scholarly journals Improved characterisation of MRSA transmission using within-host bacterial sequence diversity

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Matthew D Hall ◽  
Matthew TG Holden ◽  
Pramot Srisomang ◽  
Weera Mahavanakul ◽  
Vanaporn Wuthiekanun ◽  
...  
Keyword(s):  
Methicillin Resistant Staphylococcus Aureus ◽  
Hospital Setting ◽  
Nucleotide Polymorphism ◽  
Bacterial Genomes ◽  
Large Dataset ◽  
Single Nucleotide ◽  
Deductive Power ◽  
Optimum Threshold ◽  
Multiple Pathogen ◽  
Bacterial Sequence

Methicillin-resistant Staphylococcus aureus (MRSA) transmission in the hospital setting has been a frequent subject of investigation using bacterial genomes, but previous approaches have not yet fully utilised the extra deductive power provided when multiple pathogen samples are acquired from each host. Here, we used a large dataset of MRSA sequences from multiply-sampled patients to reconstruct colonisation of individuals in a high-transmission setting in a hospital in Thailand. We reconstructed transmission trees for MRSA. We also investigated transmission between anatomical sites on the same individual, finding that this either occurs repeatedly or involves a wide transmission bottleneck. We examined the between-subject bottleneck, finding considerable variation in the amount of diversity transmitted. Finally, we compared our approach to the simpler method of identifying transmission pairs using single nucleotide polymorphism (SNP) counts. This suggested that the optimum threshold for identifying a pair is 39 SNPs, if sensitivities and specificities are equally weighted.

scholarly journals Rapid Open-Source SNP-Based Clustering Offers an Alternative to Core Genome MLST for Outbreak Tracing in a Hospital Setting

2021 ◽  
Vol 12 ◽  
Author(s):  
Judit Szarvas ◽  
Mette Damkjaer Bartels ◽  
Henrik Westh ◽  
Ole Lund
Keyword(s):  
Open Source ◽  
Core Genome ◽  
Hospital Setting ◽  
Epidemiological Data ◽  
Resistant Bacteria ◽  
Whole Genome ◽  
Nucleotide Polymorphism ◽  
Analysis Pipeline ◽  
Single Nucleotide ◽  
Healthcare Settings

Traditional genotyping methods for infection control of antimicrobial-resistant bacteria in healthcare settings have been supplemented by whole-genome sequencing (WGS), often relying on a gene-based approach, e.g., core genome multilocus sequence typing (cgMLST), to cluster-related samples. In this study, we compared clusters of methicillin-resistant Staphylococcus aureus (MRSA) and Enterococcus faecium analyzed with the commercial cgMLST software Ridom SeqSphere+ and with an open-source single-nucleotide polymorphism (SNP)-based phylogenetic analysis pipeline (PAPABAC). A total of 5,655 MRSA and 2,572 E. faecium patient isolates, collected between 2013 and 2018, were processed. Clusters of 1,844 MRSA and 1,355 E. faecium isolates were compared to cgMLST results, and epidemiological data were included when available. The phylogenies inferred by the two different technologies were highly concordant, and the MRSA SNP tree re-captured known hospital-related outbreaks and epidemiologically linked samples. PAPABAC has the advantage over Ridom SeqSphere+ to generate stable, referable clusters without the need for sequence assembly, and it is a free-of-charge, open-source alternative to the commercial software.

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