Insight into the Significance ofAspergillus fumigatus cyp51APolymorphisms

ABSTRACTTriazole antifungal compounds are the first treatment choice for invasive aspergillosis. However, in the last decade the rate of azole resistance amongAspergillus fumigatusstrains has increased notoriously. The main resistance mechanisms are well defined and mostly related to point mutations of the azole target, 14-α sterol demethylase (cyp51A), with or without tandem repeat integrations in thecyp51Apromoter. Furthermore, different combinations of five Cyp51A mutations (F46Y, M172V, N248T, D255E, and E427K) have been reported worldwide in about 10% of allA. fumigatusisolates tested. The azole susceptibility profile of these strains shows elevated azole MICs, although on the basis of the azole susceptibility breakpoints, these strains are not considered azole resistant. The purpose of the study was to determine whether thesecyp51Apolymorphisms (single nucleotide polymorphisms [SNPs]) are responsible for the azole susceptibility profile and whether they are reflected in a poorer azole treatment responsein vivothat could compromise patient treatment and outcome. A mutant with acyp51Adeletion was generated and became fully susceptible to all azoles tested. Also, threecyp51Agene constructions with different combinations of SNPs were generated and reintroduced into an azole-susceptible wild-type (WT) strain (the ΔakuBKU80strain). The alternative model hostGalleria mellonellawas used to compare the virulence and voriconazole response ofG. mellonellalarvae infected withA. fumigatusstrains with WTcyp51Aorcyp51Awith SNPs. All strains were pathogenic inG. mellonellalarvae, although they did not respond similarly to voriconazole therapeutic doses. Finally, the full genomes of these strains were sequenced and analyzed in comparison with those ofA. fumigatusWT strains, revealing that they belong to different strain clusters or lineages.

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Causal Role of Single Nucleotide Polymorphisms within themprFGene of Staphylococcus aureus in Daptomycin Resistance

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01184-13 ◽

2013 ◽

Vol 57 (11) ◽

pp. 5658-5664 ◽

Cited By ~ 48

Author(s):

Soo-Jin Yang ◽

Nagendra N. Mishra ◽

Aileen Rubio ◽

Arnold S. Bayer

Keyword(s):

Staphylococcus Aureus ◽

Single Nucleotide Polymorphisms ◽

Point Mutations ◽

Nucleotide Polymorphisms ◽

Wild Type ◽

Single Nucleotide ◽

Content Type ◽

Reading Frame ◽

A Charge

ABSTRACTSingle nucleotide polymorphisms (SNPs) within themprFopen reading frame (ORF) have been commonly observed in daptomycin-resistant (DAPr)Staphylococcus aureusstrains. Such SNPs are usually associated with a gain-in-function phenotype, in terms of either increased synthesis or enhanced translocation (flipping) of lysyl-phosphatidylglycerol (L-PG). However, it is unclear if suchmprFSNPs are causal in DAPrstrains or are merely a biomarker for this phenotype. In this study, we used an isogenic set ofS. aureusstrains: (i) Newman, (ii) its isogenic ΔmprFmutant, and (iii) several intransplasmid complementation constructs, expressing either a wild-type or point-mutated form of themprFORF cloned from two isogenic DAP-susceptible (DAPs)-DAPrstrain pairs (616-701 and MRSA11/11-REF2145). Complementation of the ΔmprFstrain with singly point-mutatedmprFgenes (mprFS295LormprFT345A) revealed that (i) individual and distinct point mutations within themprFORF can recapitulate phenotypes observed in donor strains (i.e., changes in DAP MICs, positive surface charge, and cell membrane phospholipid profiles) and (ii) these gain-in-function SNPs (i.e., enhanced L-PG synthesis) likely promote reduced DAP binding toS. aureusby a charge repulsion mechanism. Thus, for these two DAPrstrains, the definedmprFSNPs appear to be causally related to this phenotype.

