scholarly journals Genome-Wide Analysis of Ruminant Staphylococcus aureus Reveals Diversification of the Core Genome

2008 ◽  
Vol 190 (19) ◽  
pp. 6302-6317 ◽  
Author(s):  
Nouri L. Ben Zakour ◽  
Daniel E. Sturdevant ◽  
Sergine Even ◽  
Caitriona M. Guinane ◽  
Corinne Barbey ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Core Genome ◽  
Allelic Variation ◽  
Genomic Variation ◽  
Economic Losses ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Extensive Variation ◽  
Genes Encoding ◽  
Genome Content

ABSTRACT Staphylococcus aureus causes disease in humans and a wide array of animals. Of note, S. aureus mastitis of ruminants, including cows, sheep, and goats, results in major economic losses worldwide. Extensive variation in genome content exists among S. aureus pathogenic clones. However, the genomic variation among S. aureus strains infecting different animal species has not been well examined. To investigate variation in the genome content of human and ruminant S. aureus, we carried out whole-genome PCR scanning (WGPS), comparative genomic hybridizations (CGH), and the directed DNA sequence analysis of strains of human, bovine, ovine, and caprine origin. Extensive variation in genome content was discovered, including host- and ruminant-specific genetic loci. Ovine and caprine strains were genetically allied, whereas bovine strains were heterogeneous in gene content. As expected, mobile genetic elements such as pathogenicity islands and bacteriophages contributed to the variation in genome content between strains. However, differences specific for ruminant strains were restricted to regions of the conserved core genome, which contained allelic variation in genes encoding proteins of known and unknown function. Many of these proteins are predicted to be exported and could play a role in host-pathogen interactions. The genomic regions of difference identified by the whole-genome approaches adopted in the current study represent excellent targets for studies of the molecular basis of S. aureus host adaptation.

scholarly journals Clostridium manihotivorum sp. nov., a novel mesophilic anaerobic bacterium that produces cassava pulp-degrading enzymes

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10343
Author(s):  
Pattsarun Cheawchanlertfa ◽  
Sawannee Sutheeworapong ◽  
Piroon Jenjaroenpun ◽  
Thidathip Wongsurawat ◽  
Intawat Nookaew ◽  
...  
Keyword(s):  
Related Species ◽  
Anaerobic Bacterium ◽  
Comparative Genomic ◽  
Whole Genome ◽  
Circular Chromosome ◽  
Closely Related Species ◽  
Degrading Enzymes ◽  
Cassava Pulp ◽  
Pectinolytic Enzymes ◽  
Genes Encoding

Background Cassava pulp is a promising starch-based biomasses, which consists of residual starch granules entrapped in plant cell wall containing non-starch polysaccharides, cellulose and hemicellulose. Strain CT4T, a novel mesophilic anaerobic bacterium isolated from soil collected from a cassava pulp landfill, has a strong ability to degrade polysaccharides in cassava pulp. This study explored a rarely described species within the genus Clostridium that possessed a group of cassava pulp-degrading enzymes. Methods A novel mesophilic anaerobic bacterium, the strain CT4T, was identified based on phylogenetic, genomic, phenotypic and chemotaxonomic analysis. The complete genome of the strain CT4T was obtained following whole-genome sequencing, assembly and annotation using both Illumina and Oxford Nanopore Technology (ONT) platforms. Results Analysis based on the 16S rRNA gene sequence indicated that strain CT4T is a species of genus Clostridium. Analysis of the whole-genome average amino acid identity (AAI) of strain CT4T and the other 665 closely related species of the genus Clostridium revealed a separated strain CT4T from the others. The results revealed that the genome consisted of a 6.3 Mb circular chromosome with 5,664 protein-coding sequences. Genome analysis result of strain CT4T revealed that it contained a set of genes encoding amylolytic-, hemicellulolytic-, cellulolytic- and pectinolytic enzymes. A comparative genomic analysis of strain CT4T with closely related species with available genomic information, C. amylolyticum SW408T, showed that strain CT4T contained more genes encoding cassava pulp-degrading enzymes, which comprised a complex mixture of amylolytic-, hemicellulolytic-, cellulolytic- and pectinolytic enzymes. This work presents the potential for saccharification of strain CT4T in the utilization of cassava pulp. Based on phylogenetic, genomic, phenotypic and chemotaxonomic data, we propose a novel species for which the name Clostridium manihotivorum sp. nov. is suggested, with the type strain CT4T (= TBRC 11758T = NBRC 114534T).

scholarly journals Genomic Diversity ofLactobacillus salivarius

2010 ◽  
Vol 77 (3) ◽  
pp. 954-965 ◽  
Author(s):  
Emma J. Raftis ◽  
Elisa Salvetti ◽  
Sandra Torriani ◽  
Giovanna E. Felis ◽  
Paul W. O'Toole
Keyword(s):  
Hot Spots ◽  
Gene Clusters ◽  
Genomic Variation ◽  
Genomic Diversity ◽  
Comparative Genomic ◽  
Phenotypic Traits ◽  
Lactobacillus Salivarius ◽  
Genome Content ◽  
High Level ◽  
Selection Of

