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Journal de Mycologie Medicale Apr 2020Limited data are available on the epidemiology and etiology of cryptococcal infections in the Middle East. We aimed to conduct the systematic review and meta-analysis to... (Meta-Analysis)
Meta-Analysis
OBJECTIVE
Limited data are available on the epidemiology and etiology of cryptococcal infections in the Middle East. We aimed to conduct the systematic review and meta-analysis to summarize the epidemiological data on prevalence of Cryptococcus species complexes in trees and their surroundings, bird guano and secretions, animals, and highlight the reported episodes of cryptococcosis in Iran.
MATERIALS AND METHODS
Twelve databases, including PubMed, Science Direct, Scopus, Proquest, Google Scholar, Embase, and the ISI Web of Science, as well as the national databases, from January 1969 to October 2019 were searched. Furthermore, gray literature (e.g., thesis, congress abstracts) was evaluated using Iran Doc and www.thesis.
RESEARCH
ac.ir. Search process was accomplished on English or Persian language articles using the following keywords: "Cryptococcus", "Cryptococcosis", "invasive fungal infection", "Humans", "Birds", "Pigeon", "Animals", "Tree", "Eucalyptus", and "Iran", both alone and in combination.
RESULTS
Overall 36 studies were eligible regarding Cryptococcus and cryptococcosis in Iran. The total prevalence rates of Cryptococcus species in the tree was 4.7% (95% CI: 2.3-7.8), and in bird guano was 20.4% (95% CI: 10.7-32.2). Cryptococcosis in animal, and human were 1.7% (95% CI: 0.01-5.1), and 2.8% (95% CI: 0.7v6.1), respectively. The highest prevalence of Cryptococcus in the trees (14.6%), and bird guano (89.4%) in Khorasan, animals (8.9%) in Chaharmahal and Bakhtiari, and human (4.4%) in Mazandaran provinces were reported.
CONCLUSIONS
Given the significant risk of Cryptococcus species for susceptible humans, mainly HIV-infected patients, it seems quite necessary to adopt concrete preventive strategies to pinpoint the environmental habitats of this yeast.
Topics: Animals; Bird Diseases; Columbidae; Cryptococcosis; Cryptococcus; Eucalyptus; Humans; Invasive Fungal Infections; Iran; Plant Diseases; Prevalence; Trees
PubMed: 31864801
DOI: 10.1016/j.mycmed.2019.100917 -
Journal of Hazardous Materials Apr 2022Fumigants have been used for decades to control soil-borne pathogens of high-value crops, and increasing evidence indicates they can affect non-target soil microbial... (Review)
Review
Fumigants have been used for decades to control soil-borne pathogens of high-value crops, and increasing evidence indicates they can affect non-target soil microbial communities. Understanding the impacts of these products on soil microorganisms is of critical importance not only for evaluating their environmental safety, but also because soil microbial communities have a central role in soil quality and nutrient cycling, plant growth, and crop production. Thus, we conducted a systematic review and metanalysis study of fumigant impacts on non-target soil microorganisms. In general, we found that fumigation decreases the bacterial diversity and abundance of total bacteria and nitrogen-cycling genes by approximately 10-50% during the first four weeks after application compared to non-treated soils. These decreases appear transient and tend to diminish or disappear after four weeks. Increases in bacterial diversity and abundance can occur after fumigation but are less common. Fumigant application can also alter bacterial community composition during the first six weeks after treatment by significantly increasing and/or decreasing the relative abundance of bacterial taxa involved in key soil functions such as N-cycling and plant-growth promotion. Knowledge gaps and areas where future research efforts should be prioritized to improve our understanding of the impact of organic fumigants on non-target soil microorganisms are discussed.
Topics: Fumigation; Nitrogen Cycle; Pesticides; Soil; Soil Microbiology
PubMed: 34999405
DOI: 10.1016/j.jhazmat.2021.128149 -
Cell and Tissue Banking Dec 2016For successful transplantation, allografts should be free of microorganisms that may cause harm to the allograft recipient. Before or during recovery and subsequent... (Review)
Review
For successful transplantation, allografts should be free of microorganisms that may cause harm to the allograft recipient. Before or during recovery and subsequent processing, tissues can become contaminated. Effective tissue recovery methods, such as minimizing recovery times (<24 h after death) and the number of experienced personnel performing recovery, are examples of factors that can affect the rate of tissue contamination at recovery. Additional factors, such as minimizing the time after asystole to recovery and the total time it takes to perform recovery, the type of recovery site, the efficacy of the skin prep performed immediately prior to recovery of tissue, and certain technical recovery procedures may also result in control of the rate of contamination. Due to the heterogeneity of reported recovery practices and experiences, it cannot be concluded if the use of other barriers and/or hygienic precautions to avoid contamination have had an effect on bioburden detected after tissue recovery. Qualified studies are lacking which indicates a need exists for evidence-based data to support methods that reduce or control bioburden.
