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Microbial Drug Resistance (Larchmont,... Oct 2020The present systematic review and meta-analysis study aimed to investigate the prevalence of class 1 integrons and their associated antibiotic resistance in... (Meta-Analysis)
Meta-Analysis
The present systematic review and meta-analysis study aimed to investigate the prevalence of class 1 integrons and their associated antibiotic resistance in uropathogenic A systematic search was conducted to identify studies meeting our inclusion criteria in the Web of Science, PubMed, Embase, Scopus, and Google Scholar electronic databases to the end of July 2019. Finally, 35 articles were selected for data extraction, and meta-analysis was performed using the metaprop program in the STATA, version 11.0, software. The pooled prevalence of class 1 integrons was 47% (95% confidence interval [CI]: 40-54), ranging from 6% to 90%. There was significant heterogeneity among the 35 studies (χ = 840.37; < 0.001; = 95.95%). The results of the subgroup analysis based on characterization of patients indicated that pooled prevalence of class 1 integrons was 52% (95% CI: 41-63; = 14 studies) and 43% (95% CI: 34-54; = 19 studies) in hospitalized and community patients, respectively. The lowest and highest prevalence of antibiotic resistance was observed for imipenem and ampicillin, respectively. According to the results of Begg's and Egger's tests, we did not find significant publication bias both in the included studies and in the subgroup analysis. The results show the high prevalence of class 1 integrons and high level of antibiotic resistance in association with those among uropathogenic . Moreover, the prevalence of class 1 integrons in Asian countries, as well as hospital-acquired urinary tract infection (UTI), was higher than in other countries and community-acquired UTI.
Topics: Anti-Bacterial Agents; Community-Acquired Infections; Cross Infection; Drug Resistance, Bacterial; Escherichia coli Infections; Humans; Integrons; Prevalence; Urinary Tract Infections; Uropathogenic Escherichia coli
PubMed: 32282274
DOI: 10.1089/mdr.2019.0467 -
Applied and Environmental Microbiology Feb 2023Site-specific recombinases (integrases) can mediate the horizontal transfer of genomic islands. The ability to integrate large DNA sequences into target sites is very...
Site-specific recombinases (integrases) can mediate the horizontal transfer of genomic islands. The ability to integrate large DNA sequences into target sites is very important for genetic engineering in prokaryotic and eukaryotic cells. Here, we characterized an unprecedented catalogue of 530 tyrosine-type integrases by examining genes potentially encoding tyrosine integrases in bacterial genomic islands. The phylogeny of putative tyrosine integrases revealed that these integrases form an evolutionary clade that is distinct from those already known and are affiliated with novel integrase groups. We systematically searched for candidate integrase genes, and their integration activities were validated in a bacterial model. We verified the integration functions of six representative novel integrases by using a two-plasmid integration system consisting of a donor plasmid carrying the integrase gene and site and a recipient plasmid harboring an site in -deficient Escherichia coli. Further quantitative reverse transcription-PCR (qRT-PCR) assays validated that the six selected integrases can be expressed with their native promoters in E. coli. The region reductions showed that the extent of sites of integrases is approximately 200 bp for integration capacity. In addition, mutational analysis showed that the conserved tyrosine at the C terminus is essential for catalysis, confirming that these candidate proteins belong to the tyrosine-type recombinase superfamily, i.e., tyrosine integrases. This study revealed that the novel integrases from bacterial genomic islands have site-specific recombination functions, which is of physiological significance for their genomic islands in bacterial chromosomes. More importantly, our discovery expands the toolbox for genetic engineering, especially for efficient integration activity. Site-specific recombinases or integrases have high specificity for DNA large fragment integration, which is urgently needed for gene editing. However, known integrases are not sufficient for meeting multiple integrations. In this work, we discovered an array of integrases through bioinformatics analysis in bacterial genomes. Phylogeny and functional assays revealed that these new integrases belong to tyrosine-type integrases and have the ability to conduct site-specific recombination. Moreover, region extent and catalysis site analysis were characterized. Our study provides the methodology for discovery of novel integrases and increases the capacity of weapon pool for genetic engineering in bacteria.
