Usage of Bacterial Whole Genome Sequencing: Outbreaks and Beyond in Pediatric Patients
Year: 2024
Type: article
Abstract: Infectious disease outbreaks in hospital settings, notably in specialized pediatric units such as neonatal intensive care units (NICUs), special care baby units (SCBUs), pediatric intensive care units and oncology wards, present critical challenges to healthcare providers.1 These outbreaks significantly contribute to morbidity and mortality, especially among patients with inherent vulnerabilities, with the situation worsening as cases with multidrug-resistant pathogens increase.2 Infants in NICUs and SCBUs are at heightened risk due to their immature immune systems and exposure to invasive procedures. Similarly, children in oncology wards, often immunocompromised due to their underlying conditions and treatments, are particularly susceptible to infectious agents. The intricate interplay of compromised immune defenses, invasive medical devices and frequent interactions with healthcare personnel in these settings necessitates prompt and effective responses to infectious disease threats and potential nosocomial outbreaks. Whole genome sequencing (WGS) of bacterial isolates offers the highest resolution of typing, providing the optimal method to assess nosocomial transmissions between patients, staff and the environment.3,4Figure 1 provides a comparison of different typing techniques.FIGURE 1.: Comparison of different typing techniques. Pulsed-field gel electrophoresis and multilocus sequencing typing (MLST) have been largely replaced by whole genome sequencing–based approaches. cgMLST indicates core-genome multilocus sequencing typing; SNP, single-nucleotide polymorphism.WGS has been transformative in managing complex transmission scenarios. Beyond its pivotal role in outbreak investigation and control, WGS also allows for molecular surveillance of environments within a hospital (eg, wastewater for antimicrobial-resistant bacterial isolates).5 In addition, WGS can also be used to identify pathogens and predict antimicrobial resistance (AMR) and virulence factors from bacterial isolates of a patient, offering a nuanced understanding of pathogen behavior and associated phenotypes.6 This technological advancement allows for tailored clinical management and therapeutic strategies, essential in choosing antimicrobial drug combinations.7 The information offered by WGS may impact clinical decision-making, particularly in NICUs, SCBUs and pediatric oncology wards where timely and precise intervention can dramatically alter patient outcomes. Unfortunately, the current work protocols for WGS in most routine diagnostic laboratories are too slow to generate real-time results with standardized protocols, hindering its application in diagnostics. Newer sequencing technologies with Oxford Nanopore Technology (Oxford Nanopore Technologies, Oxford, United Kingdom) and optimized automatized protocols from Illumina (Illumina, San Diego, CA) may overcome this hurdle. It is also worth noting that most studies are focused on bacteria, with parasite and fungal outbreaks less well documented, likely due to the size and complexity of the respective genomes. In more ideal study settings, WGS has already been shown to impact patient treatment.8,9 This review explores the multifaceted impact of WGS in pediatric infectious disease management, underscoring its value in enhancing patient care across various high-risk hospital settings. WGS IN OUTBREAK INVESTIGATIONS Since pioneering MRSA investigations listed in Table, Supplemental Digital Content 1, https://links.lww.com/INF/F773, WGS has revolutionized outbreak investigations in pediatric cohorts, serving as a more advanced successor to traditional, lower resolution methods such as pulsed-field gel electrophoresis, random amplified polymorphic DNA, spa-typing and multilocus sequencing typing. This transition marks a significant leap in epidemiological investigations, especially in the high-risk environment of NICUs. Unlike pulsed-field gel electrophoresis, which requires a lot of hands-on time and the results of which are not easily transferrable between laboratories, and other more traditional techniques, which are no longer recommended for outbreak investigation, WGS offers an unparalleled resolution that can differentiate between genetically similar organisms, as well as the sharing of raw data for use by other laboratories. Precision is crucial, where identifying the precise features of a pathogen can have direct implications on infection control measures. Underlying the usability of WGS are quality control (QC) and robust analysis. QC steps are important in the preanalytic, analytic and postanalytic stages. The analytical QC is usually performed by a bioinformatic pipeline, examples of which include Bacpipe (github.com/wholeGenomeSequencingAnalysisPipeline/BacPipe), Nullarbor (tseemann.github.io/nullarbor/) and IMMense (Figure, Supplemental Digital Content 2, https://links.lww.com/INF/F774). Under ISO-accredited conditions, QC ensures data accuracy that the correct sample has been sequenced, without contamination, and to acceptable read depth. Comparison of isolate genomes proceeds generally via either (1) core-genome multilocus sequencing typing using thousands of bacterial genes or (2) whole genome single-nucleotide variant comparison using millions of nucleotides, allowing the discrimination of strains that would appear identical with less sophisticated typing methods. Future pipelines may present all-in-one solutions, from DNA to report; however, these advances, such as identifying transmission clusters and integrating epidemiologic data, are not trivial. Many case studies highlight the effectiveness of WGS in providing deeper insights into NICU outbreak epidemiology than contemporary typing techniques (Table, Supplemental Digital Content 1, https://links.lww.com/INF/F773). In the complex setting of an NICU, where patients are often exposed to various microbes, WGS helps to accurately map the transmission pathways of infections and delineate highly related lineages of pathogens. An overview of outbreaks studied using WGS (Table, Supplemental Digital Content 1, https://links.lww.com/INF/F773) shows how the technology was used first to investigate cases from 2009, with increasing use over the years. Studies have been performed in all corners of the world, in countries with highly variable resources, sometimes with in-house equipment and sometimes through collaboration. A wide range of pathogens have been investigated, highlighting the susceptibility of neonates to infection. While some of these studies are retrospective and some describe more surveillance studies and findings of links between patients or not, in many cases, WGS has been used to rule-in or rule-out isolate relatedness and, therefore, investigate transmission mechanisms and sources. Sometimes, results are unexpected, with multifocal outbreaks often identified. Even where