ABSTRACTStrains ofLactobacillus salivariusare increasingly employed as probiotic agents for humans or animals. Despite the diversity of environmental sources from which they have been isolated, the genomic diversity ofL. salivariushas been poorly characterized, and the implications of this diversity for strain selection have not been examined. To tackle this, we applied comparative genomic hybridization (CGH) and multilocus sequence typing (MLST) to 33 strains derived from humans, animals, or food. The CGH, based on total genome content, including small plasmids, identified 18 major regions of genomic variation, or hot spots for variation. Three major divisions were thus identified, with only a subset of the human isolates constituting an ecologically discernible group. Omission of the small plasmids from the CGH or analysis by MLST provided broadly concordant fine divisions and separated human-derived and animal-derived strains more clearly. The two gene clusters for exopolysaccharide (EPS) biosynthesis corresponded to regions of significant genomic diversity. The CGH-based groupings of these regions did not correlate with levels of production of bound or released EPS. Furthermore, EPS production was significantly modulated by available carbohydrate. In addition to proving difficult to predict from the gene content, EPS production levels correlated inversely with production of biofilms, a trait considered desirable in probiotic commensals.L. salivariusdisplays a high level of genomic diversity, and while selection ofL. salivariusstrains for probiotic use can be informed by CGH or MLST, it also requires pragmatic experimental validation of desired phenotypic traits.

scholarly journals Genomic Analysis of Curtobacterium Flaccumfaciens Reveals the Differences Between Pathogenic and Nonpathogenic Strains

2021 ◽  
Author(s):  
Qingde Li ◽  
Lianjun Sun
Keyword(s):  
Core Genome ◽  
Genomic Analysis ◽  
Pectate Lyase ◽  
Economic Losses ◽  
Positive Bacterium ◽  
Citrate Cycle ◽  
The Core ◽  
Genomic Level ◽  
Genes Encoding ◽  
Genome Phylogeny

Abstract Purpose Curtobacterium flaccumfaciens is a Gram-positive bacterium which has been isolated from different plants and abiotic environment. Curtobacterium. flaccumfaciens pv. flaccumfaciens (Cff) is a pathogenic bacterium that infects legume, which is causing great economic losses. At the genomic level, the metabolic and phylogenetic characteristics, and differences in pathogenicity between pathogenic and nonpathogenic C. flaccumfaciens strains have not been analyzed in detail. Methods Therefore, in order to discuss the differences in genome, phylogeny, gene function and mobile genetic elements between pathogenic and nonpathogenic strains, pangenomics and comparative genomics were used in this study to analyze 12 C. flaccumfaciens strains. Result The pangenome of C. flaccumfaciens is open. Phylogenetic analysis showed that there was no correlation between the phylogeny and pathogenicity of C. flaccumfaciens. KAAS annotation of the core genome shows that the citrate cycle was incomplete. In addition, gene islands analysis of the three pathogenicity-related genes encoding for pectate lyase, serine protease and cellulases showed that they only existed in the Cffs and LMG3645 strains. LMG3645 might be a pathogenic strain. Conclusion This study clearly and reliably revealed the differences between the pathogenic and nonpathogenic strains of C. flaccumfaciens at the genomic level, and paves the way for further research on its pathogenicity.

scholarly journals Comparative Genomics of Staphylococcus aureus Musculoskeletal Isolates

2005 ◽  
Vol 187 (2) ◽  
pp. 576-592 ◽  
Author(s):  
James E. Cassat ◽  
Paul M. Dunman ◽  
Fionnuala McAleese ◽  
Ellen Murphy ◽  
Steven J. Projan ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Animal Models ◽  
The Other ◽  
Clinical Isolates ◽  
Comparative Genomic ◽  
Musculoskeletal Infection ◽  
Resource Center ◽  
Distinct Cluster ◽  
Genome Content ◽  
Lines Of Evidence

ABSTRACT Much of the research aimed at defining the pathogenesis of Staphylococcus aureus has been done with a limited number of strains, most notably the 8325-4 derivative RN6390. Several lines of evidence indicate that this strain is unique by comparison to clinical isolates of S. aureus. Based on this, we have focused our efforts on two clinical isolates (UAMS-1 and UAMS-601), both of which are hypervirulent in our animal models of musculoskeletal infection. In this study, we used comparative genomic hybridization to assess the genome content of these two isolates relative to RN6390 and each of seven sequenced S. aureus isolates. Our comparisons were done by using an amplicon-based microarray from the Pathogen Functional Genomics Resource Center and an Affymetrix GeneChip that collectively represent the genomes of all seven sequenced strains. Our results confirmed that UAMS-1 and UAMS-601 share specific attributes that distinguish them from RN6390. Potentially important differences included the presence of cna and the absence of isaB, sarT, sarU, and sasG in the UAMS isolates. Among the sequenced strains, the UAMS isolates were most closely related to the dominant European clone EMRSA-16. In contrast, RN6390, NCTC 8325, and COL formed a distinct cluster that, by comparison to the other four sequenced strains (Mu50, N315, MW2, and SANGER-476), was the most distantly related to the UAMS isolates and EMRSA-16.

