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Genes Oct 2022Objective: The Beijing strain of Mycobacterium tuberculosis (MTB) is controversially presented as the predominant genotype and is more drug resistant to rifampicin and... (Meta-Analysis)
Meta-Analysis Review
Comparison on Major Gene Mutations Related to Rifampicin and Isoniazid Resistance between Beijing and Non-Beijing Strains of : A Systematic Review and Bayesian Meta-Analysis.
Objective: The Beijing strain of Mycobacterium tuberculosis (MTB) is controversially presented as the predominant genotype and is more drug resistant to rifampicin and isoniazid compared to the non-Beijing strain. We aimed to compare the major gene mutations related to rifampicin and isoniazid drug resistance between Beijing and non-Beijing genotypes, and to extract the best evidence using the evidence-based methods for improving the service of TB control programs based on genetics of MTB. Method: Literature was searched in Google Scholar, PubMed and CNKI Database. Data analysis was conducted in R software. The conventional and Bayesian random-effects models were employed for meta-analysis, combining the examinations of publication bias and sensitivity. Results: Of the 8785 strains in the pooled studies, 5225 were identified as Beijing strains and 3560 as non-Beijing strains. The maximum and minimum strain sizes were 876 and 55, respectively. The mutations prevalence of rpoB, katG, inhA and oxyR-ahpC in Beijing strains was 52.40% (2738/5225), 57.88% (2781/4805), 12.75% (454/3562) and 6.26% (108/1724), respectively, and that in non-Beijing strains was 26.12% (930/3560), 28.65% (834/2911), 10.67% (157/1472) and 7.21% (33/458), separately. The pooled posterior value of OR for the mutations of rpoB was 2.72 ((95% confidence interval (CI): 1.90, 3.94) times higher in Beijing than in non-Beijing strains. That value for katG was 3.22 (95% CI: 2.12, 4.90) times. The estimate for inhA was 1.41 (95% CI: 0.97, 2.08) times higher in the non-Beijing than in Beijing strains. That for oxyR-ahpC was 1.46 (95% CI: 0.87, 2.48) times. The principal patterns of the variants for the mutations of the four genes were rpoB S531L, katG S315T, inhA-15C > T and oxyR-ahpC intergenic region. Conclusion: The mutations in rpoB and katG genes in Beijing are significantly more common than that in non-Beijing strains of MTB. We do not have sufficient evidence to support that the prevalence of mutations of inhA and oxyR-ahpC is higher in non-Beijing than in Beijing strains, which provides a reference basis for clinical medication selection.
Topics: Isoniazid; Mycobacterium tuberculosis; Rifampin; Antitubercular Agents; Bayes Theorem; Microbial Sensitivity Tests; Bacterial Proteins; Mutation; DNA, Intergenic
PubMed: 36292734
DOI: 10.3390/genes13101849 -
Marine Drugs Apr 2022Fucoxanthin, belonging to the xanthophyll class of carotenoids, is a natural antioxidant pigment of marine algae, including brown macroalgae and diatoms. It represents... (Review)
Review
Fucoxanthin, belonging to the xanthophyll class of carotenoids, is a natural antioxidant pigment of marine algae, including brown macroalgae and diatoms. It represents 10% of the total carotenoids in nature. The plethora of scientific evidence supports the potential benefits of nutraceutical and pharmaceutical uses of fucoxanthin for boosting human health and disease management. Due to its unique chemical structure and action as a single compound with multi-targets of health effects, it has attracted mounting attention from the scientific community, resulting in an escalated number of scientific publications from January 2017 to February 2022. Fucoxanthin has remained the most popular option for anti-cancer and anti-tumor activity, followed by protection against inflammatory, oxidative stress-related, nervous system, obesity, hepatic, diabetic, kidney, cardiac, skin, respiratory and microbial diseases, in a variety of model systems. Despite much pharmacological evidence from in vitro and in vivo findings, fucoxanthin in clinical research is still not satisfactory, because only one clinical study on obesity management was reported in the last five years. Additionally, pharmacokinetics, safety, toxicity, functional stability, and clinical perspective of fucoxanthin are substantially addressed. Nevertheless, fucoxanthin and its derivatives are shown to be safe, non-toxic, and readily available upon administration. This review will provide pharmacological insights into fucoxanthin, underlying the diverse molecular mechanisms of health benefits. However, it requires more activity-oriented translational research in humans before it can be used as a multi-target drug.
