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Clinical Microbiology and Infection :... Dec 2022The intestinal microbiome provides a reservoir for antibiotic resistance genes (ARGs). The neonatal microbiome is more susceptible to disturbance from external factors... (Review)
Review
BACKGROUND
The intestinal microbiome provides a reservoir for antibiotic resistance genes (ARGs). The neonatal microbiome is more susceptible to disturbance from external factors than the established microbiome in later life.
OBJECTIVES
In this review, we systematically summarize studies which investigated the intestinal resistome in neonates.
DATA SOURCES
MEDLINE and Embase databases were searched.
STUDY ELIGIBILITY CRITERIA
We included original studies which investigated ARGs in stool or rectal swabs in neonates using molecular diagnostics.
METHODS OF DATA SYNTHESIS
Two authors independently extracted data, which were summarized in tables.
RESULTS
Our search identified 2701 studies, of which 23 (22 cohorts) were included. The studies show that the neonatal intestine harbours a high abundance and variety of ARGs, even in the absence of direct antibiotic exposure. The most commonly found ARGs confer resistance to aminoglycosides, β-lactams, macrolides, tetracyclines, or multidrug resistance. There is evidence that ARGs can be transferred from mothers to neonates. Interestingly, however, compared to mothers, neonates are reported to have a higher abundance of ARGs. One likely reason for this is the bacterial phylogenetic composition with a high abundance of Gammaproteobacteria in neonatal stool. Factors that have been associated with a higher abundance of ARGs are intrapartum and neonatal antibiotic use. Breastfeeding and neonatal probiotic use have been associated with a lower abundance of ARGs. Antibiotics during pregnancy, delivery mode, or sex are reported to have little effect. However, this might be because studies were underpowered and because it is difficult to account for effect modifiers.
CONCLUSIONS
The neonatal intestine seems to have a lower colonization resistance, which could make it easier for antibiotic-resistant populations to establish themselves. Future studies will help in the development of evidence-based interventions to modulate the abundance of ARGs in neonates, for example, by the use of pre- and probiotics and bacteriophages.
Topics: Infant, Newborn; Pregnancy; Female; Humans; Phylogeny; Drug Resistance, Microbial; Anti-Bacterial Agents; Bacteria; Intestines
PubMed: 35868586
DOI: 10.1016/j.cmi.2022.07.014 -
Frontiers in Cellular and Infection... 2022A prosthetic joint infection (PJI) is a devastating complication following total joint arthroplasties with poor prognosis. Identifying an accurate and prompt diagnostic... (Meta-Analysis)
Meta-Analysis Review
BACKGROUND
A prosthetic joint infection (PJI) is a devastating complication following total joint arthroplasties with poor prognosis. Identifying an accurate and prompt diagnostic method is particularly important for PJI. Recently, the diagnostic value of metagenomic next-generation sequencing (mNGS) in detecting PJI has attracted much attention, while the evidence of its accuracy is quite limited. Thus, this study aimed to evaluate the accuracy of mNGS for the diagnosis of PJI.
METHODS
We summarized published studies to identify the potential diagnostic value of mNGS for PJI patients by searching online databases using keywords such as "prosthetic joint infection", "PJI", and "metagenomic sequencing". Ten of 380 studies with 955 patients in total were included. The included studies provided sufficient data for the completion of 2-by-2 tables. We calculated the sensitivity, specificity, and area under the SROC curve (AUC) to evaluate mNGS for PJI diagnosis.
RESULTS
We found that the pooled diagnostic sensitivity and specificity of mNGS for PJI were 0.93 (95% CI, 0.83 to 0.97) and 0.95 (95% CI, 0.92 to 0.97), respectively. Positive and negative likelihood ratios were 18.3 (95% CI, 10.9 to 30.6) and 0.07 (95% CI, 0.03 to 0.18), respectively. The area under the curve was 0.96 (95% CI, 0.93 to 0.97).
CONCLUSION
Metagenomic next-generation sequencing displays high accuracy in the diagnosis of PJI, especially for culture-negative cases.
