scholarly journals Integrated Genome-Wide Analysis of an Isogenic Pair of Pseudomonas aeruginosa Clinical Isolates with Differential Antimicrobial Resistance to Ceftolozane/Tazobactam, Ceftazidime/Avibactam, and Piperacillin/Tazobactam

2020 ◽  
Vol 21 (3) ◽  
pp. 1026 ◽  
Author(s):  
Weihua Huang ◽  
Joelle El Hamouche ◽  
Guiqing Wang ◽  
Melissa Smith ◽  
Changhong Yin ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Pseudomonas Aeruginosa ◽  
Antimicrobial Resistance ◽  
Multidrug Resistant ◽  
Clinical Isolates ◽  
Epigenetic Mechanism ◽  
Phenotypic Change ◽  
Genome Wide ◽  
Family Protein ◽  
Significant Difference

Multidrug-resistant (MDR) Pseudomonas aeruginosa is one of the main causes of morbidity and mortality in hospitalized patients and the leading cause of nosocomial infections. We investigated, here, two MDR P. aeruginosa clinical isolates from a hospitalized patient with differential antimicrobial resistance to ceftazidime/avibactam (CZA), ceftolozane/tazobactam (C/T), and piperacillin/tazobactam (P/T). Their assembled complete genomes revealed they belonged to ST235, a widespread MDR clone; and were isogenic with only a single nucleotide variant, causing G183D mutation in AmpC β-lactamase, responsible for a phenotypic change from susceptible to resistant to CZA and C/T. Further epigenomic profiling uncovered two conserved DNA methylation motifs targeted by two distinct putative methyltransferase-containing restriction-modification systems, respectively; more intriguingly, there was a significant difference between the paired isolates in the pattern of genomic DNA methylation and modifications. Moreover, genome-wide gene expression profiling demonstrated the inheritable genomic methylation and modification induced 14 genes being differentially regulated, of which only toxR (downregulated), a regulatory transcription factor, had its promoter region differentially methylate and modified. Since highly expressed opdQ encodes an OprD porin family protein, therefore, we proposed an epigenetic regulation of opdQ expression pertinent to the phenotypic change of P. aeruginosa from resistant to susceptible to P/T. The disclosed epigenetic mechanism controlling phenotypic antimicrobial resistance deserves further experimental investigation.

Genome-wide Differential-based Analysis of the Relationship between DNA Methylation and Gene Expression in Cancer

2019 ◽  
Vol 14 (8) ◽  
pp. 783-792 ◽  
Author(s):  
Yuanyuan Zhang ◽  
Chuanhua Kou ◽  
Shudong Wang ◽  
Yulin Zhang
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Epigenetic Modification ◽  
Epigenetic Mechanism ◽  
Gene Body ◽  
Differential Analysis ◽  
Promoter Regions ◽  
Genome Wide ◽  
Significant Difference ◽  
The Relationship

Background:: DNA methylation is an epigenetic modification that plays an important role in regulating gene expression. There is evidence that the hypermethylation of promoter regions always causes gene silencing. However, how the methylation patterns of other regions in the genome, such as gene body and 3’UTR, affect gene expression is unknown. Objective:: The study aimed to fully explore the relationship between DNA methylation and expression throughout the genome-wide analysis which is important in understanding the function of DNA methylation essentially. Method:: In this paper, we develop a heuristic framework to analyze the relationship between the methylated change in different regions and that of the corresponding gene expression based on differential analysis. Results:: To understande the methylated function of different genomic regions, a gene is divided into seven functional regions. By applying the method in five cancer datasets from the Synapse database, it was found that methylated regions with a significant difference between cases and controls were almost uniformly distributed in the seven regions of the genome. Also, the effect of DNA methylation in different regions on gene expression was different. For example, there was a higher percentage of positive relationships in 1stExon, gene body and 3’UTR than in TSS1500 and TSS200. The functional analysis of genes with a significant positive and negative correlation between DNA methylation and gene expression demonstrated the epigenetic mechanism of cancerassociated genes. Conclusion:: Differential based analysis helps us to recognize the change in DNA methylation and how this change affects the change in gene expression. It provides a basis for further integrating gene expression and DNA methylation data to identify disease-associated biomarkers.