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Interrogation of Related Clinical Pan-Azole-Resistant Aspergillus fumigatus Strains: G138C, Y431C, and G434C Single Nucleotide Polymorphisms incyp51A, Upregulation ofcyp51A, and Integration and Activation of TransposonAtf1in thecyp51APromoter

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00517-11 ◽

2011 ◽

Vol 55 (11) ◽

pp. 5113-5121 ◽

Cited By ~ 63

Author(s):

Ahmed M. Albarrag ◽

Michael J. Anderson ◽

Susan J. Howard ◽

Geoff D. Robson ◽

Peter A. Warn ◽

...

Keyword(s):

Aspergillus Fumigatus ◽

Resistance Mechanisms ◽

Start Codon ◽

Azole Resistance ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Content Type ◽

Transcription Start Sites ◽

Chronic Pulmonary Aspergillosis

ABSTRACTMultipleAspergillus fumigatusisolates from a patient with two aspergillomas complicating chronic pulmonary aspergillosis were pan-azole resistant. Microsatellite typing was identical for all isolates despite major phenotypic and some growth rate differences. Three differentcyp51Amutations were found (G138C, Y431C, and G434C), of which the first two were demonstrated by heterologous expression in a hypersusceptibleSaccharomyces cerevisiaestrain to be at least partly responsible for elevated MICs.cyp51Aandcyp51Bgene duplication was excluded, but increased expression ofcyp51Awas demonstrated in three isolates selected for additional study (7-to 13-fold increases). In the isolate with the greatestcyp51Aexpression, anAft1transposon was found inserted 370 bp upstream of the start codon of thecyp51Agene, an integration location never previously demonstrated inAspergillus. Two transcription start sites were identified at 49 and 136 bp upstream of the start codon. The role of theAft1transposon, if any, in modulatingcyp51Aexpression remains to be established. Increased mRNA expression of the transportersAfuMDR1andAfuMDR4also was demonstrated in some isolates, which could contribute to azole resistance or simply represent a stress response. The diversity of confirmed and possible azole resistance mechanisms demonstrated in a single series of isogenic isolates is remarkable, indicating the ability ofA. fumigatusto adapt in the clinical setting.

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Interactions of COMT and ALDH2 Genetic Polymorphisms on Symptoms of Parkinson’s Disease

Brain Sciences ◽

10.3390/brainsci11030361 ◽

2021 ◽

Vol 11 (3) ◽

pp. 361

Author(s):

Rwei-Ling Yu ◽

Shao-Ching Tu ◽

Ruey-Meei Wu ◽

Pei-An Lu ◽

Chun-Hsiang Tan

Keyword(s):

Parkinson’S Disease ◽

Parkinson's Disease ◽

Detrimental Effect ◽

Personal Hygiene ◽

Nucleotide Polymorphisms ◽

Monoamine Neurotransmitters ◽

Single Nucleotide ◽

Detrimental Impact ◽

Reduced Activity ◽

Insight Into

(1) Background: Monoamine neurotransmitters play essential roles in the normal functioning of our nervous system. However, the metabolism of monoamine neurotransmitters is accompanied by the production of neurotoxic metabolites, and inefficient removal of the metabolites has been suggested to cause neurodegeneration. (2) Methods: To examine the effect of reduced activity of catechol-O-methyltransferase (COMT) and aldehyde dehydrogenase 2 (ALDH2) conferred by single nucleotide polymorphisms COMT rs4680(A) and ALDH2 rs671(A) on the symptoms of patients with Parkinson’s disease (PD), a total of 114 PD patients were recruited cross-sectionally and received genotyping for rs4680 and rs671 along with MDS-UPDRS evaluation. (3) Results: We found that patients carrying rs4680(A) had more severe bradykinesia in the upper extremity and rest tremor. Besides, patients carrying rs671(A) had more difficulty maintaining personal hygiene, while patients with genotype rs671(GG) had higher scores in the item “depressed mood.” More importantly, we found the effect of rs4680 to be moderated by rs671 SNP for the symptom of “hand movements.” The detrimental impact of rs4680(A) is more pronounced in the presence of genotype rs671(GG). (4) Conclusions: This study facilitates a deeper understanding of the detrimental effect of reduced activity of COMT and ALDH2 conferred by genetic variation and provides novel insight into the interactions between enzymes metabolizing monoamine neurotransmitters in the pathogenesis of PD.

