scholarly journals Single nucleotide polymorphism leads to daptomycin resistance causing amino acid substitution—T345I in MprF of clinically isolated MRSA strains

PLoS ONE ◽  
2021 ◽  
Vol 16 (1) ◽  
pp. e0245732
Author(s):  
Masaki Nakamura ◽  
Hayato Kawada ◽  
Hiroki Uchida ◽  
Yusuke Takagi ◽  
Shuichi Obata ◽  
...  
Keyword(s):  
Amino Acid ◽  
Surface Charge ◽  
Mutant Strain ◽  
Amino Acid Substitution ◽  
Growth Speed ◽  
Subsequent Increase ◽  
Exchange Method ◽  
Single Nucleotide ◽  
Positive Surface Charge ◽  
Mrsa Strains

Daptomycin (DAP) is one of the most potent antibiotics used for the treatment of methicillin-resistant Staphylococcus aureus (MRSA) infections. Due to an increase in its administration for combating MRSA infections, DAP non-susceptible (DAP-NS) MRSA strains have recently been reported in clinical settings. The presence of single nucleotide polymorphisms (SNPs) in the multiple peptide resistance factor (mprF) gene is the most frequently reported cause for the evolution of DAP-NS MRSA strains; however, there are some variations of SNPs that could lead to DAP-NS. In this study, we used two clinical MRSA strains, including DAP susceptible (DAP-S) and DAP-NS, isolated from the same patient at different time points. We introduced T345I SNP to mprF of the DAP-S MRSA strain using the gene exchange method with pIMAY vector. Further, we investigated the phenotype of the mutant strain, including drug susceptibility, cell surface positive charge, and growth speed. The mutant strain exhibited (i) resistance to DAP, (ii) up-regulation of positive surface charge, (iii) slower growth speed, and (iv) thickened cell walls. Hence, the SNP in mprF may have caused an up-regulation in MprF function, with a subsequent increase in positive surface charge. Cumulatively, these results demonstrated that the T345I amino acid substitution in mprF represents one of the primary causes of DAP-NS in MRSA strains.

scholarly journals A single amino acid substitution (157 Gly----Val) in a phosphoglycerate kinase variant (PGK Shizuoka) associated with chronic hemolysis and myoglobinuria

Blood ◽  
1992 ◽  
Vol 79 (6) ◽  
pp. 1582-1585
Author(s):  
H Fujii ◽  
H Kanno ◽  
A Hirono ◽  
T Shiomura ◽  
S Miwa
Keyword(s):  
Amino Acid ◽  
Amino Acid Substitution ◽  
Messenger Rna ◽  
Phosphoglycerate Kinase ◽  
Single Amino Acid Substitution ◽  
Single Amino Acid ◽  
Kinetic Properties ◽  
Total Blood ◽  
Single Nucleotide ◽  
Chronic Hemolysis

We have determined a single amino acid substitution in a new phosphoglycerate kinase (PGK) variant, PGK Shizuoka, associated with chronic hemolysis and myoglobinuria. PGK Shizuoka had an extremely low enzyme activity with normal kinetic properties and normal electrophoretic mobility. Total blood cell RNA of the patient was reverse-transcribed and amplified by the polymerase chain reaction. A single nucleotide substitution from guanine to thymine at position 473 of PGK messenger RNA was found. This nucleotide change causes a single amino acid substitution from Gly to Val at the 157th position, which is located in the NH2-terminal domain of the enzyme. This mutation creates a new Bst XI cleavage site in exon 5, and we thus confirmed the mutation in the variant gene. The replacement of Gly by Val is considered to affect enzyme catalysis.

scholarly journals A Single Amino Acid Change in the Response Regulator PhoP, Acquired duringYersinia pestisEvolution, Affects PhoP Target Gene Transcription and Polymyxin B Susceptibility

2018 ◽  
Vol 200 (9) ◽  
pp. e00050-18 ◽  
Author(s):  
Hana S. Fukuto ◽  
Viveka Vadyvaloo ◽  
Joseph B. McPhee ◽  
Hendrik N. Poinar ◽  
Edward C. Holmes ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Substitution ◽  
Target Gene ◽  
Response Regulator ◽  
Polymyxin B ◽  
Single Amino Acid ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Content Type ◽  
Virulent Strains

