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FEMS Microbiology Reviews Jan 2024Rhizosphere microbes play critical roles for plant's growth and health. Among them, the beneficial rhizobacteria have the potential to be developed as the biofertilizer...
Rhizosphere microbes play critical roles for plant's growth and health. Among them, the beneficial rhizobacteria have the potential to be developed as the biofertilizer or bioinoculants for sustaining the agricultural development. The efficient rhizosphere colonization of these rhizobacteria is a prerequisite for exerting their plant beneficial functions, but the colonizing process and underlying mechanisms have not been thoroughly reviewed, especially for the nonsymbiotic beneficial rhizobacteria. This review systematically analyzed the root colonizing process of the nonsymbiotic rhizobacteria and compared it with that of the symbiotic and pathogenic bacteria. This review also highlighted the approaches to improve the root colonization efficiency and proposed to study the rhizobacterial colonization from a holistic perspective of the rhizosphere microbiome under more natural conditions.
Topics: Alphaproteobacteria; Bacteria; Plant Roots; Rhizosphere; Soil Microbiology; Symbiosis
PubMed: 38093453
DOI: 10.1093/femsre/fuad066 -
Infection Dec 2021Differentiating Acinetobacter baumannii complex (ABC) infection from colonization remains difficult and further complicated in polymicrobial infections. (Meta-Analysis)
Meta-Analysis Review
Systematic review and meta-analysis of the proportion and associated mortality of polymicrobial (vs monomicrobial) pulmonary and bloodstream infections by Acinetobacter baumannii complex.
BACKGROUND
Differentiating Acinetobacter baumannii complex (ABC) infection from colonization remains difficult and further complicated in polymicrobial infections.
PURPOSE
To assess the frequency of polymicrobial ABC infections and associated mortality. We hypothesized a lower mortality in polymicrobial infections if ABC isolation reflects colonization in some polymicrobial infections.
METHODS
A systematic review was conducted in PubMed, Scopus and CENTRAL for studies reporting ABC pulmonary and bloodstream infections. The proportion of infections that were polymicrobial and the magnitude of the association between polymicrobial (vs monomicrobial) infection and mortality were estimated with meta-analyses.
RESULTS
Based on 80 studies (9759 infections) from 23 countries, the pooled proportion of polymicrobial infection was 27% (95% CI 22-31%) and was similarly high for bloodstream and pulmonary infections. Polymicrobial infection was variably and insufficiently defined in most (95%) studies. Considerable heterogeneity (I = 95%) was observed that persisted in subgroup analyses and meta-regressions. Based on 17 studies (2675 infections), polymicrobial infection was associated with lower 28-day mortality (OR = 0.75, 95% CI 0.58-0.98, I = 36%). However, polymicrobial infection was not associated with in-hospital mortality (OR = 0.97, 95% CI 0.69-1.35, I = 0%) based on 14 studies (953 infections). The quality of evidence (GRADE) for the association of polymicrobial (vs monomicrobial) infection with mortality was low and at high risk of bias.
CONCLUSION
Polymicrobial ABC infections are common and may be associated with lower 28-day mortality. Considering the heterogeneity of polymicrobial infections and limitations of the available literature, more research is required to clarify the clinical impact of polymicrobial (vs monomicrobial) ABC infection.
Topics: Acinetobacter baumannii; Bacteremia; Coinfection; Humans; Retrospective Studies; Sepsis
PubMed: 34260054
DOI: 10.1007/s15010-021-01663-0 -
PloS One 2015Healthcare-related infections caused by extended-spectrum beta-lactamase (ESBL)-producing Klebsiella spp. are of major concern. To control transmission, deep... (Meta-Analysis)
Meta-Analysis Review
Healthcare-related infections caused by extended-spectrum beta-lactamase (ESBL)-producing Klebsiella spp. are of major concern. To control transmission, deep understanding of the transmission mechanisms is needed. This systematic review aimed to identify risk factors and sources, clonal relatedness using molecular techniques, and the most effective control strategies for ESBL-producing Klebsiella spp. A systematic search of PubMed, Embase, and Outbreak Database was performed. We identified 2771 articles from November 25th, 1960 until April 7th, 2014 of which 148 were included in the systematic review and 23 in a random-effects meta-analysis study. The random-effects meta-analyses showed that underlying disease or condition (odds ratio [OR] = 6.25; 95% confidence interval [CI] = 2.85 to 13.66) generated the highest pooled estimate. ESBL-producing Klebsiella spp. were spread through person-to-person contact and via sources in the environment; we identified both monoclonal and polyclonal presence. Multi-faceted interventions are needed to prevent transmission of ESBL-producing Klebsiella spp.
