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British Journal of Cancer May 2022Substantial evidence indicates that dysbiosis of the gut microbial community is associated with colorectal neoplasia. This review aims to systematically summarise the...
BACKGROUND
Substantial evidence indicates that dysbiosis of the gut microbial community is associated with colorectal neoplasia. This review aims to systematically summarise the microbial markers associated with colorectal neoplasia and to assess their predictive performance.
METHODS
A comprehensive literature search of MEDLINE and EMBASE databases was performed to identify eligible studies. Observational studies exploring the associations between microbial biomarkers and colorectal neoplasia were included. We also included prediction studies that constructed models using microbial markers to predict CRC and adenomas. Risk of bias for included observational and prediction studies was assessed.
RESULTS
Forty-five studies were included to assess the associations between microbial markers and colorectal neoplasia. Nine faecal microbiotas (i.e., Fusobacterium, Enterococcus, Porphyromonas, Salmonella, Pseudomonas, Peptostreptococcus, Actinomyces, Bifidobacterium and Roseburia), two oral pathogens (i.e., Treponema denticola and Prevotella intermedia) and serum antibody levels response to Streptococcus gallolyticus subspecies gallolyticus were found to be consistently associated with colorectal neoplasia. Thirty studies reported prediction models using microbial markers, and 83.3% of these models had acceptable-to-good discrimination (AUROC > 0.75). The results of predictive performance were promising, but most of the studies were limited to small number of cases (range: 9-485 cases) and lack of independent external validation (76.7%).
CONCLUSIONS
This review provides insight into the evidence supporting the association between different types of microbial species and their predictive value for colorectal neoplasia. Prediction models developed from case-control studies require further external validation in high-quality prospective studies. Further studies should assess the feasibility and impact of incorporating microbial biomarkers in CRC screening programme.
Topics: Adenoma; Biomarkers; Colorectal Neoplasms; Dysbiosis; Humans; Prospective Studies
PubMed: 35292756
DOI: 10.1038/s41416-022-01740-7 -
Microorganisms Jan 2024The global pandemic was caused by the SARS-CoV-2 virus, known as COVID-19, which primarily affects the respiratory and intestinal systems and impacts the microbial... (Review)
Review
The global pandemic was caused by the SARS-CoV-2 virus, known as COVID-19, which primarily affects the respiratory and intestinal systems and impacts the microbial communities of patients. This systematic review involved a comprehensive search across the major literature databases to explore the relationship between lactobacilli and COVID-19. Our emphasis was on investigations employing NGS technologies to explore this connection. Our analysis of nine selected studies revealed that lactobacilli have a reduced abundance in the disease and an association with disease severity. The protective mechanisms of lactobacilli in COVID-19 and other viral infections are likely to be multifaceted, involving complex interactions between the microbiota, the host immune system, and the virus itself. Moreover, upon closely examining the NGS methodologies and associated statistical analyses in each research study, we have noted concerns regarding the approach used to delineate the varying abundance of lactobacilli, which involves potential biases and the exclusion of pertinent data elements. These findings provide new insight into the relationship between COVID-19 and lactobacilli, highlighting the potential for microbiota modulation in COVID-19 treatment.
PubMed: 38399688
DOI: 10.3390/microorganisms12020284 -
Inflammatory Bowel Diseases Jun 2015The intestinal microbiota is involved in the pathogenesis of inflammatory bowel disease. A reduction in the diversity of the intestinal microbiota as well as specific... (Review)
Review
BACKGROUND
The intestinal microbiota is involved in the pathogenesis of inflammatory bowel disease. A reduction in the diversity of the intestinal microbiota as well as specific taxonomic and functional shifts have been reported in Crohn's disease and may play a central role in the inflammatory process. The aim was to systematically review recent developments in the structural and functional changes observed in the gastrointestinal microbiome in patients with Crohn's Disease.
