scholarly journals Comparative genome analysis of a multidrug-resistant Pseudomonas aeruginosa sequence type 277 clone that harbours two copies of the blaSPM-1 gene and multiple single nucleotide polymorphisms in other resistance-associated genes

2019 ◽  
Author(s):  
Ana Paula Barbosa do Nascimento ◽  
Fernando Medeiros Filho ◽  
Hério Sousa ◽  
Hermes Senger ◽  
Rodolpho Mattos Albano ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Antimicrobial Resistance ◽  
Single Nucleotide Polymorphisms ◽  
Multidrug Resistant ◽  
Sequence Type ◽  
Genomic Islands ◽  
Genome Comparison ◽  
Nucleotide Polymorphisms ◽  
Emerging Pathogens ◽  
Single Nucleotide

AbstractPseudomonas aeruginosa is one of the most common pathogens related to healthcare-associated infections. The Brazilian isolate, named CCBH4851, is a multidrug-resistant clone belonging to the sequence type 277. The antimicrobial resistance mechanisms of the CCBH4851 strain are associated with the presence of blaSPM-1 gene, encoding a metallo-beta-lactamase, in addition to other exogenously acquired genes. Whole-genome sequencing studies focusing on emerging pathogens are essential to identify physiological key aspects that may lead to the exposure of new targets for therapy. This study was designed to characterize the genome of Pseudomonas aeruginosa CCBH4851 through the detection of genomic features and genome comparison with other Pseudomonas aeruginosa strains. The CCBH4851 closed genome showed features that were consistent with data reported for the specie. However, comparative genomics revealed the absence of genes important for pathogenesis. On the other hand, CCBH4851 genome contained acquired genomic islands that carry additional virulence and antimicrobial resistance-related genes. The presence of single nucleotide polymorphisms in the core genome, mainly those located in resistance-associated genes, suggests that these mutations could influence the multidrug-resistant behavior of CCBH4851. Overall, the characterization of Pseudomonas aeruginosa CCBH4851 complete genome revealed several features that could directly impact the profile of virulence and antibiotic resistance of this pathogen in infectious outbreaks.

scholarly journals Multidrug-Resistant Sequence Type 235 Pseudomonas aeruginosa Clinical Isolates Producing IMP-26 with Increased Carbapenem-Hydrolyzing Activities in Vietnam

2016 ◽  
Vol 60 (11) ◽  
pp. 6853-6858 ◽  
Author(s):  
Tatsuya Tada ◽  
Pham Hong Nhung ◽  
Tohru Miyoshi-Akiyama ◽  
Kayo Shimada ◽  
Mitsuhiro Tsuchiya ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Multidrug Resistant ◽  
Sequence Type ◽  
Clinical Isolates ◽  
Medical Setting ◽  
Single Nucleotide ◽  
Content Type ◽  
E Coli ◽  
Whole Genomes ◽  
Encoding Genes

ABSTRACTForty clinical isolates of multidrug-resistantPseudomonas aeruginosawere obtained in a medical setting in Hanoi, Vietnam. Whole genomes of all 40 isolates were sequenced by MiSeq (Illumina), and phylogenic trees were constructed from the single nucleotide polymorphism concatemers. Of these 40 isolates, 24 (60.0%) harbored metallo-β-lactamase-encoding genes, includingblaIMP-15,blaIMP-26,blaIMP-51, and/orblaNDM-1. Of these 24 isolates, 12 harboredblaIMP-26and belonged to sequence type 235 (ST235).Escherichia coliexpressingblaIMP-26was significantly more resistant to doripenem and meropenem thanE. coliexpressingblaIMP-1andblaIMP-15. IMP-26 showed higher catalytic activity against doripenem and meropenem than IMP-1 and against all carbapenems tested, including doripenem, imipenem, meropenem, and panipenem, than did IMP-15. These data suggest that clinical isolates of multidrug-resistant ST235P. aeruginosaproducing IMP-26 with increased carbapenem-hydrolyzing activities are spreading in medical settings in Vietnam.

scholarly journals Genomic analyses of multidrug resistant Pseudomonas aeruginosa PA1 resequenced by single-molecule real-time sequencing