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Mycobacterium chimaera genomics with regard to epidemiological and clinical investigations conducted for the open-chest post-surgical Mycobacterium chimaera infections outbreak

Open Forum Infectious Diseases ◽

10.1093/ofid/ofab192 ◽

2021 ◽

Author(s):

Emmanuel Lecorche ◽

Côme Daniau ◽

Kevin La ◽

Faiza Mougari ◽

Hanaa Benmansour ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Clinical Isolates ◽

Whole Genome ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Healthcare Facilities ◽

Open Chest

Abstract Background Post-surgical infections due to Mycobacterium chimaera appeared as a novel nosocomial threat in 2015, with a worldwide outbreak due to contaminated heater-cooler units used in open chest surgery. We report the results of investigations conducted in France including whole genome sequencing comparison of patient and HCU isolates. Methods We sought M. chimaera infection cases from 2010 onwards through national epidemiological investigations in healthcare facilities performing cardiopulmonary bypass together with a survey on good practices and systematic heater-cooler unit microbial analyses. Clinical and HCU isolates were subjected to whole genome sequencing analyzed with regards to the reference outbreak strain Zuerich-1. Results Only two clinical cases were shown to be related to the outbreak, although 23% (41/175) heater-cooler units were declared positive for M. avium complex. Specific measures to prevent infection were applied in 89% (50/56) healthcare facilities although only 14% (8/56) of them followed the manufacturer maintenance recommendations. Whole genome sequencing comparison showed that the clinical isolates and 72% (26/36) of heater-cooler unit isolates belonged to the epidemic cluster. Within clinical isolates, 5 to 9 non-synonymous single nucleotide polymorphisms were observed, among which an in vivo mutation in a putative efflux pump gene observed in a clinical isolate obtained for one patient under antimicrobial treatment. Conclusions Cases of post-surgical M. chimaera infections were declared to be rare in France, although heater-cooler units were contaminated as in other countries. Genomic analyses confirmed the connection to the outbreak and identified specific single nucleotide polymorphisms, including one suggesting fitness evolution in vivo.

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Emergence of Resistance Mutations in Salmonella enterica Serovar Typhi Against Fluoroquinolones

Open Forum Infectious Diseases ◽

10.1093/ofid/ofx230 ◽

2017 ◽

Vol 4 (4) ◽

Cited By ~ 5

Author(s):

Takashi Matono ◽

Masatomo Morita ◽

Koji Yahara ◽

Ken-ichi Lee ◽

Hidemasa Izumiya ◽

...

Keyword(s):

Salmonella Enterica ◽

Evolutionary Process ◽

Resistance Mechanisms ◽

Single Mutation ◽

Nucleotide Polymorphisms ◽

Resistance Mutations ◽

Single Nucleotide ◽

Salmonella Enterica Serovar Typhi ◽

Resistant Strains ◽

Emergence Of Resistance

Abstract Background Little is known about the evolutionary process and emergence time of resistance mutations to fluoroquinolone in Salmonella enterica serovar Typhi. Methods We analyzed S. Typhi isolates collected from returned travelers between 2001 and 2016. Based on ciprofloxacin susceptibility, isolates were categorized as highly resistant (minimum inhibitory concentration [MIC] ≥ 4 μg/mL [CIPHR]), resistant (MIC = 1–2 μg/mL [CIPR]), intermediate susceptible (MIC = 0.12–0.5 μg/mL [CIPI]), and susceptible (MIC ≤ 0.06 μg/mL [CIPS]). Results A total of 107 isolates (33 CIPHR, 14 CIPR, 30 CIPI, and 30 CIPS) were analyzed by whole-genome sequencing; 2461 single nucleotide polymorphisms (SNPs) were identified. CIPS had no mutations in the gyrA or parC genes, while each CIPI had 1 of 3 single mutations in gyrA (encoding Ser83Phe [63.3%], Ser83Tyr [33.3%], or Asp87Asn [3.3%]). CIPHR had the same 3 mutations: 2 SNPs in gyrA (encoding Ser83Phe and Asp87Asn) and a third in parC (encoding Ser80Ile). CIPHR shared a common ancestor with CIPR and CIPI isolates harboring a single mutation in gyrA encoding Ser83Phe, suggesting that CIPHR emerged 16 to 23 years ago. Conclusions Three SNPs—2 in gyrA and 1 in parC—are present in S. Typhi strains highly resistant to fluoroquinolone, which were found to have evolved in 1993–2000, approximately 10 years after the beginning of the ciprofloxacin era. Highly resistant strains with survival advantages arose from strains harboring a single mutation in gyrA encoding Ser83Phe. Judicious use of fluoroquinolones is warranted to prevent acceleration of such resistance mechanisms in the future.

