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Cureus Mar 2020Endodontic treatment failure may occur due to different causes such as persistence of bacteria, root canals that are poorly cleaned and obturated, improper coronal seal... (Review)
Review
Endodontic treatment failure may occur due to different causes such as persistence of bacteria, root canals that are poorly cleaned and obturated, improper coronal seal (leakage), and untreated canals (missed canals). The main reason for endodontic failure is the presence of some species of bacteria inside the root canal system such as Enterococcus (E.) faecalis. Those bacteria are more resistant to disinfection agents, causing a persistent intra-radicular or extra-radicular infection. The current review aims to compile all the current studies concerning Enterococcus faecalis as a dental root canal pathogen that causes endodontic failure. In this systemic review, two databases, PubMed and Google Scholar, were searched using specific inclusion and exclusion criteria. Among 2943 studies, only 11 met the inclusion criteria and were included in the review for further analysis. The 11 studies give prominence to the high distribution of Enterococcus faecalis within the root canal system. These studies investigated different aspects of Enterococcus faecalis, including its prevalence, resistance mechanisms, characteristics, express survival genes, and treatment. The compiled data observed that most of the studies highlight Enterococcus faecalis as the primary pathogen associated with endodontic treatment. It has characteristic proprieties that make it capable of escaping disinfection means. Furthermore, clinical trials are required to examine E. faecalis and may provide valuable information about novel microbial detection methods to decrease the number of E. faecalis within the root canal system.
PubMed: 32292671
DOI: 10.7759/cureus.7257 -
Mini Reviews in Medicinal Chemistry 2021In the era of antimicrobial resistance, fungal pathogens are not an exception. Several strategies, including antimicrobial stewardship programs and high throughput...
In the era of antimicrobial resistance, fungal pathogens are not an exception. Several strategies, including antimicrobial stewardship programs and high throughput screening of new drugs, are being implemented. Several recent studies have demonstrated the effectiveness of plant compounds with antifungal activity. In this systematic review, we examine the use of natural compounds as a possible avenue to fight fungal infections produced by Candida albicans, the most common human fungal pathogen. Electronic literature searches were conducted through PubMed/MEDLINE, Cochrane, and Science Direct limited to the 5 years. A total of 131 articles were included, with 186 plants extracts evaluated. Although the majority of the natural extracts exhibited antifungal activities against C. albicans (both in vivo and in vitro), the strongest antifungal activity was obtained from Lawsonia inermis, Pelargonium graveolens, Camellia sinensis, Mentha piperita, and Citrus latifolia. The main components with proven antifungal activities were phenolic compounds such as gallic acid, thymol, and flavonoids (especially catechin), polyphenols such as tannins, terpenoids and saponins. The incorporation of nanotechnology greatly enhances the antifungal properties of these natural compounds. Further research is needed to fully characterize the composition of all herbal extracts with antifungal activity as well as the mechanisms of action of the active compounds.
Topics: Antifungal Agents; Camellia sinensis; Candida albicans; Citrus; Humans; Lawsonia Plant; Mentha piperita; Microbial Sensitivity Tests; Pelargonium; Plant Extracts
PubMed: 32600229
DOI: 10.2174/1389557520666200628032116 -
Clinical Microbiology and Infection :... Dec 2020Bacterial co-pathogens are commonly identified in viral respiratory infections and are important causes of morbidity and mortality. The prevalence of bacterial infection... (Meta-Analysis)
Meta-Analysis
BACKGROUND
Bacterial co-pathogens are commonly identified in viral respiratory infections and are important causes of morbidity and mortality. The prevalence of bacterial infection in patients infected with SARS-CoV-2 is not well understood.
AIMS
To determine the prevalence of bacterial co-infection (at presentation) and secondary infection (after presentation) in patients with COVID-19.
SOURCES
We performed a systematic search of MEDLINE, OVID Epub and EMBASE databases for English language literature from 2019 to April 16, 2020. Studies were included if they (a) evaluated patients with confirmed COVID-19 and (b) reported the prevalence of acute bacterial infection.
CONTENT
Data were extracted by a single reviewer and cross-checked by a second reviewer. The main outcome was the proportion of COVID-19 patients with an acute bacterial infection. Any bacteria detected from non-respiratory-tract or non-bloodstream sources were excluded. Of 1308 studies screened, 24 were eligible and included in the rapid review representing 3338 patients with COVID-19 evaluated for acute bacterial infection. In the meta-analysis, bacterial co-infection (estimated on presentation) was identified in 3.5% of patients (95%CI 0.4-6.7%) and secondary bacterial infection in 14.3% of patients (95%CI 9.6-18.9%). The overall proportion of COVID-19 patients with bacterial infection was 6.9% (95%CI 4.3-9.5%). Bacterial infection was more common in critically ill patients (8.1%, 95%CI 2.3-13.8%). The majority of patients with COVID-19 received antibiotics (71.9%, 95%CI 56.1 to 87.7%).
