Efflux pump gene expression study using RNA-seq in multidrug-resistant TB

2021 ◽  
Vol 25 (12) ◽  
pp. 974-981
Author(s):  
J. J. Lee ◽  
H. Y. Kang ◽  
W-I. Lee ◽  
S. Y. Cho ◽  
Y. J. Kim ◽  
...  
Keyword(s):  
Wild Type Strain ◽  
Efflux Pump ◽  
Expression Patterns ◽  
Resistance Mechanism ◽  
Multidrug Resistant ◽  
Regulatory Genes ◽  
Control Group ◽  
Rna Expression ◽  
Rna Seq ◽  
Expression Study

BACKGROUND: The mechanism underlying kanamycin (KM) resistance in Mycobacterium tuberculosis is not well understood, although efflux pump proteins are thought to play a role. This study used RNA-seq data to investigate changes in the expression levels of efflux pump genes following exposure to KM.METHODS: RNA expression of efflux pump and regulatory genes following exposure to different concentrations of KM (minimum inhibitory concentration MIC 25 and MIC50) in rrs wild-type strain and rrs A1401G mutated strain were compared with the control group.RESULTS: The selected strains had differential RNA expression patterns. Among the 71 putative efflux pump and regulatory genes, 46 had significant fold changes, and 12 genes (Rv0842, Rv1146, Rv1258c, Rv1473, Rv1686c, Rv1687c, Rv1877, Rv2038c, Rv3065, Rv3197a, Rv3728 and Rv3789) that were overexpressed following exposure to KM were thought to contribute to drug resistance. Rv3197A (whiB7) showed a distinct fold change based on the concentration of KM.CONCLUSION: The significant changes in the expression of the efflux pump and regulatory genes following exposure to KM may provide insights into the identification of a new resistance mechanism.

Logic programming to infer complex RNA expression patterns from RNA-seq data

2016 ◽  
pp. bbw117 ◽  
Author(s):  
Tyler Weirick ◽  
Giuseppe Militello ◽  
Yuliya Ponomareva ◽  
David John ◽  
Claudia Döring ◽  
...  
Keyword(s):  
Logic Programming ◽  
Expression Patterns ◽  
Rna Expression ◽  
Rna Seq

scholarly journals Insights into the Resistome and Phylogenomics of a ST195 Multidrug-Resistant Acinetobacter baumannii Clinical Isolate from the Czech Republic

Life ◽  
2021 ◽  
Vol 11 (10) ◽  
pp. 1079
Author(s):  
Patrik Mlynarcik ◽  
Monika Dolejska ◽  
Iva Vagnerova ◽  
Jana Petrzelova ◽  
Iva Sukkar ◽  
...  
Keyword(s):  
Acinetobacter Baumannii ◽  
Clinical Isolate ◽  
Efflux Pump ◽  
Resistance Mechanism ◽  
Carbapenem Resistance ◽  
Multidrug Resistant ◽  
Clinical Settings ◽  
Sequencing Analysis ◽  
Pump System ◽  
The Czech Republic

Increasing antimicrobial resistance in nosocomial pathogens, such as Acinetobacter baumannii, is becoming a serious threat to public health. It is necessary to detect β-lactamase-producing microorganisms in clinical settings to be able to control the spread of carbapenem resistance. This study was conducted to evaluate the presence of β-lactamases in a selected clinical isolate of A. baumannii of ST2P/ST195Ox and to characterize possible enzymes, as well as its β-lactam resistome, using PCR and whole-genome sequencing analysis. PCR and sequencing confirmed that the isolate harbored five bla gene alleles, namely, blaADC-73, blaTEM-1, blaOXA-23, blaOXA-58 and blaOXA-66, as well as aminoglycosides, macrolides, sulfonamides and tetracyclines resistance determinants, which were either chromosomally and/or plasmid located. Furthermore, a gene order comparison using MAUVE alignment showed multiple changes compared with the clinical isolate of Malaysian A. baumannii AC30 genome and 76 regions with high homology. This study suggests that resistance to β-lactams in this A. baumannii isolate is mainly due to an overproduction of β-lactamases in combination with other resistance mechanism (efflux pump system).

