Whole Genome Sequence Analysis of Brucella melitensis Phylogeny and Virulence Factors

Brucellosis has a wide range of clinical severity in humans that remains poorly understood. Whole genome sequencing (WGS) analysis may be able to detect variation in virulence genes. We used Brucella melitensis sequences in the NCBI Sequence Read Archive (SRA) database to assemble 248 whole genomes, and additionally, assembled 27 B. melitensis genomes from samples of human patients in Southern Israel. We searched the 275 assembled genomes for the 43 B. melitensis virulence genes in the Virulence Factors of Pathogenic Bacteria Database (VFDB) and 10 other published putative virulence genes. We explored pan-genome variation across the genomes and in a pilot analysis, explored single nucleotide polymorphism (SNP) variation among the ten putative virulence genes. More than 99% of the genomes had sequences for all Brucella melitensis virulence genes included in the VFDB. The 10 other virulence genes of interest were present across all the genomes, but three of these genes had SNP variation associated with particular Brucella melitensis genotypes. SNP variation was also seen within the Israeli genomes obtained from a small geographic region. While the Brucella genome is highly conserved, this novel and large whole genome study of Brucella demonstrates the ability of whole genome and pan-genome analysis to screen multiple genomes and identify SNP variation in both known and novel virulence genes that could be associated with differential disease virulence. Further development of whole genome techniques and linkage with clinical metadata on disease outcomes could shed light on whether such variation in the Brucella genome plays a role in pathogenesis.

Download Full-text

Virulence analysis of 81 of Pseudomonas aeruginosa genomes available in public sequence databases

10.21203/rs.2.10146/v1 ◽

2019 ◽

Author(s):

Marcin Brzozowski ◽

Joanna Barbara Jursa-Kulesza ◽

Danuta Kosik-Bogacka

Keyword(s):

Pseudomonas Aeruginosa ◽

Virulence Genes ◽

Opportunistic Infections ◽

Pearson Correlation ◽

Whole Genome Sequence ◽

Whole Genome ◽

Secretion Systems ◽

Wide Range ◽

Genes Encoding ◽

Sequence Databases

Abstract Background Pseudomonas aeruginosa is a pathogen capable of causing a wide range of severe opportunistic infections. Its genome contains numerous virulence genes encoding secretion systems of different types, structures responsible for adhesion and motility, toxins, proteases, siderophores, and others. The aim of this study is to analyse virulence, population structure, and distribution of highly divergent genes among 81 P. aeruginosa strains available in whole genome sequence databases. Results For this purpose, 260 virulence genes were searched in 81 different P. aeruginosa whole genomes that were available in databases. We identified most of the virulence genes as core and softcore genes. The most of the highly divergent sequences encoding pyoverdines, flagella and pilA were acknowledged as accessory, because of the differences in sequence among different alleles of those genes. Phylogenetic tree revealed the existence of three genetic groups of P. aeruginosa. Strains of the first clade were characterised as ExoS positive, whiles genomes of the second clade were ExoU positive. The member of third clade, PA7 strain was the only strain deprived of all T3SS genes. The analysis of pyoverdine locus facilitated finding a new pyoverdine type similar to pyoverdine type III. This newly described variant was present in 7 different strains. It contained a gene that was probably created by the fusion of pilD and pilI genes. In order to determine the coexistence of genes encoding exoenzymes, flagella and pyoverdines, Pearson correlation coefficients were calculated. There were significant correlations between genes encoding ExoS/ExoU-type strains and genes encoding type-A/type-B flagella. The correlation also occurred between Conclusion This study facilitates describing genetic differences of various P. aeruginosa strains based on Pseudomonas aeruginosa whole genome information from online databases. We conclude that most P. aeruginosa virulence genes are present in more than 95% of available genomes of the species. There are correlations of occurrence of different P. aeruginosa accessory virulence genes.