IMPLICATIONS
Bacterial co-infection is relatively infrequent in hospitalized patients with COVID-19. The majority of these patients may not require empirical antibacterial treatment.
Topics: Asia; Bacteria; Bacterial Infections; COVID-19; Coinfection; Critical Illness; Data Management; Female; Humans; Male; Pandemics; Prevalence; Respiratory Tract Infections; United States
PubMed: 32711058
DOI: 10.1016/j.cmi.2020.07.016 -
Infection Control and Hospital... Apr 2024To identify and report the pathogens and sources of contamination associated with bronchoscopy-related outbreaks and pseudo-outbreaks. (Review)
Review
OBJECTIVE
To identify and report the pathogens and sources of contamination associated with bronchoscopy-related outbreaks and pseudo-outbreaks.
DESIGN
Systematic review.
SETTING
Inpatient and outpatient outbreaks and pseudo-outbreaks after bronchoscopy.
METHODS
PubMed/Medline databases were searched according to Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines, using the search terms "bronchoscopy," "outbreak," and "pseudo-outbreak" from inception until December 31, 2022. From eligible publications, data were extracted regarding the type of event, pathogen involved, and source of contamination. Pearson correlation was used to identify correlations between variables.
RESULTS
In total, 74 studies describing 23 outbreaks and 52 pseudo-outbreaks were included in this review. The major pathogens identified in these studies were , , nontuberculous mycobacteria (NTM), , , , , and fungi. The primary sources of contamination were the use of contaminated water or contaminated topical anesthetics, dysfunction and contamination of bronchoscopes or automatic endoscope reprocessors, and inadequate disinfection of the bronchoscopes following procedures. Correlations were identified between primary bronchoscope defects and the identification of (r = 0.351; = .002) and (r = 0.346; = .002), and between the presence of a contaminated water source and NTM (r = 0.331; = .004) or (r = 0.280; = .015).
CONCLUSIONS
Continued vigilance in bronchoscopy disinfection practices remains essential because outbreaks and pseudo-outbreaks continue to pose a significant risk to patient care, emphasizing the importance of stringent disinfection and quality control measures.
Topics: Humans; Bronchoscopy; Cross Infection; Equipment Contamination; Bronchoscopes; Pseudomonas aeruginosa; Disease Outbreaks; Nontuberculous Mycobacteria; Klebsiella pneumoniae; Water
PubMed: 38099453
DOI: 10.1017/ice.2023.250 -
Systematic Reviews Oct 2023Food-borne diseases are a global public health issue with 1 in 10 people falling ill after eating contaminated food every year. In response, the food industry has... (Meta-Analysis)
Meta-Analysis Review
Food-borne diseases are a global public health issue with 1 in 10 people falling ill after eating contaminated food every year. In response, the food industry has implemented several new pathogen control strategies, such as biotechnological tools using the direct application of bacteriophages for biological control. We have undertaken a systematic review and meta-analysis that evaluated the efficiency of patented phages as a biological control for food-borne pathogens and determined the physical-chemical characteristics of the antimicrobial effect. Included and excluded criteria was developed. Included criteria: Phage patent files with an application in biological control on food and scientific articles and book chapters that used phages patented for food biological control. Excluded criteria: Patent documents, scientific articles, and book chapters that included phage therapy in humans, animals, and biological control on plants but did not have an application on food were not considered in our study. The systematic analysis identified 77 documents, 46 scientific articles, and 31 documents of patents and 23 articles was included in the meta-analysis. Listeria monocytogenes and Salmonella sp. comprised most of the targets identified in the screening, so that we focused on these strains to do the meta-analysis. There are a total of 383 and 192 experiments for Listeria and Salmonella phages for quantitative data analysis.Indexing databases for the bibliographic search (Scopus, Web of Science (WoS) and PubMed (Medline) were addressed by an automated script written in Python 3 Python Core Team (2015) and deposited on GitHub ( https://github.com/glenjasper ).A random-effects meta-analysis revealed (i) significant antimicrobial effect of Listeria phages in apple, apple juice, pear, and pear juice, (ii) significant antimicrobial effect of Salmonella phages in eggs, apple, and ready-to-eat chicken, (iii) no heterogeneity was identified in either meta-analysis, (iv) publication bias was detected for Listeria phages but not for Salmonella phages. (v) ListShield and Felix01 phages showed the best result for Listeria and Salmonella biological control, respectively, (vi) concentration of phage and bacteria, time and food had significant effect in the biological control of Listeria, (vii) temperature and time had a significant effect on the antimicrobial activity of Salmonella phages. The systematic review and meta-analyses to determine the efficiency of bacteriophages previously patented against pathogenic bacteria on dairy products, meat, fruits and vegetables. Besides, the discovering of key factors for efficacy, so that future applications of phage biotechnology in foods can be optimally deployed.