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The Implications of CaMK2A And MeCP2 Signalings In The Cognitive Ability of Adolescents

10.21203/rs.3.rs-506538/v1 ◽

2021 ◽

Author(s):

Li-Ching Lee ◽

Ming-Tsan Su ◽

Hsing-Ying Huang ◽

Ying-Chun Cho ◽

Ting-Kuang Yeh ◽

...

Keyword(s):

High School Students ◽

Single Nucleotide Polymorphisms ◽

Cognitive Ability ◽

Signaling Pathway ◽

Collective Effects ◽

Nucleotide Polymorphisms ◽

School Students ◽

Single Nucleotide ◽

Glutamatergic Signaling

Abstract The glutamatergic signaling pathway is involved in molecular learning and human cognitive ability. Specific single nucleotide polymorphisms (SNPs) in the genes encoding NMDA receptor subunits have been associated with neuropsychiatric disorders by altering glutamate transmission. But how these polymorphisms associated with cognition and brain psychological activities were rarely been explored in healthy adolescents. In this study, we screened SNPs of the glutamatergic signaling pathway to identify genetic variants associated with cognitive ability. We found that single nucleotide polymorphisms (SNPs) in subunits of ionotropic glutamate receptors, including GRIA1, GRINN1, GRIN2B, GRIN2C, GRIN3A, GRIN3B, and Calcium/ Calmodulin-dependent protein kinase II α (CaMK2A) associated with the cognitive function of students. Importantly, the plasma CaMK2A levels correlated positively with the cognitive ability of senior high school students in Taiwan. We demonstrated that the elevated CaMK2A increased its autophosphorylation at T286 and increased the expression of its downstream targets, including GRIA1 and phosphor GRIA1 in vivo. Additionally, the Methyl CpG binding protein 2 (MeCP2), a downstream target of CaMK2A, can activate the expression of CaMK2A, suggesting that MeCP2 and CaMK2A could form a positive feedback loop. In summary, we concluded that members of the glutamatergic signaling, CaMK2A, and MeCP2 were implicated in the cognitive ability of adolescents, and alternating in the CaMK2A expressing may have collective effects on the cognitive ability of youths.

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Assessing Genetic Diversity among Brettanomyces Yeasts by DNA Fingerprinting and Whole-Genome Sequencing

Applied and Environmental Microbiology ◽

10.1128/aem.00601-14 ◽

2014 ◽

Vol 80 (14) ◽

pp. 4398-4413 ◽

Cited By ~ 45

Author(s):

Sam Crauwels ◽

Bo Zhu ◽

Jan Steensels ◽

Pieter Busschaert ◽

Gorik De Samblanx ◽

...