Topics: Integrases; Genomic Islands; Escherichia coli; Tyrosine; Plasmids; Bacteriophages; Attachment Sites, Microbiological
PubMed: 36719242
DOI: 10.1128/aem.01738-22 -
Molecular Oral Microbiology Aug 2022The objective of this review was to assess the prevalence of antibiotic resistance genes in the oral cavity and identify mobile genetic elements (MGEs) important in... (Review)
Review
The objective of this review was to assess the prevalence of antibiotic resistance genes in the oral cavity and identify mobile genetic elements (MGEs) important in disseminating them. Additionally, to assess if age, geographic location, oral site, bacterial strains and oral disease influence the prevalence of these genes. Three electronic databases (Medline, Embase and the Cochrane Library) were used to search the literature. Journals and the grey literature were also hand searched. English language studies from January 2000 to November 2020 were selected. Primary screening was performed on the titles and abstracts of 1509 articles generated. One hundred and forty-seven full texts were obtained to conduct the second screening with strict inclusion and exclusion criteria. Forty-four final articles agreed with the inclusion criteria. Half of the studies were classed as low quality. tet(M) was the most prevalent gene overall and the conjugative transposon Tn916 the most common MGE associated with antibiotic resistance genes in the oral cavity. In babies delivered vaginally, tet(M) was more prevalent, whilst tet(Q) was more prevalent in those delivered by C-section. Generally, countries with higher consumption of antibiotics had higher numbers of antibiotic resistance genes. Agricultural as well as medical use of antibiotics in a country should always be considered. Between healthy, periodontitis and peri-implantitis subjects, there was no difference in the prevalence of tet(M); however, erm(B), tet(M) and tet(O) were higher in carious active children than the non-carious group. Subjects with poor oral hygiene have more pathogenic bacteria that carry resistance genes compared to those with good oral hygiene. Enterococcus faecalis isolates demonstrated significant tetracycline resistance (tet(M) up to 60% prevalence in samples) and erythromycin resistance (erm(B) up to 61.9% prevalence in samples), periodontal pathogens showed significant beta-lactam resistance with blaZ and cfxA present in up to 90%-97% of samples and the normal oral flora had a high level of erythromycin resistance with mef(A/E) present in 65% of Streptococcus salivarius isolates. The most common resistance gene was tet(M) in root canals, cfxA in subgingival plaque, erm(B) in supragingival plaque and tet(W) in 100% of whole saliva samples. The review highlights that although many studies in this area have been performed, 50% were classed as low quality. We advise the following recommendations to allow firm conclusions to be drawn from future work: the use of large sample sizes, investigate a broad range of antibiotic resistance genes, improved methodologies and reporting to improve the quality of genetic testing in microbiology and randomisation of subject selection.
Topics: Anti-Bacterial Agents; Bacteria; Child; Drug Resistance, Bacterial; Erythromycin; Humans; Interspersed Repetitive Sequences; Microbial Sensitivity Tests; Mouth; Prevalence
PubMed: 35674142
DOI: 10.1111/omi.12375 -
International Journal of Molecular... Jan 2022Human endogenous retroviruses (HERVs) are remnants of ancient retroviral infections that have become fixed in the human genome. While HERV genes are typically silenced...
Human endogenous retroviruses (HERVs) are remnants of ancient retroviral infections that have become fixed in the human genome. While HERV genes are typically silenced in healthy somatic cells, there are numerous reports of HERV transcription and translation across a wide spectrum of cancers, while T and B cell responses against HERV proteins have been detected in cancer patients. This review systematically categorizes the published evidence on the expression of and adaptive immune response against specific HERVs in distinct cancer types. A systematic literature search was performed using Medical Search Headings (MeSH) in the PubMed/Medline database. Papers were included if they described the translational activity of HERVs. We present multiple tables that pair the protein expression of specific HERVs and cancer types with information on the quality of the evidence. We find that HERV-K is the most investigated HERV. HERV-W (syncytin-1) is the second-most investigated, while other HERVs have received less attention. From a therapeutic perspective, HERV-K and HERV-E are the only HERVs with experimental demonstration of effective targeted therapies, but unspecific approaches using antiviral and demethylating agents in combination with chemo- and immunotherapies have also been investigated.