Topics: Allografts; Cell Culture Techniques; Decontamination; Humans; Specimen Handling; Sterilization; Tissue Banks; Transplantation, Homologous
PubMed: 27761677
DOI: 10.1007/s10561-016-9590-5 -
Current Nutrition Reports Sep 2022Cancers are a leading cause of death in humans and for many other species. Diet has often been associated with cancers, and the microbiome is an essential mediator... (Review)
Review
PURPOSE OF REVIEW
Cancers are a leading cause of death in humans and for many other species. Diet has often been associated with cancers, and the microbiome is an essential mediator between diet and cancers. Here, we review the work on cancer and the microbiome across species to search for broad patterns of susceptibility associated with different microbial species.
RECENT FINDINGS
Some microbes, such as Helicobacter bacteria, papillomaviruses, and the carnivore-associated Fusobacteria, consistently induce tumorigenesis in humans and other species. Other microbes, such as the milk-associated Lactobacillus, consistently inhibit tumorigenesis in humans and other species. We systematically reviewed over a thousand published articles and identified links between diet, microbes, and cancers in several species of mammals, birds, and flies. Future work should examine a larger variety of host species to discover new model organisms for human preclinical trials, to better understand the observed variance in cancer prevalence across species, and to discover which microbes and diets are associated with cancers across species. Ultimately, this could help identify microbial and dietary interventions to diagnose, prevent, and treat cancers in humans as well as other animals.
Topics: Animals; Carcinogenesis; Diet; Humans; Mammals; Microbiota; Neoplasms
PubMed: 35704266
DOI: 10.1007/s13668-022-00420-5 -
Gut Microbes Dec 2023Loss of response to therapy in inflammatory bowel disease (IBD) has led to a surge in research focusing on precision medicine. Three systematic reviews have been... (Review)
Review
Loss of response to therapy in inflammatory bowel disease (IBD) has led to a surge in research focusing on precision medicine. Three systematic reviews have been published investigating the associations between gut microbiota and disease activity or IBD therapy. We performed a systematic review to investigate the microbiome predictors of response to advanced therapy in IBD. Unlike previous studies, our review focused on predictors of response to therapy; so the included studies assessed microbiome predictors before the proposed time of response or remission. We also provide an update of the available data on mycobiomes and viromes. We highlight key themes in the literature that may serve as future biomarkers of treatment response: the abundance of fecal SCFA-producing bacteria and opportunistic bacteria, metabolic pathways related to butyrate synthesis, and non-butyrate metabolomic predictors, including bile acids (BAs), amino acids, and lipids, as well as mycobiome predictors of response.