Topics: Carotenoids; Humans; Neoplasms; Seaweed; Xanthophylls
PubMed: 35621930
DOI: 10.3390/md20050279 -
Journal of Applied Microbiology Dec 2022The molecular ecology of Staphylococcus aureus, Staphylococcus pseudintermedius and their methicillin-resistant strains in healthy dogs and cats could serve as good... (Review)
Review
Nasal Staphylococcus aureus and S. pseudintermedius carriage in healthy dogs and cats: a systematic review of their antibiotic resistance, virulence and genetic lineages of zoonotic relevance.
The molecular ecology of Staphylococcus aureus, Staphylococcus pseudintermedius and their methicillin-resistant strains in healthy dogs and cats could serve as good models to understand the concept of bacterial zoonosis due to animal companionship. This study aims to provide insights into pooled prevalence, genetic lineages, virulence and antimicrobial resistance (AMR) among healthy dogs and cats. Original research and brief communication articles published from 2001 to 2021 that reported the nasal detection of S. aureus and S. pseudintermedius in healthy dogs and cats in the community, homes and outside veterinary clinics were examined and analysed. Forty-nine studies were eligible and included in this systematic review. The pooled prevalence of nasal carriage of S. aureus/methicillin-resistant S. aureus (MRSA) in healthy dogs and cats were 10.9% (95% CI: 10.1-11.9)/2.8% (95% CI: 2.4-3.2) and 3.2% (95% CI: 1.9-4.8)/0.5% (95% CI: 0.0-1.1), respectively. Conversely, the pooled prevalence of S. pseudintermedius/methicillin-resistant S. pseudintermedius (MRSP) in healthy dogs and cats were 18.3% (95% CI: 17.1-19.7)/3.1% (95% CI: 2.5-3.7) and 1.3% (95% CI: 0.6-2.4)/1.2% (95% CI: 0.6-2.3), respectively. Although highly diverse genetic lineages of S. aureus were detected in healthy dogs and cats, MSSA-CC1/CC5/CC22/CC45/CC121/CC398 and MRSA-CC5/CC93/CC22/CC30 were mostly reported in dogs; and MSSA-CC5/CC8/CC15/CC48 and MRSA-CC22/CC30/CC80 in cats. Of note, MSSA-CC398 isolates (spa-types t034 and t5883) were detected in dogs. Genetic lineages often associated with MSSP/MRSP were ST20/ST71, highlighting the frequent detection of the epidemic European MRSP-ST71 clone in dogs. S. aureus isolates carrying the luk-S/F-PV, tst, eta, etb and etd genes were seldomly detected in dogs, and luk-S/F-PV was the unique virulence factor reported in isolates of cats. S. pseudintermedius isolates harbouring the luk-S/F-I, seint and expA genes were frequently found, especially in dogs. High and diverse rates of AMR were noted, especially among MRSA/MRSP isolates. There is a need for additional studies on the molecular characterization of isolates from countries with under-studied nasal staphylococci isolates.
Topics: Cats; Dogs; Animals; Staphylococcus aureus; Methicillin-Resistant Staphylococcus aureus; Virulence; Cat Diseases; Dog Diseases; Staphylococcal Infections; Methicillin Resistance; Anti-Bacterial Agents; Microbial Sensitivity Tests
PubMed: 36063061
DOI: 10.1111/jam.15803 -
PLoS Medicine Jun 2023Inappropriate antimicrobial usage is a key driver of antimicrobial resistance (AMR). Low- and middle-income countries (LMICs) are disproportionately burdened by AMR and...
