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Microbial Pathogenesis Nov 2022Vibrio cholera (V. cholera) is a facultative pathogen that colonizes the small intestine and produces cholerae toxin as the primary virulence factor that causes cholera... (Meta-Analysis)
Meta-Analysis Review
BACKGROUND
Vibrio cholera (V. cholera) is a facultative pathogen that colonizes the small intestine and produces cholerae toxin as the primary virulence factor that causes cholera and fatal diarrhea in humans. In recent decades, V. cholera has emerged as a notorious multidrug-resistant enteric pathogen. This meta-analysis estimated the pooled proportion of V. cholera antimicrobial resistance against RNA and DNA effective antibiotics.
METHOD
A systematic search was performed for relevant literature until 05 June 2021 in PubMed, Scopus, Embase, and Web of Science databases. Freeman-Tukey double arcsine transformation was performed to estimate weighted pooled resistance (WPR).
RESULTS
The meta-analysis were included 164 articles. The WPR of V. cholera were as follows 76% [67,84] to furazolidone, 65% [29,94] to nitrofurantoin, 55% [44,66] to nalidixic acid, 10% [2,23] to rifampicin, 4%(0, 12) to novobiocin, 4% [2,6] to norfloxacin, 3% [1,4] to ciprofloxacin, 1%(0, 3) to sparofloxacin, 0%(0, 3) to levofloxacin, 0%(0, 2) to ofloxacin, 0%(0, 0) to gatifloxacin.
CONCLUSION
V. cholera is a severe problem in Asia and Africa, especially in South Asian countries. The resistance patterns are various in geographical regions. novobiocin 0% (0, 0), and ofloxacin 0% (0, 1) in Africa, gatifloxacin 0% (0, 0), and levofloxacin 0% (0, 6) in Asia and ciprofloxacin 0% (0, 2) in North America are most effective antibiotis. The resistance rate to furazolidone, nalidixic acid, nitrofurantoin, and cephalothin has increased over the years. Monitoring antibiotic resistance and prescribing an appropriate antibiotic is vital to control resistance.
Topics: Humans; Anti-Bacterial Agents; Cephalothin; Cholera; Cholera Toxin; Ciprofloxacin; Furazolidone; Gatifloxacin; Levofloxacin; Microbial Sensitivity Tests; Nalidixic Acid; Nitrofurantoin; Norfloxacin; Novobiocin; Rifampin; Vibrio cholerae; Virulence Factors; Drug Resistance, Bacterial
PubMed: 35537594
DOI: 10.1016/j.micpath.2022.105514 -
Water Research Apr 2021The emergence of next generation sequencing (NGS) is revolutionizing the potential to address complex microbiological challenges in the water industry. NGS technologies... (Review)
Review
The emergence of next generation sequencing (NGS) is revolutionizing the potential to address complex microbiological challenges in the water industry. NGS technologies can provide holistic insight into microbial communities and their functional capacities in water and wastewater systems, thus eliminating the need to develop a new assay for each target organism or gene. However, several barriers have hampered wide-scale adoption of NGS by the water industry, including cost, need for specialized expertise and equipment, challenges with data analysis and interpretation, lack of standardized methods, and the rapid pace of development of new technologies. In this critical review, we provide an overview of the current state of the science of NGS technologies as they apply to water, wastewater, and recycled water. In addition, a systematic literature review was conducted in which we identified over 600 peer-reviewed journal articles on this topic and summarized their contributions to six key areas relevant to the water and wastewater fields: taxonomic classification and pathogen detection, functional and catabolic gene characterization, antimicrobial resistance (AMR) profiling, bacterial toxicity characterization, Cyanobacteria and harmful algal bloom identification, and virus characterization. For each application, we have presented key trends, noteworthy advancements, and proposed future directions. Finally, key needs to advance NGS technologies for broader application in water and wastewater fields are assessed.
Topics: Cyanobacteria; Harmful Algal Bloom; High-Throughput Nucleotide Sequencing; Wastewater; Water
PubMed: 33610927
DOI: 10.1016/j.watres.2021.116907 -
Clinical Microbiology and Infection :... Dec 2023Early identification of extended-spectrum ß-lactamase (ESBL) and carbapenemase-producing Enterobacterales (CP-CRE) is critical for timely therapy. Rapid phenotypic... (Meta-Analysis)
Meta-Analysis Review
Rapid phenotypic testing for detection of carbapenemase- or extended-spectrum ß-lactamase-producing Enterobacterales directly from blood cultures: a systematic review and meta-analysis.