Topics: Humans; Gastrointestinal Microbiome; Inflammatory Bowel Diseases; Feces; Fecal Microbiota Transplantation; Biomarkers
PubMed: 38044504
DOI: 10.1080/19490976.2023.2287073 -
AJR. American Journal of Roentgenology Apr 2023The reported sensitivity and yield of image-guided biopsies for diskitis-osteomyelitis vary widely. The purpose of this study was to perform a systematic review of the... (Meta-Analysis)
Meta-Analysis Review
The reported sensitivity and yield of image-guided biopsies for diskitis-osteomyelitis vary widely. The purpose of this study was to perform a systematic review of the literature and meta-analysis of pooled sensitivity data to elucidate strategies for optimal image-guided biopsies among patients suspected to have diskitis-osteomyelitis. A comprehensive literature search was performed for studies of patient populations with proven or suspected diskitis-osteomyelitis that included percutaneous image-guided biopsy as part of the workup algorithm. Type of pathogens, imaging modality used for biopsy guidance, tissue targeted, antibiotic administration at the time of biopsy, true microbiology positives, true microbiology negatives, false microbiology positives, false microbiology negatives, disease (i.e., diskitis-osteomyelitis) positives as determined by reference standard, true infection positives (i.e., positive microbiology or pathology results), and total number of biopsies performed were extracted from the studies. Microbiology sensitivity, microbiology biopsy yield, and infection sensitivity were calculated from the pooled data. These terms and the data required to calculate them were also defined in detail. Thirty-six articles satisfied inclusion criteria and were used for analysis. The pooled microbiology sensitivity, infection sensitivity, and microbiology biopsy yields were 46.6%, 70.0%, and 26.7%, respectively. Mycobacterium tuberculosis-only microbiology sensitivity was significantly higher than both pyogenic bacteria and mixed-organism microbiology sensitivity ( < .001). was the most common causative organism (28.6%). Pooled microbiology sensitivity was not significantly different for CT guidance and fluoroscopy guidance ( = .16). There was a statistically significant difference between pooled microbiology sensitivity of bone/end plate (45.5%) and disk/paravertebral soft-tissue (64.8%) image-guided biopsies ( < .001). There was no statistically significant difference in pooled microbiology sensitivities for patients who received antibiotics before the procedure (46.2%) and those who did not (44.6%) ( = .70). Image guidance by CT or fluoroscopy does not affect microbiology yield, disk and paravertebral soft-tissue biopsies should be considered over bone and end plate biopsies, and preprocedural antibiotic administration does not appear to impact biopsy results. Understanding and correctly applying reported statistics contribute to appropriate interpretation of the abundant literature on this topic and optimization of care for patients with diskitis-osteomyelitis.
Topics: Humans; Discitis; Image-Guided Biopsy; Biopsy; Osteomyelitis; Bone and Bones; Anti-Bacterial Agents; Retrospective Studies
PubMed: 36222488
DOI: 10.2214/AJR.22.28423 -
APMIS : Acta Pathologica,... May 2023An abscess is a collection of pus forming a cavity in the tissue, for example, the skin. They are generally perceived as the result of infection but infection is not... (Review)
Review
An abscess is a collection of pus forming a cavity in the tissue, for example, the skin. They are generally perceived as the result of infection but infection is not mandatory for the diagnosis. Skin abscesses may occur independently (primary) or be part of other diseases such as the recurrent inflammatory skin disease hidradenitis suppurativa (HS). HS is noninfectious but nevertheless abscesses are a common differential diagnosis. The purpose of this study is to review the microbiome of bacteria positive primary skin abscesses in order to explore the reported microbiota. EMBASE, MEDLINER, and COCHRANE LIBRABRY were searched on 9th of October 2021 for microbiome, skin, and abscesses. Studies with more than 10 patients reporting the microbiome in human skin-abscesses were included and studies with abscess microbiota sampled from HS patients, microbiota not sampled from skin-abscesses, missing information on microbiome data, sampling bias, studies in other language than English or Danish, reviews and meta-analyses were excluded. In total 11 studies were included for further analysis. S. aureus is likely to dominate the microbiome of bacteria positive primary skin abscesses in contrast to the polymicrobial microbiome of HS.
Topics: Humans; Abscess; Staphylococcus aureus; Skin; Hidradenitis Suppurativa; Bacteria; Microbiota
PubMed: 36861497
DOI: 10.1111/apm.13304 -
Nutrition in Clinical Practice :... Jun 2017Human milk-associated microbes are among the first to colonize the infant gut and may help to shape both short- and long-term infant health outcomes. We performed a... (Review)
Review
Human milk-associated microbes are among the first to colonize the infant gut and may help to shape both short- and long-term infant health outcomes. We performed a systematic review to characterize the microbiota of human milk. Relevant primary studies were identified through a comprehensive search of PubMed (January 1, 1964, to June 31, 2015). Included studies were conducted among healthy mothers, were written in English, identified bacteria in human milk, used culture-independent methods, and reported primary results at the genus level. Twelve studies satisfied inclusion criteria. All varied in geographic location and human milk collection/storage/analytic methods. Streptococcus was identified in human milk samples in 11 studies (91.6%) and Staphylococcus in 10 (83.3%); both were predominant genera in 6 (50%). Eight of the 12 studies used conventional ribosomal RNA (rRNA) polymerase chain reaction (PCR), of which 7 (87.5%) identified Streptococcus and 6 (80%) identified Staphylococcus as present. Of these 8 studies, 2 (25%) identified Streptococcus and Staphylococcus as predominant genera. Four of the 12 studies used next-generation sequencing (NGS), all of which identified Streptococcus and Staphylococcus as present and predominant genera. Relative to conventional rRNA PCR, NGS is a more sensitive method to identify/quantify bacterial genera in human milk, suggesting the predominance of Streptococcus and Staphylococcus may be underestimated in studies using older methods. These genera, Streptococcus and Staphylococcus, may be universally predominant in human milk, regardless of differences in geographic location or analytic methods. Primary studies designed to evaluate the effect of these 2 genera on short- and long-term infant outcomes are warranted.