BACKGROUND
Inappropriate antimicrobial usage is a key driver of antimicrobial resistance (AMR). Low- and middle-income countries (LMICs) are disproportionately burdened by AMR and young children are especially vulnerable to infections with AMR-bearing pathogens. The impact of antibiotics on the microbiome, selection, persistence, and horizontal spread of AMR genes is insufficiently characterized and understood in children in LMICs. This systematic review aims to collate and evaluate the available literature describing the impact of antibiotics on the infant gut microbiome and resistome in LMICs.
METHODS AND FINDINGS
In this systematic review, we searched the online databases MEDLINE (1946 to 28 January 2023), EMBASE (1947 to 28 January 2023), SCOPUS (1945 to 29 January 2023), WHO Global Index Medicus (searched up to 29 January 2023), and SciELO (searched up to 29 January 2023). A total of 4,369 articles were retrieved across the databases. Duplicates were removed resulting in 2,748 unique articles. Screening by title and abstract excluded 2,666 articles, 92 articles were assessed based on the full text, and 10 studies met the eligibility criteria that included human studies conducted in LMICs among children below the age of 2 that reported gut microbiome composition and/or resistome composition (AMR genes) following antibiotic usage. The included studies were all randomized control trials (RCTs) and were assessed for risk of bias using the Cochrane risk-of-bias for randomized studies tool. Overall, antibiotics reduced gut microbiome diversity and increased antibiotic-specific resistance gene abundance in antibiotic treatment groups as compared to the placebo. The most widely tested antibiotic was azithromycin that decreased the diversity of the gut microbiome and significantly increased macrolide resistance as early as 5 days posttreatment. A major limitation of this study was paucity of available studies that cover this subject area. Specifically, the range of antibiotics assessed did not include the most commonly used antibiotics in LMIC populations.
CONCLUSION
In this study, we observed that antibiotics significantly reduce the diversity and alter the composition of the infant gut microbiome in LMICs, while concomitantly selecting for resistance genes whose persistence can last for months following treatment. Considerable heterogeneity in study methodology, timing and duration of sampling, and sequencing methodology in currently available research limit insights into antibiotic impacts on the microbiome and resistome in children in LMICs. More research is urgently needed to fill this gap in order to better understand whether antibiotic-driven reductions in microbiome diversity and selection of AMR genes place LMIC children at risk for adverse health outcomes, including infections with AMR-bearing pathogens.
Topics: Infant; Child; Humans; Child, Preschool; Anti-Bacterial Agents; Developing Countries; Gastrointestinal Microbiome; Azithromycin; Drug Resistance, Microbial
PubMed: 37368871
DOI: 10.1371/journal.pmed.1004235 -
The European Respiratory Journal Jan 2017Only 25% of multidrug-resistant tuberculosis (MDR-TB) cases are currently diagnosed. Line probe assays (LPAs) enable rapid drug-susceptibility testing for rifampicin... (Meta-Analysis)
Meta-Analysis Review
Only 25% of multidrug-resistant tuberculosis (MDR-TB) cases are currently diagnosed. Line probe assays (LPAs) enable rapid drug-susceptibility testing for rifampicin (RIF) and isoniazid (INH) resistance and Mycobacterium tuberculosis detection. Genotype MTBDRplusV1 was WHO-endorsed in 2008 but newer LPAs have since been developed.This systematic review evaluated three LPAs: Hain Genotype MTBDRplusV1, MTBDRplusV2 and Nipro NTM+MDRTB. Study quality was assessed with QUADAS-2. Bivariate random-effects meta-analyses were performed for direct and indirect testing. Results for RIF and INH resistance were compared to phenotypic and composite (incorporating sequencing) reference standards. M. tuberculosis detection results were compared to culture.74 unique studies were included. For RIF resistance (21 225 samples), pooled sensitivity and specificity (with 95% confidence intervals) were 96.7% (95.6-97.5%) and 98.8% (98.2-99.2%). For INH resistance (20 954 samples), pooled sensitivity and specificity were 90.2% (88.2-91.9%) and 99.2% (98.7-99.5%). Results were similar for direct and indirect testing and across LPAs. Using a composite reference standard, specificity increased marginally. For M. tuberculosis detection (3451 samples), pooled sensitivity was 94% (89.4-99.4%) for smear-positive specimens and 44% (20.2-71.7%) for smear-negative specimens.In patients with pulmonary TB, LPAs have high sensitivity and specificity for RIF resistance and high specificity and good sensitivity for INH resistance. This meta-analysis provides evidence for policy and practice.
