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Preventive Veterinary Medicine Sep 2023In the last decades, a more prudent and rational use of antimicrobials has been progressively directed towards animal production to reduce antimicrobial selective... (Meta-Analysis)
Meta-Analysis Review
BACKGROUND
In the last decades, a more prudent and rational use of antimicrobials has been progressively directed towards animal production to reduce antimicrobial selective pressure and antimicrobial resistance (AMR) in microorganisms and safeguard the antimicrobial efficacy of treatments in human medicine. This systematic review evaluated the effectiveness of interventions that have been applied to reduce or improve veterinary antimicrobial usage and aimed at decreasing resistant bacteria in chicken broiler and pig production contexts.
METHODS
Original articles were identified by searching PubMed™, Scopus™, The Cochrane Library™, and Web of Science™, and grey literature by searching DANS EASY™, WorldCat™ and RCAAP™. Inclusion criteria included: chicken broiler or pig populations (predestined for meat production), interventions intended to reduce/improve antimicrobial use, comparator with standard or no use of antimicrobials, outcomes related to prevalence of resistant bacteria, farm level studies, original data, and analytical observational studies. Data was extracted from eligible studies and meta-analysis using random or fixed effects models was conducted for combinations including type of intervention, bacterial species, production type and animal populations. Models were selected according to heterogeneity between studies. The effectiveness of interventions was assessed using pooled odds ratio of resistance to antimicrobial substances/classes by bacteria for associations between animal populations with and without intervention.
RESULTS
A total of 46 studies were eligible for review. For chicken broilers, most interventions were identified as antimicrobial restrictions on all non-therapeutic use (46%), complete restriction (27%), and prohibition on antimicrobials used for growth promotion (23%). As for pig populations, restrictions were mainly observed on all non-therapeutic use (37%), complete restriction (37%) and group treatments (22%). For meta-analysis, 21 studies were pooled after assessment of existing combinations. These combinations demonstrated a protective effect for most antimicrobial classes in Escherichia coli, Campylobacter and Enterococcus isolates from samples of chicken broilers as well in Escherichia coli and Campylobacter spp. from samples of pigs, compared to animals raised under conventional production or without intervention. Increased odds of resistance were only observed for cephalosporins in E. coli and broilers raised without antimicrobials, and to fluoroquinolones and quinolones in Campylobacter and pigs raised without antimicrobials, compared to conventional production.
CONCLUSIONS
Our study indicates that organic production, antimicrobial-free farms, and group treatment restrictions are recommended for AMR reduction, providing information that may support decision-making to tackle AMR and better reporting to improve comparability of results between studies.
Topics: Humans; Animals; Swine; Anti-Bacterial Agents; Chickens; Drug Resistance, Bacterial; Escherichia coli; Anti-Infective Agents; Campylobacter
PubMed: 37639825
DOI: 10.1016/j.prevetmed.2023.106002 -
Brazilian Journal of Microbiology :... Sep 2023Collared and white-lipped peccaries are sympatric and are distributed in most of South America and in the humid tropical forests of Mexico and Central America.... (Review)
Review
Collared and white-lipped peccaries are sympatric and are distributed in most of South America and in the humid tropical forests of Mexico and Central America. Historically, these species have been used as a source of protein by traditional and/or indigenous human communities, but currently they have been used for legal consumption in different countries. Thus, there has been greater interaction between these wild species and domestic animals and humans, enabling microbial interactions between different niches. The present study presents a systematic review of the literature on the microbial community of collared peccaries and white-lipped peccaries distributed throughout the world, focusing on experimental studies related to the detection of microorganisms as well as the prevalence of the animal species and its characterization of the studied population, in situ or ex situ. Seventy-two studies were selected, mainly in South American countries, related to different species of microorganisms isolated or serologically detected (viruses, bacteria, fungi, and parasites), either as microbiota, pathogens or commensals, many of which are of zoonotic interest, such as Leptospira, Toxoplasma, Brucella, among others. Therefore, these wild mammals are characterized as sentinel agents of anthropic action and require the implementation of studies in relation to their contribution to the spread of microorganisms, being a potential source of amplification and transmission of pathogens.
