Multi-site implementation of whole genome sequencing for hospital infection control: A prospective genomic epidemiological analysis

Sherry, Norelle L; Gorrie, Claire L.; Kwong, Jason C; Higgs, Charlie; Stuart, Rhonda L.; Marshall, Caroline; Ballard, Susan A; Sait, Michelle; Korman, Tony M.; Slavin, Monica; Lee, Robyn S; Graham, Maryza; Leroi, Marcel; Worth, Leon J.; Chan, Hiu Tat; Seemann, Torsten; Grayson, M Lindsay; Howden, Benjamin P

doi:10.1016/j.lanwpc.2022.100446

Cited by 17 publications

(13 citation statements)

References 33 publications

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“…Prior studies have characterized healthcare-associated VRE transmission rates ranging from 60-80%. 9,34 Consistent with these prior reports, we found that 70% of VRE isolates in our study were genetically linked to one another when we considered both clinical and rectal swab isolates, however this proportion fell to only 53% when we considered clinical isolates only. Together these findings suggest that the inclusion of rectal swabs increases clustering of related isolates, and may improve both within and between patient lineage tracking.…”

Section: Discussionsupporting

confidence: 91%

Genomic sequencing surveillance of patients colonized with vancomycin-resistantEnterococcus(VRE) improves detection of hospital-associated transmission

Sundermann,

Rangachar Srinivasa,

Mills

et al. 2024

Preprint

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Background: Vancomycin-resistant enterococcal (VRE) infections pose significant challenges in healthcare. Transmission dynamics of VRE are complex, often involving patient colonization and subsequent transmission through various healthcare-associated vectors. We utilized a whole genome sequencing (WGS) surveillance program at our institution to better understand the contribution of clinical and colonizing isolates to VRE transmission. Methods: We performed whole genome sequencing on 352 VRE clinical isolates collected over 34 months and 891 rectal screening isolates collected over a 9-month nested period, and used single nucleotide polymorphisms to assess relatedness. We then performed a geo-temporal transmission analysis considering both clinical and rectal screening isolates compared with clinical isolates alone, and calculated 30-day outcomes of patients. Results: VRE rectal carriage constituted 87.3% of VRE acquisition, with an average monthly acquisition rate of 7.6 per 1000 patient days. We identified 185 genetically related clusters containing 2-42 isolates and encompassing 69.6% of all isolates in the dataset. The inclusion of rectal swab isolates increased the detection of clinical isolate clusters (from 53% to 67%, P<0.01). Geo-temporal analysis identified hotspot locations of VRE transmission. Patients with clinical VRE isolates that were closely related to previously sampled rectal swab isolates experienced 30-day ICU admission (17.5%), hospital readmission (9.2%), and death (13.3%). Conclusions: Our findings describe the high burden of VRE transmission at our hospital and shed light on the importance of using WGS surveillance of both clinical and rectal screening isolates to better understand the transmission of this pathogen. This study highlights the potential utility of incorporating WGS surveillance of VRE into routine hospital practice for improving infection prevention and patient safety.

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Section: Discussionsupporting

confidence: 91%

Genomic sequencing surveillance of patients colonized with vancomycin-resistantEnterococcus(VRE) improves detection of hospital-associated transmission

Sundermann,

Rangachar Srinivasa,

Mills

et al. 2024

Preprint

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“…However, these techniques can lack discriminatory power and/or reproducibility and therefore analyses have increasingly been replaced by whole genome sequencing (WGS) [7]. WGS has been widely used to study outbreaks retrospectively [8][9][10][11] and, to some extent, prospectively [12,13], and is considered the gold standard approach to determining isolate relatedness. However, implementation in the routine clinical setting is still limited by availability, turnaround time, relative cost, and the specialist bioinformatics expertise required to process data and interpret outputs.…”

Section: Introductionmentioning

confidence: 99%

WITHDRAWN: Evaluation of Fourier Transform Infrared spectroscopy (IR Biotyper) as a complement to Whole genome sequencing (WGS) to characteriseEnterobacter cloacae,Citrobacter freundiiandKlebsiella pneumoniaeisolates recovered from hospital sinks

Aranega-Bou¹,

Cornbill²,

Rodger

et al. 2023

Preprint

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Whole genome sequencing (WGS) of healthcare-associated pathogens is recognised as the gold standard for isolate typing and the recognition of transmission networks and outbreaks. However, it remains reasonably expensive to process small numbers of isolates in real-time, and frequently requires specific expertise to enable both sequencing and the analysis of sequencing outputs, limiting its generalisability and turnaround. Spectrometry has revolutionised species identification in clinical laboratory workflows, and has more recently been applied to strain-level identification to facilitate low-cost, routine strain typing in clinical laboratories. However, studies to date of its clinical performance for strain-level typing are conflicting, and limited evaluation has been undertaken on environmental healthcare-associated isolates. We therefore compared its performance with WGS for Enterobacter cloacae, Citrobacter freundii and Klebsiella pneumoniae isolated from sink drains across nine hospitals and investigated whether it could be used as a screening tool prior to WGS. We found its sensitivity and specificity to cluster isolates when compared with WGS were generally poor and highly variable dependent on species and the single nucleotide polymorphism (SNP) distance threshold used to cluster isolates.

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“…Resistance in healthcare pathogens spreads in narrower or wider patient and hospital networks [20,21]. Depending on the pathogen, the extent of clonal versus horizontal spread may differ, as well as transmissibility potential.…”

Section: Hospital Pathogen Surveillance -It Is Mainly About Resistancementioning

confidence: 99%

Taking hospital pathogen surveillance to the next level

et al. 2023

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High-throughput bacterial genomic sequencing and subsequent analyses can produce large volumes of high-quality data rapidly. Advances in sequencing technology, with commensurate developments in bioinformatics, have increased the speed and efficiency with which it is possible to apply genomics to outbreak analysis and broader public health surveillance. This approach has been focused on targeted pathogenic taxa, such as Mycobacteria, and diseases corresponding to different modes of transmission, including food-and-water-borne diseases (FWDs) and sexually transmitted infections (STIs). In addition, major healthcare-associated pathogens such as methicillin-resistant Staphylococcus aureus , vancomycin-resistant enterococci and carbapenemase-producing Klebsiella pneumoniae are the focus of research projects and initiatives to understand transmission dynamics and temporal trends on both local and global scales. Here, we discuss current and future public health priorities relating to genome-based surveillance of major healthcare-associated pathogens. We highlight the specific challenges for the surveillance of healthcare-associated infections (HAIs), and how recent technical advances might be deployed most effectively to mitigate the increasing public health burden they cause.

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Multi-site implementation of whole genome sequencing for hospital infection control: A prospective genomic epidemiological analysis

Cited by 17 publications

References 33 publications

Genomic sequencing surveillance of patients colonized with vancomycin-resistantEnterococcus(VRE) improves detection of hospital-associated transmission

Genomic sequencing surveillance of patients colonized with vancomycin-resistantEnterococcus(VRE) improves detection of hospital-associated transmission

WITHDRAWN: Evaluation of Fourier Transform Infrared spectroscopy (IR Biotyper) as a complement to Whole genome sequencing (WGS) to characteriseEnterobacter cloacae,Citrobacter freundiiandKlebsiella pneumoniaeisolates recovered from hospital sinks

Taking hospital pathogen surveillance to the next level

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