Topics: Anti-Infective Agents; Bacteriophages; Foodborne Diseases; Listeria monocytogenes; Meat
PubMed: 37898821
DOI: 10.1186/s13643-023-02352-9 -
Liver International : Official Journal... Oct 2017While hepatitis C exemplifies the role of host genetics in infectious diseases outcomes, there is no comprehensive overview of polymorphisms influencing spontaneous... (Meta-Analysis)
Meta-Analysis Review
While hepatitis C exemplifies the role of host genetics in infectious diseases outcomes, there is no comprehensive overview of polymorphisms influencing spontaneous and/or treatment-induced hepatitis C virus clearance. We performed a systematic review and meta-analysis of host polymorphisms associated with these phenotypes. Literature search was conducted using combinations of keywords in three databases. Studies were reviewed and relevant data systematically extracted for subsequent meta-analyses. Polymorphisms from candidate gene studies were tested in two cohorts of HCV-infected patients with available genomic data. The literature search yielded 8'294 citations, among which 262 studies were selected. In the meta-analysis of 27 HLA studies, the most significant associations with spontaneous hepatitis C virus clearance included DQB1*02, DQB1*03, DRB1*04 and DRB1*11. In the meta-analysis of 16 studies of KIR genes and their HLA-ligands, KIR2DS3 was associated with both spontaneous and treatment-induced clearance, and the HLA-C2 ligand with failure to spontaneously clear the virus. In a pooled analysis of 105 candidate genes and two genome-wide association studies, we observed associations of single nucleotide polymorphisms from nine genes (EIF2AK2, IFNAR2, ITPA, MBL2, MX1, OASL, SPP1, TGFB1, TNK2) with response to interferon-based therapy. Meta-analysis of 141 studies confirmed the association of IFNL3/4 polymorphisms with spontaneous and treatment-induced hepatitis C virus clearance, even in previously underpowered groups, such as hepatitis C virus genotypes 2/3-infected patients. This study may contribute to a better understanding of hepatitis C virus immunopathogenesis and highlights the complex role of host genetics in hepatitis C virus clearance.
Topics: Antiviral Agents; Genotype; HLA Antigens; Hepacivirus; Hepatitis C; Host-Pathogen Interactions; Humans; Odds Ratio; Phenotype; Polymorphism, Single Nucleotide; Receptors, KIR; Sustained Virologic Response; Treatment Outcome
PubMed: 28261910
DOI: 10.1111/liv.13401 -
Microorganisms Jun 2023A set of diseases caused by fungi and oomycetes are responsible for large losses in annual world cocoa production. Managing the impact caused by these diseases is very... (Review)
Review
A set of diseases caused by fungi and oomycetes are responsible for large losses in annual world cocoa production. Managing the impact caused by these diseases is very complex because a common solution has yet to be found for different pathogens. In this context, the systematic knowledge of L. pathogens' molecular characteristics may help researchers understand the possibilities and limitations of cocoa disease management strategies. This work systematically organized and summarized the main findings of omics studies of eukaryotic pathogens, focusing on the plant-pathogen interaction and production dynamics. Using the PRISMA protocol and a semiautomated process, we selected papers from the Scopus and Web of Science databases and collected data from the selected papers. From the initial 3169 studies, 149 were selected. The first author's affiliations were mostly from two countries, Brazil (55%) and the USA (22%). The most frequent genera were (105 studies), (59 studies) and (13 studies). The systematic review database includes papers reporting the whole-genome sequence from six cocoa pathogens and evidence of some necrosis-inducing-like proteins, which are common in pathogen genomes. This review contributes to the knowledge about diseases, providing an integrated discussion of pathogens' molecular characteristics, common mechanisms of pathogenicity and how this knowledge is produced worldwide.
PubMed: 37375069
DOI: 10.3390/microorganisms11061567 -
Andrology Sep 2015The relationship between mycoplasma and ureaplasma infection and male infertility has been studied widely; however, results remain controversial. This meta-analysis... (Meta-Analysis)
Meta-Analysis Review
The relationship between mycoplasma and ureaplasma infection and male infertility has been studied widely; however, results remain controversial. This meta-analysis investigated the association between genital ureaplasmas (Ureaplasma urealyticum, Ureaplasma parvum) and mycoplasmas (Mycoplasma hominis, Mycoplasma genitalium), and risk of male infertility. Differences in prevalence of ureaplasma and mycoplasma infection between China and the rest of the world were also compared. Study data were collected from PubMed, Embase and the China National Knowledge Infrastructure. Summary odds ratio (OR) with 95% confidence interval (CI) was applied to assess the relationship. Heterogeneity testing and publication bias testing were also performed. A total of 14 studies were used: five case-control studies with 611 infertile cases and 506 controls featuring U. urealyticum infection, and nine case-control studies with 2410 cases and 1223 controls concerning M. hominis infection. Two other infection (U. parvum and M. genitalium) were featured in five and three studies, respectively. The meta-analysis results indicated that U. parvum and M. genitalium are not associated with male infertility. However, a significant relationship existed between U. urealyticum and M. hominis and male infertility. Comparing the global average with China, a significantly higher positive rate of U. urealyticum, but a significantly lower positive rate of M. hominis, was observed in both the infertile and control groups in China.