Topics: Humans; Klebsiella; Klebsiella Infections; Risk Factors; beta-Lactam Resistance; beta-Lactamases
PubMed: 26485570
DOI: 10.1371/journal.pone.0140754 -
United European Gastroenterology Journal Feb 2024Gastric cancer is the fifth most common cancer globally, with about 75% of cases occurring in Asia. While chronic atrophic gastritis (CAG) and intestinal metaplasia (IM)... (Meta-Analysis)
Meta-Analysis
BACKGROUND
Gastric cancer is the fifth most common cancer globally, with about 75% of cases occurring in Asia. While chronic atrophic gastritis (CAG) and intestinal metaplasia (IM) are well-recognized preneoplastic gastric lesions, we determined the prevalence and temporal trend of CAG and IM in Asia over the past 50 years.
METHODS
In this systematic review and meta-analysis, we searched PubMed, Embase, MEDLINE, Scopus, and Web of Science for studies reporting the prevalence of CAG and IM in Asia (according to the United Nations geoscheme) published between 1970 and 2022. Heterogeneity was assessed by the I index and Cochran Q test. We adopted the random effects model to estimate the pooled prevalence and 95% confidence interval (CI). The slope of prevalence was estimated as a function of time in simple linear regression and weighted meta-regression models to demonstrate the temporal trend. Studies that reported the odds ratio (OR) of Helicobacter pylori infection and CAG/IM were analyzed separately to compile a pooled OR with a 95% CI. This study was registered in INPLASY2022120028.
RESULTS
Of the 81 studies from 19 Asian countries identified, the pooled prevalence for CAG and IM in Asia was 26.1% (95%CI: 22.7-30.0) and 22.9% (95%CI: 19.7-26.6), respectively. Over the past 5 decades, there was a significant decline in the prevalence of IM (slope in adjusted meta-regression models: -0.79 [95%CI: -1.28 to -0.26], P = 0.003), but there was no significant change in the pooled prevalence of CAG. Within Asia, the prevalence varied significantly among different regions. Southern Asia reported the highest pooled prevalence of CAG (42.9%, 95%CI: 27.5%-67.1%), while Western Asia reported the lowest level (12.7%, 95%CI: 5.0%-32.3%). For IM, Eastern Asia reported the highest prevalence (27.1%, 95%CI: 21.1-34.9), with the lowest prevalence reported in Western Asia (3.1%; 95% CI 1.2%-8.0%). H. pylori infection was linked to CAG and IM with OR of 2.16 (95%CI: 2.09-2.22) and 1.64 (95%CI: 1.57-1.72), respectively.
CONCLUSION
This updated meta-analysis showed that up to 26% of study individuals in Asia harbored preneoplastic gastric lesions. There was a declining temporal trend in the prevalence of IM, but not for CAG, in Asia.
Topics: Humans; Prevalence; Helicobacter Infections; Helicobacter pylori; Gastritis, Atrophic; Asia
PubMed: 38084663
DOI: 10.1002/ueg2.12507 -
BMC Microbiology Dec 2023There is a link between Helicobacter pylori (HP) infection and small intestinal bacterial overgrowth (SIBO) with nonspecific digestive symptoms. Nonetheless, whether HP... (Meta-Analysis)
Meta-Analysis
BACKGROUND
There is a link between Helicobacter pylori (HP) infection and small intestinal bacterial overgrowth (SIBO) with nonspecific digestive symptoms. Nonetheless, whether HP infection is associated with SIBO in adults remains unclear. Based on a meta-analysis, we evaluated this relationship.
