Coolen, J. | bioRxiv Science

bioRxiv2021

A prioritized and validated resource of mitochondrial proteins in Plasmodium identifies leads to unique biology

Plasmodium species have a single mitochondrion that is essential for their survival and has been successfully targeted by anti-malarial drugs. Most mitochondrial proteins are imported into this organelle and our picture of the Plasmodium mitochondrial proteome remains incomplete. Many data sources contain information about mitochondrial localization, including proteome and gene expression profiles, orthology to mitochondrial proteins from other species, co-evolutionary relationships, and amino acid sequences, each with different coverage and reliability. To obtain a comprehensive, prioritized list of Plasmodium falciparum mitochondrial proteins, we rigorously analyzed and integrated eight datasets using Bayesian statistics into a predictive score per protein for mitochondrial localization. At a corrected false discovery rate of 25%, we identified 445 proteins with a sensitivity of 87% and a specificity of 97%. They include proteins that have not been identified as mitochondrial in other eukaryotes but have characterized homologs in bacteria that are involved in metabolism or translation. Mitochondrial localization of seven Plasmodium berghei orthologs was confirmed by epitope labeling and co-localization with a mitochondrial marker protein. One of these belongs to a newly identified apicomplexan mitochondrial protein family that in P. falciparum has four members. With the experimentally validated mitochondrial proteins and the complete ranked P. falciparum proteome, which we have named PlasmoMitoCarta, we present a resource to study unique proteins of Plasmodium mitochondria.

bioinformatics↗

bioRxiv2019

Surveillance-embedded genomic outbreak resolution of methicillin-susceptible Staphylococcus aureus in a neonatal intensive care unit

BackgroundWe observed an increase in methicillin-susceptible Staphylococcus aureus (MSSA) infections among neonates at a Dutch third level neonatal intensive care unit. Weekly surveillance data of MSSA carriage among neonates and cross-sectional screenings of health care workers (HCWs) were available for outbreak tracing. While traditional typing of MSSA isolates by staphylococcal protein A gene (spa typing) and Multiple-Locus Variable number tandem repeat Analysis (MLVA) suggested that nosocomial transmission had contributed to the infections, here they lacked the resolution to draw solid conclusions.\n\nMethodsMSSA isolates from neonatal infections, carriage surveillance, and HCWs were subjected to whole-genome sequencing and compared by a series of automated tools including de novo assembly, identification and localization of high-quality single nucleotide polymorphisms, and in-depth analysis of subsets of isolates. Outbreaks were defined as isolates that were more closely related than was to be expected from the genetic diversity in background surveillance.\n\nResultsGenomic analysis identified isolates that had been unjustly assigned to clusters based on MLVA typing, while spa typing was concordant but of insufficient resolution. Detailing particular subsets of isolates further improved resolution and although it provided evidence that HCWs were involved in multiple outbreaks, it alleviated heavy concerns about one particular HCW. Genomic clustering of isolates based on deviations from background surveillance matched epidemiological patient linkage. Compared to MLVA typing, the genomic analysis demonstrated more, shorter, and re-assorted nosocomial transmission chains during this outbreak.\n\nConclusionsIn this study the improved resolution and accuracy of genomic outbreak analyses compared to spa typing and MLVA substantially altered the view on outbreaks, along with apposite outbreak measures. Inclusion of the circulating background population has the potential to overcome current issues in genomic outbreak inference.

microbiology↗