scholarly journals Genome Analysis of Antimicrobial Resistance Genes and Virulence Factors in Multidrug-Resistant Campylobacter fetus Subspecies Isolated from Sheath Wash

2020 ◽  
Vol 10 (4) ◽  
pp. 465-480
Author(s):  
Mpinda Edoaurd Tshipamba ◽  
Ngoma Lubanza ◽  
Mulunda Mwanza
Keyword(s):  
Antibiotic Resistance ◽  
Virulence Factors ◽  
Efflux Pump ◽  
Resistance Mechanism ◽  
Multidrug Resistant ◽  
Diffusion Method ◽  
Genetic Profile ◽  
Multidrug Efflux Pump ◽  
Campylobacter Fetus ◽  
Antimicrobial Resistance Genes

Campylobacter fetus subspecies are mostly characterized by reproductions problems in cattle and sheep. This study aimed to study the genetic profile and assess the genes mechanism of resistance and their virulence factors using genome sequence analysis. A total of 59 confirmed Campylobacter fetus subspecies based on molecular assays and DNA sequencing were subjected to antimicrobial susceptibility test against 14 antibiotic agents representing the five classes of antibiotics using the disc diffusion method. In addition, sequencing the genome of all strains induced complete resistance against all tested antibiotics. The results of the antimicrobial test indicated that 54.4% had a resistance profile, 26.3% were intermediate, while 19.3% were observed to be susceptible. The Whole Genome Sequencing (WGS) result revealed the presence of different genes, such as Broad-specificity multidrug efflux pump and 16S rRNA (guanine527-N7)-methyltransferase (gidB), efflux pump conferring antibiotic resistance (MacA and MacB), protein-altering cell wall charge conferring antibiotic resistance (PgsA), which have never been reported in Campylobacter fetus subspecies. The WGS also revealed the presence of genes that involved in colonization, adhesion, motility, and invasion, such as type IV secretion system protein (VirD4), S-Layer, cytolethal distending toxin (A, B, and C), Campylobacter invasion antigen (CiaB), and fic domain protein (fic) were among important CDS. The presence of these uncommon genes explains the resistance of Campylobacter fetus subspecies against different tested antibiotics. The results of this study can be used to implement molecular surveillance of Campylobacter fetus subspecies and conduct further studies on the resistance mechanism in these subspecies.

scholarly journals A novel genome editing platform for drug resistantAcinetobacter baumanniirevealed an AdeR-unrelated tigecycline resistance mechanism

2016 ◽  
pp. AAC.01275-16 ◽  
Author(s):  
Vincent Trebosc ◽  
Sarah Gartenmann ◽  
Kevin Royet ◽  
Pablo Manfredi ◽  
Marcus Tötzl ◽  
...  
Keyword(s):  
Genome Editing ◽  
Efflux Pump ◽  
Treatment Options ◽  
Resistance Mechanism ◽  
Multidrug Resistant ◽  
Clinical Isolates ◽  
Future Research ◽  
Drug Resistant ◽  
Loss Of Function ◽  
Drug Resistant Phenotype

Infections with the Gram-negative coccobacillusAcinetobacter baumanniiare a major threat in hospital settings. The progressing emergence of multidrug resistant clinical strains significantly reduces the treatment options for clinicians to fightA. baumanniiinfections. The current lack of robust methods to genetically manipulate drug resistantA. baumanniiisolates impedes research on resistance and virulence mechanisms in clinically relevant strains. In this study we developed a highly efficient and versatile genome editing platform enabling the markerless modification of the genome ofA. baumanniiclinical and laboratory strains, regardless of their resistance profile.We applied this method for the deletion of AdeR, a transcription factor that regulates the expression of the AdeABC efflux pump in tigecycline resistantA. baumannii, to evaluate its function as a putative drug target. Loss ofadeRreduced the MIC90of tigecycline from 25 μg/ml in the parental strains to 3.1 μg/ml in theΔadeRmutants indicating its importance in the drug resistant phenotype. However, 60% of the clinical isolates remained non-susceptible to tigecycline afteradeRdeletion. Evolution of artificial tigecycline resistance in two strains followed by whole genome sequencing revealed loss of function mutations intrm,suggesting its role in an alternative AdeABC-independent tigecycline resistance mechanism. This finding was strengthened by the confirmation oftrmdisruption in the majority of the tigecycline resistant clinical isolates. This study highlights the development and application of a powerful genome editing platform forA. baumanniienabling future research on drug resistance and virulence pathways in clinical relevant strains.

scholarly journals Structure and expression of the human MDR (P-glycoprotein) gene family.