RESULTS
Observational studies relevant to our research were identified by searching PubMed, Embase, the Cochrane Library, and the Web of Science. We evaluated between-study heterogeneity using the Cochrane Q test and estimated the I statistic. Random-effects models were used when significant heterogeneity was observed; otherwise, fixed-effects models were used. Ten datasets from eight studies, including 874 patients, were involved in the meta-analysis. It was shown that HP infection was related to a higher odds of SIBO (odds ratio [OR]: 1.82, 95% confidence interval: 1.29 to 2.58, p < 0.001) with mild heterogeneity (p for Cochrane Q test = 0.11, I = 7%). Subgroup analyses showed that HP infection was related to SIBO in young patients (mean age < 48 years, OR: 2.68, 95% CI: 1.67 to 4.28, p < 0.001; I = 15%) but not in older patients (mean age ≥ 48 years, OR: 1.15, 95% CI: 0.69 to 1.92, p < 0.60; I = 1%; p for subgroup difference = 0.02). Subgroup analyses further indicated that the association was not significantly affected by the country of study, comorbidities, exposure to proton pump inhibitors, or methods of evaluating HP infection and SIBO.
CONCLUSIONS
HP infection may be related to SIBO in adults, which supports the detection of SIBO in patients with digestive symptoms and HP infection.
Topics: Adult; Humans; Middle Aged; Intestine, Small; Helicobacter pylori; Helicobacter Infections; Proton Pump Inhibitors
PubMed: 38053022
DOI: 10.1186/s12866-023-03063-w -
The Korean Journal of Internal Medicine Jan 2024There may be many predictors of anticoagulation-related gastrointestinal bleeding (GIB), but until now, systematic reviews and assessments of the certainty of the... (Meta-Analysis)
Meta-Analysis
BACKGROUND/AIMS
There may be many predictors of anticoagulation-related gastrointestinal bleeding (GIB), but until now, systematic reviews and assessments of the certainty of the evidence have not been published. We conducted a systematic review to identify all risk factors for anticoagulant-associated GIB to inform risk prediction in the management of anticoagulation- related GIB.
METHODS
A systematic review and meta-analysis were conducted to search PubMed, EMBASE, Web of Science, and Cochrane Library databases (from inception through January 21, 2022) using the following search terms: anticoagulants, heparin, warfarin, dabigatran, rivaroxaban, apixaban, DOACs, gastrointestinal hemorrhage, risk factors. According to inclusion and exclusion criteria, studies of risk factors for anticoagulation-related GIB were identified. Risk factors for anticoagulant-associated GIB were used as the outcome index of this review.
RESULTS
We included 34 studies in our analysis. For anticoagulant-associated GIB, moderate-certainty evidence showed a probable association with older age, kidney disease, concomitant use of aspirin, concomitant use of the antiplatelet agent, heart failure, myocardial infarction, hematochezia, renal failure, coronary artery disease, helicobacter pylori infection, social risk factors, alcohol use, smoking, anemia, history of sleep apnea, chronic obstructive pulmonary disease, international normalized ratio (INR), obesity et al. Some of these factors are not included in current GIB risk prediction models. such as anemia, co-administration of gemfibrozil, co-administration of verapamil or diltiazem, INR, heart failure, myocardial infarction, etc.
CONCLUSION
The study found that anemia, co-administration of gemfibrozil, co-administration of verapamil or diltiazem, INR, heart failure, myocardial infarction et al. were associated with anticoagulation-related GIB, and these factors were not in the existing prediction models. This study informs risk prediction for anticoagulant-associated GIB, it also informs guidelines for GIB prevention and future research.
Topics: Humans; Anemia; Anticoagulants; Diltiazem; Gastrointestinal Hemorrhage; Gemfibrozil; Heart Failure; Helicobacter Infections; Helicobacter pylori; Myocardial Infarction; Risk Factors; Verapamil
PubMed: 38062723
DOI: 10.3904/kjim.2023.098 -
Surgery May 2023The aim of this meta-analysis and systematic review was to evaluate the association between intraoperative bile cultures and postoperative complications of patients... (Meta-Analysis)
Meta-Analysis Review
BACKGROUND
The aim of this meta-analysis and systematic review was to evaluate the association between intraoperative bile cultures and postoperative complications of patients undergoing pancreaticoduodenectomy.
