A Comparative Transcriptome Between Anti-drug Sensitive and Resistant Candida auris in China

Candida auris emerged as a pathogenic species of fungus that causes severe and invasive outbreaks worldwide. The fungus exhibits high intrinsic resistance rates to various first-line antifungals, and the underlying molecular mechanism responsible for its multidrug resistance is still unclear. In this study, a transcriptomic analysis was performed between two C. auris isolates that exhibited different anti-drug patterns by RNA-sequencing, namely, CX1 (anti-drug sensitive) and CX2 (resistant). Transcriptomic analysis results revealed 541 upregulated and 453 downregulated genes in the resistant C. auris strain compared with the susceptible strain. In addition, our findings highlight the presence of potential differentially expressed genes (DEGs), which may play a role in drug resistance, including genes involved in ergosterol and efflux pump biosynthesis such as SNQ2, CDR4, ARB1, MDR1, MRR1, and ERG genes. We also found that Hsp related genes were upregulated for expression in the anti-drug-resistant strain. Biofilm formation and growth conditions were also compared between the two isolates. Our study provides novel clues for future studies in terms of understanding multidrug resistance mechanisms of C. auris strains.

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Role of the AheABC Efflux Pump in Aeromonas hydrophila Intrinsic Multidrug Resistance

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.01052-07 ◽

2008 ◽

Vol 52 (4) ◽

pp. 1559-1563 ◽

Cited By ~ 26

Author(s):

Mathieu Hernould ◽

Séverine Gagné ◽

Michel Fournier ◽

Claudine Quentin ◽

Corinne Arpin

Keyword(s):

Multidrug Resistance ◽

Aeromonas Hydrophila ◽

Efflux Pump ◽

Gene Inactivation ◽

Multidrug Efflux ◽

Intrinsic Resistance

ABSTRACT Gene inactivation and complementation experiments showed that the tripartite AheABC efflux pump of Aeromonas hydrophila extruded at least 13 substrates, including nine antibiotics. The use of phenylalanine-arginine-β-naphthylamide (PAβN) revealed an additional system(s) contributing to intrinsic resistance. This is the first analysis of the role of multidrug efflux systems in Aeromonas spp.

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Impact of an Intervention to Control Imipenem-Resistant Acinetobacter baumannii and Its Resistance Mechanisms: An 8-Year Survey

Frontiers in Microbiology ◽

10.3389/fmicb.2020.610109 ◽

2021 ◽

Vol 11 ◽

Cited By ~ 1

Author(s):

Lida Chen ◽

Pinghai Tan ◽

Jianming Zeng ◽

Xuegao Yu ◽

Yimei Cai ◽

...

Keyword(s):

Drug Resistance ◽

Acinetobacter Baumannii ◽

Bacterial Resistance ◽

Efflux Pump ◽

Resistance Mechanism ◽

Resistance Mechanisms ◽

Multi Drug Resistance ◽

Minimal Inhibitory Concentrations ◽

Resistance Rates ◽

The Impact

BackgroundThis study aimed to examine the impact of an intervention carried out in 2011 to combat multi-drug resistance and outbreaks of imipenem-resistant Acinetobacter baumannii (IRAB), and to explore its resistance mechanism.MethodsA total of 2572 isolates of A. baumannii, including 1673 IRAB isolates, were collected between 2007 and 2014. An intervention was implemented to control A. baumannii resistance and outbreaks. Antimicrobial susceptibility was tested by calculating minimal inhibitory concentrations (MICs), and outbreaks were typed using pulsed-field gel electrophoresis (PFGE). Resistance mechanisms were explored by polymerase chain reaction (PCR) and whole genome sequencing (WGS).ResultsFollowing the intervention in 2011, the resistance rates of A. baumannii to almost all tested antibiotics decreased, from 85.3 to 72.6% for imipenem, 100 to 80.8% for ceftriaxone, and 45.0 to 6.9% for tigecycline. The intervention resulted in a decrease in the number (seven to five), duration (8–3 months), and departments (five to three) affected by outbreaks; no outbreaks occurred in 2011. After the intervention, only blaAMPC (76.47 to 100%) and blaTEM–1 (75.74 to 96.92%) increased (P < 0.0001); whereas blaGES–1 (32.35 to 3.07%), blaPER–1 (21.32 to 1.54%), blaOXA–58 (60.29 to 1.54%), carO (37.50 to 7.69%), and adeB (9.56 to 3.08%) decreased (P < 0.0001). Interestingly, the frequency of class B β-lactamase genes decreased from 91.18% (blaSPM–1) and 61.03% (blaIMP–1) to 0%, while that of class D blaOXA–23 increased to 96.92% (P < 0.0001). WGS showed that the major PFGE types causing outbreaks each year (type 01, 11, 18, 23, 26, and 31) carried the same resistance genes (blaKPC–1, blaADC–25, blaOXA–66, and adeABC), AdeR-S mutations (G186V and A136V), and a partially blocked porin channel CarO. Meanwhile, plasmids harboring blaOXA–23 were found after the intervention.ConclusionThe intervention was highly effective in reducing multi-drug resistance of A. baumannii and IRAB outbreaks in the long term. The resistance mechanisms of IRAB may involve genes encoding β-lactamases, efflux pump overexpression, outer membrane porin blockade, and plasmids; in particular, clonal spread of blaOXA–23 was the major cause of outbreaks. Similar interventions may also help reduce bacterial resistance rates and outbreaks in other hospitals.