scholarly journals Characterization of Genome-Wide DNA Methylation and Hydroxymethylation in Mouse Arcuate Nucleus of Hypothalamus During Puberty Process

2020 ◽  
Vol 11 ◽  
Author(s):  
Yihang Shen ◽  
Shasha Zhou ◽  
Xiaodong Zhao ◽  
Hua Li ◽  
Jielin Sun
Keyword(s):  
Dna Methylation ◽  
Arcuate Nucleus ◽  
Epigenetic Mechanism ◽  
Promoter Regions ◽  
Gonadotropin Secretion ◽  
Dna Hydroxymethylation ◽  
Genome Wide ◽  
Significant Difference ◽  
Gnrh Release ◽  
Hypothalamic Arcuate Nucleus

Background: Pulsatile pituitary gonadotropin secretion governed by hypothalamic gonadotropin-releasing hormone (GnRH) is essential for the pubertal onset. The epigenetic mechanism underlying the activation of GnRH-dependent regulatory axis in hypothalamus remains elusive. This study aims to explore the potential correlation between the signature of DNA (hydroxyl)methylation and pubertal process.Methods: Hypothalamic arcuate nucleus (ARC) of mouse at early (4-weeks) and late pubertal (8-weeks) stages underwent RNA-, RRBS-, and RRHP-seq to investigate the genome-wide profiles of transcriptome, differential DNA methylation and hydroxymethylation.Results: A series of differential expressed genes (DEGs) involved in sexual development could be separated into three subgroups with the significant difference of DNA methylation or hydroxymethylation or both in promoter regions. Compared to DNA methylation, DNA hydroxymethylation partook in more signaling pathways including synapse morphology, channel activity and glial development, which could enhance transsynaptic change and glia-to-neuron communication to faciliate GnRH release. The correlation between transcription and these epigenetic modifications indicated that DNA hydroxymethylation impacted with gene transcription independently of DNA methylation spanning puberty.Conclusion: Our results characterized the hydroxymethylation pattern and provided an insight into the novel epigenetic regulation on gene expression during pubertal process.

scholarly journals Detection of extended spectrum beta-lactamase genes in Pseudomonas aeruginosa isolated from patients in rural Eastern Cape Province, South Africa

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Mojisola C. Hosu ◽  
Sandeep D. Vasaikar ◽  
Grace E. Okuthe ◽  
Teke Apalata
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Antimicrobial Resistance ◽  
Multidrug Resistant ◽  
High Rate ◽  
Infection Prevention And Control ◽  
Beta Lactamase ◽  
Eastern Cape ◽  
Extended Spectrum Beta Lactamase ◽  
Extended Spectrum ◽  
Resistance Patterns

AbstractThe proliferation of extended spectrum beta-lactamase (ESBL) producing Pseudomonas aeruginosa represent a major public health threat. In this study, we evaluated the antimicrobial resistance patterns of P. aeruginosa strains and characterized the ESBLs and Metallo- β-lactamases (MBL) produced. Strains of P. aeruginosa cultured from patients who attended Nelson Mandela Academic Hospital and other clinics in the four district municipalities of the Eastern Cape between August 2017 and May 2019 were identified; antimicrobial susceptibility testing was carried out against thirteen clinically relevant antibiotics using the BioMérieux VITEK 2 and confirmed by Beckman autoSCAN-4 System. Real-time PCR was done using Roche Light Cycler 2.0 to detect the presence of ESBLs; blaSHV, blaTEM and blaCTX-M genes; and MBLs; blaIMP, blaVIM. Strains of P. aeruginosa demonstrated resistance to wide-ranging clinically relevant antibiotics including piperacillin (64.2%), followed by aztreonam (57.8%), cefepime (51.5%), ceftazidime (51.0%), piperacillin/tazobactam (50.5%), and imipenem (46.6%). A total of 75 (36.8%) multidrug-resistant (MDR) strains were observed of the total pool of isolates. The blaTEM, blaSHV and blaCTX-M was detected in 79.3%, 69.5% and 31.7% isolates (n = 82), respectively. The blaIMP was detected in 1.25% while no blaVIM was detected in any of the strains tested. The study showed a high rate of MDR P. aeruginosa in our setting. The vast majority of these resistant strains carried blaTEM and blaSHV genes. Continuous monitoring of antimicrobial resistance and strict compliance towards infection prevention and control practices are the best defence against spread of MDR P. aeruginosa.