METHODS
A detailed literature search was performed from January 2015 to July 2022 in PubMed, Web of Science, Google Scholar, and EMBASE for related research publications. The data were extracted, screened, and graded independently. An analysis of pooled data was performed, and a risk ratio with corresponding confidence intervals was calculated and summarized.
RESULTS
A total of 8 articles were included with 1,778 pancreaticoduodenectomy patients who had an intraoperative bile culture performed. A systematic review demonstrated that some of the most common organisms isolated in a positive intraoperative bile culture were Enterococcus species, Klebsiella species, and E. coli. Four studies also showed that specific microorganisms were associated with specific postoperative complications (surgical site infection and intra-abdominal abscess). The postoperative complications that were evaluated for an association with a positive intraoperative bile culture were surgical site infections (risk ratio = 2.33, 95% confidence interval [1.47-3.69], P < .01), delayed gastric emptying (risk ratio = 1.23, 95% confidence interval [0.63-2.38], P = n.s.), 90-day mortality (risk ratio = 0.68, 95% confidence interval [0.01-52.76], P = n.s.), postoperative pancreatic hemorrhage (risk ratio = 1.70, 95% confidence interval [0.33-8.74], P = n.s.), intra-abdominal abscess (risk ratio = 1.70, 95% confidence interval [0.38-7.56], P = n.s.), and postoperative pancreatic fistula (risk ratio = 0.97, 95% confidence interval [0.72-1.32], P = n.s.).
CONCLUSION
The cumulative data suggest that a positive intraoperative bile culture has no association with predicting the postoperative complications of delayed gastric emptying, 90-day mortality, postoperative pancreatic hemorrhage, intra-abdominal abscess, or postoperative pancreatic fistula. However, the data also suggest that a positive intraoperative bile culture was associated with a patient developing a surgical site infection.
Topics: Humans; Pancreaticoduodenectomy; Surgical Wound Infection; Pancreatic Fistula; Bile; Gastroparesis; Escherichia coli; Pancreatic Diseases; Postoperative Hemorrhage; Abdominal Abscess; Postoperative Complications
PubMed: 36707272
DOI: 10.1016/j.surg.2022.12.012 -
Antimicrobial Agents and Chemotherapy May 2019The duration of antibiotic therapy for bacteremia due to is not well defined. We sought to evaluate the clinical outcomes with shorter- versus longer-course treatment.... (Meta-Analysis)
Meta-Analysis Review
The duration of antibiotic therapy for bacteremia due to is not well defined. We sought to evaluate the clinical outcomes with shorter- versus longer-course treatment. We performed a systematic search of the PubMed and EMBASE databases through May 2018. Studies presenting comparative outcomes between patients receiving antibiotic treatment for ≤10 days ("short-course") and those treated for >10 days ("long-course") were considered eligible. Four retrospective cohort studies and one randomized controlled trial comprising 2,865 patients met the inclusion criteria. The short- and long-course antibiotic treatments did not differ in 30-day all-cause mortality (1,374 patients; risk ratio [RR] = 0.99; 95% confidence interval [CI], 0.69 to 1.43), 90-day all-cause mortality (1,750 patients; RR = 1.16; 95% CI, 0.81 to 1.66), clinical cure (1,080 patients; RR = 1.02; 95% CI, 0.96 to 1.08), or relapse at 90 days (1,750 patients; RR = 1.08; 95% CI, 0.69 to 1.67). In patients with bacteremia due to , the short- and long-course antibiotic treatments did not differ significantly in terms of clinical outcomes. Further well-designed studies are needed before treatment for 10 days or less is adopted in clinical practice.
Topics: Anti-Bacterial Agents; Bacteremia; Enterobacteriaceae; Humans; Sepsis
PubMed: 30803971
DOI: 10.1128/AAC.02495-18 -
International Journal of Environmental... Mar 2020The aim of this systematic review was to investigate the effectiveness of various disinfection methods available for stethoscopes. In March 2019, we performed a search...