Topics: Animals; Antibody Formation; Endogenous Retroviruses; Host-Pathogen Interactions; Humans; Neoplasms; Retroviridae Infections; Viral Proteins
PubMed: 35163254
DOI: 10.3390/ijms23031330 -
The Journal of Surgical Research Aug 2019Human endogenous retroviruses (HERVs) are genetic elements in the human genome, which resulted from ancient retroviral germline infections. HERVs have strong...
BACKGROUND
Human endogenous retroviruses (HERVs) are genetic elements in the human genome, which resulted from ancient retroviral germline infections. HERVs have strong transcriptional promoters and enhancers that affect a cell's transcriptome. They also encode proteins that can exert effects in human cells. This review examines how our increased understanding of HERVs have led to their potential use as biomarkers and immunologic targets.
MATERIAL AND METHODS
PubMed/Medline, Embase, Web of Science, and Cochrane databases were used in a systematic search to identify all articles studying the potential impact of HERVs on surgical diseases. The search included studies that involved clinical patient samples in diseases including cancer, inflammatory conditions, and autoimmune disease. Articles focused on conditions not routinely managed by surgeons were excluded.
RESULTS
Eighty six articles met inclusion and quality criteria for this review and were included. Breast cancer and melanoma have robust evidence regarding the use of HERVs as potential tumor markers and immunologic targets. Reported evidence of the activity of HERVs in colorectal cancer, pancreatic cancer, hepatocellular cancer, prostate and ovarian cancer, germ cell tumors as well as idiopathic pulmonary hypertension, and the inflammatory response in burns was also reviewed.
CONCLUSIONS
Increasingly convincing evidence indicates that HERVs may play a role in solid organ malignancy and present important biomarkers or immunologic targets in multiple cancers. Innovative investigation of HERVs is a valuable focus of translational research and can deepen our understanding of cellular physiology and the effects of endogenous retroviruses on human biology. As strategies for treatment continue to focus on genome-based interventions, understanding the impact of endogenous retroviruses on human disease will be critical.
Topics: Antineoplastic Agents, Immunological; Biomarkers, Tumor; Endogenous Retroviruses; Gene Expression Regulation, Neoplastic; Genome, Human; Humans; Neoplasms; Transcriptome; Translational Research, Biomedical
PubMed: 30933828
DOI: 10.1016/j.jss.2019.02.009 -
Ethiopian Journal of Health Sciences Sep 2019Acinetobacter baumannii is an important opportunistic nosocomial pathogen. Class 1 integrons in A. baumannii plays a significant role in antibiotic resistance.... (Meta-Analysis)
Meta-Analysis
BACKGROUND
Acinetobacter baumannii is an important opportunistic nosocomial pathogen. Class 1 integrons in A. baumannii plays a significant role in antibiotic resistance. Therefore, this study aimed to investigate the prevalence of integrons and antibiotic resistance pattern in A. baumannii isolated from clinical samples of Iranian patients.
METHODS
The Medical Subject Headings (MeSH) and the keywords with the help of Boolean operators ("AND" or "OR") were used alone or in combination to conduct the search. The searching process was conducted in the Web of Science, PubMed, Cochrane Library, Scopus, and Google Scholar databases and, also Iranian databases. The search was restricted to relevant English and Persian cross-sectional publications reporting the prevalence of Int1 in A. baumannii isolated from clinical samples from 1 January 2000 to 31 December 2018. The data were analyzed using Comprehensive Meta-Analysis software. Regarding the heterogeneity of studies, the random effects model was used. Cochrane Q and I tests was used to evaluate statistical heterogeneity between the studies.
RESULTS
Fifteen studies were included in the analysis. The combined prevalence of class 1 integrons in A. baumannii was 55.2% (95% CI: 44.8-65.1). The pooled prevalence of MDR A. baumannii isolates was 68.1%. The highest resistance belonged to Aztreonam, followed by Ciprofloxacin, and Ceftazidime with a resistance rate of 97.6%, 92.8%, and 91.6%, respectively. Tobramycin was reported as an effective antibiotic.