cases are not genomically linked, sources such as unsealed construction areas can be identified, and the sources of the pathogens can be resolved. Screening of patients, healthcare workers and environmental locations such as cots and sinks is also in many cases critical and can reveal potential sources or transmission routes. While original sources of infection are rarely traced unambiguously, improved or reiterated infection control measures are often the key to outbreak resolution. An important benefit of WGS is the ability to identify genes encoding AMR determinants and virulence factors, which are often used in case interpretation. The adoption of WGS in NICUs has not only enhanced the resolution and accuracy of outbreak investigations but also facilitated a more rapid response to infectious threats. While clearly not all outbreak investigations have been published, WGS plays a pivotal role in the epidemiological landscape of NICUs already in many hospitals around the globe, offering new avenues for understanding and combating neonatal infections. CHALLENGES IN IMPLEMENTATION OF WGS Despite its advantages, the implementation of WGS faces several challenges. One of the primary concerns is the turnaround time. In outbreak situations, especially in critical care settings such as NICUs, time is of the essence. Traditional WGS processes can take several days to yield results, which may delay crucial interventions. This is due to the need for bacterial isolation, technical workflows and bioinformatic analysis. Accessibility and cost are additional barriers: setting up and maintaining WGS facilities require significant investment, making it challenging for smaller or resource-limited healthcare settings to adopt this technology. The cost factor extends to the initial setup and to the ongoing operations, including reagents and maintenance. Recent analyses point to overall savings compared with the costs associated with healthcare-associated infections10,11 although more data are needed.12 The need for standardization and bioinformatics expertise cannot be overstated. WGS generates a vast amount of data that requires specialized skills for accurate interpretation. This necessity means that healthcare facilities must either train existing staff in bioinformatics or hire experts, both of which can be costly and time-consuming. Furthermore, standardization across different platforms and institutions is crucial to ensure comparability and consistency of WGS data, but this is less of an issue with WGS compared with other techniques. It is unclear if the new In Vitro Diagnostics Regulation in Europe will affect epidemiological surveillance, as there is often no direct patient treatment consequence during outbreak investigation. Ideally, patient-related sample WGS should be processed in an ISO-accredited laboratory. This guarantees that quality management is in place, including participation in external QCs. However, if AMR prediction is used to change the antibiotic treatment, then the In Vitro Diagnostics Regulation will apply, increasing the regulatory burden. WGS AS THE NEW GOLD STANDARD AND ONGOING DEVELOPMENTS The evolution of WGS has given rise to the “sequence first” approach in outbreak investigation, which generates a continuous surveillance environment.13 This approach involves utilizing WGS as a primary tool for early detection and intervention, rather than as a retrospective analysis tool. By implementing routine genomic surveillance, healthcare facilities can gain an early warning of transmission events, potentially identifying and curtailing outbreaks before they escalate. This proactive stance is particularly advantageous in pediatric care settings, where early intervention can significantly reduce the spread of infection and improve patient care outcomes. In general, prospective surveillance of high-risk pathogens is also more cost-efficient than “waiting” for an outbreak.10,11 Furthermore, as WGS technologies continue to advance, it is anticipated that the costs associated with sequencing and turnaround times will decrease, making it more accessible to a broader range of healthcare settings, including smaller hospitals and clinics in resource-limited environments. The development of smaller benchtop sequencers is a significant leap forward in this regard. These compact instruments are exemplified by models such as the Oxford Nanopore MinION and the Illumina iSeq and MiniSeq. They require lower investment, offer shorter running times, are more user-friendly and require less specialized training compared with their predecessors. Moreover, advancements in rapid library preparation methods and automation have significantly reduced the time from sample collection to analysis, with some systems now capable of delivering results in less than a day.14 Automation of laboratory and analytical workflows are necessary to further improve data quality and reduce costs. As methods develop, metagenomic-based diagnostics, removing the requirement for bacterial isolation, may enter more common use. The connection and sharing of WGS data for national and global surveillance can also improve data interpretation and understanding of pathogen transmissions over larger scales. Databases such as the Swiss Pathogen Surveillance Platform (SPSP.ch) support these efforts. CONCLUSIONS WGS has revolutionized outbreak investigation in NICUs, marking a significant advancement in pediatric infectious diseases. By offering unprecedented accuracy in identifying related pathogenic isolates, WGS has become an indispensable tool in NICUs and SCBUs, where rapid and precise identification of outbreak sources is crucial. WGS also allows the investigation of AMR determinants and virulence factors, which may inform on measures to implement. The findings may also play a role in preventing future incidents. As we look to the future, WGS is poised to play an even more integral role in NICU and other pediatric settings and beyond. Its evolving application, from an adjunct in outbreak investigations to a mainstay in routine genomic surveillance, is expected to bring about significant improvements in patient outcomes. The continued advancement of WGS technology, coupled with decreasing costs and increased accessibility, will see its integration into standard care practices. We also anticipate the use of artificial intelligence in the analysis, interpretation and reporting of data to healthcare personnel. In conclusion, WGS stands at the forefront of a new era in pediatric infectious disease management, offering hope and enhanced care to the most vulnerable patients in our healthcare system. ACKNOWLEDGMENTS The authors thank the Microbial Genomics Sequencing Team at the Institute of Medical Microbiology, University of Zurich, for their technical support.
Institution: University of Zurich
Language: English
Subfield: Infectious Diseases
Field: Medicine
Domain: Health Sciences
Open Access status: green
OpenAlex ID: W4403719285