Download Full-text

Pseudomonas aeruginosa PA80 is a cystic fibrosis isolate deficient in RhlRI quorum sensing

Scientific Reports ◽

10.1038/s41598-021-85100-0 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Syed A. K. Shifat Ahmed ◽

Michelle Rudden ◽

Sabrina M. Elias ◽

Thomas J. Smyth ◽

Roger Marchant ◽

...

Keyword(s):

Cystic Fibrosis ◽

Pseudomonas Aeruginosa ◽

Quorum Sensing ◽

Virulence Factors ◽

Genomic Islands ◽

Clinical Strain ◽

Whole Genome ◽

Synonymous Mutations ◽

Wide Range

AbstractPseudomonas aeruginosa uses quorum sensing (QS) to modulate the expression of several virulence factors that enable it to establish severe infections. The QS system in P. aeruginosa is complex, intricate and is dominated by two main N-acyl-homoserine lactone circuits, LasRI and RhlRI. These two QS systems work in a hierarchical fashion with LasRI at the top, directly regulating RhlRI. Together these QS circuits regulate several virulence associated genes, metabolites, and enzymes in P. aeruginosa. Paradoxically, LasR mutants are frequently isolated from chronic P. aeruginosa infections, typically among cystic fibrosis (CF) patients. This suggests P. aeruginosa can undergo significant evolutionary pathoadaptation to persist in long term chronic infections. In contrast, mutations in the RhlRI system are less common. Here, we have isolated a clinical strain of P. aeruginosa from a CF patient that has deleted the transcriptional regulator RhlR entirely. Whole genome sequencing shows the rhlR locus is deleted in PA80 alongside a few non-synonymous mutations in virulence factors including protease lasA and rhamnolipid rhlA, rhlB, rhlC. Importantly we did not observe any mutations in the LasRI QS system. PA80 does not appear to have an accumulation of mutations typically associated with several hallmark pathoadaptive genes (i.e., mexT, mucA, algR, rpoN, exsS, ampR). Whole genome comparisons show that P. aeruginosa strain PA80 is closely related to the hypervirulent Liverpool epidemic strain (LES) LESB58. PA80 also contains several genomic islands (GI’s) encoding virulence and/or resistance determinants homologous to LESB58. To further understand the effect of these mutations in PA80 QS regulatory and virulence associated genes, we compared transcriptional expression of genes and phenotypic effects with isogenic mutants in the genetic reference strain PAO1. In PAO1, we show that deletion of rhlR has a much more significant impact on the expression of a wide range of virulence associated factors rather than deletion of lasR. In PA80, no QS regulatory genes were expressed, which we attribute to the inactivation of the RhlRI QS system by deletion of rhlR and mutation of rhlI. This study demonstrates that inactivation of the LasRI system does not impact RhlRI regulated virulence factors. PA80 has bypassed the common pathoadaptive mutations observed in LasR by targeting the RhlRI system. This suggests that RhlRI is a significant target for the long-term persistence of P. aeruginosa in chronic CF patients. This raises important questions in targeting QS systems for therapeutic interventions.

Download Full-text

Analysis of virulence factors and emm typing of Streptococcus pyogenes clinical isolates.

10.7287/peerj.preprints.27649v1 ◽

2019 ◽

Author(s):

Gustavo Enck Sambrano ◽

Gustavo P Riboldi ◽

Keli C Reiter ◽

Thiago Galvão da Silva Paim ◽

Neidmar Correa Tolfo ◽

...

