Co-existence of virulence factors and antibiotic resistance in new Klebsiella pneumoniae clones emerging in south of Italy

Abstract Background Endemic presence of Klebsiella pneumoniae resistant to carbapenem in Italy has been due principally to the clonal expansion of CC258 isolates; however, recent studies suggest an ongoing epidemiological change in this geographical area. Methods 50 K. pneumoniae strains, 25 carbapenem-resistant (CR-Kp) and 25 susceptible (CS-Kp), collected from march 2014 to march 2016 at the Laboratory of Bacteriology of the Paolo Giaccone Polyclinic University hospital of Palermo, Italy, were characterized for antibiotic susceptibility and fully sequenced by next generation sequencing (NGS) for the in silico analysis of resistome, virulome, multi-locus sequence typing (MLST) and core single nucleotide polymorphism (SNP) genotypes Results MLST in silico analysis of CR-Kp showed that 52% of isolates belonged to CC258, followed by ST395 (12%), ST307 (12%), ST392 (8%), ST348 (8%), ST405 (4%) and ST101 (4%). In the CS-Kp group, the most represented isolate was ST405 (20%), followed by ST392 and ST15 (12%), ST395, ST307 and ST1727 (8%). The in silico β-lactamase analysis of the CR-Kp group showed that the most detected gene was blaSHV (100%), followed by blaTEM (92%), blaKPC (88%), blaOXA (88%) and blaCTX-M (32%). The virulome analysis detected mrk operon in all studied isolates, and wzi-2 was found in three CR-Kp isolates (12%). Furthermore, the distribution of virulence genes encoding for the yersiniabactin system, its receptor fyuA and the aerobactin system did not show significant distribution differences between CR-Kp and CS-Kp, whereas the Klebsiella ferrous iron uptake system (kfuA, kfuB and kfuC genes), the two-component system kvgAS and the microcin E495 were significantly (p < 0.05) prevalent in the CS-Kp group compared to the CR-Kp group. Core SNP genotyping, correlating with the MLST data, allowed greater strain tracking and discrimination than MLST analysis. Conclusions Our data support the idea that an epidemiological change is ongoing in the Palermo area (Sicily, Italy). In addition, our analysis revealed the co-existence of antibiotic resistance and virulence factors in CR-Kp isolates; this characteristic should be considered for future genomic surveillance studies.

Download Full-text

Characterization and risk association of polymorphisms in Aurora kinases A, B and C with genetic susceptibility to gastric cancer development

BMC Cancer ◽

10.1186/s12885-019-6133-z ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 1

Author(s):

Aner Mesic ◽

Marija Rogar ◽

Petra Hudler ◽

Nurija Bilalovic ◽

Izet Eminovic ◽

...

Keyword(s):

Gastric Cancer ◽

Transcription Factors ◽

In Silico ◽

In Silico Analysis ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Mitotic Kinases ◽