The aim of this systematic review was to investigate the effectiveness of various disinfection methods available for stethoscopes. In March 2019, we performed a search in PubMed and Scopus using the search terms: "reducing stethoscopes contamination" and "disinfection stethoscopes"; the Mesh terms used in PubMed were "Decontamination/methods" or "Disinfection/methods" and "Stethoscopes/microbiology". Selection criteria were: English language; at least one disinfection method tested. A total of 253 publications were screened. After title, abstract, and full-text analysis, 17 papers were included in the systematic review. Ethanol at 90%, Ethanol-Based Hands Sanitizer (EBHS), triclosan, chlorhexidine, isopropyl alcohol, 66% ethyl alcohol, sodium hypochlorite, and benzalkonium chloride have been proven to lower the presence of bacteria on stethoscopes' surfaces. In addition, alcohol wipes show effective results. A wearable device emitting ultraviolet C by Light-Emitting Diode (LED) resulted efficacious against common microorganisms involved in Healthcare Associated Infections. The cover impregnated with silver ions seemed to be associated with significantly higher colony counts. Instead, copper stethoscopes surface reduced bacterial load. The disinfection of stethoscopes appears to be essential. There are many valid methods available; the choice depends on various factors, such as the cost, availability, and practicality.
Topics: Aged; Child; Cohort Studies; Cross-Sectional Studies; Disinfection; Double-Blind Method; Escherichia coli; Humans; Methicillin-Resistant Staphylococcus aureus; Pilot Projects; Prospective Studies; Staphylococcus aureus; Stethoscopes
PubMed: 32182989
DOI: 10.3390/ijerph17061856 -
International Journal of Food... Feb 2020Campylobacter and Salmonella, particularly non-typhoidal Salmonella, are important bacterial enteric pathogens of humans which are often carried asymptomatically in... (Meta-Analysis)
Meta-Analysis Review
BACKGROUND
Campylobacter and Salmonella, particularly non-typhoidal Salmonella, are important bacterial enteric pathogens of humans which are often carried asymptomatically in animal reservoirs. Bacterial foodborne infections, including those derived from meat, are associated with illness and death globally but the burden is disproportionately high in Africa. Commercial meat production is increasing and intensifying in many African countries, creating opportunities and threats for food safety.
METHODS
Following Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) guidelines, we searched six databases for English language studies published through June 2016, that reported Campylobacter or Salmonella carriage or infection prevalence in food animals and contamination prevalence in food animal products from African countries. A random effects meta-analysis and multivariable logistic regression were used to estimate the species-specific prevalence of Salmonella and Campylobacter and assess relationships between sample type and region and the detection or isolation of either pathogen.
RESULTS
Seventy-three studies reporting Campylobacter and 187 studies reporting Salmonella across 27 African countries were represented. Adjusted prevalence calculations estimate Campylobacter detection in 37.7% (95% CI 31.6-44.3) of 11,828 poultry samples; 24.6% (95% CI 18.0-32.7) of 1975 pig samples; 17.8% (95% CI 12.6-24.5) of 2907 goat samples; 12.6% (95% CI 8.4-18.5) of 2382 sheep samples; and 12.3% (95% CI 9.5-15.8) of 6545 cattle samples. Salmonella were detected in 13.9% (95% CI 11.7-16.4) of 25,430 poultry samples; 13.1% (95% CI 9.3-18.3) of 5467 pig samples; 9.3% (95% CI 7.2-12.1) of 2988 camel samples; 5.3% (95% CI 4.0-6.8) of 72,292 cattle samples; 4.8% (95% CI 3.6-6.3) of 11,335 sheep samples; and 3.4% (95% CI 2.2-5.2) of 4904 goat samples. 'External' samples (e.g. hide, feathers) were significantly more likely to be contaminated by both pathogens than 'gut' (e.g. faeces, cloaca) while meat and organs were significantly less likely to be contaminated than gut samples.
CONCLUSIONS
This study demonstrated widespread prevalence of Campylobacter species and Salmonella serovars in African food animals and meat, particularly in samples of poultry and pig origin. Source attribution studies could help ascertain which food animals are contributing to human campylobacteriosis and salmonellosis and direct potential food safety interventions.
Topics: Africa; Animals; Campylobacter; Campylobacter Infections; Cattle; Feces; Food Contamination; Food Microbiology; Humans; Meat; Meat Products; Poultry; Prevalence; Salmonella; Salmonella Infections, Animal; Sheep; Swine
PubMed: 31710971
DOI: 10.1016/j.ijfoodmicro.2019.108382