Comparison of Prevalence, Antimicrobial Resistance, and Occurrence of Multidrug-Resistant Salmonella in Antimicrobial-Free and Conventional Pig Production

2006 ◽  
Vol 69 (4) ◽  
pp. 743-748 ◽  
Author(s):  
WONDWOSSEN A. GEBREYES ◽  
SIDDHARTHA THAKUR ◽  
W. E. MORGAN MORROW
Keyword(s):  
Antimicrobial Resistance ◽  
Production Systems ◽  
Multidrug Resistant ◽  
Resistance Pattern ◽  
Swine Production ◽  
Significant Difference ◽  
Conventional Farms ◽  
Resistance Patterns ◽  
Conventional Systems ◽  
On Farm

Conventional swine production evolved to routinely use antimicrobials, and common occurrence of antimicrobial-resistant Salmonella has been reported. There is a paucity of information on the antimicrobial resistance of Salmonella in swine production in the absence of antimicrobial selective pressure. Therefore, we compared the prevalence and antimicrobial resistance of Salmonella isolated from antimicrobial-free and conventional production systems. A total of 889 pigs and 743 carcasses were sampled in the study. Salmonella prevalence was significantly higher among the antimicrobial-free systems (15.2%) than the conventional systems (4.2%) (odds ratio [OR] = 4.23; P < 0.05). Antimicrobial resistance was detected against 10 of the 12 antimicrobials tested. The highest frequency of resistance was found against tetracycline (80%), followed by streptomycin (43.4%) and sulfamethoxazole (36%). Frequency of resistance to most classes of antimicrobials (except tetracycline) was significantly higher among conventional farms than antimicrobial-free farms, with ORs ranging from 2.84 for chloramphenicol to 23.22 for kanamycin at the on-farm level. A total of 28 antimicrobial resistance patterns were detected. A resistance pattern with streptomycin, sulfamethoxazole, and tetracycline (n = 130) was the most common multidrug resistance pattern. There was no significant difference in the proportion of isolates with this pattern between the conventional (19.5%) and the antimicrobial-free systems (18%) (OR = 1.8; P > 0.05). A pentaresistance pattern with ampicillin, chloramphenicol, streptomycin, sulfamethoxazole, and tetracycline was strongly associated with antimicrobial-free groups (OR = 5.4; P = 0.01). While showing the higher likelihood of finding antimicrobial resistance among conventional herds, this study also implies that specific multidrug-resistant strains may occur on antimicrobial-free farms. A longitudinal study with a representative sample size is needed to reach more conclusive results of the associations detected in this study.

scholarly journals Detection of Extended-Spectrum β-Lactamases in Clinical Isolates of Pseudomonas aeruginosa

2006 ◽  
Vol 50 (9) ◽  
pp. 2990-2995 ◽  
Author(s):  
Xiaofei Jiang ◽  
Zhe Zhang ◽  
Min Li ◽  
Danqiu Zhou ◽  
Feiyi Ruan ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Multidrug Resistant ◽  
Clinical Isolates ◽  
Screening Methods ◽  
Extended Spectrum ◽  
Pcr Product ◽  
Amoxicillin Clavulanate ◽  
Synergy Test ◽  
Esbl Producers ◽  
Disk Test