Genes Encoding ◽

Silico Analysis ◽

Control Study

Abstract Background Single nucleotide polymorphisms (SNPs) in genes encoding mitotic kinases could influence development and progression of gastric cancer (GC). Methods Case-control study of nine SNPs in mitotic genes was conducted using qPCR. The study included 116 GC patients and 203 controls. In silico analysis was performed to evaluate the effects of polymorphisms on transcription factors binding sites. Results The AURKA rs1047972 genotypes (CT vs. CC: OR, 1.96; 95% CI, 1.05–3.65; p = 0.033; CC + TT vs. CT: OR, 1.94; 95% CI, 1.04–3.60; p = 0.036) and rs911160 (CC vs. GG: OR, 5.56; 95% CI, 1.24–24.81; p = 0.025; GG + CG vs. CC: OR, 5.26; 95% CI, 1.19–23.22; p = 0.028), were associated with increased GC risk, whereas certain rs8173 genotypes (CG vs. CC: OR, 0.60; 95% CI, 0.36–0.99; p = 0.049; GG vs. CC: OR, 0.38; 95% CI, 0.18–0.79; p = 0.010; CC + CG vs. GG: OR, 0.49; 95% CI, 0.25–0.98; p = 0.043) were protective. Association with increased GC risk was demonstrated for AURKB rs2241909 (GG + AG vs. AA: OR, 1.61; 95% CI, 1.01–2.56; p = 0.041) and rs2289590 (AC vs. AA: OR, 2.41; 95% CI, 1.47–3.98; p = 0.001; CC vs. AA: OR, 6.77; 95% CI, 2.24–20.47; p = 0.001; AA+AC vs. CC: OR, 4.23; 95% CI, 1.44–12.40; p = 0.009). Furthermore, AURKC rs11084490 (GG + CG vs. CC: OR, 1.71; 95% CI, 1.04–2.81; p = 0.033) was associated with increased GC risk. A combined analysis of five SNPs, associated with an increased GC risk, detected polymorphism profiles where all the combinations contribute to the higher GC risk, with an OR increased 1.51-fold for the rs1047972(CT)/rs11084490(CG + GG) to 2.29-fold for the rs1047972(CT)/rs911160(CC) combinations. In silico analysis for rs911160 and rs2289590 demonstrated that different transcription factors preferentially bind to polymorphic sites, indicating that AURKA and AURKB could be regulated differently depending on the presence of particular allele. Conclusions Our results revealed that AURKA (rs1047972 and rs911160), AURKB (rs2241909 and rs2289590) and AURKC (rs11084490) are associated with a higher risk of GC susceptibility. Our findings also showed that the combined effect of these SNPs may influence GC risk, thus indicating the significance of assessing multiple polymorphisms, jointly. The study was conducted on a less numerous but ethnically homogeneous Bosnian population, therefore further investigations in larger and multiethnic groups and the assessment of functional impact of the results are needed to strengthen the findings.

Download Full-text

In silico analysis as a strategy to identify candidate epitopes with human IgG reactivity to study Porphyromonas gingivalis virulence factors

AMB Express ◽

10.1186/s13568-019-0757-x ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 3

Author(s):

Ellen Karla Nobre dos Santos-Lima ◽

Kizzes Araújo Paiva Andrade Cardoso ◽

Patrícia Mares de Miranda ◽

Ana Carla Montino Pimentel ◽

Paulo Cirino de Carvalho-Filho ◽

...

Keyword(s):

Porphyromonas Gingivalis ◽

Virulence Factors ◽

In Silico ◽

In Silico Analysis ◽

Human Igg ◽

Silico Analysis

Download Full-text

In Silico Analysis of Regulatory cis-Elements in the Promoters of Genes Encoding Apoplastic Invertase and Sucrose Synthase in Silver Birch

Russian Journal of Developmental Biology ◽

10.1134/s1062360420050082 ◽

2020 ◽

Vol 51 (5) ◽

pp. 323-335 ◽

Cited By ~ 1

Author(s):

T. V. Tarelkina ◽

N. A. Galibina ◽

Yu. L. Moshchenskaya ◽

L. L. Novitskaya

Keyword(s):

In Silico ◽

Sucrose Synthase ◽

In Silico Analysis ◽

Silver Birch ◽

Cis Elements ◽

Apoplastic Invertase ◽

Genes Encoding ◽

Silico Analysis

Download Full-text

In Silico Analysis of Antibiotic Resistance Genes in the Gut Microflora of Individuals from Diverse Geographies and Age-Groups

PLoS ONE ◽

10.1371/journal.pone.0083823 ◽

2013 ◽

Vol 8 (12) ◽

pp. e83823 ◽

Cited By ~ 49

Author(s):

Tarini Shankar Ghosh ◽

Sourav Sen Gupta ◽

Gopinath Balakrish Nair ◽

Sharmila S. Mande

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

In Silico ◽

Age Groups ◽

Antibiotic Resistance Genes ◽

In Silico Analysis ◽

Gut Microflora ◽

Silico Analysis

Download Full-text

Mobilization of the nonconjugative virulence plasmid from hypervirulent Klebsiella pneumoniae

Genome Medicine ◽

10.1186/s13073-021-00936-5 ◽

2021 ◽

Vol 13 (1) ◽

Author(s):

Yanping Xu ◽

Jianfeng Zhang ◽

Meng Wang ◽

Meng Liu ◽

Guitian Liu ◽

...