Topics: Food Microbiology; Humans; Infant; Microbiota; Milk, Human; Staphylococcus; Streptococcus
PubMed: 27679525
DOI: 10.1177/0884533616670150 -
APMIS : Acta Pathologica,... Mar 2020Pseudomonas aeruginosa is generally described as ubiquitous in natural settings, such as soil and water. However, because anecdotal observations and published reports... (Meta-Analysis)
Meta-Analysis
Pseudomonas aeruginosa is generally described as ubiquitous in natural settings, such as soil and water. However, because anecdotal observations and published reports have questioned whether or not this description is true, we undertook a rigorous study using three methods to investigate the occurrence of P. aeruginosa: We investigated environmental samples, analyzed 16S rRNA data, and undertook a systematic review and meta-analysis of published data. The environmental sample screening identified P. aeruginosa as significantly associated with hydrocarbon and pesticide-contaminated environments and feces, as compared to uncontaminated environments in which its prevalence was relatively low. The 16S rRNA data analysis showed that P. aeruginosa sequences were present in all habitats but were most abundant in samples from human and animals. Similarly, the meta-analysis revealed that samples obtained from environments with intense human contact had a higher prevalence of P. aeruginosa compared to those with less human contact. Thus, we found a clear tendency of P. aeruginosa to be present in places closely linked with human activity. Although P. aeruginosa may be ubiquitous in nature, it is usually scarce in pristine environments. Thus, we suggest that P. aeruginosa should be described as a bacterium largely found in locations associated with human activity.
Topics: Animals; Environment; Environmental Microbiology; Humans; Pseudomonas Infections; Pseudomonas aeruginosa; RNA, Ribosomal, 16S
PubMed: 31709616
DOI: 10.1111/apm.13010 -
Indian Journal of Ophthalmology Aug 2017The purpose of this study was to review the incidence and microbiology of acute postcataract surgery endophthalmitis in India. (Review)
Review
PURPOSE
The purpose of this study was to review the incidence and microbiology of acute postcataract surgery endophthalmitis in India.
METHODS
Systematic review of English-language PubMed referenced articles on endophthalmitis in India published in the past 21 years (January 1992-December 2012), and retrospective chart review of 2 major eye care facilities in India in the past 5 years (January 2010-December 2014) were done. The incidence data were collected from articles that described "in-house" endophthalmitis and the microbiology data were collected from all articles. Both incidence and microbiological data of endophthalmitis were collected from two large eye care facilities. Case reports were excluded, except for the articles on cluster infection.
RESULTS
Six of 99 published articles reported the incidence of "in-house" acute postcataract surgery endophthalmitis, 8 articles reported the microbiology spectrum, and 11 articles described cluster infection. The clinical endophthalmitis incidence was between 0.04% and 0.15%. In two large eye care facilities, the clinical endophthalmitis incidence was 0.08% and 0.16%; the culture proven endophthalmitis was 0.02% and 0.08%. Gram-positive cocci (44%-64.8%; commonly, Staphylococcus species), and Gram-negative bacilli (26.2%-43%; commonly Pseudomonas species) were common bacteria in south India. Fungi (16.7%-70%; commonly Aspergillus flavus) were the common organisms in north India. Pseudomonas aeruginosa (73.3%) was the major organism in cluster infections.
CONCLUSIONS
The incidence of postcataract surgery clinical endophthalmitis in India is nearly similar to the world literature. There is a regional difference in microbiological spectrum. A registry with regular and uniform national reporting will help formulate region specific management guidelines.
Topics: Cataract Extraction; Endophthalmitis; Eye Infections; Forecasting; Humans; Incidence; India; Microbial Sensitivity Tests; Surgical Wound Infection
PubMed: 28820151
DOI: 10.4103/ijo.IJO_509_17