Topics: Antitubercular Agents; DNA Probes; Drug Resistance, Multiple, Bacterial; Humans; Isoniazid; Microbial Sensitivity Tests; Mycobacterium tuberculosis; Nucleic Acid Amplification Techniques; Rifampin; Sensitivity and Specificity; Sputum; Tuberculosis, Multidrug-Resistant; Tuberculosis, Pulmonary
PubMed: 28100546
DOI: 10.1183/13993003.01075-2016 -
The Science of the Total Environment Feb 2023Cover cropping is commonly acknowledged to promote soil health in agriculture. However, contradictory findings on the benefits of cover crops for soil health, crop... (Review)
Review
Cover cropping is commonly acknowledged to promote soil health in agriculture. However, contradictory findings on the benefits of cover crops for soil health, crop productivity, economic and ecological factors, as well as the influence of inherent soil parameters on such benefits exist in the scientific literature. Here, we critically assessed evidence of cover crop benefits through a systematic review of the published literature. To access relevant papers, we searched the literature for cover crops and soil health indicators using Scopus (1996-2020), ScienceDirect (1996-2020) and Google scholar (1970-1996) with specific keywords and combinations. Only English research papers including experimental plots and control groups were considered. We analyzed 102 unique peer-reviewed papers and 1494 corresponding unique plots encompassing various cover crops, soil textures, climates, management systems and experimental duration (1-3 years, 4-6 years, 7-10 years and over 10 years). Strong evidence suggests that cover crops can enhance soil structure and promote soil health by improving soil physical and chemical properties, including saturated hydraulic conductivity (mean net change of 105.6 %), total organic carbon (10.1 %), and total nitrogen (20.2 %). On the other hand, cover crops exhibit weak effects on properties like bulk density and microporosity with fairly low values of net change. In most cases, cover crops increase the soil carbon content, including microbial biomass carbon (19.5 %) and particulate organic carbon (49.5 %). In this systematic review, we found limited studies on the effect of cover crops on soil health as influenced by soil texture, regional climate, rainfall and duration of the cover crop practices. The paucity of long-term regional systematic research of soil physics, chemistry and biology makes it difficult to forecast future implications of cover crops on soil health indicators.
Topics: Soil; Agriculture; Crop Production; Crops, Agricultural; Carbon
PubMed: 36470378
DOI: 10.1016/j.scitotenv.2022.160600 -
World Journal of Gastroenterology Dec 2017To critically evaluate previous scientific evidence on Fusobacterium's role in colorectal neoplasia development. (Review)
Review
AIM
To critically evaluate previous scientific evidence on Fusobacterium's role in colorectal neoplasia development.
METHODS
Two independent investigators systematically reviewed all original scientific articles published between January, 2000, and July, 2017, using PubMed, EMBASE, and MEDLINE. A total of 355 articles were screened at the abstract level. Of these, only original scientific human, animal, and in vitro studies investigating and its relationship with colorectal cancer (CRC) were included in the analysis. Abstracts, review articles, studies investigating other colonic diseases, and studies written in other languages than English were excluded from our analysis. Ninety articles were included after removing duplicates, resolving disagreements between the two reviewers, and applying the above criteria.
