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Journal of Advanced Research Sep 2023The rapid and reliable detection of pathogenic bacteria at an early stage is a highly significant research field for public health. However, most traditional approaches... (Review)
Review
BACKGROUND
The rapid and reliable detection of pathogenic bacteria at an early stage is a highly significant research field for public health. However, most traditional approaches for pathogen identification are time-consuming and labour-intensive, which may cause physicians making inappropriate treatment decisions based on an incomplete diagnosis of patients with unknown infections, leading to increased morbidity and mortality. Therefore, novel methods are constantly required to face the emerging challenges of bacterial detection and identification. In particular, Raman spectroscopy (RS) is becoming an attractive method for rapid and accurate detection of bacterial pathogens in recent years, among which the newly developed surface-enhanced Raman spectroscopy (SERS) shows the most promising potential.
AIM OF REVIEW
Recent advances in pathogen detection and diagnosis of bacterial infections were discussed with focuses on the development of the SERS approaches and its applications in complex clinical settings.
KEY SCIENTIFIC CONCEPTS OF REVIEW
The current review describes bacterial classification using surface enhanced Raman spectroscopy (SERS) for developing a rapid and more accurate method for the identification of bacterial pathogens in clinical diagnosis. The initial part of this review gives a brief overview of the mechanism of SERS technology and development of the SERS approach to detect bacterial pathogens in complex samples. The development of the label-based and label-free SERS strategies and several novel SERS-compatible technologies in clinical applications, as well as the analytical procedures and examples of chemometric methods for SERS, are introduced. The computational challenges of pre-processing spectra and the highlights of the limitations and perspectives of the SERS technique are also discussed.Taken together, this systematic review provides an overall summary of the SERS technique and its application potential for direct bacterial diagnosis in clinical samples such as blood, urine and sputum, etc.
Topics: Humans; Spectrum Analysis, Raman; Bacteria; Bacterial Infections
PubMed: 36549439
DOI: 10.1016/j.jare.2022.11.010 -
Pathogens (Basel, Switzerland) Sep 2022Background Human African trypanocide resistance (HATr) is a challenge for the eradication of Human African Trypansomiaisis (HAT) following the widespread emergence of... (Review)
Review
Background Human African trypanocide resistance (HATr) is a challenge for the eradication of Human African Trypansomiaisis (HAT) following the widespread emergence of increased monotherapy drug treatment failures against Trypanosoma brucei gambiense and T. b. rhodesiense that are associated with changes in pathogen receptors. Methods: Electronic searches of 12 databases and 3 Google search websites for human African trypanocide resistance were performed using a keyword search criterion applied to both laboratory and clinical studies. Fifty-one publications were identified and included in this study using the PRISMA checklist. Data were analyzed using RevMan and random effect sizes were computed for the statistics at the 95% confidence interval. Results: Pentamidine/melarsoprol/nifurtimox cross-resistance is associated with loss of the T. brucei adenosine transporter 1/purine 2 gene (TbAT1/P2), aquaglyceroporins (TbAQP) 2 and 3, followed by the high affinity pentamidine melarsoprol transporter (HAPT) 1. In addition, the loss of the amino acid transporter (AAT) 6 is associated with eflornithine resistance. Nifurtimox/eflornithine combination therapy resistance is associated with AAT6 and nitroreductase loss, and high resistance and parasite regrowth is responsible for treatment relapse. In clinical studies, the TbAT1 proportion of total random effects was 68% (95% CI: 38.0−91.6); I2 = 96.99% (95% CI: 94.6−98.3). Treatment failure rates were highest with melarsoprol followed by eflornithine at 41.49% (95% CI: 24.94−59.09) and 6.56% (3.06−11.25) respectively. HATr-resistant phenotypes used in most laboratory experiments demonstrated significantly higher pentamidine resistance than other trypanocides. Conclusion: The emergence of drug resistance across the spectrum of trypanocidal agents that are used to treat HAT is a major threat to the global WHO target to eliminate HAT by 2030. T. brucei strains were largely resistant to diamidines and the use of high trypanocide concentrations in clinical studies have proved fatal in humans. Studies to develop novel chemotherapeutical agents and identify alternative protein targets could help to reduce the emergence and spread of HATr.