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Ascarids exposed: a method for in vitro drug exposure and gene expression analysis of anthelmintic naïve Parascaris spp

Parasitology ◽

10.1017/s0031182020000189 ◽

2020 ◽

Vol 147 (6) ◽

pp. 659-666 ◽

Cited By ~ 2

Author(s):

J. A. Scare ◽

P. Dini ◽

J. K. Norris ◽

A. E. Steuer ◽

K. Scoggin ◽

...

Keyword(s):

Drug Exposure ◽

Anthelmintic Resistance ◽

Resistance Mechanisms ◽

Transcriptomic Analysis ◽

Rna Seq ◽

Future Studies ◽

Drug Concentrations ◽

Drug Detoxification ◽

Phenotypic Responses

AbstractAscarid parasites infect a variety of hosts and regular anthelmintic treatment is recommended for all species. Parascaris spp. is the only ascarid species with widespread anthelmintic resistance, which allows for the study of resistance mechanisms. The purpose of this study was to establish an in vitro drug exposure protocol for adult anthelmintic-naïve Parascaris spp. and report a preliminary transcriptomic analysis in response to drug exposure. Live worms were harvested from foal necropsies and maintained in RPMI-1640 at 37 °C. Serial dilutions of oxibendazole (OBZ) and ivermectin (IVM) were prepared for in vitro drug exposure, and worm viability was monitored over time. In a second drug trial, worms were used for transcriptomic analysis. The final drug concentrations employed were OBZ at 40.1 μm (10 μg mL−1) and IVM at 1.1 μm (1 μg mL−1) for 24 and 3 h, respectively. The RNA-seq analysis revealed numerous differentially expressed genes, with some being potentially related to drug detoxification and regulatory mechanisms. This report provides a method for in vitro drug exposure and the phenotypic responses for Parascaris spp., which could be extrapolated to other ascarid parasites. Finally, it also provides preliminary transcriptomic data following drug exposure as a reference point for future studies of Parascaris spp.

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Prevalence and mechanisms of azole resistance in clinical isolates of Aspergillus section Fumigati species in a Canadian tertiary care centre, 2000 to 2013

Journal of Antimicrobial Chemotherapy ◽

10.1093/jac/dkz534 ◽

2019 ◽

Vol 75 (4) ◽

pp. 849-858

Author(s):

Maxime Parent-Michaud ◽

Philippe J Dufresne ◽

Eric Fournier ◽

Benjamin Folch ◽

Christine Martineau ◽

...

Keyword(s):