2016 ◽  
Vol 36 (6) ◽  
Author(s):  
Gang Li ◽  
Mengyu Shen ◽  
Shuai Le ◽  
Yinling Tan ◽  
Ming Li ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Real Time ◽  
Single Molecule ◽  
De Novo ◽  
Phylogenetic Analyses ◽  
Multidrug Resistant ◽  
Genomic Islands ◽  
Read Length ◽  
Genome Comparison ◽  
Genomic Analyses

As a third-generation sequencing (TGS) method, single-molecule real-time (SMRT) technology provides long read length, and it is well suited for resequencing projects and de novo assembly. In the present study, Pseudomonas aeruginosa PA1 was characterized and resequenced using SMRT technology. PA1 was also subjected to genomic, comparative and pan-genomic analyses. The multidrug resistant strain PA1 possesses a 6,498,072 bp genome and a sequence type of ST-782. The genome of PA1 was also visualized, and the results revealed the details of general genome annotations, virulence factors, regulatory proteins (RPs), secretion system proteins, type II toxin–antitoxin (T–A) pairs and genomic islands. Whole genome comparison analysis suggested that PA1 exhibits similarity to other P. aeruginosa strains but differs in terms of horizontal gene transfer (HGT) regions, such as prophages and genomic islands. Phylogenetic analyses based on 16S rRNA sequences demonstrated that PA1 is closely related to PAO1, and P. aeruginosa strains can be divided into two main groups. The pan-genome of P. aeruginosa consists of a core genome of approximately 4,000 genes and an accessory genome of at least 6,600 genes. The present study presented a detailed, visualized and comparative analysis of the PA1 genome, to enhance our understanding of this notorious pathogen.

scholarly journals Whole-Genome Comparison of Mycobacterium tuberculosis Clinical and Laboratory Strains

2002 ◽  
Vol 184 (19) ◽  
pp. 5479-5490 ◽  
Author(s):  
R. D. Fleischmann ◽  
D. Alland ◽  
J. A. Eisen ◽  
L. Carpenter ◽  
O. White ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Single Nucleotide Polymorphisms ◽  
Gene Family ◽  
Genome Comparison ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Disease Pathogenesis ◽  
Single Nucleotide ◽  
Polymorphic Loci ◽  
Whole Genome Comparison

ABSTRACT Virulence and immunity are poorly understood in Mycobacterium tuberculosis. We sequenced the complete genome of the M. tuberculosis clinical strain CDC1551 and performed a whole-genome comparison with the laboratory strain H37Rv in order to identify polymorphic sequences with potential relevance to disease pathogenesis, immunity, and evolution. We found large-sequence and single-nucleotide polymorphisms in numerous genes. Polymorphic loci included a phospholipase C, a membrane lipoprotein, members of an adenylate cyclase gene family, and members of the PE/PPE gene family, some of which have been implicated in virulence or the host immune response. Several gene families, including the PE/PPE gene family, also had significantly higher synonymous and nonsynonymous substitution frequencies compared to the genome as a whole. We tested a large sample of M. tuberculosis clinical isolates for a subset of the large-sequence and single-nucleotide polymorphisms and found widespread genetic variability at many of these loci. We performed phylogenetic and epidemiological analysis to investigate the evolutionary relationships among isolates and the origins of specific polymorphic loci. A number of these polymorphisms appear to have occurred multiple times as independent events, suggesting that these changes may be under selective pressure. Together, these results demonstrate that polymorphisms among M. tuberculosis strains are more extensive than initially anticipated, and genetic variation may have an important role in disease pathogenesis and immunity.

scholarly journals Single nucleotide polymorphisms may explain the contrasting phenotypes of two variants of a multidrug-resistant Mycobacterium tuberculosis strain

Tuberculosis ◽  
2017 ◽  
Vol 103 ◽  
pp. 28-36 ◽  
Author(s):  
María Mercedes Bigi ◽  
Beatriz Lopez ◽  
Federico Carlos Blanco ◽  
María del Carmen Sasiain ◽  
Silvia De la Barrera ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Single Nucleotide Polymorphisms ◽  
Multidrug Resistant ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Tuberculosis Strain ◽  
Mycobacterium Tuberculosis Strain

scholarly journals Genomic Characteristics of Colistin-Resistant Salmonella enterica subsp. enterica Serovar Infantis from Poultry Farms in the Republic of Serbia