PubMed: 36297157
DOI: 10.3390/pathogens11101100 -
Pathogens (Basel, Switzerland) Feb 2023Current inflammatory bowel disease (IBD) treatments including non-biological, biological, and nutritional therapies aim to achieve remission and mucosal healing.... (Review)
Review
Current inflammatory bowel disease (IBD) treatments including non-biological, biological, and nutritional therapies aim to achieve remission and mucosal healing. Treatment efficacy, however, is highly variable, and there is growing evidence that the gut microbiota influences therapeutic efficacy. The aim of this study was to conduct a systematic review and meta-analysis to define changes in the gut microbiota following IBD treatment and to identify microbial predictors of treatment response. A systematic search using MEDLINE/Embase and PubMed was performed in July 2022. The review was conducted based on the Preferred Reporting Items for Systematic reviews and Meta-Analyses guidelines. Studies were included if they reported longitudinal microbiota analysis (>2 weeks) using next-generation sequencing or high-throughput sequencing of faecal/mucosal samples from IBD patients commencing treatment. Meta-analysis on alpha-diversity changes following infliximab treatment was conducted. Thirty-nine studies met the inclusion criteria, and four studies were included in the meta-analysis. An increase in alpha diversity was observed following treatment with 5-aminosalicylates, corticosteroids, and biological therapies in most studies. Characteristic signatures involving the enrichment of short-chain-fatty-acid-producing bacteria including and a reduction of pathogenic bacteria including various Proteobacteria were demonstrated following treatment with specific signatures identified based on treatment outcome. The meta-analysis demonstrated a statistically significant increase in bacterial richness following infliximab treatment (standardised mean difference -1.16 (-1.50, -0.83), < 0.00001). Conclusion: Distinct microbial signatures are seen following treatment and are associated with treatment response. The interrogation of large longitudinal studies is needed to establish the link between the gut microbiota and IBD therapeutic outcomes.
PubMed: 36839534
DOI: 10.3390/pathogens12020262 -
Frontiers in Veterinary Science 2021is a worldwide emerging zoonotic tick-borne pathogen transmitted by ticks and naturally maintained in complex and incompletely assessed enzootic cycles. Several... (Review)
Review
is a worldwide emerging zoonotic tick-borne pathogen transmitted by ticks and naturally maintained in complex and incompletely assessed enzootic cycles. Several studies have demonstrated an extensive genetic variability with variable host tropisms and pathogenicity. However, the relationship between genetic diversity and modified pathogenicity is not yet understood. Because of their proximity to humans, dogs are potential sentinels for the transmission of vector-borne pathogens. Furthermore, the strong molecular similarity between human and canine isolates of in Europe and the USA and the positive association in the distribution of human and canine cases in the USA emphasizes the epidemiological role of dogs. infects and survives within neutrophils by disregulating neutrophil functions and evading specific immune responses. Moreover, the complex interaction between the bacterium and the infected host immune system contribute to induce inflammatory injuries. Canine granulocytic anaplasmosis is an acute febrile illness characterized by lethargy, inappetence, weight loss and musculoskeletal pain. Hematological and biochemistry profile modifications associated with this disease are unspecific and include thrombocytopenia, anemia, morulae within neutrophils and increased liver enzymes activity. Coinfections with other tick-borne pathogens (TBPs) may occur, especially with , complicating the clinical presentation, diagnosis and response to treatment. Although clinical studies have been published in dogs, it remains unclear if several clinical signs and clinicopathological abnormalities can be related to this infection.
PubMed: 34250067
DOI: 10.3389/fvets.2021.686644 -
Water Research X Jan 2023The safe management of fecal sludge from the 3.4 billion people worldwide that use onsite sanitation systems can greatly reduce the global infectious disease burden.... (Review)
Review
The safe management of fecal sludge from the 3.4 billion people worldwide that use onsite sanitation systems can greatly reduce the global infectious disease burden. However, there is limited knowledge about the role of design, operational, and environmental factors on pathogen survival in pit latrines, urine diverting desiccation toilets, and other types of onsite toilets. We conducted a systematic literature review and meta-analysis to characterize pathogen reduction rates in fecal sludge, feces, and human excreta with respect to pH, temperature, moisture content, and the use of additives for desiccation, alkalinization, or disinfection. A meta-analysis of 1,382 data points extracted from 243 experiments described in 26 articles revealed significant differences between the decay rates and T values of pathogens and indicators from different microbial groups. The overall median T values were 4.8 days, 29 days, >341 days, and 429 days for bacteria, viruses, protozoan (oo)cysts, and eggs, respectively. As expected, higher pH values, higher temperatures, and the application of lime all significantly predicted greater pathogen reduction rates but the use of lime by itself was more effective for bacteria and viruses than for eggs, unless urea was also added. In multiple lab-scale experiments, the application of urea with enough lime or ash to reach a pH of 10 - 12 and a sustained concentration of 2,000 - 6,000 mg/L of non-protonated NHN reduced eggs more rapidly than without urea. In general, the storage of fecal sludge for 6 months adequately controls hazards from viruses and bacteria, but much longer storage times or alkaline treatment with urea and low moisture or heat is needed to control hazards from protozoa and helminths. More research is needed to demonstrate the efficacy of lime, ash, and urea in the field. More studies of protozoan pathogens are also needed, as very few qualifying experiments were found for this group.
