scholarly journals Genome-wide comparison of four MRSA clinical isolates from Germany and Hungary

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10185
Author(s):  
Romen Singh Naorem ◽  
Jochen Blom ◽  
Csaba Fekete
Keyword(s):  
Genome Analysis ◽  
Genetic Background ◽  
Multiple Drug Resistance ◽  
Clinical Isolates ◽  
Ecological Niches ◽  
Comparative Genome Analysis ◽  
Pathogenic Potential ◽  
Comparative Genome ◽  
Pan Genome ◽  
Niche Adaptation

Staphylococcus aureus is a drug-resistant pathogen, capable of colonizing diverse ecological niches and causing a broad spectrum of infections related to a community and healthcare. In this study, we choose four methicillin-resistant S. aureus (MRSA) clinical isolates from Germany and Hungary based on our previous polyphasic characterization finding. We assumed that the selected strains have a different genetic background in terms of the presence of resistance and virulence genes, prophages, plasmids, and secondary metabolite biosynthesis genes that may play a crucial role in niche adaptation and pathogenesis. To clarify these assumptions, we performed a comparative genome analysis of these strains and observed many differences in their genomic compositions. The Hungarian isolates (SA H27 and SA H32) with ST22-SCCmec type IVa have fewer genes for multiple-drug resistance, virulence, and prophages reported in Germany isolates. Germany isolate, SA G6 acquires aminoglycoside (ant(6)-Ia and aph(3’)-III) and nucleoside (sat-4) resistance genes via phage transduction and may determine its pathogenic potential. The comparative genome study allowed the segregation of isolates of geographical origin and differentiation of the clinical isolates from the commensal isolates. This study suggested that Germany and Hungarian isolates are genetically diverse and showing variation among them due to the gain or loss of mobile genetic elements (MGEs). An interesting finding is the addition of SA G6 genome responsible for the drastic decline of the core/pan-genome ratio curve and causing the pan-genome to open wider. Functional characterizations revealed that S. aureus isolates survival are maintained by the amino acids catabolism and favor adaptation to growing in a protein-rich medium. The dispersible and singleton genes content of S. aureus genomes allows us to understand the genetic variation among the CC5 and CC22 groups. The strains with the same genetic background were clustered together, which suggests that these strains are highly alike; however, comparative genome analysis exposed that the acquisition of phage elements, and plasmids through the events of MGEs transfer contribute to differences in their phenotypic characters. This comparative genome analysis would improve the knowledge about the pathogenic S. aureus strain’s characterization, and responsible for clinically important phenotypic differences among the S. aureus strains.

scholarly journals Comparative genomics of Klebsiella michiganensis BD177 and related members of Klebsiella sp. reveal the symbiotic relationship with Bactrocera dorsalis

BMC Genetics ◽  
2020 ◽  
Vol 21 (S2) ◽  
Author(s):  
Zhaohui Cai ◽  
Qiongyu Guo ◽  
Zhichao Yao ◽  
Wenping Zheng ◽  
Junfei Xie ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Complete Genome ◽  
Type Strain ◽  
Bactrocera Dorsalis ◽  
Symbiotic Relationship ◽  
Comparative Genome Analysis ◽  
Circular Chromosome ◽  
Comparative Genome ◽  
Ecological Fitness ◽  
Pan Genome

Abstract Background Bactrocera dorsalis is a destructive polyphagous and highly invasive insect pest of tropical and subtropical species of fruit and vegetable crops. The sterile insect technique (SIT) has been used for decades to control insect pests of agricultural, veterinary, and human health importance. Irradiation of pupae in SIT can reduce the ecological fitness of the sterile insects. Our previous study has shown that a gut bacterial strain BD177 that could restore ecological fitness by promoting host food intake and metabolic activities. Results Using long-read sequence technologies, we assembled the complete genome of K. michiganensis BD177 strain. The complete genome of K. michiganensis BD177 comprises one circular chromosome and four plasmids with a GC content of 55.03%. The pan-genome analysis was performed on 119 genomes (strain BD177 genome and 118 out of 128 published Klebsiella sp. genomes since ten were discarded). The pan-genome includes a total of 49305 gene clusters, a small number of 858 core genes, and a high number of accessory (10566) genes. Pan-genome and average nucleotide identity (ANI) analysis showed that BD177 is more similar to the type strain K. michiganensis DSM2544, while away from the type strain K. oxytoca ATCC13182. Comparative genome analysis with 21 K. oxytoca and 12 K. michiganensis strains, identified 213 unique genes, several of them related to amino acid metabolism, metabolism of cofactors and vitamins, and xenobiotics biodegradation and metabolism in BD177 genome. Conclusions Phylogenomics analysis reclassified strain BD177 as a member of the species K. michiganensis. Comparative genome analysis suggested that K. michiganensis BD177 has the strain-specific ability to provide three essential amino acids (phenylalanine, tryptophan and methionine) and two vitamins B (folate and riboflavin) to B. dorsalis. The clear classification status of BD177 strain and identification of unique genetic characteristics may contribute to expanding our understanding of the symbiotic relationship of gut microbiota and B. dorsalis.