Antibiotics ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 886
Author(s):  
Branko Jovčić ◽  
Katarina Novović ◽  
Brankica Filipić ◽  
Maja Velhner ◽  
Dalibor Todorović ◽  
...  
Keyword(s):  
Susceptibility Testing ◽  
Multidrug Resistant ◽  
Sequence Type ◽  
Nucleotide Polymorphisms ◽  
Salmonella Spp ◽  
Single Nucleotide ◽  
Poultry Farms ◽  
The Republic ◽  
First Time ◽  
Sequence Types

The antimicrobial susceptibility testing was conducted on 174 single isolates from poultry farms in Serbia and it was determined that seven Salmonella spp. were multidrug resistant. Sixteen serotypes were detected, but only serotype Infantis confirmed reduced susceptibility to colistin. Seven colistin resistant Salmonella Infantis were studied in detail using the WGS approach. Three sequence types were identified corresponding to different epizootiology region. The isolate from the Province of Vojvodina 3842 and isolates from Jagodina (92 and 821) are represented by the sequence type ST413 and ST11, respectively. Four isolates from Kraljevo are ST32, a common S. Infantis sequence type in humans, poultry and food. The fosfomycin resistance gene fosA7 in isolate 3842 and the vgaA gene in isolate 8418/2948 encoding resistance to pleuromutilins were reported for the first time in serovar Infantis. The changes in relative expression of the phoP/Q, mgrB and pmrA/B genes were detected. Single nucleotide polymorphisms of the pmrB gene, including transitions Val164Gly or Val164Met, and Arg92Pro are described. Analyses of quinolone resistance determining region revealed substitutions Ser83Tyr in GyrA protein and Thr57Ser and Ser80Arg in ParC protein. Based on WGS data, there are two major clusters among analyzed Salmonella Infantis isolates from central Serbia.

scholarly journals Structure of Pseudomonas aeruginosa Populations Analyzed by Single Nucleotide Polymorphism and Pulsed-Field Gel Electrophoresis Genotyping

2004 ◽  
Vol 186 (13) ◽  
pp. 4228-4237 ◽  
Author(s):  
Gracia Morales ◽  
Lutz Wiehlmann ◽  
Peter Gudowius ◽  
Christian van Delden ◽  
Burkhard Tümmler ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Core Genome ◽  
Genomic Islands ◽  
Clinical Settings ◽  
Nucleotide Polymorphisms ◽  
Natural Habitats ◽  
Single Nucleotide ◽  
Genetic Fingerprint ◽  
A Genome ◽  
Conserved Core

ABSTRACT Pseudomonas aeruginosa has a wide ecological distribution that includes natural habitats and clinical settings. To analyze the population structure and distribution of P. aeruginosa, a collection of 111 isolates of diverse habitats and geographical origin, most of which contained a genome with a different SpeI macrorestriction profile, was typed by restriction fragment length polymorphism based on 14 single nucleotide polymorphisms (SNPs) located at seven conserved loci of the core genome (oriC, oprL, fliC, alkB2, citS, oprI, and ampC). The combination of these SNPs plus the type of fliC present (a or b) allowed the assignment of a genetic fingerprint to each strain, thus providing a simple tool for the discrimination of P. aeruginosa strains. Thirteen of the 91 identified SNP genotypes were found in two or more strains. In several cases, strains sharing their SNP genotype had different SpeI macrorestriction profiles. The highly virulent CHA strain shared its SNP genotype with other strains that had different SpeI genotypes and which had been isolated from nonclinical habitats. The reference strain PAO1 also shared its SNP genotype with other strains that had different SpeI genotypes. The P. aeruginosa chromosome contains a conserved core genome and variable amounts of accessory DNA segments (genomic islands and islets) that can be horizontally transferred among strains. The fact that some SNP genotypes were overrepresented in the P. aeruginosa population studied and that several strains sharing an SNP genotype had different SpeI macrorestriction profiles supports the idea that changes occur at a higher rate in the accessory DNA segments than in the conserved core genome.

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