Keyword(s):

Virulence Factors ◽

Streptococcus Pyogenes ◽

Virulence Genes ◽

Clinical Isolates ◽

Pcr Analysis ◽

Tissue Tropism ◽

Factors Analysis ◽

Wide Range ◽

Group A ◽

Micro Organisms

Background: Streptococcus pyogenes, a Group A streptococci (GAS), is an important human pathogen that causes a wide range of infections. Methods: Twenty five clinical isolates of S. pyogenes were submitted to an emm typing and to a Real-time PCR analysis for 23 important virulence factors. Results: Fourteen emm types were found and the emm1 type was the most prevalent. The majority of the isolates were classified as emm pattern E, followed by A-C3. No pattern D was found. Among the virulence factors, the most prevalent were SpeG, Slo, C5a-peptidase and SPNA. Phage encoded virulence genes were also found among the strains, such as mf-2, SpeJ and SpeL. Discussion: The emm1 type was the most prevalent while the 13 others M types were distributed along the strains. No tissue tropism was found on the isolates. The virulence factors analysis demonstrated that chromosomally and phage-encoded genes were found, which confers a potential for high virulent micro-organisms.

Download Full-text

Analysis of virulence factors and emm typing of Streptococcus pyogenes clinical isolates.

10.7287/peerj.preprints.27649 ◽

2019 ◽

Author(s):

Gustavo Enck Sambrano ◽

Gustavo P Riboldi ◽

Keli C Reiter ◽

Thiago Galvão da Silva Paim ◽

Neidmar Correa Tolfo ◽

...

Keyword(s):

Virulence Factors ◽

Streptococcus Pyogenes ◽

Virulence Genes ◽

Clinical Isolates ◽

Pcr Analysis ◽

Tissue Tropism ◽

Factors Analysis ◽

Wide Range ◽

Group A ◽

Micro Organisms

Download Full-text

Coagulase-Negative Staphylococci Pathogenomics

International Journal of Molecular Sciences ◽

10.3390/ijms20051215 ◽

2019 ◽

Vol 20 (5) ◽

pp. 1215 ◽

Cited By ~ 19

Author(s):

Xavier Argemi ◽

Yves Hansmann ◽

Kevin Prola ◽

Gilles Prévost

Keyword(s):

Staphylococcus Aureus ◽

Virulence Factors ◽

Molecular Basis ◽

Sequence Data ◽

Commensal Bacteria ◽

Whole Genome Sequence ◽

Whole Genome ◽

Genome Sequences ◽

Coagulase Negative Staphylococci ◽

Major Pathogens

Coagulase-negative Staphylococci (CoNS) are skin commensal bacteria. Besides their role in maintaining homeostasis, CoNS have emerged as major pathogens in nosocomial settings. Several studies have investigated the molecular basis for this emergence and identified multiple putative virulence factors with regards to Staphylococcus aureus pathogenicity. In the last decade, numerous CoNS whole-genome sequences have been released, leading to the identification of numerous putative virulence factors. Koch’s postulates and the molecular rendition of these postulates, established by Stanley Falkow in 1988, do not explain the microbial pathogenicity of CoNS. However, whole-genome sequence data has shed new light on CoNS pathogenicity. In this review, we analyzed the contribution of genomics in defining CoNS virulence, focusing on the most frequent and pathogenic CoNS species: S. epidermidis, S. haemolyticus, S. saprophyticus, S. capitis, and S. lugdunensis.

Download Full-text

Insights into Brevibacillus borstelensis AK1 through Whole Genome Sequencing: A Thermophilic Bacterium Isolated from a Hot Spring in Saudi Arabia

BioMed Research International ◽

10.1155/2018/5862437 ◽

2018 ◽

Vol 2018 ◽

pp. 1-9 ◽

Cited By ~ 4

Author(s):

Amjad B. Khalil ◽

Neelamegam Sivakumar ◽

Muhammad Arslan ◽

Hamna Saleem ◽

Sami Qarawi

Keyword(s):