ABSTRACTYersinia pestis, the causative agent of plague, evolved from the closely related pathogenYersinia pseudotuberculosis. During its emergence,Y. pestisis believed to have acquired its unique pathogenic characteristics through numerous gene gains/losses, genomic rearrangements, and single nucleotide polymorphism (SNP) changes. One such SNP creates a single amino acid variation in the DNA binding domain of PhoP, the response regulator in the PhoP/PhoQ two-component system.Y. pseudotuberculosisand the basal human-avirulent strains ofY. pestisharbor glycines at position 215 of PhoP, whereas the modern human-virulent strains (e.g., KIM and CO92) harbor serines at this residue. Since PhoP plays multiple roles in the adaptation ofY. pestisto stressful host conditions, we tested whether this amino acid substitution affects PhoP activity or the ability ofY. pestisto survive in host environments. Compared to the parental KIM6+ strain carrying the modern allele ofphoP(phoP-S215), a derivative carrying the basal allele (phoP-G215) exhibited slightly defective growth under a low-Mg2+condition and decreased transcription of a PhoP target gene,ugd, as well as an ∼8-fold increase in the susceptibility to the antimicrobial peptide polymyxin B. ThephoP-G215strain showed no apparent defect in flea colonization, although aphoP-null mutant showed decreased flea infectivity in competition experiments. Our results suggest that the amino acid variation at position 215 of PhoP causes subtle changes in the PhoP activity and raise the possibility that the change in this residue have contributed to the evolution of increased virulence inY. pestis.IMPORTANCEY. pestisacquired a single nucleotide polymorphism (SNP) inphoPwhen the highly human-virulent strains diverged from less virulent basal strains, resulting in an amino acid substitution in the DNA binding domain of the PhoP response regulator. We show thatY. pestiscarrying the modernphoPallele has an increased ability to induce the PhoP-regulatedugdgene and resist antimicrobial peptides compared to an isogenic strain carrying the basal allele. Given the important roles PhoP plays in host adaptation, the results raise an intriguing possibility that this amino acid substitution contributed to the evolution of increased virulence inY. pestis. Additionally, we present the first evidence thatphoPconfers a survival fitness advantage toY. pestisinside the flea midgut.

scholarly journals InMeRF: prediction of pathogenicity of missense variants by individual modeling for each amino acid substitution

2020 ◽  
Vol 2 (2) ◽  
Author(s):  
Jun-ichi Takeda ◽  
Kentaro Nanatsue ◽  
Ryosuke Yamagishi ◽  
Mikako Ito ◽  
Nobuhiko Haga ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Substitution ◽  
Operating Characteristic ◽  
Radical Change ◽  
Training Dataset ◽  
Single Nucleotide ◽  
Amino Acid Properties ◽  
Genome Wide ◽  
Mutation Database ◽  
Fold Cross Validation

Abstract In predicting the pathogenicity of a nonsynonymous single-nucleotide variant (nsSNV), a radical change in amino acid properties is prone to be classified as being pathogenic. However, not all such nsSNVs are associated with human diseases. We generated random forest (RF) models individually for each amino acid substitution to differentiate pathogenic nsSNVs in the Human Gene Mutation Database and common nsSNVs in dbSNP. We named a set of our models ‘Individual Meta RF’ (InMeRF). Ten-fold cross-validation of InMeRF showed that the areas under the curves (AUCs) of receiver operating characteristic (ROC) and precision–recall curves were on average 0.941 and 0.957, respectively. To compare InMeRF with seven other tools, the eight tools were generated using the same training dataset, and were compared using the same three testing datasets. ROC-AUCs of InMeRF were ranked first in the eight tools. We applied InMeRF to 155 pathogenic and 125 common nsSNVs in seven major genes causing congenital myasthenic syndromes, as well as in VANGL1 causing spina bifida, and found that the sensitivity and specificity of InMeRF were 0.942 and 0.848, respectively. We made the InMeRF web service, and also made genome-wide InMeRF scores available online (https://www.med.nagoya-u.ac.jp/neurogenetics/InMeRF/).

scholarly journals 712. Identification of a Novel Tedizolid Resistance Mutation in rpoB of Methicillin-Resistant Staphylococcus aureus

