Infection prevention and control insights from a decade of pathogen whole-genome sequencing

Abstract

Pathogen whole-genome sequencing has become an important tool for understanding the transmission and epidemiology of infectious diseases. It has improved our understanding of sources of infection and transmission routes for important healthcare-associated pathogens, including Clostridioides difficile and Staphylococcus aureus . Transmission from known infected or colonised patients in hospitals may explain fewer cases than previously thought and multiple introductions of these pathogens from the community may play a greater a role. The findings have had important implications for infection prevention and control. Sequencing has identified heterogeneity within pathogen species, with some subtypes transmitting and persisting in hospitals better than others. It has identified sources of infection in healthcare-associated outbreaks of food-borne pathogens, Candida auris and Mycobacterium chimera , as well as individuals or groups involved in transmission and historical sources of infection. SARS-CoV-2 sequencing has been central to tracking variants during the COVID-19 pandemic and has helped understand transmission to and from patients and healthcare workers despite prevention efforts. Metagenomic sequencing is an emerging technology for culture-independent diagnosis of infection and antimicrobial resistance. In future, sequencing is likely to become more accessible and widely available. Real-time use in hospitals may allow infection prevention and control teams to identify transmission and to target interventions. It may also provide surveillance and infection control benchmarking. Attention to ethical and well-being issues arising from sequencing identifying individuals involved in transmission is important. Pathogen whole-genome sequencing has provided an incredible new lens to understand the epidemiology of healthcare-associated infection and to better control and prevent these infections.

Evaluation of miniaturized Illumina DNA preparation protocols for SARS-CoV-2 whole genome sequencing

“…The use of WGS has become an important aspect of the international response to the COVID-19 pandemic [ 25 ] and will be the focus of future pandemics [ 26 , 27 ]. With the ever-increasing demands of WGS, it has become necessary to look at ways of reducing the cost of library preparation methods.…”

Combination of Whole Genome Sequencing and Metagenomics for Microbiological Diagnostics

“…Whole genome sequencing (WGS) and metagenomics use different approaches to determine the genomic content in a sample. WGS aims to analyze the whole genome of a single bacterial colony, while amplicon-based marker gene sequencing (e.g., 16S/ITS) or shotgun metagenomics focuses on microbial communities within a sample, usually without culture [ 9 , 10 ]. The costs per sequenced nucleotide have substantially decreased during the past decade [ 11 , 12 ] due to the expansion of sequencing capacities, the development of cost-effective technologies, advances in laboratory automation, and the progression of standardized workflows [ 13 , 14 ].…”

“…Successfully linking the genotype to the phenotype for clinical applications requires a profound understanding of the diagnostic process, for example, when and how linking both types of information is appropriate. Sequencing capacity was further boosted during the COVID-19 pandemic [ 10 , 18 ], with more than 13.9 million SARS-CoV-2 genomes sequenced and made publicly available ( ; accessed on 9 August 2022). This massive sequencing effort also resulted in a high degree of standardized analytical protocols and increased awareness of quality control of the sequencing data [ 19 ].…”

Repeated transmission of SARS-CoV-2 in an overcrowded Irish emergency department elucidated by whole-genome sequencing

“…Whole genome sequencing (WGS) has emerged as an important tool for characterising the epidemiology and patterns of transmission of a wide variety of microbial pathogens [ 5 , 6 , 7 ], and has been shown to offer higher resolution for comparative analyses during outbreak investigations than traditional typing techniques [ 8 ]. In recent years, the development of affordable, high-throughput, massively-parallel next generation sequencing (NGS) platforms has meant that sequencing is now feasible for diagnostic purposes in routine clinical microbiology laboratories [ 5 , 8 ], and can deliver actionable results to IPC teams in hospitals within clinically meaningful timeframes [ 9 , 10 ]. Throughout the COVID-19 pandemic, the unprecedented scale of genomic data generated worldwide has provided important insights into the evolution and pathogenesis of the SARS-CoV-2 virus.…”