RESULTS
Seventy-two abstracts were included in this review. The effects of host genetics, disease phenotype, and inflammatory bowel disease treatment on the gastrointestinal microbiome in Crohn's disease were reviewed, and taxonomic shifts in patients with early and established disease were described. The relative abundance of Bacteroidetes is increased and Firmicutes decreased in Crohn's disease compared with healthy controls. Enterobacteriaceae, specifically Eschericia coli, is enriched in Crohn's disease. Faecalibacterium prausnitzii is found at lower abundance in Crohn's disease and in those with postoperative recurrence. Observed functional changes include major shifts in oxidative stress pathways, a decrease in butanoate and propanoate metabolism gene expression, lower levels of butyrate, and other short-chain fatty acids, decreased carbohydrate metabolism, and decreased amino acid biosynthesis.
CONCLUSIONS
Changes in microbial composition and function have been described, although a causative role remains to be established. Larger, prospective, and longitudinal studies are required with deep interrogation of the microbiome if causality is to be determined, and refined microbial manipulation is to emerge as a focused therapy.
Topics: Bacteroidetes; Crohn Disease; Escherichia coli; Firmicutes; Gastrointestinal Microbiome; Humans
PubMed: 25844959
DOI: 10.1097/MIB.0000000000000382 -
Antimicrobial Resistance and Infection... Apr 2022Vibrio cholerae O1/O139 were the predominant circulating serogroups exhibiting multi-drug resistance (MDR) during the cholera outbreak which led to cholera treatment... (Meta-Analysis)
Meta-Analysis Review
BACKGROUND
Vibrio cholerae O1/O139 were the predominant circulating serogroups exhibiting multi-drug resistance (MDR) during the cholera outbreak which led to cholera treatment failures.
OBJECTIVE
This meta-analysis aimed to evaluate the weighted pooled resistance (WPR) rates in V. cholerae O1/O139 isolates obtained from environmental samples.
METHODS
We systematically searched the articles in PubMed, Scopus, and Embase (until January 2020). Subgroup analyses were then employed by publication year, geographic areas, and the quality of studies. Statistical analyses were conducted using STATA software (ver. 14.0).
RESULTS
A total of 20 studies investigating 648 environmental V. cholerae O1/O139 isolates were analysed. The majority of the studies were originated from Asia (n = 9). In addition, a large number of studies (n = 15 i.e. 71.4%) included in the meta-analysis revealed the resistance to cotrimoxazole and ciprofloxacin. The WPR rates were as follows: cotrimoxazole 59%, erythromycin 28%, tetracycline 14%, doxycycline 5%, and ciprofloxacin 0%. There was increased resistance to nalidixic acid, cotrimoxazole, furazolidone, and tetracycline while a decreased resistance to amoxicillin, ciprofloxacin, erythromycin, chloramphenicol, ampicillin, streptomycin, and ceftriaxone was observed during the years 2000-2020. A significant decrease in the doxycycline and ciprofloxacin-resistance rates in V. cholerae O1/O139 isolates was reported over the years 2011-2020 which represents a decrease in 2001-2010 (p < 0.05).
CONCLUSIONS
Fluoroquinolones, gentamicin, ceftriaxone, doxycycline, kanamycin, and cefotaxime showed the highest effectiveness and the lowest resistance rate. However, the main interest is the rise of antimicrobial resistance in V. cholerae strains especially in low-income countries or endemic areas, and therefore, continuous surveillance, careful appropriate AST, and limitation on improper antibiotic usage are crucial.
Topics: Anti-Bacterial Agents; Ceftriaxone; Cholera; Ciprofloxacin; Doxycycline; Drug Resistance, Bacterial; Erythromycin; Humans; Microbial Sensitivity Tests; Trimethoprim, Sulfamethoxazole Drug Combination; Vibrio cholerae O1; Vibrio cholerae O139
PubMed: 35468830
DOI: 10.1186/s13756-022-01100-3 -
Sheng Wu Gong Cheng Xue Bao = Chinese... May 2021Filamentous fungi are important industrial microorganisms that play important roles in the production of bio-based products such as organic acids, proteins and secondary...
Filamentous fungi are important industrial microorganisms that play important roles in the production of bio-based products such as organic acids, proteins and secondary metabolites. The development of metabolic engineering and its enabling techniques have greatly promoted the design, construction and application of filamentous fungal cell factories. This article systematically reviews the development of filamentous fungal cell factories constructed through metabolic engineering, and discusses the challenges and future perspectives for systems metabolic engineering of filamentous fungi.