Topics: China; Genital Diseases, Male; Humans; Infertility, Male; Male; Mycoplasma Infections; Mycoplasma genitalium; Mycoplasma hominis; Ureaplasma; Ureaplasma Infections; Ureaplasma urealyticum
PubMed: 26311339
DOI: 10.1111/andr.12078 -
Viruses Jul 2022Arctic regions are ecologically significant for the environmental persistence and geographic dissemination of influenza A viruses (IAVs) by avian hosts and other... (Review)
Review
Arctic regions are ecologically significant for the environmental persistence and geographic dissemination of influenza A viruses (IAVs) by avian hosts and other wildlife species. Data describing the epidemiology and ecology of IAVs among wildlife in the arctic are less frequently published compared to southern temperate regions, where prevalence and subtype diversity are more routinely documented. Following PRISMA guidelines, this systematic review addresses this gap by describing the prevalence, spatiotemporal distribution, and ecological characteristics of IAVs detected among wildlife and the environment in this understudied region of the globe. The literature search was performed in PubMed and Google Scholar using a set of pre-defined search terms to identify publications reporting on IAVs in Arctic regions between 1978 and February 2022. A total of 2125 articles were initially screened, 267 were assessed for eligibility, and 71 articles met inclusion criteria. IAVs have been detected in multiple wildlife species in all Arctic regions, including seabirds, shorebirds, waterfowl, seals, sea lions, whales, and terrestrial mammals, and in the environment. Isolates from wild birds comprise the majority of documented viruses derived from wildlife; however, among all animals and environmental matrices, 26 unique low and highly pathogenic subtypes have been characterized in the scientific literature from Arctic regions. Pooled prevalence across studies indicates 4.23% for wild birds, 3.42% among tested environmental matrices, and seroprevalences of 9.29% and 1.69% among marine and terrestrial mammals, respectively. Surveillance data are geographically biased, with most data from the Alaskan Arctic and many fewer reports from the Russian, Canadian, North Atlantic, and Western European Arctic. We highlight multiple important aspects of wildlife host, pathogen, and environmental ecology of IAVs in Arctic regions, including the role of avian migration and breeding cycles for the global spread of IAVs, evidence of inter-species and inter-continental reassortment at high latitudes, and how climate change-driven ecosystem shifts, including changes in the seasonal availability and distribution of dietary resources, have the potential to alter host-pathogen-environment dynamics in Arctic regions. We conclude by identifying gaps in knowledge and propose priorities for future research.
Topics: Animals; Animals, Wild; Arctic Regions; Birds; Canada; Ecosystem; Influenza A virus; Influenza in Birds; Mammals
PubMed: 35891510
DOI: 10.3390/v14071531 -
Salud Publica de Mexico Dec 2020Objetivo. Describir la evidencia sobre la presencia e infectividad de SARS-CoV-2 y otros coronavirus en aguas residuales y su potencial uso como herramienta de...
Objetivo. Describir la evidencia sobre la presencia e infectividad de SARS-CoV-2 y otros coronavirus en aguas residuales y su potencial uso como herramienta de vigilancia epidemiológica. Material y métodos. Búsqueda de publicaciones en PubMed y medRxiv desde enero 2003 hasta el 8 de junio de 2020 de acuerdo con la guía de revisiones rápidas de Cochrane. Resultados. Se incluyeron 29 publicaciones. El ARN de SARS-CoV-2 no infectivo se encontró en agua residual hospitalaria, agua residual cruda, tratada y lodos de plantas de tratamiento. Los niveles cuantitativos de ARN viral en agua residual presentan relación con el número de casos de Covid-19. SARS-CoV-1 y otros coronavirus permanecieron infectivos en agua residual cruda hasta por dos días. Conclusiones. Hasta esta revisión no existe evidencia sobre la presencia de virus infectivos de SARS-CoV-2 en agua residual cruda o tratada. La cuantificación de ARN de SARS-CoV-2 en agua residual es útil para la vigilancia epidemiológica.
Topics: Coronavirus; Mexico; RNA, Viral; Severe acute respiratory syndrome-related coronavirus; SARS-CoV-2; Virulence; Wastewater; Wastewater-Based Epidemiological Monitoring; Water Microbiology
PubMed: 33984206
DOI: 10.21149/11783