ABSTRACT With the occurrence of extended-spectrum β-lactamases (ESBLs) in Pseudomonas aeruginosa being increasingly reported worldwide, there is a need for a reliable test to detect ESBLs in clinical isolates of P. aeruginosa. In our study, a total of 75 clinical isolates of P. aeruginosa were studied. Nitrocefin tests were performed to detect the β-lactamase enzyme; isoelectric focusing electrophoresis, PCR, and PCR product sequencing were designed to further characterize the contained ESBLs. Various ESBL-screening methods were designed to compare the reliabilities of detecting ESBLs in clinical isolates of P. aeruginosa whose β-lactamases were well characterized. Thirty-four of 36 multidrug-resistant P. aeruginosa clinical isolates were positive for ESBLs. bla VEB-3 was the most prevalent ESBL gene in P. aeruginosa in our study. Among the total of 34 isolates that were considered ESBL producers, 20 strains were positive using conventional combined disk tests and 10 strains were positive using a conventional double-disk synergy test (DDST) with amoxicillin-clavulanate, expanded-spectrum cephalosporins, aztreonam, and cefepime. Modifications of the combined disk test and DDST, which consisted of shorter distances between disks (20 mm instead of 30 mm) and the use of three different plates that contained cloxacillin (200 μg/ml) alone, Phe-Arg β-naphthylamide dihydrochloride (MC-207,110; 20 μg/ml) alone, and both cloxacillin (200 μg/ml) and MC-207,110 (20 μg/ml) increased the sensitivity of the tests to 78.8%, 91.18%, 85.29%, and 97.06%.

scholarly journals Staphylococcus aureus Infections in Malaysia: A Review of Antimicrobial Resistance and Characteristics of the Clinical Isolates, 1990–2017

Antibiotics ◽  
2019 ◽  
Vol 8 (3) ◽  
pp. 128 ◽  
Author(s):  
Ainal Mardziah Che Hamzah ◽  
Chew Chieng Yeo ◽  
Suat Moi Puah ◽  
Kek Heng Chua ◽  
Ching Hoong Chew
Keyword(s):  
Staphylococcus Aureus ◽  
Antimicrobial Resistance ◽  
Sccmec Type ◽  
Epidemiological Data ◽  
Multidrug Resistant ◽  
Clinical Isolates ◽  
Type Iv ◽  
Resistant Strains ◽  
Vancomycin Resistant ◽  
Comprehensive Surveillance

Staphylococcus aureus is an important nosocomial pathogen and its multidrug resistant strains, particularly methicillin-resistant S. aureus (MRSA), poses a serious threat to public health due to its limited therapeutic options. The increasing MRSA resistance towards vancomycin, which is the current drug of last resort, gives a great challenge to the treatment and management of MRSA infections. While vancomycin resistance among Malaysian MRSA isolates has yet to be documented, a case of vancomycin resistant S. aureus has been reported in our neighboring country, Indonesia. In this review, we present the antimicrobial resistance profiles of S. aureus clinical isolates in Malaysia with data obtained from the Malaysian National Surveillance on Antimicrobial Resistance (NSAR) reports as well as various peer-reviewed published records spanning a period of nearly three decades (1990–2017). We also review the clonal types and characteristics of Malaysian S. aureus isolates, where hospital-associated (HA) MRSA isolates tend to carry staphylococcal cassette chromosome mec (SCCmec) type III and were of sequence type (ST)239, whereas community-associated (CA) isolates are mostly SCCmec type IV/V and ST30. More comprehensive surveillance data that include molecular epidemiological data would enable further in-depth understanding of Malaysian S. aureus isolates.

scholarly journals Enhancement of pyocyanin production by subinhibitory concentration of royal jelly in Pseudomonas aeruginosa

F1000Research ◽  
2021 ◽  
Vol 10 ◽  
pp. 14
Author(s):  
Dina Auliya Amly ◽  
Puspita Hajardhini ◽  
Alma Linggar Jonarta ◽  
Heribertus Dedy Kusuma Yulianto ◽  
Heni Susilowati
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Bacterial Growth ◽  
Biofilm Formation ◽  
Royal Jelly ◽  
Microtiter Plate ◽  
Multidrug Resistant ◽  
Clinical Isolates ◽  
Antibiotic Tolerance ◽  
Subinhibitory Concentration ◽  
Pyocyanin Production