1989 ◽  
Vol 9 (9) ◽  
pp. 3808-3820 ◽  
Author(s):  
J E Chin ◽  
R Soffir ◽  
K E Noonan ◽  
K Choi ◽  
I B Roninson
Keyword(s):  
Gene Family ◽  
Cell Lines ◽  
Efflux Pump ◽  
Expression Patterns ◽  
Multidrug Resistant ◽  
Resistant Cell ◽  
Mdr1 Gene ◽  
Glycoprotein Gene ◽  
P Glycoprotein ◽  
Mdr Genes

The human MDR (P-glycoprotein) gene family is known to include two members, MDR1 and MDR2. The product of the MDR1 gene, which is responsible for resistance to different cytotoxic drugs (multidrug resistance), appears to serve as an energy-dependent efflux pump for various lipophilic compounds. The function of the MDR2 gene remains unknown. We have examined the structure of the human MDR gene family by Southern hybridization of DNA from different multidrug-resistant cell lines with subfragments of MDR1 cDNA and by cloning and sequencing of genomic fragments. We have found no evidence for any other cross-hybridizing MDR genes. The sequence of two exons of the MDR2 gene was determined from genomic clones. Hybridization with single-exon probes showed that the human MDR1 gene is closely related to two genes in mouse and hamster DNA, whereas MDR2 corresponds to one rodent gene. The human MDR locus was mapped by field-inversion gel electrophoresis, and both MDR genes were found to be linked within 330 kilobases. The expression patterns of the human MDR genes were examined by enzymatic amplification of cDNA. In multidrug-resistant cell lines, increased expression of MDR1 mRNA was paralleled by a smaller increase in the levels of MDR2 mRNA. In normal human tissues, MDR2 was coexpressed with MDR1 in the liver, kidney, adrenal gland, and spleen. MDR1 expression was also detected in colon, lung, stomach, esophagus, muscle, breast, and bladder.

scholarly journals Amidochelocardin Overcomes Resistance Mechanisms Exerted on Tetracyclines and Natural Chelocardin

Antibiotics ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 619
Author(s):  
Fabienne Hennessen ◽  
Marcus Miethke ◽  
Nestor Zaburannyi ◽  
Maria Loose ◽  
Tadeja Lukežič ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Efflux Pump ◽  
Resistance Mechanism ◽  
Tetracycline Resistance ◽  
Multidrug Resistant ◽  
Resistance Mechanisms ◽  
Resistance Breaking ◽  
Pharmaceutical Properties ◽  
Tract Infections

The reassessment of known but neglected natural compounds is a vital strategy for providing novel lead structures urgently needed to overcome antimicrobial resistance. Scaffolds with resistance-breaking properties represent the most promising candidates for a successful translation into future therapeutics. Our study focuses on chelocardin, a member of the atypical tetracyclines, and its bioengineered derivative amidochelocardin, both showing broad-spectrum antibacterial activity within the ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) panel. Further lead development of chelocardins requires extensive biological and chemical profiling to achieve favorable pharmaceutical properties and efficacy. This study shows that both molecules possess resistance-breaking properties enabling the escape from most common tetracycline resistance mechanisms. Further, we show that these compounds are potent candidates for treatment of urinary tract infections due to their in vitro activity against a large panel of multidrug-resistant uropathogenic clinical isolates. In addition, the mechanism of resistance to natural chelocardin was identified as relying on efflux processes, both in the chelocardin producer Amycolatopsis sulphurea and in the pathogen Klebsiella pneumoniae. Resistance development in Klebsiella led primarily to mutations in ramR, causing increased expression of the acrAB-tolC efflux pump. Most importantly, amidochelocardin overcomes this resistance mechanism, revealing not only the improved activity profile but also superior resistance-breaking properties of this novel antibacterial compound.