Saudi Arabia ◽

Hot Spring ◽

Gc Content ◽

Morphological Characterization ◽

Thermophilic Bacterium ◽

Whole Genome Sequence ◽

Strictly Aerobic ◽

Whole Genome ◽

Aerobic Bacterium ◽

Wide Range

Brevibacillus borstelensis AK1 is a thermophile which grows between the temperatures of 45°C and 70°C. The present study is an extended genome report of B. borstelensis AK1 along with the morphological characterization. The strain is isolated from a hot spring in Saudi Arabia (southeast of the city Gazan). It is observed that the strain AK1 is rod-shaped, motile, and strictly aerobic bacterium. The whole genome sequence resulted in 29 contigs with a total length of 5,155,092 bp. In total, 3,946 protein-coding genes and 139 RNA genes were identified. Comparison with the previously submitted strains of B. borstelensis strains illustrates that strain AK1 has a small genome size but high GC content. The strain possesses putative genes for degradation of a wide range of substrates including polyethylene (plastic) and long-chain hydrocarbons. These genomic features may be useful for future environmental/biotechnological applications.

Download Full-text

Virulence Gene Pattern of Pasteurella multocida Isolates of Buffalo in Association to Capsule Biosynthesis Genes

Indian Journal of Animal Research ◽

10.18805/ijar.b-3977 ◽

2020 ◽

Author(s):

N. Sujatha ◽

K. Lakshmi Kavitha ◽

K.V. Subramanyam ◽

T. Srinivasa Rao ◽

R.N. Ramani Pushpa

Keyword(s):

Virulence Factors ◽

Pasteurella Multocida ◽

Virulence Genes ◽

Systemic Disease ◽

Virulence Gene ◽

Disease Status ◽

Host Cells ◽

Wide Range ◽

Serotype B ◽

Apparently Healthy

Background: Pasteurella multocida is the causative agent of many economically important diseases in a wide range of hosts. The mechanisms by which these bacteria can invade the mucosa, evade innate immunity and cause systemic disease are slowly being elucidated. Many key virulence factors are yet to be identified, including those required for initial attachment and invasion of host cells and for persistence in a relatively nutrient poor and hostile environment. This has led to intensive research to understand host adaptation mechanisms and virulence factors in order to develop effective vaccines. Methods: The present study was carried out to know the distribution of virulence genes viz., haemoglobin binding proteins (hgbA and hgbB), outer membrane protein (ompH), fimbrial antigen (ptfA), filamentous haemagglutinin (pfhA) and transferrin binding protein (tbpA) by PCR in P. multocida CapA isolates from apparently healthy or carrier animals and CapB isolates from field Haemorrhagic septicemia (HS) cases to monitor the epidemiological associations of virulence genes in Cap A and Cap B isolates.Result: The study revealed that all the six virulence associated genes were present in Cap B isolates. None of the Cap A isolates harboured tbpA and pfhA genes. These two genes were closely related to serotype B causing Haemorrhagic septicemia and were epidemiologically associated with disease status.

Download Full-text

Whole-Genome Sequence of Leptospira interrogans Serovar Hardjo Subtype Hardjoprajitno Strain Norma, Isolated from Cattle in a Leptospirosis Outbreak in Brazil

Genome Announcements ◽

10.1128/genomea.01302-15 ◽

2015 ◽

Vol 3 (6) ◽

Cited By ~ 4

Author(s):

M. R. V. Cosate ◽

S. C. Soares ◽

T. A. Mendes ◽

R. T. Raittz ◽

E. C. Moreira ◽

...

Keyword(s):

Genome Sequence ◽

Pathogenic Bacteria ◽

Global Distribution ◽

Whole Genome Sequence ◽

Leptospira Interrogans ◽

Whole Genome

Leptospirosis is caused by pathogenic bacteria of the genus Leptospira spp. This neglected re-emergent disease has global distribution and relevance in veterinary production. Here, we report the whole-genome sequence and annotation of Leptospira interrogans serovar Hardjo subtype Hardjoprajitno strain Norma, isolated from cattle in a livestock leptospirosis outbreak in Brazil.

