VRprofile: gene-cluster-detection-based profiling of virulence and antibiotic resistance traits encoded within genome sequences of pathogenic bacteria

Pathogenomics of Virulence Traits of Plesiomonas shigelloides That Were Deemed Inconclusive by Traditional Experimental Approaches

One of the major challenges of modern medicine includes the failure of conventional protocols to characterize the pathogenicity of emerging pathogens. This is particularly apparent in the case of Plesiomonas shigelloides. Although a number of infections have been linked to this microorganism, experimental evidence of its virulence factors (VFs), obtained by traditional approaches, is somewhat inconclusive. Hence, it remains unclear whether P. shigelloides is a true or opportunistic one. In the current study, four publicly available whole-genome sequences of P. shigelloides (GN7, NCTC10360, 302-73, and LS1) were profiled using bioinformatics platforms to determine the putative candidate VFs to characterize the bacterial pathogenicity. Overall, 134 unique open reading frames (ORFs) were identified that were homologous or orthologous to virulence genes identified in other pathogens. Of these, 52.24% (70/134) were jointly shared by the strains. The numbers of strain-specific virulence traits were 4 in LS1; 7 in NCTC10360; 10 in 302-73; and 15 in GN7. The pathogenicity islands (PAIs) common to all the strains accounted for 24.07% ORFs. The numbers of PAIs exclusive to each strain were 8 in 302-73; 11 in NCTC10360; 14 in GN7; and 18 in LS1. A PAI encoding Vibrio cholerae ToxR-activated gene d protein was specific to 302-73, GN7, and NCTC10360 strains. Out of 33 antibiotic multi-resistance genes identified, 16 (48.48%) genes were intrinsic to all strains. Further, 17 (22.08%) of 77 antibiotic resistance islands were found in all the strains. Out of 23 identified distinct insertion sequences, 13 were only harbored by strain LS1. The number of intact prophages identified in the strains was 1 in GN7; 2 in 302-73; and 2 in NCTC10360. Further, 1 CRISPR element was identified in LS1; 2 in NCTC10360; and 8 in 302-73. Fifteen (78.95%) of 19 secretion systems and secretion effector variants were identified in all the strains. In conclusion, certain P. shigelloides strains might possess VFs associated with gastroenteritis and extraintestinal infections. However, the role of host factors in the onset of infections should not be undermined.

The Core- and Pan-Genomic Analyses of the Genus Comamonas: From Environmental Adaptation to Potential Virulence

Comamonas is often reported to be one of the major members of microbial communities in various natural and engineered environments. Versatile catabolic capabilities of Comamonas have been studied extensively in the last decade. In contrast, little is known about the ecological roles and adaptation of Comamonas to different environments as well as the virulence of potentially pathogenic Comamonas strains. In this study, we provide genomic insights into the potential ecological roles and virulence of Comamonas by analysing the entire gene set (pangenome) and the genes present in all genomes (core genome) using 34 genomes of 11 different Comamonas species. The analyses revealed that the metabolic pathways enabling Comamonas to acquire energy from various nutrient sources are well conserved. Genes for denitrification and ammonification are abundant in Comamonas, suggesting that Comamonas plays an important role in the nitrogen biogeochemical cycle. They also encode sophisticated redox sensory systems and diverse c-di-GMP controlling systems, allowing them to be able to effectively adjust their biofilm lifestyle to changing environments. The virulence factors in Comamonas were found to be highly species-specific. The conserved strategies used by potentially pathogenic Comamonas for surface adherence, motility control, nutrient acquisition and stress tolerance were also revealed.