scholarly journals Whole-genome sequence analyses of Glaesserella parasuis isolates reveals extensive genomic variation and diverse antibiotic resistance determinants

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9293
Author(s):  
Xiulin Wan ◽  
Xinhui Li ◽  
Todd Osmundson ◽  
Chunling Li ◽  
He Yan
Keyword(s):  
Antibiotic Resistance ◽  
Genetic Variation ◽  
Genome Sequence ◽  
Resistance Genes ◽  
Genomic Variation ◽  
Whole Genome Sequence ◽  
Comparative Genomic ◽  
Broad Host Range ◽  
Whole Genome ◽  
Resistance Determinants

Background Glaesserella parasuis (G. parasuis) is a respiratory pathogen of swine and the etiological agent of Glässer’s disease. The structural organization of genetic information, antibiotic resistance genes, potential pathogenicity, and evolutionary relationships among global G. parasuis strains remain unclear. The aim of this study was to better understand patterns of genetic variation, antibiotic resistance factors, and virulence mechanisms of this pathogen. Methods The whole-genome sequence of a ST328 isolate from diseased swine in China was determined using Pacbio RS II and Illumina MiSeq platforms and compared with 54 isolates from China sequenced in this study and 39 strains from China and eigtht other countries sequenced by previously. Patterns of genetic variation, antibiotic resistance, and virulence mechanisms were investigated in relation to the phylogeny of the isolates. Electrotransformation experiments were performed to confirm the ability of pYL1—a plasmid observed in ST328—to confer antibiotic resistance. Results The ST328 genome contained a novel Tn6678 transposon harbouring a unique resistance determinant. It also contained a small broad-host-range plasmid pYL1 carrying aac(6’)-Ie-aph(2”)-Ia and blaROB-1; when transferred to Staphylococcus aureus RN4220 by electroporation, this plasmid was highly stable under kanamycin selection. Most (85.13–91.74%) of the genetic variation between G. parasuis isolates was observed in the accessory genomes. Phylogenetic analysis revealed two major subgroups distinguished by country of origin, serotype, and multilocus sequence type (MLST). Novel virulence factors (gigP, malQ, and gmhA) and drug resistance genes (norA, bacA, ksgA, and bcr) in G. parasuis were identified. Resistance determinants (sul2, aph(3”)-Ib, norA, bacA, ksgA, and bcr) were widespread across isolates, regardless of serovar, isolation source, or geographical location. Conclusions Our comparative genomic analysis of worldwide G. parasuis isolates provides valuable insight into the emergence and transmission of G. parasuis in the swine industry. The result suggests the importance of transposon-related and/or plasmid-related gene variations in the evolution of G. parasuis.

scholarly journals Genomic Analysis of Staphylococcus aureus Isolates Associated With Peracute Non-gangrenous or Gangrenous Mastitis and Comparison With Other Mastitis-Associated Staphylococcus aureus Isolates

2021 ◽  
Vol 12 ◽  
Author(s):  
Silja Åvall-Jääskeläinen ◽  
Joanna Koort ◽  
Heli Simojoki ◽  
Suvi Taponen
Keyword(s):  
Staphylococcus Aureus ◽  
Clinical Outcome ◽  
Virulence Factors ◽  
Virulence Genes ◽  
Allelic Variation ◽  
Bovine Mastitis ◽  
Genomic Analysis ◽  
Virulence Gene ◽  
Clinical Mastitis ◽  
Comparative Genomic

Staphylococcus aureus is a highly prevalent cause of mastitis in dairy herds worldwide, capable of causing outcomes that vary from subclinical to peracute gangrenous mastitis. We performed a comparative genomic analysis between 14 isolates of S. aureus, originating from peracute bovine mastitis with very severe signs (9 gangrenous, 5 non-gangrenous) and six isolates originating from subclinical or clinical mastitis with mild to moderate signs, to find differences that could be associated with the clinical outcome of mastitis. Of the 296 virulence factors studied, 219 were detected in all isolates. No difference in the presence of virulence genes was detected between the peracute and control groups. None of the virulence factors were significantly associated with only a single study group. Most of the variation in virulence gene profiles existed between the clonal complexes. Our isolates belonged to five clonal complexes (CC97, CC133, CC151, CC479, and CC522), of which CC522 has previously been detected only in isolates originating from caprine and ovine mastitis, but not from bovine mastitis. For statistical analysis, we sorted the CCs into two groups. The group of CCs including CC133, CC479, and CC522 was associated with gangrenous mastitis, in contrast to the group of CCs including CC97 and CC151. The presence of virulence genes does not explain the clinical outcome of mastitis, but may be affected by allelic variation, and especially different regulation and thus expression in the virulence genes.

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