BACKGROUND
Early identification of extended-spectrum ß-lactamase (ESBL) and carbapenemase-producing Enterobacterales (CP-CRE) is critical for timely therapy. Rapid phenotypic tests identifying these resistance mechanisms from pure bacterial colonies have been developed.
OBJECTIVES
To determine the operating characteristics of available rapid phenotypic tests when applied directly to positive blood cultures.
METHODS OF DATA SYNTHESIS
Bivariate random effects models were used unless convergence was not achieved where we used separate univariate models for sensitivity and specificity.
DATA SOURCES
MEDLINE, CENTRAL, Embase, BIOSIS, and Scopus from inception to 16 March 2021.
STUDY ELIGIBILITY CRITERIA
Studies using any rapid phenotypic assay for detection of ESBL or CP-CRE directly from blood cultures positive for Enterobacterales, including those utilizing spiked blood cultures. Case reports/series, posters, abstracts, review articles, those with ≤5 resistant isolates, and studies lacking data or without full text were excluded.
PARTICIPANTS
Consecutive patient samples (main analysis) or spiked blood cultures (sensitivity analysis).
TESTS
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry assays (MALDI-TOF) and commercially available chromogenic or immunogenic assays.
REFERENCE STANDARD
Conventional laboratory methods and/or polymerase chain reaction (PCR).
ASSESSMENT OF RISK OF BIAS
Quality Assessment of Diagnostic Accuracy Studies Version 2 (QUADAS-2).
RESULTS
For detection of the ESBL phenotype the respective pooled sensitivities and specificities for consecutive clinical samples were as follows: 94% (95% CI 93-99%) and 97% (95% CI 95-100%) for MALDI-TOF/mass spectrometry (n = 1); and 98% (95% CI 92-100%) and 100% (95% CI 96-100%) for chromogenic assays (n = 7). For the CP-CRE phenotype the respective pooled sensitivity and specificities for consecutive clinical samples were as follows: 100% (95% CI 99-100%) and 100% (95% CI 100-100%) for MALDI-TOF (n = 2); 96% (95% CI 77-99%) and 100% (95% CI 81-100%) for chromogenic assays (n = 4); and 98% (95% CI 96-100%) and 100% (95% CI 100-100%) for immunogenic testing (n = 2).
CONCLUSIONS
Rapid phenotypic assays that can be directly applied to positive blood cultures to detect ESBL and carbapenemase production from Enterobacterales exist and, although clinical studies are limited, they appear to have high sensitivity and specificity. Their potential to facilitate patient care through timely identification of bacterial resistance should be further explored.
Topics: Humans; Anti-Bacterial Agents; Blood Culture; beta-Lactamases; Bacterial Proteins; Phenotype; Microbial Sensitivity Tests
PubMed: 37722531
DOI: 10.1016/j.cmi.2023.09.007 -
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 -
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 -
Journal of Clinical Microbiology Sep 2023rRNA gene Sanger sequencing is being used for the identification of cultured pathogens. A new diagnostic approach is sequencing of uncultured samples by using the... (Meta-Analysis)
Meta-Analysis
Direct 16S/18S rRNA Gene PCR Followed by Sanger Sequencing as a Clinical Diagnostic Tool for Detection of Bacterial and Fungal Infections: a Systematic Review and Meta-Analysis.
rRNA gene Sanger sequencing is being used for the identification of cultured pathogens. A new diagnostic approach is sequencing of uncultured samples by using the commercial DNA extraction and sequencing platform SepsiTest (ST). The goal was to analyze the clinical performance of ST with a focus on nongrowing pathogens and the impact on antibiotic therapy. A literature search used PubMed/Medline, Cochrane, Science Direct, and Google Scholar. Eligibility followed PRISMA-P criteria. Quality and risk of bias were assessed drawing on QUADAS-2 (quality assessment of diagnostic accuracy studies, revised) criteria. Meta-analyses were performed regarding accuracy metrics compared to standard references and the added value of ST in terms of extra found pathogens. We identified 25 studies on sepsis, infectious endocarditis, bacterial meningitis, joint infections, pyomyositis, and various diseases from routine diagnosis. Patients with suspected infections of purportedly sterile body sites originated from various hospital wards. The overall sensitivity (79%; 95% confidence interval [CI], 73 to 84%) and specificity (83%; 95% CI, 72 to 90%) were accompanied by large effect sizes. ST-related positivity was 32% (95% CI, 30 to 34%), which was significantly higher than the culture positivity (20%; 95% CI, 18 to 22%). The overall added value of ST was 14% (95% CI, 10 to 20%) for all samples. With 130 relevant taxa, ST uncovered high microbial richness. Four studies demonstrated changes of antibiotic treatment at 12% (95% CI, 9 to 15%) of all patients upon availability of ST results. ST appears to be an approach for the diagnosis of nongrowing pathogens. The potential clinical role of this agnostic molecular diagnostic tool is discussed regarding changes of antibiotic treatment in cases where culture stays negative.