2018 ◽  
Vol 5 (suppl_1) ◽  
pp. S256-S256
Author(s):  
Brian Werth ◽  
Kelsi Penewit ◽  
Stephen Salipante ◽  
Tianwei Shen ◽  
Libin Xu ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Substitution ◽  
Novel Mutation ◽  
Resistance Mutation ◽  
Serial Passage ◽  
Single Nucleotide Variant ◽  
23S Rrna ◽  
Single Nucleotide ◽  
Chloramphenicol Resistance ◽  
Methicillin Resistant

Abstract Background Tedizolid (TDZ) is an oxazolidinone antimicrobial with broad-spectrum activity against Gram-positive bacteria including methicillin-resistant S. aureus (MRSA). Resistance to TDZ is uncommon but mutations in the 23S rRNA target as well as in the transferable rRNA methyltransferase gene cfr, which also mediate resistance to linezolid and chloramphenicol have been implicated. The objective of this study was to determine whether other TDZ resistance pathways exist in MRSA. Methods Using a well-characterized MRSA strain, N315, we selected for TDZ resistance by serial passage in escalating concentrations of TDZ in Mueller Hinton broth (MHB) starting with 0.5× the MIC. Once visible growth was achieved a sample of the broth was diluted 1:1,000 into fresh MHB with twice the previous concentration of TDZ until an isolate with an MIC of ≥4 mg/mL was recovered. This MIC was selected since it is 1 dilution above the breakpoint for resistance ≥2 mg/L). This isolate was subjected to whole genome sequencing (WGS) and MICs to other antimicrobials were assessed. Homology modeling was performed to evaluate the potential impact of the mutation on target protein function. Results After 10 days of serial passage we recovered a stable mutant with a TDZ MIC of 4 mg/L. WGS revealed a single nucleotide variant (A1345G) in the rpoB gene corresponding to an amino acid substitution at D449N. The following table and figure summarize the changes in drug susceptibility between the parent and evolved strain and reveals the location of the amino acid substitution relative to the TDZ binding site. Conclusion We have identified a novel mutation in the RNA polymerase gene, rpoB, that mediates oxazolidinone and chloramphenicol resistance. This variant lies outside of the rifampin resistance determinant clusters of rpoB that span from 1,384 to 1,464 and 1,543 to 1,590, and as expected did not affect rifampin susceptibility. The underlying molecular mechanism by which this single nucleotide variant confers TDZ resistance remains unclear but may involve transcriptional modulation by altered sigma factor binding. Disclosures All authors: No reported disclosures.

scholarly journals Frequency and Distribution of Single-Nucleotide Polymorphisms withinmprFin Methicillin-Resistant Staphylococcus aureus Clinical Isolates and Their Role in Cross-Resistance to Daptomycin and Host Defense Antimicrobial Peptides

2015 ◽  
Vol 59 (8) ◽  
pp. 4930-4937 ◽  
Author(s):  
Arnold S. Bayer ◽  
Nagendra N. Mishra ◽  
Liang Chen ◽  
Barry N. Kreiswirth ◽  
Aileen Rubio ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Single Nucleotide Polymorphisms ◽  
Surface Charge ◽  
Host Defense ◽  
Cross Resistance ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Methicillin Resistant ◽  
Content Type ◽  
Positive Surface Charge

ABSTRACTMprF is responsible for the lysinylation of phosphatidylglycerol (PG) to synthesize the positively charged phospholipid (PL) species, lysyl-PG (L-PG). It has been proposed that the single-nucleotide polymorphisms (SNPs) within themprFopen reading frame (ORF) are associated with a gain-in-function phenotype in terms of daptomycin resistance inStaphylococcus aureus. (Note that although the official term is daptomycin nonsusceptibility, we use the term daptomycin resistance in this paper for ease of presentation.) Using 22 daptomycin-susceptible (DAPs)/daptomycin-resistant (DAPr) clinical methicillin-resistantS. aureus(MRSA) strain pairs, we assessed (i) the frequencies and distribution of putativemprFgain-in-function SNPs, (ii) the relationships of the SNPs to both daptomycin resistance and cross-resistance to the prototypical endovascular host defense peptide (HDP) thrombin-induced platelet microbicidal protein (tPMP), and (iii) the impact ofmprFSNPs on positive surface charge phenotype and modifications of membrane PL profiles. Most of themprFSNPs identified in our DAPrstrains were clustered within the two MprF loci, (i) the central bifunctional domain and (ii) the C-terminal synthase domain. Moreover, we were able to correlate the presence and location ofmprFSNPs in DAPrstrains with HDP cross-resistance, positive surface charge, and L-PG profiles. Although DAPrstrains withmprFSNPs in the bifunctional domain showed higher resistance to tPMPs than DAPrstrains with SNPs in the synthase domain, this relationship was not observed in positive surface charge assays. These results demonstrated that both charge-mediated and -unrelated mechanisms are involved in DAP resistance and HDP cross-resistance inS. aureus.