Comparative Analysis of Genomic Island Prediction Tools

Tools for genomic island prediction use strategies for genomic comparison analysis and sequence composition analysis. The goal of comparative analysis is to identify unique regions in the genomes of related organisms, whereas sequence composition analysis evaluates and relates the composition of specific regions with other regions in the genome. The goal of this study was to qualitatively and quantitatively evaluate extant genomic island predictors. We chose tools reported to produce significant results using sequence composition prediction, comparative genomics, and hybrid genomics methods. To maintain diversity, the tools were applied to eight complete genomes of organisms with distinct characteristics and belonging to different families. Escherichia coli CFT073 was used as a control and considered as the gold standard because its islands were previously curated in vitro. The results of predictions with the gold standard were manually curated, and the content and characteristics of each predicted island were analyzed. For other organisms, we created GenBank (GBK) files using Artemis software for each predicted island. We copied only the amino acid sequences from the coding sequence and constructed a multi-FASTA file for each predictor. We used BLASTp to compare all results and generate hits to evaluate similarities and differences among the predictions. Comparison of the results with the gold standard revealed that GIPSy produced the best results, covering ~91% of the composition and regions of the islands, followed by Alien Hunter (81%), IslandViewer (47.8%), Predict Bias (31%), GI Hunter (17%), and Zisland Explorer (16%). The tools with the best results in the analyzes of the set of organisms were the same ones that presented better performance in the tests with the gold standard.

Dissemination of Genetic Acquisition/Loss Provides a Variety of Quorum Sensing Regulatory Properties in Pseudoalteromonas

A bstract: Quorum sensing (QS) enables single-celled bacteria to communicate with chemical signals in order to synchronize group-level bacterial behavior. Pseudoalteromonas are marine bacteria found in versatile environments, of which QS regulation for their habitat adaptation is extremely fragmentary. To distinguish genes required for QS regulation in Pseudoalteromonas, comparative genomics was deployed to define the pan-genomics for twelve isolates and previously-sequenced genomes, of which acyl-homoserine lactone (AHL)-based QS traits were characterized. Additionally, transposon mutagenesis was used to identify the essential QS regulatory genes in the selected Pseudoalteromonas isolate. A remarkable feature showed that AHL-based colorization intensity of biosensors induced by Pseudoalteromonas most likely correlates with QS regulators genetic heterogeneity within the genus. This is supported by the relative expression levels of two of the main QS regulatory genes (luxO and rpoN) analyzed in representative Pseudoalteromonas isolates. Notably, comprehensive QS regulatory schema and the working model proposed in Pseudoalteromonas seem to phylogenetically include the network architectures derived from Escherichia coli, Pseudomonas, and Vibrio. Several associated genes were mapped by transposon mutagenesis. Among them, a right origin-binding protein-encoding gene (robp) was functionally identified as a positive QS regulatory gene. This gene lies on a genomic instable region and exists in the aforementioned bioinformatically recruited QS regulatory schema. The obtained data emphasize that the distinctly- and hierarchically-organized mechanisms probably target QS association in Pseudoalteromonas dynamic genomes, thus leading to bacterial ability to accommodate their adaption fitness and survival advantages.

Impacts of horizontal gene transfer on the compact genome of the clavulanic acid-producing Streptomyces strain F613-1

Mobile genetic elements involved in mediating horizontal transfer events contribute to bacterial evolution, and bacterial genomic plasticity and instability result in variation in functional genetic information in Streptomyces secondary metabolism. In a previous study, we reported the complete genome sequence of the industrial Streptomyces strain F613-1, which produces high yields of clavulanic acid. In this study, we used comparative genomics and bioinformatics to investigate the unique genomic features of this strain. Taken together, comparative genomics were used to systematically investigate secondary metabolism capabilities and indicated that frequent exchange of genetic materials between Streptomyces replicons may shape the remarkable diversities in their secondary metabolite repertoires. Moreover, a 136.9-kb giant region of plasticity (RGP) was found in the F613-1 chromosome, and the chromosome and plasmid pSCL4 are densely packed with an exceptionally large variety of potential secondary metabolic gene clusters, involving several determinants putatively accounting for antibiotic production. In addition, the differences in the architecture and size of plasmid pSCL4 between F613-1 and ATCC 27064 suggest that the pSCL4 plasmid could evolve from pSCL4-like and pSCL2-like extrachromosomal replicons. Furthermore, the genomic analyses revealed that strain F613-1 has developed specific genomic architectures and genetic patterns that are well suited to meet the requirements of industrial innovation processes.

Indexed variation graphs for efficient and accurate resistome profiling

Motivation

Antimicrobial resistance (AMR) remains a major threat to global health. Profiling the collective AMR genes within a metagenome (the 'resistome') facilitates greater understanding of AMR gene diversity and dynamics. In turn, this can allow for gene surveillance, individualized treatment of bacterial infections and more sustainable use of antimicrobials. However, resistome profiling can be complicated by high similarity between reference genes, as well as the sheer volume of sequencing data and the complexity of analysis workflows. We have developed an efficient and accurate method for resistome profiling that addresses these complications and improves upon currently available tools.