Keyword(s):

Genetic Diversity ◽

Dna Fingerprinting ◽

Wine Industry ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Content Type ◽

Carbon And Nitrogen ◽

Spoilage Yeasts ◽

Off Flavors ◽

Carbon And Nitrogen Metabolism

ABSTRACTBrettanomycesyeasts, with the speciesBrettanomyces(Dekkera)bruxellensisbeing the most important one, are generally reported to be spoilage yeasts in the beer and wine industry due to the production of phenolic off flavors. However,B. bruxellensisis also known to be a beneficial contributor in certain fermentation processes, such as the production of certain specialty beers. Nevertheless, despite its economic importance,Brettanomycesyeasts remain poorly understood at the genetic and genomic levels. In this study, the genetic relationship between more than 50Brettanomycesstrains from all presently known species and from several sources was studied using a combination of DNA fingerprinting techniques. This revealed an intriguing correlation between theB. bruxellensisfingerprints and the respective isolation source. To further explore this relationship, we sequenced a (beneficial) beer isolate ofB. bruxellensis(VIB X9085; ST05.12/22) and compared its genome sequence with the genome sequences of two wine spoilage strains (AWRI 1499 and CBS 2499). ST05.12/22 was found to be substantially different from both wine strains, especially at the level of single nucleotide polymorphisms (SNPs). In addition, there were major differences in the genome structures between the strains investigated, including the presence of large duplications and deletions. Gene content analysis revealed the presence of 20 genes which were present in both wine strains but absent in the beer strain, including many genes involved in carbon and nitrogen metabolism, and vice versa, no genes that were missing in both AWRI 1499 and CBS 2499 were found in ST05.12/22. Together, this study provides tools to discriminateBrettanomycesstrains and provides a first glimpse at the genetic diversity and genome plasticity ofB. bruxellensis.

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Dissecting the Structure-Function Relationship of a Fungicidal Peptide Derived from the Constant Region of Human Immunoglobulins

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01753-15 ◽

2016 ◽

Vol 60 (4) ◽

pp. 2435-2442 ◽

Cited By ~ 5

Author(s):

Tecla Ciociola ◽

Thelma A. Pertinhez ◽

Laura Giovati ◽

Martina Sperindè ◽

Walter Magliani ◽

...

Keyword(s):

Self Assembly ◽

Galleria Mellonella ◽

Critical Role ◽

Yeast Cells ◽

Therapeutic Effects ◽

Constant Region ◽

Content Type ◽

Complementarity Determining Regions

ABSTRACTSynthetic peptides encompassing sequences related to the complementarity-determining regions of antibodies or derived from their constant region (Fc peptides) were proven to exert differential antimicrobial, antiviral, antitumor, and/or immunomodulatory activitiesin vitroand/orin vivo, regardless of the specificity and isotype of the parental antibody. Alanine substitution derivatives of these peptides exhibited unaltered, increased, or decreased candidacidal activitiesin vitro. The bioactive IgG-derived Fc N10K peptide (NQVSLTCLVK) spontaneously self-assembles, a feature previously recognized as relevant for the therapeutic activity of another antibody-derived peptide. We evaluated the contribution of each residue to the peptide self-assembling capability by circular-dichroism spectroscopy. The interaction of the N10K peptide and its derivatives withCandida albicanscells was studied by confocal, transmission, and scanning electron microscopy. The apoptosis and autophagy induction profiles in yeast cells treated with the peptides were evaluated by flow cytometry, and the therapeutic efficacy against candidal infection was studied in aGalleria mellonellamodel. Overall, the results indicate a critical role for some residues in the self-assembly process and a correlation of that capability with the candidacidal activities of the peptidesin vitroand their therapeutic effectsin vivo.

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A SNP in the Cache 1 Signaling Domain of Diguanylate Cyclase STM1987 Leads to Increased In Vivo Fitness of Invasive Salmonella Strains

Infection and Immunity ◽

10.1128/iai.00810-20 ◽

2021 ◽

Vol 89 (4) ◽

Author(s):

Akosiererem S. Sokaribo ◽

Lindsay R. Balezantis ◽

Keith D. MacKenzie ◽

Yejun Wang ◽

Melissa B. Palmer ◽

...