Topics: Arthritis, Infectious; High-Throughput Nucleotide Sequencing; Humans; Metagenomics; Prosthesis-Related Infections; Sensitivity and Specificity; Synovial Fluid
PubMed: 35755833
DOI: 10.3389/fcimb.2022.875822 -
European Journal of Clinical... Jun 2022The early diagnosis of bacterial meningoencephalitis (BM/E) is difficult, and delay in diagnosis can cause complications leading to neurological impairment/death. In... (Meta-Analysis)
Meta-Analysis
The early diagnosis of bacterial meningoencephalitis (BM/E) is difficult, and delay in diagnosis can cause complications leading to neurological impairment/death. In cases of unexplained BM/E, the metagenomic NGS (mNGS) offers an advantage over conventional methods, especially when a rare pathogen is implicated or the patient is on antibiotics. This study aims to evaluate and compare the diagnostic efficacy of mNGS for the diagnosis of BM/E using cerebrospinal fluid (CSF) specimens versus a composite reference standard (CRS). The electronic databases (Embase, PubMed, and Web of Science) were searched up to 15 June 2021. Studies such as cohort, case-control, prospective, or retrospective studies that assessed the diagnostic efficacy of mNGS in suspected bacterial meningitis/encephalitis cases were included. Ten studies met the inclusion criteria, including three retrospective and seven prospective studies. The sensitivity of mNGS for diagnosis of BM/E from CSF samples ranged from 33 (95% CI: 13-62) to 98% (95% CI: 76-99). The specificity of mNGS ranged from 67 (95% CI: 55-78) to 98% (95% CI: 95-99). The estimated AUC (area under curve) by hierarchical summary receiver operating characteristic (HSROC) of the studies being analyzed was 0.912. The meta-regression analysis demonstrated that the different types of studies (single-center vs. multi-center) had an effect on the specificity of mNGS for BM/E compared with CRS (90% vs. 96%, meta-regression P < 0.05). The current analysis revealed moderate diagnostic accuracy of mNGS. This approach can be helpful, especially in cases of undiagnosed BM/E by identification of organism and subsequently accelerating the patient management.
Topics: High-Throughput Nucleotide Sequencing; Humans; Infectious Encephalitis; Meningitis, Bacterial; Meningoencephalitis; Metagenomics; Prospective Studies; Retrospective Studies; Sensitivity and Specificity
PubMed: 35474146
DOI: 10.1007/s10096-022-04445-0 -
Frontiers in Medicine 2022The fight against (MTB) has been going on for thousands of years, while it still poses a threat to human health. In addition to routine detections, metagenomic...
The fight against (MTB) has been going on for thousands of years, while it still poses a threat to human health. In addition to routine detections, metagenomic next-generation sequencing (mNGS) has begun to show presence as a comprehensive and hypothesis-free test. It can not only detect MTB without isolating specific pathogens but also suggest the co-infection pathogens or underlying tumor simultaneously, which is of benefit to assist in comprehensive clinical diagnosis. It also shows the potential to detect multiple drug resistance sites for precise treatment. However, considering the cost performance compared with conventional assays (especially Xpert MTB/RIF), mNGS seems to be overqualified for patients with mild and typical symptoms. Technology optimization of sequencing and analyzing should be conducted to improve the positive rate and broaden the applicable fields.
PubMed: 35433724
DOI: 10.3389/fmed.2022.802719 -
The Science of the Total Environment Aug 2022The global rise in industrialization and vehicularization has led to the increasing trend in the use of different crude oil types. Among these mobil oil has major...
The global rise in industrialization and vehicularization has led to the increasing trend in the use of different crude oil types. Among these mobil oil has major application in automobiles and different machines. The combustion of mobil oil renders a non-usable form that ultimately enters the environment thereby causing problems to environmental health. The aliphatic and aromatic hydrocarbon fraction of mobil oil has serious human and environmental health hazards. These components upon interaction with soil affect its fertility and microbial diversity. The recent advancement in the omics approach viz. metagenomics, metatranscriptomics and metaproteomics has led to increased efficiency for the use of microbial based remediation strategy. Additionally, the use of biosurfactants further aids in increasing the bioavailability and thus biodegradation of crude oil constituents. The combination of more than one approach could serve as an effective tool for efficient reduction of oil contamination from diverse ecosystems. To the best of our knowledge only a few publications on mobil oil have been published in the last decade. This systematic review could be extremely useful in designing a micro-bioremediation strategy for aquatic and terrestrial ecosystems contaminated with mobil oil or petroleum hydrocarbons that is both efficient and feasible. The state-of-art information and future research directions have been discussed to address the issue efficiently.
Topics: Biodegradation, Environmental; Ecosystem; Humans; Hydrocarbons; Petroleum; Petroleum Pollution; Soil Microbiology; Soil Pollutants
PubMed: 35395309
DOI: 10.1016/j.scitotenv.2022.155083 -
International Urogynecology Journal May 2022The objective was to systemically review the current literature on the association of gut, vaginal, and urinary dysbiosis in female patients with overactive bladder...