Results

Our method combines a variation graph representation of gene sets with a locality-sensitive hashing Forest indexing scheme to allow for fast classification of metagenomic sequence reads using similarity-search queries. Subsequent hierarchical local alignment of classified reads against graph traversals enables accurate reconstruction of full-length gene sequences using a scoring scheme. We provide our implementation, graphing Resistance Out Of meTagenomes (GROOT), and show it to be both faster and more accurate than a current reference-dependent tool for resistome profiling. GROOT runs on a laptop and can process a typical 2 gigabyte metagenome in 2 min using a single CPU. Our method is not restricted to resistome profiling and has the potential to improve current metagenomic workflows.

Availability and implementation

GROOT is written in Go and is available at https://github.com/will-rowe/groot (MIT license).

Supplementary information

Supplementary data are available at Bioinformatics online.

Whole-Genome-Sequencing characterization of bloodstream infection-causing hypervirulent Klebsiella pneumoniae of capsular serotype K2 and ST374

Hypervirulent K. pneumoniae variants (hvKP) have been increasingly reported worldwide, causing metastasis of severe infections such as liver abscesses and bacteremia. The capsular serotype K2 hvKP strains show diverse multi-locus sequence types (MLSTs), but with limited genetics and virulence information. In this study, we report a hypermucoviscous K. pneumoniae strain, RJF293, isolated from a human bloodstream sample in a Chinese hospital. It caused a metastatic infection and fatal septic shock in a critical patient. The microbiological features and genetic background were investigated with multiple approaches. The Strain RJF293 was determined to be multilocis sequence type (ST) 374 and serotype K2, displayed a median lethal dose (LD50) of 1.5 × 10² CFU in BALB/c mice and was as virulent as the ST23 K1 serotype hvKP strain NTUH-K2044 in a mouse lethality assay. Whole genome sequencing revealed that the RJF293 genome codes for 32 putative virulence factors and exhibits a unique presence/absence pattern in comparison to the other 105 completely sequenced K. pneumoniae genomes. Whole genome SNP-based phylogenetic analysis revealed that strain RJF293 formed a single clade, distant from those containing either ST66 or ST86 hvKP. Compared to the other sequenced hvKP chromosomes, RJF293 contains several strain-variable regions, including one prophage, one ICEKp1 family integrative and conjugative element and six large genomic islands. The sequencing of the first complete genome of an ST374 K2 hvKP clinical strain should reinforce our understanding of the epidemiology and virulence mechanisms of this bloodstream infection-causing hvKP with clinical significance.

Alterations of Salmonella enterica Serovar Typhimurium Antibiotic Resistance under Environmental Pressure

Microbial horizontal gene transfer is a continuous process that shapes bacterial genomic adaptation to the environment and the composition of concurrent microbial ecology. This includes the potential impact of synthetic antibiotic utilization in farm animal production on overall antibiotic resistance issues; however, the mechanisms behind the evolution of microbial communities are not fully understood. We explored potential mechanisms by experimentally examining the relatedness of phylogenetic inference between multidrug-resistant Salmonella enterica serovar Typhimurium isolates and pathogenic Salmonella Typhimurium strains based on genome-wide single-nucleotide polymorphism (SNP) comparisons. Antibiotic-resistant S Typhimurium isolates in a simulated farm environment barely lost their resistance, whereas sensitive S Typhimurium isolates in soils gradually acquired higher tetracycline resistance under antibiotic pressure and manipulated differential expression of antibiotic-resistant genes. The expeditious development of antibiotic resistance and the ensuing genetic alterations in antimicrobial resistance genes in S Typhimurium warrant effective actions to control the dissemination of Salmonella antibiotic resistance.IMPORTANCE Antibiotic resistance is attributed to the misuse or overuse of antibiotics in agriculture, and antibiotic resistance genes can also be transferred to bacteria under environmental stress. In this study, we report a unidirectional alteration in antibiotic resistance from susceptibility to increased resistance. Highly sensitive Salmonella enterica serovar Typhimurium isolates from organic farm systems quickly acquired tetracycline resistance under antibiotic pressure in simulated farm soil environments within 2 weeks, with expression of antibiotic resistance-related genes that was significantly upregulated. Conversely, originally resistant S Typhimurium isolates from conventional farm systems lost little of their resistance when transferred to environments without antibiotic pressure. Additionally, multidrug-resistant S Typhimurium isolates genetically shared relevancy with pathogenic S Typhimurium isolates, whereas susceptible isolates clustered with nonpathogenic strains. These results provide detailed discussion and explanation about the genetic alterations and simultaneous acquisition of antibiotic resistance in S Typhimurium in agricultural environments.