scholarly journals Discovery of new antibacterial accramycins from a genetic variant of the soil bacterium, Streptomyces sp. MA37

2020 ◽  
Author(s):  
Fleurdeliz Maglangit ◽  
Yuting Zhang ◽  
Kwaku Kyeremeh ◽  
Hai Deng
Keyword(s):  
Wild Type Strain ◽  
Biosynthetic Gene Cluster ◽  
Multidrug Resistant ◽  
Regulatory Genes ◽  
Negative Regulator ◽  
Clinical Isolates ◽  
Wild Type ◽  
In The Wild ◽  
A Minor ◽  
New Metabolites

AbstractContinued mining of natural products from the strain Streptomyces sp. MA37 in our laboratory led to the discovery of a minor specialised metabolite (SM) called accramycin A. Owing to its low yield (0.2mg/L) in the wild type strain, we investigated the roles of regulatory genes in the corresponding biosynthetic gene cluster (acc BGC) through gene inactivation with the aim of improving the titre of this compound. One of the resulting mutants (ΔaccJ) dramatically upregulated the production of accramycin A 1 by 330-fold (66mg/L). Furthermore, ten new metabolites, accramycins B-K 2-11, were discovered, together with two known compounds, naphthacemycin B112 and fasamycin C 13 from the mutant extract. This suggested that accJ, annotated as Multiple Antibiotic Resistance Regulator (MarR), is a negative regulator gene in the accramycin biosynthesis. Compounds 1-13 inhibited the Gram-positive pathogens (S. aureus, E. faecalis) and clinical isolates, E. faecium (K59-68 and K60-39), and S. haemolyticus with minimal inhibitory concentration (MIC) values in the range of 1.5-12.5µg/mL. Remarkably, compounds 1-13 displayed superior activity against K60-39 (MIC = 3.1-6.3µg/mL) than ampicillin (MIC = 25µg/mL), and offer promising potential for the development of accramycin-based antibiotics that target multidrug-resistant Enterococcus clinical isolates. Our results highlight the importance of identifying the roles of regulatory genes in natural product discovery.

Structure and expression of the human MDR (P-glycoprotein) gene family

1989 ◽  
Vol 9 (9) ◽  
pp. 3808-3820
Author(s):  
J E Chin ◽  
R Soffir ◽  
K E Noonan ◽  
K Choi ◽  
I B Roninson
Keyword(s):  
Gene Family ◽  
Cell Lines ◽  
Efflux Pump ◽  
Expression Patterns ◽  
Multidrug Resistant ◽  
Resistant Cell ◽  
Mdr1 Gene ◽  
Glycoprotein Gene ◽  
P Glycoprotein ◽  
Mdr Genes

The human MDR (P-glycoprotein) gene family is known to include two members, MDR1 and MDR2. The product of the MDR1 gene, which is responsible for resistance to different cytotoxic drugs (multidrug resistance), appears to serve as an energy-dependent efflux pump for various lipophilic compounds. The function of the MDR2 gene remains unknown. We have examined the structure of the human MDR gene family by Southern hybridization of DNA from different multidrug-resistant cell lines with subfragments of MDR1 cDNA and by cloning and sequencing of genomic fragments. We have found no evidence for any other cross-hybridizing MDR genes. The sequence of two exons of the MDR2 gene was determined from genomic clones. Hybridization with single-exon probes showed that the human MDR1 gene is closely related to two genes in mouse and hamster DNA, whereas MDR2 corresponds to one rodent gene. The human MDR locus was mapped by field-inversion gel electrophoresis, and both MDR genes were found to be linked within 330 kilobases. The expression patterns of the human MDR genes were examined by enzymatic amplification of cDNA. In multidrug-resistant cell lines, increased expression of MDR1 mRNA was paralleled by a smaller increase in the levels of MDR2 mRNA. In normal human tissues, MDR2 was coexpressed with MDR1 in the liver, kidney, adrenal gland, and spleen. MDR1 expression was also detected in colon, lung, stomach, esophagus, muscle, breast, and bladder.

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