Topics: Fungi; Metabolic Engineering
PubMed: 34085447
DOI: 10.13345/j.cjb.200723 -
Frontiers in Immunology 2024Increasing evidence indicates the microbial ecology of chronic obstructive pulmonary disease (COPD) is intricately associated with the disease's status and severity, and... (Meta-Analysis)
Meta-Analysis
BACKGROUND
Increasing evidence indicates the microbial ecology of chronic obstructive pulmonary disease (COPD) is intricately associated with the disease's status and severity, and distinct microbial ecological variations exist between COPD and healthy control (HC). This systematic review and meta-analysis aimed to summarize microbial diversity indices and taxa relative abundance of oral, airway, and intestine microbiota of different stages of COPD and HC to make comparisons.
METHODS
A comprehensive systematic literature search was conducted in PubMed, Embase, the Web of Science, and the Cochrane Library databases to identify relevant English articles on the oral, airway, and intestine microbiota in COPD published between 2003 and 8 May 2023. Information on microbial diversity indices and taxa relative abundance of oral, airway, and intestine microbiota was collected for comparison between different stages of COPD and HC.
RESULTS
A total of 20 studies were included in this review, involving a total of 337 HC participants, 511 COPD patients, and 154 AECOPD patients. We observed that no significant differences in alpha diversity between the participant groups, but beta diversity was significantly different in half of the included studies. Compared to HC, , , , and of oral microbiota in SCOPD were reduced at the genus level. Most studies supported that , , and were increased, but , , , , and were decreased at the genus level in the airway microbiota of SCOPD. However, the abundance of , and genera exhibited an increase, whereas and showed a decrease in the airway microbiota of AECOPD compared to HC. And of intestine microbiota in SCOPD was reduced at the genus level.
CONCLUSION
The majority of published research findings supported that COPD exhibited decreased alpha diversity compared to HC. However, our meta-analysis does not confirm it. In order to further investigate the characteristics and mechanisms of microbiome in the oral-airway- intestine axis of COPD patients, larger-scale and more rigorous studies are needed.
SYSTEMATIC REVIEW REGISTRATION
PROSPERO (https://www.crd.york.ac.uk/prospero/), identifier CRD42023418726.
Topics: Pulmonary Disease, Chronic Obstructive; Humans; Gastrointestinal Microbiome; Mouth; Microbiota; Bacteria
PubMed: 38779669
DOI: 10.3389/fimmu.2024.1407439 -
Antimicrobial Agents and Chemotherapy Sep 2015Pyrazinamide (PZA) is an important first-line drug in the treatment of tuberculosis (TB) and of significant interest to the HIV-infected community due to the prevalence... (Review)
Review
Pyrazinamide (PZA) is an important first-line drug in the treatment of tuberculosis (TB) and of significant interest to the HIV-infected community due to the prevalence of TB-HIV coinfection in some regions of the world. The mechanism of resistance to PZA is unlike that of any other anti-TB drug. The gene pncA, encoding pyrazinamidase (PZase), is associated with resistance to PZA. However, because single mutations in PZase have a low prevalence, the individual sensitivities are low. Hundreds of distinct mutations in the enzyme have been associated with resistance, while some only appear in susceptible isolates. This makes interpretation of molecular testing difficult and often leads to the simplification that any PZase mutation causes resistance. This systematic review reports a comprehensive global list of mutations observed in PZase and its promoter region in clinical strains, their phenotypic association, their global frequencies and diversity, the method of phenotypic determination, their MIC values when given, and the method of MIC determination and assesses the strength of the association between mutations and phenotypic resistance to PZA. In this systematic review, we report global statistics for 641 mutations in 171 (of 187) codons from 2,760 resistant strains and 96 mutations from 3,329 susceptible strains reported in 61 studies. For diagnostics, individual mutations (or any subset) were not sufficiently sensitive. Assuming similar error profiles of the 5 phenotyping platforms included in this study, the entire enzyme and its promoter provide a combined estimated sensitivity of 83%. This review highlights the need for identification of an alternative mechanism(s) of resistance, at least for the unexplained 17% of cases.
