Author Correction: Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis

Prophage-encoded immune evasion factors are critical for Staphylococcus aureus host infection, switching, and adaptation

Staphylococcus aureus is a multi-host pathogen that causes infections in animals and humans globally. The specific genetic loci-and the extent to which they drive cross-species switching, transmissibility, and adaptation-are not well understood. Here, we conducted a population genomic study of 437 S. aureus isolates to identify bacterial genetic variation that determines infection of human and animal hosts through a genome-wide association study (GWAS) using linear mixed models. We found genetic variants tagging φSa3 prophage-encoded immune evasion genes associated with human hosts, which contributed ~99.9% of the overall heritability (~88%), highlighting their key role in S. aureus human infection. Furthermore, GWAS of pairs of phylogenetically matched human and animal isolates confirmed and uncovered additional loci not implicated in GWAS of unmatched isolates. Our findings reveal the loci that are critical for S. aureus host transmissibility, infection, switching, and adaptation and how their spread alters the specificity of host-adapted clones.

Tracking resistomes, virulence genes, and bacterial pathogens in long-term manure-amended greenhouse soils

Organic manure has been implicated as an important source of antibiotic resistance genes (ARGs) in agricultural soils. However, the profiles of biocide resistance genes (BRGs), metal resistance genes (MRGs) and virulence genes (VGs) and their bacterial hosts in manure-amended soils remain largely unknown. Herein, a systematic metagenome-based survey was conducted to comprehensively explore the changes in resistomes, VGs and their bacterial hosts, mobile genetic elements (MGEs), and pathogenic bacteria in manure-amended greenhouse soils. Many manure-borne ARGs, BRGs, MRGs, VGs, and bacterial pathogens could be transferred into soils by applying manures, and their abundance and diversity were markedly positively correlated with greenhouse planting years (manure amendment years). The main ARGs transferred from manures to soils conferred resistance to tetracycline, aminoglycoside, and macrolide-lincosamide-streptogramin. Both statistical analysis and gene arrangements showed a good positive co-occurrence pattern of ARGs/BRGs/MRGs/VGs and MGEs. Furthermore, bacterial hosts of resistomes and VGs were significantly changed in the greenhouse soils in comparison with the field soils. Our findings confirmed the migration and dissemination of resistomes, VGs, and bacterial pathogens, and their accumulation and persistence were correlated with the continuous application of manures.

Excessive Parallelism in Protein Evolution of Lake Baikal Amphipod Species Flock

Repeated emergence of similar adaptations is often explained by parallel evolution of underlying genes. However, evidence of parallel evolution at amino acid level is limited. When the analyzed species are highly divergent, this can be due to epistatic interactions underlying the dynamic nature of the amino acid preferences: The same amino acid substitution may have different phenotypic effects on different genetic backgrounds. Distantly related species also often inhabit radically different environments, which makes the emergence of parallel adaptations less likely. Here, we hypothesize that parallel molecular adaptations are more prevalent between closely related species. We analyze the rate of parallel evolution in genome-size sets of orthologous genes in three groups of species with widely ranging levels of divergence: 46 species of the relatively recent lake Baikal amphipod radiation, a species flock of very closely related cichlids, and a set of significantly more divergent vertebrates. Strikingly, in genes of amphipods, the rate of parallel substitutions at nonsynonymous sites exceeded that at synonymous sites, suggesting rampant selection driving parallel adaptation. At sites of parallel substitutions, the intraspecies polymorphism is low, suggesting that parallelism has been driven by positive selection and is therefore adaptive. By contrast, in cichlids, the rate of nonsynonymous parallel evolution was similar to that at synonymous sites, whereas in vertebrates, this rate was lower than that at synonymous sites, indicating that in these groups of species, parallel substitutions are mainly fixed by drift.

Whole-genome sequencing and Mycobacterium tuberculosis: Challenges in sample preparation and sequencing data analysis

The numbers of patients with tuberculosis (TB) caused by resistant strains are still alarming. Therefore, it is necessary to determine resistance more quickly and precisely, than it is with the currently used phenotypic and genotypic methods. In recent years, technological advances have been made and the whole-genome sequencing (WGS) method has been introduced as a part of routine diagnostics in clinical laboratories. Comparing a wide range of mycobacterial genomic variations with a reference genome leads to a consistent evaluation of molecular-epidemiology and resistance of Mycobacterium tuberculosis (M. tuberculosis) to a wide range of anti-TB drugs. The quality of the obtained sequencing data is closely related to the type of sample and the method used for DNA extraction and sequencing library preparation. Moreover, the correct interpretation of results is also influenced by a bioinformatic data processing. A large number of bioinformatics pipelines are currently available, the sensitivity of which varies due to the different sizes of databases containing relevant mutations. This review focuses on the individual steps included in the sequencing workflow and factors that may affect the interpretation of final results.