NGSocomial Infections: High-Resolution Views of Hospital-Acquired Infections Through Genomic Epidemiology

Greninger, Alexander L.; Zerr, Danielle M.

doi:10.1093/jpids/piab074

Cited by 11 publications

(5 citation statements)

References 115 publications

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“…Nosocomial transmission of respiratory pathogens remains a threat to recovering patients [ 261 ], and they were able to identify SARS-CoV-2 from hospital air, together with other respiratory pathogens of interest such as human adenoviruses, respiratory syncytial virus, and influenza B. In hospital settings, HC can be employed for the identification and genotyping of pathogens for genomic epidemiology, to reduce the spread of nosocomial infecitons [ 262 ].. From clinical to environmental samples, HC proved to be a useful and versatile technique during the recent pandemic, cementing its value in the toolbox of molecular biologists.…”

Section: Case Study: Sars-cov-2mentioning

confidence: 99%

Hybrid-Capture Target Enrichment in Human Pathogens: Identification, Evolution, Biosurveillance, and Genomic Epidemiology

Quek,

2024

Pathogens

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High-throughput sequencing (HTS) has revolutionised the field of pathogen genomics, enabling the direct recovery of pathogen genomes from clinical and environmental samples. However, pathogen nucleic acids are often overwhelmed by those of the host, requiring deep metagenomic sequencing to recover sufficient sequences for downstream analyses (e.g., identification and genome characterisation). To circumvent this, hybrid-capture target enrichment (HC) is able to enrich pathogen nucleic acids across multiple scales of divergences and taxa, depending on the panel used. In this review, we outline the applications of HC in human pathogens—bacteria, fungi, parasites and viruses—including identification, genomic epidemiology, antimicrobial resistance genotyping, and evolution. Importantly, we explored the applicability of HC to clinical metagenomics, which ultimately requires more work before it is a reliable and accurate tool for clinical diagnosis. Relatedly, the utility of HC was exemplified by COVID-19, which was used as a case study to illustrate the maturity of HC for recovering pathogen sequences. As we unravel the origins of COVID-19, zoonoses remain more relevant than ever. Therefore, the role of HC in biosurveillance studies is also highlighted in this review, which is critical in preparing us for the next pandemic. We also found that while HC is a popular tool to study viruses, it remains underutilised in parasites and fungi and, to a lesser extent, bacteria. Finally, weevaluated the future of HC with respect to bait design in the eukaryotic groups and the prospect of combining HC with long-read HTS.

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Section: Case Study: Sars-cov-2mentioning

confidence: 99%

Hybrid-Capture Target Enrichment in Human Pathogens: Identification, Evolution, Biosurveillance, and Genomic Epidemiology

Quek,

2024

Pathogens

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“…Another application is environmental pathogen surveillance, for example, the detection of C. auris in wastewater with the use of NGS [ 87 ]. Outbreak investigation and clustering of cases can also be investigated to delineate the course of nosocomial transmission [ 88 ].…”

Section: Other Emerging Modalities Of Nucleic-acid-based Molecular Di...mentioning

confidence: 99%

Nucleic-Acid-Based Molecular Fungal Diagnostics: A Way to a Better Future

Gudisa,

Harchand,

Rudramurthy

2024

Diagnostics

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The world has seen a tremendous increase in the number of fungal infections during the past two decades. Recently, the World Health Organisation released the pathogen priority list for fungal infections, signifying the importance of these infections in the fields of research and public health. Microbiology laboratories demand an upgrade in the diagnostic system to keep up with the increased burden of these infections. Diagnosis of fungal infections using conventional techniques has always faced limitations in terms of specificity, sensitivity, and turnaround time. Although these methods are the core pillars of the diagnosis, there is an increased need for molecular approaches. Molecular techniques have revolutionised the field of fungal diagnostics. The diverse array of molecular techniques, including techniques like Polymerase Chain Reaction (PCR), have emerged as a cornerstone in fungal diagnostics. Molecular techniques have transformed fungal diagnostics, providing powerful tools for the rapid and accurate identification of pathogens. As these technologies continue to evolve, their integration into routine clinical practice holds the promise of improving patient outcomes through timely and targeted antifungal interventions. This review will cover the molecular approaches involved in fungal diagnostics, moving from the basic techniques to the advanced-level nucleic-acid-based molecular approaches providing a high throughput and decreased turnaround time for the diagnosis of serious fungal infections.

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“…In the clinical laboratory, WGS has proved valuable in hospital infection prevention programs by being able to identify and track outbreaks within a hospital [ 62 , 63 ]. A large portion of the published work has used WGS in tracking outbreaks of the most common nosocomial pathogens of methicillin-resistant Staphylococcus aureus [ 64 , 65 , 66 ] and Clostridiodes difficile [ 67 , 68 , 69 ].…”

Section: Whole Genome Sequencing Of Microorganismsmentioning

confidence: 99%

Next Generation and Other Sequencing Technologies in Diagnostic Microbiology and Infectious Diseases

Hilt

Ferrieri

2022

Genes

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Next-generation sequencing (NGS) technologies have become increasingly available for use in the clinical microbiology diagnostic environment. There are three main applications of these technologies in the clinical microbiology laboratory: whole genome sequencing (WGS), targeted metagenomics sequencing and shotgun metagenomics sequencing. These applications are being utilized for initial identification of pathogenic organisms, the detection of antimicrobial resistance mechanisms and for epidemiologic tracking of organisms within and outside hospital systems. In this review, we analyze these three applications and provide a comprehensive summary of how these applications are currently being used in public health, basic research, and clinical microbiology laboratory environments. In the public health arena, WGS is being used to identify and epidemiologically track food borne outbreaks and disease surveillance. In clinical hospital systems, WGS is used to identify multi-drug-resistant nosocomial infections and track the transmission of these organisms. In addition, we examine how metagenomics sequencing approaches (targeted and shotgun) are being used to circumvent the traditional and biased microbiology culture methods to identify potential pathogens directly from specimens. We also expand on the important factors to consider when implementing these technologies, and what is possible for these technologies in infectious disease diagnosis in the next 5 years.

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NGSocomial Infections: High-Resolution Views of Hospital-Acquired Infections Through Genomic Epidemiology

Cited by 11 publications

References 115 publications

Hybrid-Capture Target Enrichment in Human Pathogens: Identification, Evolution, Biosurveillance, and Genomic Epidemiology

Hybrid-Capture Target Enrichment in Human Pathogens: Identification, Evolution, Biosurveillance, and Genomic Epidemiology

Nucleic-Acid-Based Molecular Fungal Diagnostics: A Way to a Better Future

Next Generation and Other Sequencing Technologies in Diagnostic Microbiology and Infectious Diseases

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