Keyword(s):

Klebsiella Pneumoniae ◽

In Silico ◽

In Silico Analysis ◽

Conjugative Plasmid ◽

Virulence Plasmid ◽

E Coli ◽

Virulence Plasmids ◽

Carbapenem Resistant ◽

Helper Plasmids ◽

Silico Analysis

Abstract Background Klebsiella pneumoniae, as a global priority pathogen, is well known for its capability of acquiring mobile genetic elements that carry resistance and/or virulence genes. Its virulence plasmid, previously deemed nonconjugative and restricted within hypervirulent K. pneumoniae (hvKP), has disseminated into classic K. pneumoniae (cKP), particularly carbapenem-resistant K. pneumoniae (CRKP), which poses alarming challenges to public health. However, the mechanism underlying its transfer from hvKP to CRKP is unclear. Methods A total of 28 sequence type (ST) 11 bloodstream infection-causing CRKP strains were collected from Ruijin Hospital in Shanghai, China, and used as recipients in conjugation assays. Transconjugants obtained from conjugation assays were confirmed by XbaI and S1 nuclease pulsed-field gel electrophoresis, PCR detection and/or whole-genome sequencing. The plasmid stability of the transconjugants was evaluated by serial culture. Genetically modified strains and constructed mimic virulence plasmids were employed to investigate the mechanisms underlying mobilization. The level of extracellular polysaccharides was measured by mucoviscosity assays and uronic acid quantification. An in silico analysis of 2608 plasmids derived from 814 completely sequenced K. pneumoniae strains available in GenBank was performed to investigate the distribution of putative helper plasmids and mobilizable virulence plasmids. Results A nonconjugative virulence plasmid was mobilized by the conjugative plasmid belonging to incompatibility group F (IncF) from the hvKP strain into ST11 CRKP strains under low extracellular polysaccharide-producing conditions or by employing intermediate E. coli strains. The virulence plasmid was mobilized via four modes: transfer alone, cotransfer with the conjugative IncF plasmid, hybrid plasmid formation due to two rounds of single-strand exchanges at specific 28-bp fusion sites or homologous recombination. According to the in silico analysis, 31.8% (242) of the putative helper plasmids and 98.8% (84/85) of the virulence plasmids carry the 28-bp fusion site. All virulence plasmids carry the origin of the transfer site. Conclusions The nonconjugative virulence plasmid in ST11 CRKP strains is putatively mobilized from hvKP or E. coli intermediates with the help of conjugative IncF plasmids. Our findings emphasize the importance of raising public awareness of the rapid dissemination of virulence plasmids and the consistent emergence of hypervirulent carbapenem-resistant K. pneumoniae (hv-CRKP) strains.

Download Full-text

The role of mobile genetic elements in evolution of cyanobacteria

Ecological genetics ◽

10.17816/ecogen9452-62 ◽

2011 ◽

Vol 9 (4) ◽

pp. 52-62

Author(s):

Lidia E Mikheeva ◽

Elena A Karbysheva ◽

Sergey V Shestakov

Keyword(s):

Gene Regulation ◽

Significant Role ◽

In Silico ◽

In Silico Analysis ◽

Whole Genome ◽

Number Of Genes ◽

Genes Encoding ◽

Adaptation Processes ◽

Silico Analysis

Possible pathways of cyanobacterial evolution are discussed on the basis of in silico analysis of fully sequenced genomes of 45 species/strains of cyanobacteria. The information on quantity and functions of different mobile elements (IS, MITE elements and group II introns) was reviewed. Positive correlation between whole genome sizes and number of genes, encoding transposases has been revealed. It is suggested that transpositions play significant role in genome rearrangements taking part in gene regulation and adaptation processes determining the directions of microevolution processes in cyanobacterial populations.

Download Full-text