RESULTS
Studies have consistently identified positive associations between , especially (), and CRC. Stronger associations were seen in CRCs proximal to the splenic flexure and CpG island methylator phenotype (CIMP)-high CRCs. There was evidence of temporality and a biological gradient, with increased DNA detection and quantity along the traditional adenoma-carcinoma sequence and in CIMP-high CRC precursors. Diet may have a differential impact on colonic enrichment; evidence suggests that high fiber diet may reduce the risk of a subset of CRCs that are DNA-positive. Data also suggest shorter CRC and disease-specific survival with increased amount of DNA in CRC tissue. The pathophysiology of enrichment of and other species in colonic tissue is unclear; however, the virulence factors and changes to the local colonic environment with disruption of the protective mucus layer may contribute. The presence of a host lectin (Gal-GalNAc) in the colonic epithelium may also mediate attachment to CRC and precursors through interaction with an protein, fibroblast activation protein 2 (FAP2). The clinical significance of detection or enrichment of in colorectal neoplasia is ambiguous, but data suggest a procarcinogenic effect of , likely due to activation of oncogenic and inflammatory pathways and modulation of the tumor immune environment. This is hypothesized to be mediated by certain strains carrying invasive properties and virulence factors such as FadA and FAP.
CONCLUSION
Evidence suggests a potential active role of , specifically , in CRC. Future prospective and experimental human studies would fill an important gap in this literature.
Topics: Animals; Carcinogenesis; Colon; Colorectal Neoplasms; CpG Islands; Fusobacterium; Fusobacterium Infections; Humans; Intestinal Mucosa; Methylation; Rectum
PubMed: 29358871
DOI: 10.3748/wjg.v23.i48.8626 -
Pediatric Research Jan 2024The first-pass meconium has been suggested as a proxy for the fetal gut microbiota because it is formed in utero. This systematic review and cohort study investigated...
BACKGROUND
The first-pass meconium has been suggested as a proxy for the fetal gut microbiota because it is formed in utero. This systematic review and cohort study investigated how pre- and perinatal factors influence the composition of the meconium microbiota.
METHODS
We performed the systematic review using Covidence by searching PubMed, Scopus, and Web of Science databases with the search terms "meconium microbiome" and "meconium microbiota". In the cohort study, we performed 16 S rRNA gene sequencing on 393 meconium samples and analyzed the sequencing data using QIIME2.
RESULTS
Our systematic review identified 69 studies exploring prenatal factors, immediate perinatal factors, and microbial composition in relation to subsequent health of infants but gave only limited comparative evidence regarding factors related to the composition of the meconium microbiota. The cohort study pointed to a low-biomass microbiota consisting of the phyla Firmicutes, Proteobacteria and Actinobacteriota and the genera Staphylococcus, Escherichia-Shigella and Lactobacillus, and indicated that immediate perinatal factors affected the composition of the meconium microbiota more than did prenatal factors.
CONCLUSIONS
This finding supports the idea that the meconium microbiota mostly starts developing during delivery.
IMPACT
It is unclear when the first-pass meconium microbiota develops, and what are the sources of the colonization. In this systematic review, we found 69 studies exploring prenatal factors, immediate perinatal factors, and microbial composition relative to subsequent health of infants, but there was no consensus on the factors affecting the meconium microbiota development. In this cohort study, immediate perinatal factors markedly affected the meconium microbiota development while prenatal factors had little effect on it. As the meconium microbiota composition was influenced by immediate perinatal factors, the present study supports the idea that the initial gut microbiota develops mainly during delivery.
Topics: Infant, Newborn; Pregnancy; Infant; Female; Humans; Meconium; Cohort Studies; Microbiota; Gastrointestinal Microbiome; Bacteria; RNA, Ribosomal, 16S
PubMed: 37591927
DOI: 10.1038/s41390-023-02783-z -
PloS One 2022Clostridium difficile is the leading cause of infectious diarrhea that develops in patients after hospitalization during antibiotic administration. It has also become a... (Meta-Analysis)
Meta-Analysis
BACKGROUND
Clostridium difficile is the leading cause of infectious diarrhea that develops in patients after hospitalization during antibiotic administration. It has also become a big issue in community-acquired diarrhea. The emergence of hypervirulent strains of C. difficile poses a major problem in hospital-associated diarrhea outbreaks and it is difficult to treat. The antimicrobial resistance in C. difficile has worsened due to the inappropriate use of broad-spectrum antibiotics including cephalosporins, clindamycin, tetracycline, and fluoroquinolones together with the emergence of hypervirulent strains.