Efflux Pump ◽

Tertiary Care ◽

Geographic Area ◽

Resistance Mechanisms ◽

Sensu Stricto ◽

Azole Resistance ◽

Intrinsic Resistance ◽

Tertiary Care Centre ◽

Combined Use ◽

Aspergillus Section

Abstract Objectives Azole resistance among Aspergillus fumigatus isolates is a growing concern worldwide. Induction of mutations during azole therapy, environment-acquired mutations caused by azole fungicides and intrinsic resistance of cryptic Fumigati species all contribute to the burden of resistance. However, there is a lack of data in Canada on this emerging threat. Methods To gain insights into the magnitude and mechanisms of resistance, a 14 year collection of Aspergillus section Fumigati comprising 999 isolates from 807 patients at a Montreal hospital was screened for azole resistance, and resistance mechanisms were investigated with the combined use of genome sequencing, 3D modelling and phenotypic efflux pump assays. Results Overall azole resistance was low (4/807 patients; 0.5%). A single azole-resistant A. fumigatus sensu stricto strain, isolated from a patient with pulmonary aspergillosis, displayed efflux-pump-mediated resistance. Three patients were colonized or infected with azole-resistant cryptic Fumigati species (one Aspergillus thermomutatus, one Aspergillus lentulus and one Aspergillus turcosus). Evidence is presented that azole resistance is efflux-pump-mediated in the A. turcosus isolate, but not in the A. lentulus and A. thermomutatus isolates. Conclusions Azole resistance is rare in our geographic area and currently driven by cryptic Fumigati species. Continued surveillance of emergence of resistance is warranted.

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Identification and Characterization of Inhibitors of Multidrug Resistance Efflux Pumps in Pseudomonas aeruginosa: Novel Agents for Combination Therapy

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.45.1.105-116.2001 ◽

2001 ◽

Vol 45 (1) ◽

pp. 105-116 ◽

Cited By ~ 527

Author(s):

Olga Lomovskaya ◽

Mark S. Warren ◽

Angela Lee ◽

Jorge Galazzo ◽

Richard Fronko ◽

...

Keyword(s):

Pseudomonas Aeruginosa ◽

Multidrug Resistance ◽

Efflux Pump ◽

Acquired Resistance ◽

Efflux Pumps ◽

Fluoroquinolone Resistance ◽

Intrinsic Resistance ◽

Fold Reduction ◽

Cell Assays ◽

In The Wild

ABSTRACT Whole-cell assays were implemented to search for efflux pump inhibitors (EPIs) of the three multidrug resistance efflux pumps (MexAB-OprM, MexCD-OprJ, MexEF-OprN) that contribute to fluoroquinolone resistance in clinical isolates of Pseudomonas aeruginosa. Secondary assays were developed to identify lead compounds with exquisite activities as inhibitors. A broad-spectrum EPI which is active against all three known Mex efflux pumps from P. aeruginosa and their close Escherichia coli efflux pump homolog (AcrAB-TolC) was discovered. When this compound, MC-207,110, was used, the intrinsic resistance of P. aeruginosa to fluoroquinolones was decreased significantly (eightfold for levofloxacin). Acquired resistance due to the overexpression of efflux pumps was also decreased (32- to 64-fold reduction in the MIC of levofloxacin). Similarly, 32- to 64-fold reductions in MICs in the presence of MC-207,110 were observed for strains with overexpressed efflux pumps and various target mutations that confer resistance to levofloxacin (e.g., gyrA andparC). We also compared the frequencies of emergence of levofloxacin-resistant variants in the wild-type strain at four times the MIC of levofloxacin (1 μg/ml) when it was used either alone or in combination with EPI. In the case of levofloxacin alone, the frequency was ∼10−7 CFU/ml. In contrast, with an EPI, the frequency was below the level of detection (<10−11). In summary, we have demonstrated that inhibition of efflux pumps (i) decreased the level of intrinsic resistance significantly, (ii) reversed acquired resistance, and (iii) resulted in a decreased frequency of emergence of P. aeruginosa strains that are highly resistant to fluoroquinolones.

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Novel ERG11 and TAC1b Mutations Associated with Azole Resistance in Candida auris

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.02663-20 ◽

2021 ◽

Vol 65 (5) ◽

Author(s):

Jizhou Li ◽

Alix T. Coste ◽

Maroussia Liechti ◽

Daniel Bachmann ◽

Dominique Sanglard ◽

...

