Key parameters for genomics-based real-time detection and tracking of multidrug-resistant bacteria: a systematic analysis

Abstract

Background Pairwise single nucleotide polymorphisms (SNPs) are a cornerstone of genomic approaches to the inference of transmission of multidrug-resistant (MDR) organisms in hospitals. However, the impact of many key analytical approaches on these inferences has not yet been systematically assessed. This study aims to make such a systematic assessment.Methods We conducted a 15-month prospective study (2-month pilot phase, 13-month implementation phase), across four hospital networks including eight hospitals in Melbourne, VIC, Australia. Patient clinical and screening samples containing one or more isolates of meticillin-resistant Staphylococcus aureus, vancomycin-resistant Enterococcus faecium, and extended-spectrum β-lactamase-producing Escherichia coli and Klebsiella pneumoniae were collected and underwent whole genome sequencing. Using the genome data from the top four most numerous sequence types from each species, 16 in total, we systematically assessed the: (1) impact of sample and reference genome diversity through multiple core genome alignments using different data subsets and reference genomes, (2) effect of masking of prophage and regions of recombination in the core genome alignments by assessing SNP distances before and after masking, (3) differences between a cumulative versus a 3-month sliding-window approach to sample genome inclusion in the dataset over time, and (4) the comparative effects each of these approaches had when applying a previously defined SNP threshold for inferring likely transmission.

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

“…Alternatively, a decentralised genomics model (local WGS and analysis, or hybrid model with centralised analysis) may also optimise TATs; the choice of model ultimately depends on the available resources in each setting. 28 Other key challenges include the optimisation of bioinformatics processes 29 and integration of epidemiologic data, without which the genomic analyses are not interpretable. 30 , 31 In our study, the linkage of genomic and epidemiologic data was impaired by poor integration with electronic medical records; this integration would be an important component for successful implementation in the future.…”

“… 32 , 34 In a pragmatic sense, if high-resolution core genome SNP methods are used for large-scale prospective genomics, then SNP thresholds are likely to be required; however, future studies in this area should be open to exploring alternative methods and thresholds. 29 , 34 , 35 , 37 …”

Phylodynamic Inference of Bacterial Outbreak Parameters Using Nanopore Sequencing

“…Phylodynamic inference on nanopore platforms is further complicated because (ideally) an outbreak reference genome is used, that is closely related to the outbreak sequence type, thus providing sufficiently high variant calling resolution for transmission inference, particularly in recent transmission chains or outbreaks ( Gorrie et al 2021 ). In addition, on bacterial time scales (years) little sequence variation will have occurred in newly emergent outbreaks, which places a disproportionate emphasis on correctly inferring the few available outbreak-specific SNPs.…”

Systematic benchmarking of ‘all-in-one’ microbial SNP calling pipelines

“…However, there is not yet a consensus on this approach. A recent systematic analysis for real-time genomics based tracking of MDR bacteria in the healthcare environment found masking of prophages had minimal effect while masking of recombination may lead to erroneous conclusions of isolate relatedness (11).…”