Background: Pseudomonas aeruginosa, a multidrug-resistant Gram-negative bacterium, produces pyocyanin, a virulence factor associated with antibiotic tolerance. High concentrations of royal jelly have an antibacterial effect, which may potentially overcome antibacterial resistance. However, in some cases, antibiotic tolerance can occur due to prolonged stress of low-dose antibacterial agents. This study aimed to investigate the effect of subinhibitory concentrations of royal jelly on bacterial growth, pyocyanin production, and biofilm formation of P. aeruginosa. Methods: Pseudomonas aeruginosa ATCC 10145 and clinical isolates were cultured in a royal jelly-containing medium to test the antibacterial activity. Pyocyanin production was observed by measuring the absorbance at 690 nm after 36 h culture and determined using extinction coefficient 4310 M-1 cm-1. Static microtiter plate biofilm assay performed to detect the biofilm formation, followed by scanning electron microscopy. Results: Royal jelly effectively inhibited the viability of both strains from a concentration of 25%. The highest production of pyocyanin was observed in the subinhibitory concentration group 6.25%, which gradually decreased along with the decrease of royal jelly concentration. Results of one-way ANOVA tests differed significantly in pyocyanin production of the two strains between the royal jelly groups. Tukey HSD test showed concentrations of 12.5%, 6.25%, and 3.125% significantly increased pyocyanin production of ATCC 10145, and the concentrations of 12.5% and 6.25% significantly increased production of the clinical isolates. Concentrations of 12.5% and 6.125% significantly induced biofilm formation of P. aeruginosa ATCC 10145, in line with the results of the SEM analysis. Conclusions: The royal jelly concentration of 25% or higher inhibits bacterial growth; however, the subinhibitory concentration increases pyocyanin production and biofilm formation in P. aeruginosa. It is advisable to determine the appropriate concentration of royal jelly to obtain beneficial virulence inhibiting activity.

scholarly journals DNA methylation regulates transcriptional homeostasis of algal endosymbiosis in the coral modelAiptasia

2017 ◽  
Author(s):  
Yong Li ◽  
Yi Jin Liew ◽  
Guoxin Cui ◽  
Maha J Cziesielski ◽  
Noura Zahran ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Molecular Mechanisms ◽  
Model System ◽  
Epigenetic Mechanism ◽  
Symbiotic Relationship ◽  
Epigenetic Mechanisms ◽  
Genome Wide ◽  
Spurious Transcription ◽  
Coral Reef Ecosystems

The symbiotic relationship between cnidarians and dinoflagellates is the cornerstone of coral reef ecosystems. Although research is focusing on the molecular mechanisms underlying this symbiosis, the role of epigenetic mechanisms, which have been implicated in transcriptional regulation and acclimation to environmental change, is unknown. To assess the role of DNA methylation in the cnidarian-dinoflagellate symbiosis, we analyzed genome-wide CpG methylation, histone associations, and transcriptomic states of symbiotic and aposymbiotic anemones in the model systemAiptasia. We find methylated genes are marked by histone H3K36me3 and show significant reduction of spurious transcription and transcriptional noise, revealing a role of DNA methylation in the maintenance of transcriptional homeostasis. Changes in DNA methylation and expression show enrichment for symbiosis-related processes such as immunity, apoptosis, phagocytosis recognition and phagosome formation, and unveil intricate interactions between the underlying pathways. Our results demonstrate that DNA methylation provides an epigenetic mechanism of transcriptional homeostasis during symbiosis.

DNA microarray for genotyping multidrug-resistant Pseudomonas aeruginosa clinical isolates

2007 ◽  
Vol 59 (3) ◽  
pp. 325-338 ◽  
Author(s):  
Jan Weile ◽  
Rolf D. Schmid ◽  
Till T. Bachmann ◽  
Milorad Susa ◽  
Cornelius Knabbe
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Dna Microarray ◽  
Multidrug Resistant ◽  
Clinical Isolates
Sign in / Sign up

Export Citation Format

Share Document