Keyword(s):

Invasive Candidiasis ◽

Efflux Pump ◽

Cumulative Effect ◽

Resistance Mechanisms ◽

Azole Resistance ◽

Candida Auris ◽

Content Type ◽

Drug Classes ◽

In The Wild

ABSTRACT Candida auris is a novel Candida species that has spread in all continents, causing nosocomial outbreaks of invasive candidiasis. C. auris has the ability to develop resistance to all antifungal drug classes. Notably, many C. auris isolates are resistant to the azole drug fluconazole, a standard therapy for invasive candidiasis. Azole resistance in C. auris can result from mutations in the azole target gene ERG11 and/or overexpression of the efflux pump Cdr1. TAC1 is a transcription factor controlling CDR1 expression in C. albicans. The role of TAC1 homologs in C. auris (TAC1a and TAC1b) remains to be better defined. In this study, we compared sequences of ERG11, TAC1a, and TAC1b between a fluconazole-susceptible and five fluconazole-resistant C. auris isolates of clade IV. Among four of the resistant isolates, we identified similar genotypes with concomitant mutations in ERG11 (F444L) and TAC1b (S611P). The simultaneous deletion of tandemly arranged TAC1a/TAC1b resulted in a decrease of MIC for fluconazole. Introduction of the ERG11 and TAC1b mutations separately and/or combined in the wild-type azole-susceptible isolate resulted in a significant increase of azole resistance with a cumulative effect of the two combined mutations. Interestingly, CDR1 expression was not significantly affected by TAC1a/TAC1b deletion or by the presence of the TAC1b S611P mutation, suggesting the existence of Tac1-dependent and Cdr1-independent azole resistance mechanisms. In conclusion, we demonstrated the role of two previously unreported mutations responsible for azole resistance in C. auris, which were a common signature among four azole-resistant isolates of clade IV.

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CraA, a Major Facilitator Superfamily Efflux Pump Associated with Chloramphenicol Resistance in Acinetobacter baumannii

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00584-09 ◽

2009 ◽

Vol 53 (9) ◽

pp. 4013-4014 ◽

Cited By ~ 67

Author(s):

I. Roca ◽

S. Marti ◽

P. Espinal ◽

P. Martínez ◽

I. Gibert ◽

...

Keyword(s):

Multidrug Resistance ◽

Acinetobacter Baumannii ◽

Antimicrobial Agents ◽

Efflux Pump ◽

Major Facilitator Superfamily ◽

Intrinsic Resistance ◽

Chloramphenicol Resistance ◽

Hospital Acquired Infections ◽

Major Facilitator ◽

Hospital Acquired

ABSTRACT Acinetobacter baumannii has been increasingly associated with hospital-acquired infections, and the presence of multidrug resistance strains is of great concern to clinicians. A. baumannii is thought to possess a great deal of intrinsic resistance to several antimicrobial agents, including chloramphenicol, although the mechanisms involved in such resistance are not well understood. In this work, we have identified a major facilitator superfamily efflux pump present in most A. baumannii strains, displaying strong substrate specificity toward chloramphenicol.

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Genome-wide analysis of experimentally evolved Candida auris reveals multiple novel mechanisms of multidrug-resistance

Access Microbiology ◽

10.1099/acmi.cc2021.po0140 ◽

2021 ◽

Vol 3 (12) ◽

Author(s):

Hans Carolus ◽

Siebe Pierson ◽

José F. Mun?oz ◽

Ana Subotić ◽

Rita B. Cruz ◽

...

Keyword(s):

Multidrug Resistance ◽

Molecular Mechanisms ◽

Efflux Pump ◽

Hot Spot ◽

Chromosome 1 ◽

Cross Resistance ◽

Future Research ◽

Candida Auris ◽

Genome Wide

Candida auris is globally recognized as an opportunistic fungal pathogen of high concern, due to its extensive multidrug-resistance (MDR). Still, molecular mechanisms of MDR are largely unexplored. This is the first account of genome wide evolution of MDR in C. auris obtained through serial in vitro exposure to azoles, polyenes and echinocandins. We show the stepwise accumulation of multiple novel mutations in genes known and unknown in antifungal drug resistance, albeit almost all new for C. auris. Echinocandin resistance was accompanied by a codon deletion in FKS1hot spot 1 and a substitution in FKS1 ‘novel’ hot spot 3. Mutations in ERG3 and CIS2 further increased the echinocandin MIC. Decreased azole susceptibility was linked to a mutation in transcription factor TAC1b and overexpression of the drug efflux pump Cdr1; a segmental duplication of chromosome 1 containing ERG11; and a whole chromosome 5 duplication, which contains TAC1b. The latter was associated with increased expression of ERG11, TAC1band CDR2, but not CDR1. The simultaneous emergence of nonsense mutations in ERG3 and ERG11 was shown to decrease amphotericin B susceptibility, accompanied with fluconazole cross resistance. A mutation in MEC3, a gene mainly known for its role in DNA damage homeostasis, further increased the polyene MIC. Overall, this study shows the alarming potential and diversity for MDR development in C. auris, even in a clade until now not associated with MDR (clade II),hereby stressing its clinical importance and the urge for future research.

