MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples
نویسندگان
چکیده
Metagenomic characterization of microbial communities has the potential to become a tool to identify pathogens in human samples. However, software tools able to extract strain-level typing information from metagenomic data are needed. Low-throughput molecular typing schema such as Multilocus Sequence Typing (MLST) are still widely used and provide a wealth of strain-level information that is currently not exploited by metagenomic methods. We introduce MetaMLST, a software tool that reconstructs the MLST loci of microorganisms present in microbial communities from metagenomic data. Tested on synthetic and spiked-in real metagenomes, the pipeline was able to reconstruct the MLST sequences with >98.5% accuracy at coverages as low as 1×. On real samples, the pipeline showed higher sensitivity than assembly-based approaches and it proved successful in identifying strains in epidemic outbreaks as well as in intestinal, skin and gastrointestinal microbiome samples.
منابع مشابه
Streaming algorithms for identification of pathogens and antibiotic resistance potential from real-time MinIONTM sequencing
The recently introduced Oxford Nanopore MinION platform generates DNA sequence data in real-time. This has great potential to shorten the sample-to-results time and is likely to have benefits such as rapid diagnosis of bacterial infection and identification of drug resistance. However, there are few tools available for streaming analysis of real-time sequencing data. Here, we present a framewor...
متن کاملAllele Intersection Analysis: A Novel Tool for Multi Locus Sequence Assignment in Multiply Infected Hosts
Wolbachia are wide-spread, endogenous α-Proteobacteria of arthropods and filarial nematodes. 15-75% of all insect species are infected with these endosymbionts that alter their host's reproduction to facilitate their spread. In recent years, many insect species infected with multiple Wolbachia strains have been identified. As the endosymbionts are not cultivable outside living cells, strain typ...
متن کاملMolecular Methods for Bacterial Strain Typing
ABSTRACT Typing of bacteria is an important part of epidemiological studies on nosocomial infections. Bacterial identification methods have dramatically improved in recent years, which is mainly due to advancements in the field of molecular biotechnology. In many cases, molecular techniques have replaced phenotypic typing methods. Currently, a wide r...
متن کاملTowards the definition of pathogenic microbe.
Identification and typing of spoilage and pathogenic microorganisms have become major objectives over the past decade in microbiology. In food, strain typing is necessary to ensure food safety and for linking cases of foodborne infections to suspected items. Recent advances in molecular biology have resulted in the development of numerous DNA-based methods for discrimination among bacterial str...
متن کاملPopulation Structure of the Bacterial Pathogen Xylella fastidiosa among Street Trees in Washington D.C.
Bacterial leaf scorch, associated with the bacterial pathogen Xylella fastidiosa, is a widely established and problematic disease of landscape ornamentals in Washington D.C. A multi-locus sequence typing analysis was performed using 10 housekeeping loci for X. fastidiosa strains in order to better understand the epidemiology of leaf scorch disease in this municipal environment. Samples were col...
متن کامل