determined strain 83 67% SARS-CoV-2-positive two successful integration determination into programs qRT-PCR testing method. further demonstrate sensitivity efficiency analysis is dependent on cycle threshold (Ct) cutoff diagnostic assay virus gene target. Use optimized Ct value referral recommended. Community-based can be utilized enhance monitoring, could considered risk identification other respiratory infections. approach offers advantages a non-invasive specimen collection, no need supervised collection healthcare worker, supply chain resiliency, distributable access, scalability.

Язык: Английский

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Genomics-based approach for detection and characterization of SARS-CoV-2 co-infections and diverse viral populations

Microbiology Spectrum, Год журнала: 2025, Номер unknown

Опубликована: Май 1, 2025

Due to the continuous genetic diversification of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) over time, co-circulation two different lineages in same region may lead co-infections within a host, situation known contribute emergence hybrid viral populations through genomic recombination. The aim this study was use genomics-based approach identify distinct SARS-CoV-2 patients with disease 2019 (COVID-19), as an indicator potential and recombination events. cohort included 41,224 serial nasopharyngeal swabs positive for RNA, prospectively collected between January 2021 April 2022 part French national surveillance program. Full-length genomes were sequenced by next-generation sequencing (COVIDseq). Intra-host single nucleotide variants (iSNVs) identified, synthetic generated establish thresholds co-infection detection. Eight hundred sixty-one samples iSNV ratios above threshold considered "potential co-infections." Peaks prevalence occurred during periods variants. Co-infection Variants Concern (VoC) confirmed 103 cases, including Alpha-Beta 12 Alpha-Delta 15 Gamma-Delta 4 Delta-Omicron 35 Omicron BA.1-BA.2 37 cases. In conclusion, our suggests higher variant/subvariant events than that previously reported using conventional approaches, particularly characterized multiple lineages, creating increased risk Our results support premise importance approaches detect virus-infected populations, closely related lineages. We implement innovative monitor diversity human population, circulation VOCs. This focused on detecting highly diverse which are facilitate can potentially new recombinant novel characteristics. Monitoring characterizing cases outbreak is key strategy better understanding evolution, especially epidemic periods. However, challenging, their often underestimated. study, we developed be implemented programs applied large datasets. Concern.

Язык: Английский

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SARS-CoV-2 genomics and impact on clinical care for COVID-19

Journal of Antimicrobial Chemotherapy, Год журнала: 2023, Номер 78(Supplement_2), С. ii25 - ii36

Опубликована: Ноя. 1, 2023

Abstract The emergence and worldwide spread of SARS-CoV-2 during the COVID-19 pandemic necessitated adaptation rapid deployment viral WGS analysis techniques that had been previously applied on a more limited basis to other pathogens, such as HIV influenza viruses. need for was driven in part by low mutation rate SARS-CoV-2, which measuring variation along entire genome sequence effectively differentiate lineages characterize evolution. Several approaches designed maximize throughput accuracy were quickly adopted surveillance labs around world. These broad-based genomic sequencing efforts revealed ongoing evolution virus, highlighted successive new variants throughout course pandemic. insights instrumental characterizing effects mutations transmissibility, immune escape tropism, turn helped guide public health policy, use monoclonal antibody therapeutics vaccine development strategies. As direct-acting antivirals treatment became widespread, potential antiviral resistance has delineate monitor global databases their emergence. Given critical role genomics international effort combat pandemic, coordinated should be made expand capacity infrastructure towards anticipation prevention future pandemics.

Язык: Английский

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Viral sequencing to inform the global elimination of dog-mediated rabies - a systematic review

One Health & Implementation Research, Год журнала: 2024, Номер 4(2), С. 15 - 37

Опубликована: Май 31, 2024

Background: Rabies is a fatal zoonotic disease, present in almost 150 countries. The “Zero by 30” initiative aims to eliminate human deaths from dog-mediated rabies globally 2030. This systematic review investigates how viral sequencing can contribute achieving the goal improving understanding of circulation and impact control measures. Methods: A comprehensive search bibliographic databases was conducted focusing on research regions with endemic published between 2000 2023, adhering Preferred Reporting Items for Systematic Reviews Meta-Analyses (PRISMA) guidelines. Data were extracted synthesised provide recommendations further application support control. Results: 220 studies identified have documented virus (RABV) sequences 94 countries, primarily using first-generation technology produce partial genomes predominantly overseas rather than in-country. Dogs be primary RABV reservoir these regions, although some more localised wildlife reservoirs. Clade classifications commonly based host association or geographical location, however, lack standardised methods nomenclature classifying lineages limited comparison at higher resolution. Cross-species transmission, both local long-distance transmission identified, quantitative inference limited. Sequence data particularly useful identifying transboundary spread incursions, investigating shifts, tracing sources rabies, endemicity typically characterised identification multiple co-circulating lineages. Conclusion: There an urgent need classification phylogeny-based RABVs, improved capacity including proficiency bioinformatics phylogenetics. Our findings emphasise critical foster international cooperation coordinate efforts reduce spread, limit reintroductions maintain progress towards 2030 target.

Язык: Английский

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Microbial genomics and genome sequencing approaches

Elsevier eBooks, Год журнала: 2025, Номер unknown, С. 3 - 20

Опубликована: Янв. 1, 2025

Язык: Английский

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