Topics: Amidohydrolases; Antitubercular Agents; Drug Resistance, Bacterial; Microbial Sensitivity Tests; Mutation; Mycobacterium tuberculosis; Pyrazinamide
PubMed: 26077261
DOI: 10.1128/AAC.00204-15 -
Journal of Clinical Microbiology Aug 2014Ethambutol (EMB) is a first-line antituberculosis drug; however, drug resistance to EMB has been increasing. Molecular drug susceptibility testing (DST), based on the... (Meta-Analysis)
Meta-Analysis Review
Ethambutol (EMB) is a first-line antituberculosis drug; however, drug resistance to EMB has been increasing. Molecular drug susceptibility testing (DST), based on the embB gene, has recently been used for rapid identification of EMB resistance. The aim of this meta-analysis was to establish the accuracy of molecular assay for detecting drug resistance to EMB. PubMed, Embase, and Web of Science were searched according to a written protocol and explicit study selection criteria. Measures of diagnostic accuracy were pooled using a random effects model. A total of 34 studies were included in the meta-analysis. The respective pooled sensitivities and specificities were 0.57 and 0.93 for PCR-DNA sequencing that targeted the embB 306 codon, 0.76 and 0.89 for PCR-DNA sequencing that targeted the embB 306, 406, and 497 codons, 0.64 and 0.70 for detecting Mycobacterium tuberculosis isolates, 0.55 and 0.78 for detecting M. tuberculosis sputum specimens using the GenoType MTBDRsl test, 0.57 and 0.87 for pyrosequencing, and 0.35 and 0.98 for PCR-restriction fragment length polymorphism. The respective pooled sensitivities and specificities were 0.55 and 0.92 when using a lower EMB concentration as the reference standard, 0.67 and 0.73 when using a higher EMB concentration as the reference standard, and 0.60 and 1.0 when using multiple reference standards. PCR-DNA sequencing using multiple sites of the embB gene as detection targets, including embB 306, 406, and 497, can be a rapid method for preliminarily screening for EMB resistance, but it does not fully replace phenotypic DST. Of the reference DST methods examined, the agreement rates were the best using MGIT 960 for molecular DST and using the proportion method on Middlebrook 7H10 media.
Topics: Antitubercular Agents; Ethambutol; Humans; Microbial Sensitivity Tests; Molecular Diagnostic Techniques; Mycobacterium tuberculosis; Pentosyltransferases; Polymerase Chain Reaction; Sensitivity and Specificity; Sequence Analysis, DNA
PubMed: 24899018
DOI: 10.1128/JCM.00560-14 -
Annals of Clinical Microbiology and... Dec 2020Campylobacter jejuni and Campylobacter coli accounts for most cases of human gastrointestinal infections. The infection occurs through ingestion of contaminated food or... (Meta-Analysis)
Meta-Analysis
Prevalence of Campylobacter species in human, animal and food of animal origin and their antimicrobial susceptibility in Ethiopia: a systematic review and meta-analysis.
BACKGROUND
Campylobacter jejuni and Campylobacter coli accounts for most cases of human gastrointestinal infections. The infection occurs through ingestion of contaminated food or water, and direct contact with feces of infected animal or human. Regardless of few local reports of Campylobacter and its antimicrobial susceptibility profile, there is no comprehensive data that show the burden of Campylobacter infection at national level in Ethiopia. This systemic review and meta-analysis aimed to determine the pooled prevalence of Campylobacter and its resistance patterns in Ethiopia from different sources.
METHOD
A comprehensive literature search of PubMed, Google scholar, Science direct and Google engine search was conducted for studies published from 2000 to July 30, 2020 on prevalence and antimicrobial susceptibility of Campylobacter in human, animal and food. The study was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) Checklist. Data from articles was extracted using a standardized data extraction format. The quality of the studies was assessed based on the Newcastle-Ottawa scale. The Q test and I test statistic were used to test heterogeneity across studies. The Pooled estimate of prevalence of Campylobacter species and its antimicrobial susceptibility profile was computed by a random effects model using STATA 16.0 software. Results were presented in forest plot, tables, funnel plot and figures with 95% confidence interval.