PubMed: 37250291
DOI: 10.1016/j.wroa.2023.100171 -
Frontiers in Genetics 2020A compound heterozygous () variant is a type of germline variant that occurs when each parent donates one alternate allele and these alleles are located at different... (Review)
Review
A compound heterozygous () variant is a type of germline variant that occurs when each parent donates one alternate allele and these alleles are located at different loci within the same gene. Pathogenic germline variants have been identified for some pediatric cancer types but in most studies, variants are overlooked. Thus, the prevalence of pathogenic variants in most pediatric cancer types is unknown. We identified 26 studies (published between 1999 and 2019) that identified a variant in at least one pediatric cancer patient. These studies encompass 21 cancer types and have collectively identified 25 different genes in which a variant occurred. However, the sequencing methods used and the number of patients and genes evaluated in each study were highly variable across the studies. In addition, methods for assessing pathogenicity of variants varied widely and were often not reported. In this review, we discuss technologies and methods for identifying variants, provide an overview of studies that have identified variants in pediatric cancer patients, provide insights into future directions in the field, and give a summary of publicly available pediatric cancer sequencing data. Although considerable insights have been gained over the last 20 years, much has yet to be learned about the involvement of variants in pediatric cancers. In future studies, larger sample sizes, more pediatric cancer types, and better pathogenicity assessment and filtering methods will be needed to move this field forward.
PubMed: 32508881
DOI: 10.3389/fgene.2020.00493 -
BMJ Open Apr 2023We aimed to summarise the prevalence of atypical pathogens in patients with severe pneumonia to understand the prevalence of severe pneumonia caused by atypical... (Meta-Analysis)
Meta-Analysis
OBJECTIVES
We aimed to summarise the prevalence of atypical pathogens in patients with severe pneumonia to understand the prevalence of severe pneumonia caused by atypical pathogens, improve clinical decision-making and guide antibiotic use.
DESIGN
Systematic review and meta-analysis.
DATA SOURCES
PubMed, Embase, Web of Science and Cochrane Library were searched through November 2022.
ELIGIBILITY CRITERIA
English language studies enrolled consecutive cases of patients diagnosed with severe pneumonia, with complete aetiological analysis.
DATA EXTRACTION AND SYNTHESIS
We conducted literature retrieval on PubMed, Embase, Web of Science and The Cochrane Library to estimate the prevalence of , and in patients with severe pneumonia. After double arcsine transformation of the data, a random-effects model was used for meta-analyses to calculate the pooled prevalence of each pathogen. Meta-regression analysis was also used to explore whether the region, different diagnostic method, study population, pneumonia categories or sample size were potential sources of heterogeneity.
RESULTS
We included 75 eligible studies with 18 379 cases of severe pneumonia. The overall prevalence of atypical pneumonia is 8.1% (95% CI 6.3% to 10.1%) In patients with severe pneumonia, the pooled estimated prevalence of , and was 1.8% (95% CI 1.0% to 2.9%), 2.8% (95% CI 1.7% to 4.3%) and 4.0% (95% CI 2.8% to 5.3%), respectively. We noted significant heterogeneity in all pooled assessments. Meta-regression showed that the pneumonia category potentially influenced the prevalence rate of . The mean age and the diagnostic method of pathogens were likely moderators for the prevalence of and , and contribute to the heterogeneity of their prevalence.
CONCLUSIONS
In severe pneumonia, atypical pathogens are notable causes, especially . The diagnostic method, regional difference, sample size and other factors contribute to the heterogeneity of prevalence. The estimated prevalence and relative heterogeneity factors can help with microbiological screening, clinical treatment and future research planning.
PROSPERO REGISTRATION NUMBER
CRD42022373950.