CONCLUSIONS
The present study reported an alarmingly high prevalence of class 1 Integrons, and MDR isolates of A. baumannii recovered from clinical samples that should be considered.
Topics: Acinetobacter Infections; Acinetobacter baumannii; Anti-Bacterial Agents; Drug Resistance, Multiple, Bacterial; Humans; Integrons; Iran; Microbial Sensitivity Tests; Prevalence
PubMed: 31666786
DOI: 10.4314/ejhs.v29i5.15 -
Current Molecular Medicine May 2023HERVs are human endogenous retroviruses, which represent about 8% of the human genome, and have various physiological functions, especially in pregnancy, embryo...
INTRODUCTION
HERVs are human endogenous retroviruses, which represent about 8% of the human genome, and have various physiological functions, especially in pregnancy, embryo development and placenta formation. However, their involvement in diseases is not well defined. Some studies have observed changes in HERV expression according to age.
OBJECTIVE
Therefore, the aim of this systematic review was to analyze their role in pathogenesis and usage as diagnosis or prognosis biomarkers in aging disorders.
METHODS
In this study, a search on the Pubmed interface was performed for papers published from January 1953 to June 1, 2021.
RESULTS
45 articles have been included, which matched the eligibility criteria and evaluated the following diseases: breast cancer, prostate cancer, amyotrophic lateral sclerosis (ALS), osteoarthritis, Alzheimer's disease, immuno-senescence, cognitive impairment, cataract, glaucoma and hypertension.
CONCLUSION
In conclusion, the results suggested that HERVs play a role in the pathogenesis and can be used as biomarkers for the diagnosis or prognosis of aging disorders.
Topics: Male; Female; Pregnancy; Humans; Endogenous Retroviruses; Biomarkers; Placenta; Prostatic Neoplasms; Aging
PubMed: 35619278
DOI: 10.2174/1566524022666220525144135 -
Journal of Burn Care & Research :... Oct 2019The role of integrons has been highlighted in antibiotic resistance among Pseudomonas aeruginosa isolates. Therefore, we here reviewed the prevalence of class 1... (Meta-Analysis)
Meta-Analysis
The role of integrons has been highlighted in antibiotic resistance among Pseudomonas aeruginosa isolates. Therefore, we here reviewed the prevalence of class 1 integrons and their correlations with antibiotic resistance of P. aeruginosa isolated from Iranian burn patients. This review was conducted according to the guidelines of Preferred Reporting Items for Systematic Review and Meta-Analyses (PRISMA). Cross-sectional and cohort studies published from January 1, 2000 until December 31, 2018 were enrolled. Meta-analysis was performed by Comprehensive Meta-Analysis (CMA) software using the random effects model, Cochran's Q, and I2 tests. Publication bias was estimated by Funnel plot and Egger's linear regression test. Nine out of 819 studies met the eligibility criteria. The overall combined prevalence of class 1 integrons in P. aeruginosa isolates was 69% (95% confidence interval [CI]: 50.5-83%). The highest combined resistance was reported against Cloxacillin (87.7%), followed by Carbenicillin (79.1%) and Ceftriaxone (77.3%). The combined prevalence of multidrug-resistant (MDR) isolates was 79.3% (95% CI: 31.1-97%). Also, a significant correlation was noted between the presence of class 1 integrons and antibiotic resistance in 55.5% of the included studies (P < .05). The results showed high prevalence of class 1 integrons, antibiotic resistance, and MDR strains in P. aeruginosa isolated from Iranian burn patients. Also, most of the included studies showed a significant correlation between the presence of class 1 integrons and antibiotic resistance.
Topics: Anti-Bacterial Agents; Burns; Drug Resistance, Multiple, Bacterial; Humans; Integrons; Prevalence; Pseudomonas Infections; Pseudomonas aeruginosa; Wound Infection
PubMed: 31326983
DOI: 10.1093/jbcr/irz135