scholarly journals A single amino acid substitution (157 Gly----Val) in a phosphoglycerate kinase variant (PGK Shizuoka) associated with chronic hemolysis and myoglobinuria

Blood ◽  
1992 ◽  
Vol 79 (6) ◽  
pp. 1582-1585 ◽  
Author(s):  
H Fujii ◽  
H Kanno ◽  
A Hirono ◽  
T Shiomura ◽  
S Miwa
Keyword(s):  
Amino Acid ◽  
Amino Acid Substitution ◽  
Messenger Rna ◽  
Phosphoglycerate Kinase ◽  
Single Amino Acid Substitution ◽  
Single Amino Acid ◽  
Kinetic Properties ◽  
Total Blood ◽  
Single Nucleotide ◽  
Chronic Hemolysis

Abstract We have determined a single amino acid substitution in a new phosphoglycerate kinase (PGK) variant, PGK Shizuoka, associated with chronic hemolysis and myoglobinuria. PGK Shizuoka had an extremely low enzyme activity with normal kinetic properties and normal electrophoretic mobility. Total blood cell RNA of the patient was reverse-transcribed and amplified by the polymerase chain reaction. A single nucleotide substitution from guanine to thymine at position 473 of PGK messenger RNA was found. This nucleotide change causes a single amino acid substitution from Gly to Val at the 157th position, which is located in the NH2-terminal domain of the enzyme. This mutation creates a new Bst XI cleavage site in exon 5, and we thus confirmed the mutation in the variant gene. The replacement of Gly by Val is considered to affect enzyme catalysis.

scholarly journals Emergence of a Novel Lamivudine-Resistant Hepatitis B Virus Variant with a Substitution Outside the YMDD Motif

2006 ◽  
Vol 50 (11) ◽  
pp. 3867-3874 ◽  
Author(s):  
Hiromi Yatsuji ◽  
Chiemi Noguchi ◽  
Nobuhiko Hiraga ◽  
Nami Mori ◽  
Masataka Tsuge ◽  
...  
Keyword(s):  
Amino Acid ◽  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Mutant Strain ◽  
Amino Acid Substitution ◽  
Nucleotide Substitution ◽  
Chronic Hepatitis B Virus ◽  
B Virus ◽  
Mutant Strains ◽  
Ymdd Motif

ABSTRACT Lamivudine is a major drug approved for treatment of chronic hepatitis B virus (HBV) infection. Emergence of drug-resistant mutants with amino acid substitutions in the YMDD motif is a well-documented problem during long-term lamivudine therapy. Here we report a novel lamivudine-resistant strain of HBV with an intact YMDD motif, which included an amino acid substitution, rtA181T, in the reverse transcriptase (RT) domain of HBV polymerase. The substitution also induced a unique amino acid substitution (W172L) in the overlapping hepatitis B surface (HBs) protein. The YMDD mutant strains were not detected even by using the sensitive peptide nucleic acid-mediated PCR clamping method. The detected nucleotide substitution was accompanied by the emergence of an additional nucleotide substitution that induced amino acid change (S331C) in the spacer domain. The rtA181T mutant strain displayed a threefold decrease in susceptibility to lamivudine in in vitro experiments in comparison with the wild type. In vivo analysis using human hepatocyte-chimeric mice confirmed the resistance of this mutant strain to lamivudine. We developed a method to detect this novel rtA181T mutation and a previously reported rtA181T mutation with the HBs stop codon using restriction fragment length polymorphism PCR and identified one patient with the latter pattern among 40 patients with lamivudine resistance. In conclusion, although the incidence is not high, we have to be careful regarding the emergence of lamivudine-resistant mutant strains with intact YMDD motif.

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