Topics: Humans; Pneumonia, Bacterial; Prevalence; Mycoplasma pneumoniae; Pneumonia, Mycoplasma; Legionella; Chlamydia
PubMed: 37041056
DOI: 10.1136/bmjopen-2022-066721 -
Journal of Clinical Medicine Sep 2022(1) Background: We aimed to systematically review the current literature to evaluate if in patients with postoperative endophthalmitis treated with pars plana... (Review)
Review
(1) Background: We aimed to systematically review the current literature to evaluate if in patients with postoperative endophthalmitis treated with pars plana vitrectomy, silicone oil tamponade could provide a useful contribution to the control and eradication of infection and if it could influence anatomical recovery and functional outcome. (2) Randomized controlled trials, cross-sectional studies, case series, and case reports published in the English language in peer-reviewed journals were included. No restriction was placed based on the study location. We used medical subject headings (MeSH) and text words. We searched MEDLINE (OVID and PubMed), Google Scholar, ISI Web of Science (Thom-on-Reuters), and the Cochrane Library (Wiley) from January 1995 to the present. To ensure literature saturation, we scanned the reference lists of included studies or relevant reviews identified through the search. Risk of Bias was assessed using the Newcastle-Ottawa scale for longitudinal studies and Cochrane risk-of-bias tool for randomized trials. (3) Results: abstracts of 75 articles were selected for full-text reading; after full-text reading, 44 articles were taken into consideration in the systematic review. 5 out of 7 in vitro experimental studies demonstrated antimicrobial activity against different species of bacteria and fungi. The use of SO as endotamponade associated with PPV led to better visual acuity and a lower rate of retinal detachment and the need for additional surgery. (4) Conclusions: Silicone oil reduces the risk of postoperative retinal detachment, especially in case of undetected retinal breaks, produces compartmentalization of the eye, may lead to early visual recovery, allows laser photocoagulation, prevents severe postoperative hypotony and has antimicrobic activity due to an inhibitory effect for several species of pathogens. Concerns regarding possible toxic effects on the retina and optic disc, compartmentalization and impaired washout of pathogen toxins have been reported. It may also influence intravitreal antibiotic distribution and clearance.
PubMed: 36143089
DOI: 10.3390/jcm11185445 -
Veterinary Research Forum : An... 2023The purpose of this review was to assess the use of plant essential oils and extracts (PEOE) in the development of antimicrobial edible films for dairy application... (Review)
Review
The purpose of this review was to assess the use of plant essential oils and extracts (PEOE) in the development of antimicrobial edible films for dairy application through a systematic review and meta-analysis. All studies published in multiple databases were explored via PRISMA protocol on November 1, 2022. According to the results, the interquartile range of pathogen reduction potential of essential oil (EO) in dairy products, irrespective of EO, film and product type, was 0.10 - 4.70 log CFU g per % concentration. The findings from 38 articles indicate that among all EOs or their compounds, Boiss in protein film, thyme in protein film, Boiss EO in protein film, -cinnamaldehyde in carbohydrate film and lemongrass EO in protein film had extraordinary pathogen reduction potential on important foodborne pathogens. In the case of plant extract, fish gelatin film with extract, whey protein isolate film loaded with oregano EO and carboxymethyl cellulose film with clove EOs had the highest antimicrobial effect on mesophilic bacteria (9.50 log CFU g per % concentration), yeast-mold (2.63 log CFU g per % concentration) and mesophilic/ psychrophilic counts (> 9.06 log CFU g per % concentration), respectively. is the primary species of interest; whereas, mesophiles and mold-yeast populations were the most investigated microbiota/mycobiota in cheese with PEOE-incorporated film. In light of these findings, the choice of PEOE at appropriate concentrations with the selection of appropriate edible film may improve the safety, sensory, and shelf life of dairy products.
PubMed: 37181858
DOI: 10.30466/vrf.2022.1986122.3730 -
Frontiers in Immunology 2020The term ocular microbiota refers to all types of commensal and pathogenic microorganisms present on or in the eye. The ocular surface is continuously exposed to the...
The term ocular microbiota refers to all types of commensal and pathogenic microorganisms present on or in the eye. The ocular surface is continuously exposed to the environment and harbors various commensals. Commensal microbes have been demonstrated to regulate host metabolism, development of immune system, and host defense against pathogen invasion. An unbalanced microbiota could lead to pathogenic microbial overgrowth and cause local or systemic inflammation. The specific antigens that irritate the deleterious immune responses in various inflammatory eye diseases remain obscure, while recent evidence implies a microbial etiology of these illnesses. The purpose of this review is to provide an overview of the literature on ocular microbiota and the role of commensal microbes in several eye diseases. In addition, this review will also discuss the interaction between microbial pathogens and host factors involved in intraocular inflammation, and evaluate therapeutic potential of targeting ocular microbiota to treat intraocular inflammation.
Topics: Animals; Eye; Eye Diseases; Humans; Immune System; Immunity; Inflammation; Microbiota
PubMed: 33424865
DOI: 10.3389/fimmu.2020.609765