RESULTS
A total of 291 articles were retrieved initially. The pooled prevalence of Campylobacter species from different sources was 10.2% (95% CI 3.79, 16.51). In this meta-analysis, the lowest prevalence was 6.0% whereas the highest prevalence was 72.7%. In the sub-group analysis, the pooled prevalence was similar in Amhara and Oromia region, higher in Gambella and lower in Sidama. Prevalence of Campylobacter was higher in animals (14.6%) compared to humans (9%). The pooled antimicrobial resistance rates of Campylobacter species to different antimicrobials ranged from 2.9-100%. Overall, higher rate of resistance was to cephalothin (67.2%), gentamicin (67.2%), and trimethoprim-sulfamethoxazole (33.3%) in Campylobacter isolates from all sources. In isolates from human, resistance to cephalothin was 83% followed by amoxicillin (80%), amoxicillin-clavulnate (36%), trimethoprim-sulfamethpxazole (32%), clindamycin (31%) and ceftriaxone (28%). On the other hand, higher rate of resistance to penicillin (100%), cephalothin (60%), ciprofloxacin (71.2%), and trimethoprim-sulfamethoxazole (39%) was recorded in isolates from animals.
CONCLUSION
The present study highlights the burden of Campylobacter species in the country and higher rate of resistance among investigated isolates. Designing appropriate prevention strategies and further local in-depth studies are recommended to establish actual epidemiological burden of the bacteria in the country.
Topics: Animals; Anti-Bacterial Agents; Campylobacter; Campylobacter Infections; Cattle; Cattle Diseases; Chickens; Drug Resistance, Multiple, Bacterial; Ethiopia; Goat Diseases; Goats; Humans; Microbial Sensitivity Tests; Poultry Diseases; Prevalence; Sheep; Sheep Diseases; Swine; Swine Diseases
PubMed: 33302968
DOI: 10.1186/s12941-020-00405-8 -
The Indian Journal of Medical Research Mar 2017Neonates present a special subgroup of population in whom optimization of antimicrobial dosing can be particularly challenging. Gram-negative infections are common in... (Review)
Review
BACKGROUND & OBJECTIVES
Neonates present a special subgroup of population in whom optimization of antimicrobial dosing can be particularly challenging. Gram-negative infections are common in neonates, and inpatient treatment along with critical care is needed for the management of these infections. Dosing recommendations are often extrapolated from evidence generated in older patient populations. This systematic review was done to identify the knowledge gaps in the pharmacokinetics-pharmacodynamics (PK-PD)-based optimized dosing schedule for parenteral antimicrobials for Gram-negative neonatal infections.
METHODS
Relevant research questions were identified. An extensive electronic and manual search methodology was used. Potentially eligible articles were screened for eligibility. The relevant data were extracted independently in a pre-specified data extraction form. Pooling of data was planned.
RESULTS
Of the 340 records screened, 24 studies were included for data extraction and incorporation in the review [carbapenems - imipenem and meropenem (n=7); aminoglycosides - amikacin and gentamicin (n=9); piperacillin-tazobactam (n=2); quinolones (n=2); third- and fourth-generation cephalosporins (n=4) and colistin nil]. For each of the drug categories, the information for all the questions that the review sought to answer was incomplete. There was a wide variability in the covariates assessed, and pooling of results could not be undertaken.
INTERPRETATION & CONCLUSIONS
There is a wide knowledge gap for determining the doses of antimicrobials used for Gram-negative infections in neonates. A different profile of newborns in the developing countries could affect the disposition of antimicrobials for Gram negative infections, necessitating the generation of PK-PD data of antimicrobials in neonates from developing countries. Further, guidelines for treatment of neonatal conditions may incorporate the evidence-based PK-PD-guided dosing regimens.
Topics: Anti-Bacterial Agents; Dose-Response Relationship, Drug; Drug Resistance, Multiple, Bacterial; Gram-Negative Bacterial Infections; Humans; Infant, Newborn; Microbial Sensitivity Tests; Pseudomonas aeruginosa
PubMed: 28749392
DOI: 10.4103/ijmr.IJMR_723_15