Keyword(s):

Acute Infection ◽

Bloodstream Infections ◽

Sub Saharan Africa ◽

Human Macrophage ◽

Diguanylate Cyclase ◽

Nucleotide Polymorphisms ◽

Cellulose Production ◽

Content Type ◽

Signaling Domain

ABSTRACT Nontyphoidal Salmonella (NTS) strains are associated with gastroenteritis worldwide but are also the leading cause of bacterial bloodstream infections in sub-Saharan Africa. The invasive NTS (iNTS) strains that cause bloodstream infections differ from standard gastroenteritis-causing strains by >700 single-nucleotide polymorphisms (SNPs). These SNPs are known to alter metabolic pathways and biofilm formation and to contribute to serum resistance and are thought to signify iNTS strains becoming human adapted, similar to typhoid fever-causing Salmonella strains. Identifying SNPs that contribute to invasion or increased virulence has been more elusive. In this study, we identified a SNP in the cache 1 signaling domain of diguanylate cyclase STM1987 in the invasive Salmonella enterica serovar Typhimurium type strain D23580. This SNP was conserved in 118 other iNTS strains analyzed and was comparatively absent in global S. Typhimurium isolates associated with gastroenteritis. STM1987 catalyzes the formation of bis-(3′,5′)-cyclic dimeric GMP (c-di-GMP) and is proposed to stimulate production of cellulose independent of the master biofilm regulator CsgD. We show that the amino acid change in STM1987 leads to a 10-fold drop in cellulose production and increased fitness in a mouse model of acute infection. Reduced cellulose production due to the SNP led to enhanced survival in both murine and human macrophage cell lines. In contrast, loss of CsgD-dependent cellulose production did not lead to any measurable change in in vivo fitness. We hypothesize that the SNP in stm1987 represents a pathoadaptive mutation for iNTS strains.

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Using Mycobacterium tuberculosis Single-Nucleotide Polymorphisms To Predict Fluoroquinolone Treatment Response

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00076-19 ◽

2019 ◽

Vol 63 (7) ◽

Cited By ~ 3

Author(s):

Marva Seifert ◽

Edmund Capparelli ◽

Donald G. Catanzaro ◽

Timothy C. Rodwell

Keyword(s):

Mycobacterium Tuberculosis ◽

Single Nucleotide Polymorphisms ◽

Specific Resistance ◽

Therapeutic Targets ◽

World Health ◽

Population Pharmacokinetic ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Content Type ◽

Level Increase

ABSTRACT Clinical phenotypic fluoroquinolone susceptibility testing of Mycobacterium tuberculosis is currently based on M. tuberculosis growth at a single critical concentration, which provides limited information for a nuanced clinical response. We propose using specific resistance-conferring M. tuberculosis mutations in gyrA together with population pharmacokinetic and pharmacodynamic modeling as a novel tool to better inform fluoroquinolone treatment decisions. We sequenced the gyrA resistance-determining region of 138 clinical M. tuberculosis isolates collected from India, Moldova, Philippines, and South Africa and then determined each strain’s MIC against ofloxacin, moxifloxacin, levofloxacin, and gatifloxacin. Strains with specific gyrA single-nucleotide polymorphisms (SNPs) were grouped into high or low drug-specific resistance categories based on their empirically measured MICs. Published population pharmacokinetic models were then used to explore the pharmacokinetics and pharmacodynamics of each fluoroquinolone relative to the empirical MIC distribution for each resistance category to make predictions about the likelihood of patients achieving defined therapeutic targets. In patients infected with M. tuberculosis isolates containing SNPs associated with a fluoroquinolone-specific low-level increase in MIC, models suggest increased fluoroquinolone dosing improved the probability of achieving therapeutic targets for gatifloxacin and moxifloxacin but not for levofloxacin and ofloxacin. In contrast, among patients with isolates harboring SNPs associated with a high-level increase in MIC, increased dosing of levofloxacin, moxifloxacin, gatifloxacin, or ofloxacin did not meaningfully improve the probability of therapeutic target attainment. We demonstrated that quantifiable fluoroquinolone drug resistance phenotypes could be predicted from rapidly detectable gyrA SNPs and used to support dosing decisions based on the likelihood of patients reaching therapeutic targets. Our findings provide further supporting evidence for the moxifloxacin clinical breakpoint recently established by the World Health Organization.

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