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Comprehensive Joint Modeling of First-Line Therapeutics in Non-Small Cell Lung Cancer

10.1101/2020.11.24.20238212 ◽

2020 ◽

Author(s):

Benjamin K Schneider ◽

Sebastien Benzekry ◽

Jonathan P Mochel

Keyword(s):

Lung Cancer ◽

Small Cell Lung Cancer ◽

Cell Lung Cancer ◽

Acquired Resistance ◽

Small Cell ◽

Individual Therapy ◽

Small Cell Lung ◽

Intrinsic Resistance ◽

First Line ◽

Resistance Rates

AbstractFirst-line antiproliferatives for non-small cell lung cancer (NSCLC) have a relatively high failure rate due to high intrinsic resistance rates and acquired resistance rates to therapy. 57% patients are diagnosed in late-stage disease due to the tendency of early-stage NSCLC to be asymptomatic. For patients first diagnosed with metastatic disease the 5-year survival rate is approximately 5%. To help accelerate the development of novel therapeutics and computer-based tools for optimizing individual therapy, we have collated data from 11 different clinical trials in NSCLC and developed a semi-mechanistic, clinical model of NSCLC growth and pharmacodynamics relative to the various therapeutics represented in the study. In this study, we have produced extremely precise estimates of clinical parameters fundamental to cancer modeling such as the rate of acquired resistance to various pharmaceuticals, the relationship between drug concentration and rate of cancer cell death, as well as the fine temporal dynamics of anti-VEGF therapy. In the simulation sets documented in this study, we have used the model to make meaningful descriptions of efficacy gain in making bevacizumab-antiproliferative combination therapy sequential, over a series of days, rather than concurrent.

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Aminoglycoside resistance mechanisms in Pseudomonas aeruginosa isolates from non-cystic fibrosis patients in Thailand

Canadian Journal of Microbiology ◽

10.1139/cjm-2012-0465 ◽

2013 ◽

Vol 59 (1) ◽

pp. 51-56 ◽

Cited By ~ 6

Author(s):

Kanchana Poonsuk ◽

Chanwit Tribuddharat ◽

Rungtip Chuanchuen

Keyword(s):

Cystic Fibrosis ◽

Pseudomonas Aeruginosa ◽

Amino Acid ◽

High Resistance ◽

Amino Acid Change ◽

Efflux Pump ◽

Resistance Mechanisms ◽

Aminoglycoside Resistance ◽

Resistance Rates

This study aimed to examine aminoglycosides (AMGs) resistance mechanisms, including the AMG-modifying enzyme genes, mexXY, rplY, nuoG, and galU, in the Pseudomonas aeruginosa non-cystic fibrosis (CF) isolates in Thailand. One hundred P. aeruginosa isolates from non-CF patients were examined for susceptibility to AMGs and for the presence of 10 AMG-modifying enzyme genes. Thirty randomly selected isolates were tested for transcription of mexXY and nuoG and mutations in rplY and galU. All the P. aeruginosa isolates exhibited simultaneous resistance to at least 4 AMGs. High resistance rates to amikacin (92%), gentamicin (95%), streptomycin (99%), and tobramycin (96%) were observed, and all isolates were resistant to kanamycin, neomycin, and spectinomycin. Nine AMG-modifying enzyme genes were detected, including aadA1 (84%), aadB (84%), aadA2 (67%), ant(2″)-Ia (72%), strA-strB (70%), aph(3′)-IIb (57%), aac(3′)-Ia (40%), and aac(6′)-IIa (27%). None of the isolates harbored aac(6′)-IIb. Of 30 isolates tested, all but 1 isolate expressed MexXY. Two isolates did not express nuoG. Six isolates carried an amino acid change in RplY, but none of the isolates harbored mutation in galU. The results indicated that the AMG-modifying enzyme genes were widespread among the P. aeruginosa non-CF isolates. The MexXY efflux pump and inactivation for rplY played a role in AMG resistance but disruption of nuoG or galU did not.

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