scholarly journals Comparative genome analysis of Salmonella enterica serovar Gallinarum biovars Pullorum and Gallinarum decodes strain specific genes

2020 ◽  
Author(s):  
Rajesh Kumar Vaid ◽  
Zoozeal Thakur ◽  
Taruna Anand ◽  
Sanjay Kumar ◽  
Bhupendra Nath Tripathi
Keyword(s):  
Genome Analysis ◽  
Salmonella Enterica ◽  
Genomic Islands ◽  
Economic Losses ◽  
Genotypic Differences ◽  
Comparative Genome Analysis ◽  
Comparative Genome ◽  
Genomic Features ◽  
Niche Adaptation ◽  
Antimicrobial Resistance Genes

Abstract Salmonella enterica serovar Gallinarum biovar Pullorum (bvP) and biovar Gallinarum (bvG) are the etiological agents of pullorum disease (PD) and fowl typhoid (FT) respectively, which cause huge economic losses to poultry industry especially in developing countries including India. Vaccination and biosecurity measures are currently being employed to control and reduce the S. Gallinarum infections. High endemicity, poor implementation of hygiene and lack of effective vaccines pose challenges in prevention and control of disease in intensively maintained poultry flocks. Comparative genome analysis unravels similarities and dissimilarities thus facilitating identification of genomic features that aids in pathogenesis, niche adaptation and in tracing of evolutionary history. The present investigation was carried out to assess the genotypic differences amongst S. enterica serovar Gallinarum strains including Indian strain S. Gallinarum Sal40 VTCCBAA614 with a focus on identification of candidate virulence factors. The comparative genome analysis revealed an open pan-genome consisting of 5091 coding sequence (CDS) with 3270 CDS belonging to core-genome, 1254 CDS to dispensable genome and strain specific genes i.e. singletons ranging from 3 to 102 amongst the analyzed strains. Moreover, the investigated strains exhibited diversity in genomic features such as genomic islands, prophage regions, toxin-antitoxin cassettes, and acquired antimicrobial resistance genes. The identified genetic differences among the S. enterica serovar Gallinarum strains could be used for bacterial typing, design of rapid and reliable diagnostics, structure based inhibitor development and vaccine design for effective infection control as well as eradication and will also form basis for future experimental investigations.

Comparative genome analysis of Ureaplasma parvum clinical isolates

2007 ◽  
Vol 158 (4) ◽  
pp. 371-378 ◽  
Author(s):  
Kuvat Momynaliev ◽  
Andrew Klubin ◽  
Vera Chelysheva ◽  
Oksana Selezneva ◽  
Tatyana Akopian ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Clinical Isolates ◽  
Comparative Genome Analysis ◽  
Comparative Genome ◽  
Ureaplasma Parvum

scholarly journals Diversity of Pseudomonas Genomes, Including Populus-Associated Isolates, as Revealed by Comparative Genome Analysis

2015 ◽  
Vol 82 (1) ◽  
pp. 375-383 ◽  
Author(s):  
Se-Ran Jun ◽  
Trudy M. Wassenaar ◽  
Intawat Nookaew ◽  
Loren Hauser ◽  
Visanu Wanchai ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Populus Deltoides ◽  
Profile Analysis ◽  
Amino Acid Identity ◽  
Ecological Niches ◽  
Comparative Genome Analysis ◽  
Comparative Genome ◽  
Content Type ◽  
Eastern Cottonwood ◽  
Genomic Clusters

ABSTRACTThePseudomonasgenus contains a metabolically versatile group of organisms that are known to occupy numerous ecological niches, including the rhizosphere and endosphere of many plants. Their diversity influences the phylogenetic diversity and heterogeneity of these communities. On the basis of average amino acid identity, comparative genome analysis of >1,000Pseudomonasgenomes, including 21Pseudomonasstrains isolated from the roots of nativePopulus deltoides(eastern cottonwood) trees resulted in consistent and robust genomic clusters with phylogenetic homogeneity. AllPseudomonas aeruginosagenomes clustered together, and these were clearly distinct from otherPseudomonasspecies groups on the basis of pangenome and core genome analyses. In contrast, the genomes ofPseudomonas fluorescenswere organized into 20 distinct genomic clusters, representing enormous diversity and heterogeneity. Most of our 21Populus-associated isolates formed three distinct subgroups within the majorP. fluorescensgroup, supported by pathway profile analysis, while two isolates were more closely related toPseudomonas chlororaphisandPseudomonas putida. Genes specific toPopulus-associated subgroups were identified. Genes specific to subgroup 1 include several sensory systems that act in two-component signal transduction, a TonB-dependent receptor, and a phosphorelay sensor. Genes specific to subgroup 2 contain hypothetical genes, and genes specific to subgroup 3 were annotated with hydrolase activity. This study justifies the need to sequence multiple isolates, especially fromP. fluorescens, which displays the most genetic variation, in order to study functional capabilities from a pangenomic perspective. This information will prove useful when choosingPseudomonasstrains for use to promote growth and increase disease resistance in plants.

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