Topics: Humans; Anti-Bacterial Agents; Bacteria; Genes, rRNA; Meta-Analysis as Topic; Mycoses; Polymerase Chain Reaction; RNA, Ribosomal, 16S; RNA, Ribosomal, 18S; Sensitivity and Specificity; Systematic Reviews as Topic
PubMed: 37367430
DOI: 10.1128/jcm.00338-23 -
Nature Communications Aug 2023Microorganisms play essential roles in the health and resilience of cnidarians. Understanding the factors influencing cnidarian microbiomes requires cross study...
Microorganisms play essential roles in the health and resilience of cnidarians. Understanding the factors influencing cnidarian microbiomes requires cross study comparisons, yet the plethora of protocols used hampers dataset integration. We unify 16S rRNA gene sequences from cnidarian microbiome studies under a single analysis pipeline. We reprocess 12,010 cnidarian microbiome samples from 186 studies, alongside 3,388 poriferan, 370 seawater samples, and 245 cultured Symbiodiniaceae, unifying ~6.5 billion sequence reads. Samples are partitioned by hypervariable region and sequencing platform to reduce sequencing variability. This systematic review uncovers an incredible diversity of 86 archaeal and bacterial phyla associated with Cnidaria, and highlights key bacteria hosted across host sub-phylum, depth, and microhabitat. Shallow (< 30 m) water Alcyonacea and Actinaria are characterized by highly shared and relatively abundant microbial communities, unlike Scleractinia and most deeper cnidarians. Utilizing the V4 region, we find that cnidarian microbial composition, richness, diversity, and structure are primarily influenced by host phylogeny, sampling depth, and ocean body, followed by microhabitat and sampling date. We identify host and geographical generalist and specific Endozoicomonas clades within Cnidaria and Porifera. This systematic review forms a framework for understanding factors governing cnidarian microbiomes and creates a baseline for assessing stress associated dysbiosis.
Topics: Animals; RNA, Ribosomal, 16S; Microbiota; Bacteria; Archaea; Anthozoa; Phylogeny
PubMed: 37580316
DOI: 10.1038/s41467-023-39876-6 -
The ISME Journal Jan 2024Genome-scale metabolic models (GEMs) are valuable tools serving systems biology and metabolic engineering. However, GEMs are still an underestimated tool in informing... (Review)
Review
Genome-scale metabolic models (GEMs) are valuable tools serving systems biology and metabolic engineering. However, GEMs are still an underestimated tool in informing microbial ecology. Since their first application for aerobic gammaproteobacterial methane oxidizers less than a decade ago, GEMs have substantially increased our understanding of the metabolism of methanotrophs, a microbial guild of high relevance for the natural and biotechnological mitigation of methane efflux to the atmosphere. Particularly, GEMs helped to elucidate critical metabolic and regulatory pathways of several methanotrophic strains, predicted microbial responses to environmental perturbations, and were used to model metabolic interactions in cocultures. Here, we conducted a systematic review of GEMs exploring aerobic methanotrophy, summarizing recent advances, pointing out weaknesses, and drawing out probable future uses of GEMs to improve our understanding of the ecology of methane oxidizers. We also focus on their potential to unravel causes and consequences when studying interactions of methane-oxidizing bacteria with other methanotrophs or members of microbial communities in general. This review aims to bridge the gap between applied sciences and microbial ecology research on methane oxidizers as model organisms and to provide an outlook for future studies.
Topics: Methane; Oxidation-Reduction; Aerobiosis; Metabolic Networks and Pathways; Models, Biological
PubMed: 38861460
DOI: 10.1093/ismejo/wrae102