Comparative genomic analysis of a naturally competent Elizabethkingia anophelis isolated from an eye infection

Elizabethkingia anophelis has now emerged as an opportunistic human pathogen. However, its mechanisms of transmission remain unexplained. Comparative genomic (CG) analysis of E. anopheles endophthalmitis strain surprisingly found from an eye infection patient with twenty-five other E. anophelis genomes revealed its potential to participate in horizontal gene transfer. CG analysis revealed that the study isolate has an open pan genome and has undergone extensive gene rearrangements. We demonstrate that the strain is naturally competent, hitherto not reported in any members of Elizabethkingia. Presence of competence related genes, mobile genetic elements, Type IV, VI secretory systems and a unique virulence factor arylsulfatase suggests a different lineage of the strain. Deciphering the genome of E. anophelis having a reservoir of antibiotic resistance genes and virulence factors associated with diverse human infections may open up avenues to deal with the myriad of its human infections and devise strategies to combat the pathogen.

Predominant gut Lactobacillus murinus strain mediates anti-inflammaging effects in calorie-restricted mice

BACKGROUND

Calorie restriction (CR), which has a potent anti-inflammaging effect, has been demonstrated to induce dramatic changes in the gut microbiota. Whether the modulated gut microbiota contributes to the attenuation of inflammation during CR is unknown, as are the members of the microbial community that may be key mediators of this process.

RESULTS

Here, we report that a unique Lactobacillus-predominated microbial community was rapidly attained in mice within 2 weeks of CR, which decreased the levels of circulating microbial antigens and systemic inflammatory markers such as tumour necrosis factor alpha (TNF-α). Lactobacillus murinus CR147, an isolate in the most abundant operational taxonomic unit (OTU) enriched by CR, downregulated interleukin-8 production in TNF-α-stimulated Caco-2 cells and significantly increased the lifespan and the brood size of the nematode Caenorhabditis elegans. In gnotobiotic mice colonized with the gut microbiota from old mice, this strain decreased their intestinal permeability and serum endotoxin load, consequently attenuating the inflammation induced by the old microbiota.

CONCLUSIONS

Our study demonstrated that a strain of Lactobacillus murinus was promoted in CR mice and causatively contributed to the attenuation of ageing-associated inflammation.

Comparative Genomics Reveals Specific Genetic Architectures in Nicotine Metabolism of Pseudomonas sp. JY-Q

Microbial degradation of nicotine is an important process to control nicotine residues in the aqueous environment. In this study, a high active nicotine degradation strain named Pseudomonas sp. JY-Q was isolated from tobacco waste extract (TWE). This strain could completely degrade 5.0 g l⁻¹ nicotine in 24 h under optimal culture conditions, and it showed some tolerance even at higher concentrations (10.0 g l⁻¹) of nicotine. The complete genome of JY-Q was sequenced to understand the mechanism by which JY-Q could degrade nicotine and tolerate such high nicotine concentrations. Comparative genomic analysis indicated that JY-Q degrades nicotine through putative novel mechanisms. Two candidate gene cluster duplications located separately at distant loci were predicted to be responsible for nicotine degradation. These two nicotine (Nic) degradation-related loci (AA098_21325—AA098_21340, AA098_03885—AA098_03900) exhibit nearly completely consistent gene organization and component synteny. The nicotinic acid (NA) degradation gene cluster (AA098_17770–AA098_17790) and Nic-like clusters were both predicted to be flanked by mobile genetic elements (MGE). Furthermore, we analyzed the regions of genomic plasticity (RGP) in the JY-Q strain and found a dynamic genome carrying a type VI secretion system (T6SS) that promotes nicotine metabolism and tolerance based on transcriptomics and used in silico methods to identify the T6SS effector protein. Thus, a novel nicotine degradation mechanism was elucidated for Pseudomonas sp. JY-Q, suggesting its potential application in the bioremediation of nicotine-contaminated environments, such as TWEs.