INTRODUCTION AND HYPOTHESIS
The objective was to systemically review the current literature on the association of gut, vaginal, and urinary dysbiosis in female patients with overactive bladder (OAB).
METHODS
We performed a comprehensive literature search following the Preferred Reporting Items for Systematic Review and Meta-analysis (PRISMA) protocols for systematic reviews. In the EMBASE, CINAHL, and Medline databases, a search was conducted using key words such as "microbiome," "microbiota," "microflora," "overactive bladder," "urge," "gut," "vaginal." Articles were screened using the online tool www.covidence.org . Two independent reviewers screened studies at each stage and resolved conflicts together. We excluded papers that discussed pediatric patients and animal studies. In total, 13 articles met this criterion, which included 6 abstracts.
RESULTS
After identifying 817 unique references, 13 articles met the criteria for data extraction. Articles were published from 2017 to 2021. No study reported the same microbiota abundance, even in healthy individuals. Overall, there was a loss of bacterial diversity in OAB patients compared with controls. Additionally, the bacterial composition of the controls and OAB patients was not significantly different, especially if the urine was collected midstream. Overall, the composition of the microbiome is dependent on the specimen collection methodology, and the metagenomic sequencing technique utilized. OAB urine microbiome is more predisposed to alteration from the gut or vaginal influences than in controls.
CONCLUSIONS
Current evidence suggested a potential relationship among gut, vaginal, and urinary microbiome in OAB patients, but there are very limited studies.
Topics: Bacteria; Child; Female; Humans; Microbiota; Urinary Bladder, Overactive; Urinary Tract; Vagina
PubMed: 35237854
DOI: 10.1007/s00192-022-05127-3 -
Microbial Ecology Feb 2023Soil is one of the most important assets of the planet Earth, responsible for maintaining the biodiversity and managing the ecosystem services for both managed and... (Review)
Review
Soil is one of the most important assets of the planet Earth, responsible for maintaining the biodiversity and managing the ecosystem services for both managed and natural ecosystems. It encompasses large proportion of microscopic biodiversity, including prokaryotes and the microscopic eukaryotes. Soil microbiome is critical in managing the soil functions, but their activities have diminutive recognition in few systems like desert land and forest ecosystems. Soil microbiome is highly dependent on abiotic and biotic factors like pH, carbon content, soil structure, texture, and vegetation, but it can notably vary with ecosystems and the respective inhabitants. Thus, unboxing this black box is essential to comprehend the basic components adding to the soil systems and supported ecosystem services. Recent advancements in the field of molecular microbial ecology have delivered commanding tools to examine this genetic trove of soil biodiversity. Objective of this review is to provide a critical evaluation of the work on the soil microbiome, especially since the advent of the NGS techniques. The review also focuses on advances in our understanding of soil communities, their interactions, and functional capabilities along with understanding their role in maneuvering the biogeochemical cycle while underlining and tapping the unprecedented metagenomics data to infer the ecological attributes of yet undiscovered soil microbiome. This review focuses key research directions that could shape the future of basic and applied research into the soil microbiome. This review has led us to understand that it is difficult to generalize that soil microbiome plays a substantiated role in shaping the soil networks and it is indeed a vital resource for sustaining the ecosystem functioning. Exploring soil microbiome will help in unlocking their roles in various soil network. It could be resourceful in exploring and forecasting its impacts on soil systems and for dealing with alleviating problems like rapid climate change.
Topics: Ecosystem; Soil; Soil Microbiology; Biodiversity; Microbiota; Climate Change
PubMed: 35112151
DOI: 10.1007/s00248-022-01962-5 -
Frontiers in Oral Health 2021In light of recent technological advances in Next-generation sequencing (NGS) and the accumulation of large, publicly available oral microbiome datasets, the need for...
