Genome-Wide Survey of Genes Under Positive Selection in Avian Pathogenic Escherichia coli Strains

Detecting Genetic Variation of Colonizing Streptococcus agalactiae Genomes in Humans: A Precision Protocol

Deciphering the genotypic diversity of within-individual pathogens and verifying the evolutionary model can help elucidate resistant genotypes, virulent subpopulations, and the mechanism of opportunistic pathogenicity. However, observed polymorphic mutations (PMs) are rare and difficult to be detected in the “dominant-lineage” model of bacterial infection due to the low frequency. The four pooled group B Streptococcus (GBS) samples were collected from the genital tracts of healthy pregnant women, and the pooled samples and the isogenic controls were genomically sequenced. Using the PMcalling program, we detected the PMs in samples and compared the results between two technical duplicates, GBS-M001T and GBS-M001C. Tested with simulated datasets, the PMcalling program showed high sensitivity especially in low-frequency PMs and reasonable specificity. The genomic sequence data from pooled samples of GBS colonizing carrier pregnant women were analyzed, and few high-frequency PMs and some low-frequency PMs were discovered, indicating a dominant-lineage evolution model. The PMs mainly were nonsynonymous and enriched in quorum sensing, glycolysis/gluconeogenesis, ATP-binding cassette (ABC) transporters, etc., suggesting antimicrobial or environmental selective pressure. The re-analysis of the published Burkholderia dolosa data showed a diverse-community model, and only a few low-frequency PMs were shared between different individuals. Genes of general control non-repressible 5-related N-acetyltransferases family, major facilitator superfamily (MFS) transporter, and ABC transporter were positive selection candidates. Our findings indicate an unreported nature of the dominant-lineage model of GBS colonization in healthy women, and a formerly not observed mutation pool in a colonized microbial community, possibly maintained by selection pressure.

A genome-wide scan of wastewater E. coli for genes under positive selection: focusing on mechanisms of antibiotic resistance

Antibiotic resistance is a global health threat and consequently, there is a need to understand the mechanisms driving its emergence. Here, we hypothesize that genes and mutations under positive selection may contribute to antibiotic resistance. We explored wastewater E. coli, whose genomes are highly diverse. We subjected 92 genomes to a statistical analysis for positively selected genes. We obtained 75 genes under positive selection and explored their potential for antibiotic resistance. We found that eight genes have functions relating to antibiotic resistance, such as biofilm formation, membrane permeability, and bacterial persistence. Finally, we correlated the presence/absence of non-synonymous mutations in positively selected sites of the genes with a function in resistance against 20 most prescribed antibiotics. We identified mutations associated with antibiotic resistance in two genes: the porin ompC and the bacterial persistence gene hipA. These mutations are located at the surface of the proteins and may hence have a direct effect on structure and function. For hipA, we hypothesize that the mutations influence its interaction with hipB and that they enhance the capacity for dormancy as a strategy to evade antibiotics. Overall, genomic data and positive selection analyses uncover novel insights into mechanisms driving antibiotic resistance.

Prolonged culture in aerobic environments alters Escherichia coli H2 production capacity

Growing interest in renewable energy continues to motivate new work on microbial biohydrogen production and in particular utilizing Escherichia coli a well-studied, facultative anaerobe. Here we characterize, for the first time the H2 production rate and capacity, of E coli isolates from the 50 000th generation of the Long-Term Evolution Experiment. Under these reaction conditions, peak production rates near or above 5 mL per hour for 100 mL of lysogeny broth (LB media) was established for the ancestral strains and batch efficiencies between 0.15 and 0.22 mL H2 produced per 1 mL LB media were achieved. All 11 isolates studied, which had been aerobically cultured in minimal media since 1988, exhibited a decreased H2 production rate or capacity with many strains unable to grow under anaerobic conditions at all. The genomes of these strains have been sequenced and a preliminary analysis of the correlations between genotype and phenotype shows that mutations in gene ydjO are exclusively observed in the two isolates which produce H2, potentially suggesting a role for this gene in the maintenance of wild type metabolic pathways in the context of diverse mutational backgrounds. These results provide hints towards uncovering new genetic targets for the pursuit of bacterial strains with increased capacity for H2 production as well as a case study in speciation and the control of phenotypic switching.