Preliminary comparative genomics revealed pathogenic potential and international spread of Staphylococcus argenteus

Background

Staphylococcus argenteus and S. schweitzeri, were recently proposed as novel species within S. aureus complex (SAC). S. argenteus has been reported in many countries and can threaten human health. S. schweitzeri has not been associated with human infections, but has been isolated from non-human primates. Questions regarding the evolution of pathogenicity of these two species will remain elusive until an exploratory evolutionary framework is established.

Results

We present genomic comparison analysis among members of SAC based on a pan-genome definition, which included 15 S. argenteus genomes (five newly sequenced), six S. schweitzeri genomes and 30 divergent S. aureus genomes. The three species had divergent core genomes and rare interspecific recombination was observed among the core genes. However, some subtypes of staphylococcal cassette chromosome mec (SCCmec) elements and prophages were present in different species. Of 111 tested virulence genes of S. aureus, 85 and 86 homologous genes were found in S. argenteus and S. schweitzeri, respectively. There was no difference in virulence gene content among the three species, but the sequence of most core virulence genes was divergent. Analysis of the agr locus and the genes in the capsular polysaccharides biosynthetic operon revealed that they both diverged before the speciation of SAC members. Furthermore, the widespread geographic distribution of S. argenteus, sequence type 2250, showed ambiguous biogeographical structure among geographically isolated populations, demonstrating an international spread of this pathogen.

Conclusions

S. argenteus has spread among several countries, and invasive infections and persistent carriage may be not limited to currently reported regions. S. argenteus probably had undergone a recent host adaption and can cause human infections with a similar pathogenic potential.

Electronic supplementary material

The online version of this article (10.1186/s12864-017-4149-9) contains supplementary material, which is available to authorized users.

Identification and Characterization of an Antibacterial Type VI Secretion System in the Carbapenem-Resistant Strain Klebsiella pneumoniae HS11286

The type VI secretion system (T6SS) is a class of sophisticated cell contact-dependent apparatus with anti-eukaryotic or anti-bacterial function. Klebsiella pneumoniae is one of the most common bacterial pathogens with resistance to the carbapenem antibiotics. However, little is known about the antibacterial T6SS in K. pneumoniae. Using core-component protein searches, we identified a putative T6SS gene cluster on the chromosome of the carbapenemase-producing K. pneumoniae (CRKP) strain HS11286. Intraspecies and interspecies competition assays revealed an antibacterial function of the HS11286 T6SS. The phospholipase Tle1^KP was found to be an effector protein that is transferred by T6SS. The overexpression of this effector gene in the periplasm caused severe growth inhibition of Escherichia coli. A sub-inhibitory concentration of β-lactam antibiotics stimulated the expression and secretion of the HS11286 T6SS and enhanced T6SS-dependent killing. It suggested that the antibiotics might be an impact factor for the T6SS secretion and antibacterial activity.

Comparative Genomics of Methanopyrus sp. SNP6 and KOL6 Revealing Genomic Regions of Plasticity Implicated in Extremely Thermophilic Profiles

Methanopyrus spp. are usually isolated from harsh niches, such as high osmotic pressure and extreme temperature. However, the molecular mechanisms for their environmental adaption are poorly understood. Archaeal species is commonly considered as primitive organism. The evolutional placement of archaea is a fundamental and intriguing scientific question. We sequenced the genomes of Methanopyrus strains SNP6 and KOL6 isolated from the Atlantic and Iceland, respectively. Comparative genomic analysis revealed genetic diversity and instability implicated in niche adaption, including a number of transporter- and integrase/transposase-related genes. Pan-genome analysis also defined the gene pool of Methanopyrus spp., in addition of ~120-Kb genomic region of plasticity impacting cognate genomic architecture. We believe that Methanopyrus genomics could facilitate efficient investigation/recognition of archaeal phylogenetic diverse patterns, as well as improve understanding of biological roles and significance of these versatile microbes.