In light of recent technological advances in Next-generation sequencing (NGS) and the accumulation of large, publicly available oral microbiome datasets, the need for meta-analysing data on caries microbiome is becoming feasible and essential. A consensus on the identification of enriched organisms in cariogenic dysbiotic biofilms would be reached. For example, members of the genus have been detected in caries biofilms, and may have an underestimated contribution to the dysbiotic process. Hence, we aimed to determine the abundance of species in dental caries in studies using NGS data. Analysis was performed according to the Preferred Reporting Items for Systematic Review and Meta-Analysis (registered at PROSPERO: CRD42020204150). Studies investigating microbial composition in saliva, dental biofilm, or carious dentin were included. Six databases and grey literature were searched. Two independent reviewers selected the papers and assessed the methodological quality. Searches retrieved 1,323 titles, from which 38 studies were included in a qualitative synthesis, comprising a total of 1,374 caries and 745 caries-free individuals. Most studies analysed 16S rRNA amplicons, and only 5 studies used shotgun metagenomics and metatranscriptomics. A geographical bias was observed. The methodological quality was downrated in 81.5% of the studies due to the lack of criteria for defining cases and standard criteria used for measurement of the condition in a reliable way. Six studies on early childhood caries (ECC) were meta-analysed, confirming a significant enrichment of spp. in caries-associated biofilms (but not saliva) when compared to caries-free controls [mean difference: 2.22 (0.54-3.90); = 0.01]. . is more abundant in individuals suffering with ECC when compared to caries-free controls (very low evidence certainty), and should be considered for further studies to observe their metabolism in dental caries. There is an urgent need for a consensus in methodologies used to allow for more rigorous comparison between NGS studies, particularly including clinical data and details of caries diagnosis, as they are currently scarce. Inconsistent reporting on the NGS data affected the cross-study comparison and the biological connexions of the relative abundances on caries microbiome.
PubMed: 35048071
DOI: 10.3389/froh.2021.770917 -
Nutrients Dec 2021Whether the gut microbiome in obesity is characterized by lower diversity and altered composition at the phylum or genus level may be more accurately investigated using... (Meta-Analysis)
Meta-Analysis
Whether the gut microbiome in obesity is characterized by lower diversity and altered composition at the phylum or genus level may be more accurately investigated using high-throughput sequencing technologies. We conducted a systematic review in PubMed and Embase including 32 cross-sectional studies assessing the gut microbiome composition by high-throughput sequencing in obese and non-obese adults. A significantly lower alpha diversity (Shannon index) in obese versus non-obese adults was observed in nine out of 22 studies, and meta-analysis of seven studies revealed a non-significant mean difference (-0.06, 95% CI -0.24, 0.12, = 81%). At the phylum level, significantly more Firmicutes and fewer Bacteroidetes in obese versus non-obese adults were observed in six out of seventeen, and in four out of eighteen studies, respectively. Meta-analyses of six studies revealed significantly higher Firmicutes (5.50, 95% 0.27, 10.73, = 81%) and non-significantly lower Bacteroidetes (-4.79, 95% CI -10.77, 1.20, = 86%). At the genus level, lower relative proportions of and and higher , , , , , , , , , , , , and were found in obese versus non-obese adults. Although a proportion of studies found lower diversity and differences in gut microbiome composition in obese versus non-obese adults, the observed heterogeneity across studies precludes clear answers.
Topics: Bacteria; Feces; Gastrointestinal Microbiome; High-Throughput Nucleotide Sequencing; Humans; Obesity
PubMed: 35010887
DOI: 10.3390/nu14010012 -
Plants (Basel, Switzerland) Dec 2021Resurrection plants have an extraordinary ability to survive extreme water loss but still revive full metabolic activity when rehydrated. These plants are useful models... (Review)
Review
Resurrection plants have an extraordinary ability to survive extreme water loss but still revive full metabolic activity when rehydrated. These plants are useful models to understand the complex biology of vegetative desiccation tolerance. Despite extensive studies of resurrection plants, many details underlying the mechanisms of desiccation tolerance remain unexplored. To summarize the progress in resurrection plant research and identify unexplored questions, we conducted a systematic review of 15 model angiosperm resurrection plants. This systematic review provides an overview of publication trends on resurrection plants, the geographical distribution of species and studies, and the methodology used. Using the Preferred Reporting Items for Systematic reviews and Meta-Analyses protocol we surveyed all publications on resurrection plants from 2000 and 2020. This yielded 185 empirical articles that matched our selection criteria. The most investigated plants were (17.5%), (13.7%), (reclassified as ) (11.9%), (8.5%), and (8.1%), with all other species accounting for less than 8% of publications. The majority of studies have been conducted in South Africa, Bulgaria, Germany, and China, but there are contributions from across the globe. Most studies were led by researchers working within the native range of the focal species, but some international and collaborative studies were also identified. The number of annual publications fluctuated, with a large but temporary increase in 2008. Many studies have employed physiological and transcriptomic methodologies to investigate the leaves of resurrection plants, but there was a paucity of studies on roots and only one metagenomic study was recovered. Based on these findings we suggest that future research focuses on resurrection plant roots and microbiome interactions to explore microbial communities associated with these plants, and their role in vegetative desiccation tolerance.
PubMed: 34961255
DOI: 10.3390/plants10122784