Genome-wide analyses reveal genes subject to positive selection in Toxoplasma gondii

Toxoplasma gondii is an important protozoan pathogen that infects many wild and domestic animals and causes infections in immunocompromised humans. However, there has been little investigation of the molecular evolutionary trajectories of this pathogenic protozoa using comparative genomics data. Here, we employed a comparative evolutionary genomics approach to identify genes that are under site- and lineage-specific positive selection in nine strains of T. gondii, including two closely related species, Neospora caninum and Hammondia hammondi. Based on the analyses of five coccidian core genomes, 4.5% of the 5788 core genome genes showed strong signals for positive selection in the site model. In addition, the branch-site model analyses in the nine T. gondii core genomes indicated that 2 to 20 genes underwent significant positive selection along each lineage leading to T. gondii strains. Many of the protein products encoded by the positively selected genes are secretory or surface proteins that have previously been implicated in host pathogenesis. The adaptive changes in these positively selected genes might be related to dynamic interactions between the host immune systems and might play a crucial role in the infection and pathogenic processes of T. gondii.

Genomic analysis of Leptospira interrogans serovar Paidjan and Dadas isolates from carrier dogs and comparative genomic analysis to detect genes under positive selection

BACKGROUND

Leptospirosis is an emerging infectious disease worldwide that can cause high morbidity and mortality rates in humans and animals. The causative spirochetes have reservoirs in mammalian hosts, but there has been limited analysis of the genomes of isolates recovered from animals. The aims of this study were to characterize genomic features of two Leptospira interrogans strains recently isolated from asymptomatic dogs in Thailand (strains CUDO5 and CDUO8), and to perform comparative genome analyses with other strains. Molecular adaptive evolution in L. interrogans as signaled by positive selection also was analyzed.

RESULTS

Whole genome sequence analysis revealed that strains CUDO5 and CUDO8 had genome sizes of approximately 4.9 Mbp with 35.1% GC contents. Using monoclonal antibodies, strains CUDO5 and CUDO8 were identified as serovars Paidjan and Dadas, respectively. These strains harbored genes known to be associated with acute and chronic infections. Using Single Nucleotide Polymorphisms phylogeny (SNPs) with 97 L. interrogans strains, CUDO5 and CUDO8 had closest genetic relatedness with each other. Nevertheless, the serovar determinant region (rfb locus) showed variations in the genes encoding sugar biosynthesis. Amongst 13 representative L. interrogans strains examined for molecular adaptive evolution through positive selection under the site-model of Phylogenetic Analysis of Maximum Likelihood, genes responsible for iron acquisition (tlyA and hbpA), motility (fliN2, flgK, and flhB) and thermal adaptation (lpxD1) were under increased selective pressure.

CONCLUSIONS

L. interrogans serovar Paidjan strain CUDO5 and serovar Dadas strain CUDO8 had close genetic relatedness as analyzed by SNPs phylogeny. They contained genes with established roles in acute and chronic leptospirosis. The rfb locus in both serovars showed gene variation associated with sugar biosynthesis. Positive selection analysis indicated that genes encoding factors involved in motility, temperature adaptation, and iron acquisition were under strong positive selection in L. interrogans. These may be associated with adaptation in the early stages of infection.

Role of hypothetical protein YicS in the pathogenicity of Avian Pathogenic Escherichia coli in vivo and in vitro

Avian Pathogenic Escherichia coli (APEC) strains belong to the extra-intestinal pathogenic group of E. coli (ExPEC) that causes colibacillosis in poultry. A variety of putative virulence factors of APEC are recognized as potent causes of pathogenicity, the mechanisms underlying their pathogenicity are still not fully understood. The role of yicS in the virulence of pathogenic E. coli is still unclear. Thus, yicS may be related to biofilm formation, which in some bacteria plays a role in pathogenicity. Therefore, the fact that this gene appears to be under positive selection pressure suggests that yicS may be associated with the pathogenicity of APEC. To better understand the role of yicS protein in APEC biological characteristics and pathogenicity, we deleted yicS in an APEC Swollen Head Syndrome strain (APEC strain SCI-07) and studied its effects by comparing wild type and isogenic mutants through comprehensive in vitro and in vivo assays. We demonstrated that yicS plays a role in pathogenicity of APEC. We suggest that the yicS gene, which encodes an exporter protein, has a significant role in biofilm formation, motility, invasion of CEC-32 and Hep-2 cells and APEC pathogenicity in a day-old chick model.