OBJECTIVE
To estimate the pooled prevalence and antimicrobial resistance pattern of C. difficile derived from hospitalized diarrheal patients, a systematic review and meta-analysis was performed.
METHODS
Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guideline was followed to review published studies conducted. We searched bibliographic databases from PubMed, Scopus, Google Scholar, and Cochrane Library for studies on the prevalence and antimicrobial susceptibility testing on C. difficile. The weighted pooled prevalence and resistance for each antimicrobial agent was calculated using a random-effects model. A funnel plot and Egger's regression test were used to see publication bias.
RESULTS
A total of 15 studies were included. Ten articles for prevalence study and 5 additional studies for antimicrobial susceptibility testing of C. difficile were included. A total of 1967/7852 (25%) C. difficile were isolated from 10 included studies for prevalence study. The overall weighted pooled proportion (WPP) of C. difficile was 30% (95% CI: 10.0-49.0; p<0.001). The analysis showed substantial heterogeneity among studies (Cochran's test = 7038.73, I2 = 99.87%; p<0.001). The weighed pooled antimicrobial resistance (WPR) were: vancomycin 3%(95% CI: 1.0-4.0, p<0.001); metronidazole 5%(95% CI: 3.0-7.0, p<0.001); clindamycin 61%(95% CI: 52.0-69.0, p<0.001); moxifloxacin 42%(95% CI: 29-54, p<0.001); tetracycline 35%(95% CI: 22-49, p<0.001); erythromycin 61%(95% CI: 48-75, p<0.001) and ciprofloxacin 64%(95% CI: 48-80; p< 0.001) using the random effect model.
CONCLUSIONS
A higher weighted pooled prevalence of C. difficile was observed. It needs a great deal of attention to decrease the prevailing prevalence. The resistance of C. difficile to metronidazole and vancomycin was low compared to other drugs used to treat C. difficile infection. Periodic antimicrobial resistance monitoring is vital for appropriate therapy of C. difficile infection.
Topics: Anti-Bacterial Agents; Anti-Infective Agents; Clostridioides difficile; Clostridium Infections; Diarrhea; Drug Resistance, Bacterial; Drug Resistance, Microbial; Dysentery; Enterocolitis, Pseudomembranous; Hospitalization; Humans; Microbial Sensitivity Tests; Prevalence
PubMed: 35025959
DOI: 10.1371/journal.pone.0262597 -
International Journal of Molecular... Aug 2022In healthy women, the cervicovaginal microbiota is characterized by the predominance of spp., whereas the overgrowth of anaerobic bacteria leads to dysbiosis, known to... (Meta-Analysis)
Meta-Analysis Review
In healthy women, the cervicovaginal microbiota is characterized by the predominance of spp., whereas the overgrowth of anaerobic bacteria leads to dysbiosis, known to increase the risk of acquiring genital infections like . In the last decade, a growing body of research has investigated the composition of the cervicovaginal microbiota associated with chlamydial infection via 16s rDNA sequencing, with contrasting results. A systematic review and a meta-analysis, performed on the alpha-diversity indices, were conducted to summarize the scientific evidence on the cervicovaginal microbiota composition in infection. Databases PubMed, Scopus and Web of Science were searched with the following strategy: "Chlamydia trachomatis" AND "micro*". The diversity indices considered for the meta-analysis were Operational Taxonomic Unit (OTU) number, Chao1, phylogenetic diversity whole tree, Shannon's, Pielou's and Simpson's diversity indexes. The search yielded 425 abstracts for initial review, of which 16 met the inclusion criteria. The results suggested that the cervicovaginal microbiota in -positive women was characterized by dominance, or by a diverse mix of facultative or strict anaerobes. The meta-analysis, instead, did not show any difference in the microbial biodiversity between -positive and healthy women. Additional research is clearly required to deepen our knowledge on the interplay between the resident microflora and in the genital microenvironment.
Topics: Chlamydia Infections; Chlamydia trachomatis; Female; Humans; Microbiota; Phylogeny; RNA, Ribosomal, 16S; Vagina
PubMed: 36076948
DOI: 10.3390/ijms23179554