Download Full-text

Determination and Structural Analysis of the Whole-Genome Sequence of Fusarium equiseti D25-1

10.21203/rs.2.24663/v1 ◽

2020 ◽

Author(s):

Xueping LI ◽

Jianhong Li ◽

Yonghong Qi ◽

Yonggang Liu ◽

Minquan Li

Keyword(s):

Molecular Mechanisms ◽

Gc Content ◽

Whole Genome Sequence ◽

Effective Control ◽

Sequence Length ◽

Comparative Genomic ◽

Whole Genome ◽

Illumina Hiseq ◽

Fusarium Equiseti ◽

Wide Range

Abstract BackgroundFusarium equiseti is a plant pathogen with a wide range of hosts and diverse effects, including probiotic activity. However, the underlying molecular mechanisms remain unclear, hindering its effective control and utilization. In this study, the Illumina HiSeq 4000 and PacBio platforms were used to sequence and assemble the whole genome of Fusarium equiseti D25-1.ResultsThe assembly included 16 fragments with a GC content of 48.01%, gap number of zero, and size of 40,776,005 bp. There were 40,110 exons and 26,281 introns having a total size of 19,787,286 bp and 2,290,434 bp, respectively. The genome had an average copy number of 333, 71, 69, 31, and 108 for tRNAs, rRNAs, sRNAs, snRNAs, and miRNAs, respectively. The total repetitive sequence length was 1,713,918 bp, accounting for 4.2033% of the genome. In total, 13,134 functional genes were annotated, accounting for 94.97% of the total gene number. Toxin-related genes, including two related to zearalenone and 23 related to trichothecene, were identified. A comparative genomic analysis supported the high quality of the F. equiseti assembly, exhibiting good collinearity with the reference strains, 3,483 species-specific genes, and 1,805 core genes. A gene family analysis revealed more than 2,500 single-copy orthologs. F. equiseti was most closely related to Fusarium pseudograminearum based on a phylogenetic analysis at the whole-genome level.ConclusionsOur comprehensive analysis of the whole genome of F. equiseti provides basic data for studies of gene expression, regulatory and functional mechanisms, evolutionary processes, as well as disease prevention and control.

Download Full-text

Distribution of Sigma factors delineates segregation of virulent and avirulent Mycobacterium

10.1101/235986 ◽

2017 ◽

Author(s):

Aayatti Mallick Gupta ◽

Sukhendu Mandal

Keyword(s):

Virulence Factors ◽

Dominant Role ◽

Phylogenetic Analyses ◽

Sigma Factors ◽

Whole Genome Sequence ◽

Wide Range ◽

Aliphatic Index ◽

Slow Growing ◽

Major Pathogens ◽

Potential Tool

AbstractSigma factors, in combination with RNA polymerase and several transcription factors play specific role in expression of housekeeping as well as various stress responsive genes in mycobacterial species. The genus Mycobacterium includes a wide range of species under major pathogens, opportunists and non-pathogens. The number and combination of sigma factors is extremely diversified among Mycobacterium. We have performed comparative genome analysis among 40 different species of Mycobacterium whose whole genome sequence is available, in order to identify the distribution of sigma factors. The study illustrate that SigC, SigD, SigG, SigH, SigK and SigI are dominant among the true pathogens. Moreover, 16S rDNA based phylogenetic analyses distinctly differentiate the slow growing Mycobacterium from the fast growers, and clusters the true pathogens from the opportunists and non-pathogens. While evaluating the similarity coefficient upon the allotment of sigma factors of different Mycobacterium species through UPGMA dendrogram analysis, it is apparent that the true pathogens are grouped separately following the similar trend observed from evolutionary approach. Sigma factors playing dominant role in pathogenicity are found stable in nature with high aliphatic index thereby remain flexible at a wide range of temperature. The comparative distribution of six well known virulence factors of Mycobacterium - PhoP, PcaA, FbpA, Mce1B, KatG and PE_PGRS and various sigma factors justify the allotment pattern of mycobacterial sigma factors among pathogenic species. The pathogenicity responsible sigma factors elicit close resemblance with few notable characters of the known virulence factors. Thus the analysis renders that the distribution of sigma factors of different species of Mycobacterium can be a potential tool to predict the pathogenicity index of this genus.

Download Full-text