Topics: Animals; Humans; One Health; Artiodactyla; Leptospira; Animals, Domestic; Microbiota
PubMed: 37380932
DOI: 10.1007/s42770-023-01046-7 -
International Journal of Molecular... Dec 2023Bacteria have existed on Earth for billions of years, exhibiting ubiquity and involvement in various biological activities. To ensure survival, bacteria usually release... (Review)
Review
Bacteria have existed on Earth for billions of years, exhibiting ubiquity and involvement in various biological activities. To ensure survival, bacteria usually release and secrete effector proteins to acquire nutrients and compete with other microorganisms for living space during long-term evolution. Consequently, bacteria have developed a range of secretion systems, which are complex macromolecular transport machines responsible for transporting proteins across the bacterial cell membranes. Among them, one particular secretion system that stands out from the rest is the type V secretion system (T5SS), known as the "autotransporter". Bacterial activities mediated by T5SS include adherence to host cells or the extracellular matrix, invasion of host cells, immune evasion and serum resistance, contact-dependent growth inhibition, cytotoxicity, intracellular flow, protease activity, autoaggregation, and biofilm formation. In a bacterial body, it is not enough to rely on T5SS alone; in most cases, T5SS cooperates with other secretion systems to carry out bacterial life activities, but regardless of how good the relationship is, there is friction between the secretion systems. T5SS and T1SS/T2SS/T3SS/T6SS all play a synergistic role in the pathogenic processes of bacteria, such as nutrient acquisition, pathogenicity enhancement, and immune modulation, but T5SS indirectly inhibits the function of T4SS. This could be considered a love-hate relationship between secretion systems. This paper uses the systematic literature review methodology to review 117 journal articles published within the period from 1995 to 2024, which are all available from the PubMed, Web of Science, and Scopus databases and aim to elucidate the link between T5SS and other secretion systems, providing clues for future prevention and control of bacterial diseases.
Topics: Type V Secretion Systems; Bacteria; Bodily Secretions; Cell Aggregation; Cell Membrane
PubMed: 38203452
DOI: 10.3390/ijms25010281 -
Clinical Laboratory Oct 2023Matrix-assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) is one of the preferred detection techniques for identification of clinical... (Review)
Review
BACKGROUND
Matrix-assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) is one of the preferred detection techniques for identification of clinical microorganisms and it has the characteristics of rapid identification, simple operation, low cost, and updatable databases. For laboratory medicine undergraduates, clinical internship is an important stage for the connection of basic theoretical knowledge and clinical practice. Internship teaching choosing MALDI-TOF MS as the content will greatly increase the popularity and applicability of the new technology in the clinical microbiology laboratory.
METHODS
With the help of electronic databases on the network, we conducted a systematic review. According to the purpose of research, we singled out forty papers. Latest studies on history, basic principles, clinical features, and applications of MALDI-TOF MS and the internship teaching contents introducing new technologies are summarized and focused on. In internship teaching, firstly we explain the historical development, basic principle and widespread applications of MALDI-TOF MS in the identification of clinical pathogenic microorganisms and the detection of antibiotic resistance. Subsequently, we instruct the students to perform the experimental operations, analyze the common problems, and find solutions. Finally, we highlight quality control and laboratory biosafety.
RESULTS
Most of the reviews published previously report the clinical features and applications of MALDI-TOF MS and the internship teaching contents choosing other new technologies. It is the first study selecting MALDI-TOF MS technology as an internship teaching content creatively. Primary outcome is that the students understand the theoretical knowledge in detail, master the operation skills of MALDI-TOF MS quickly, and obtain excellent internship performances in the clinical internship through the internship teaching. Secondary outcome is that it is a help to cultivate medical students' train of thought for scientific research and to understand the application of the new technology in clinical testing and scientific research.
CONCLUSIONS
Laboratory medicine undergraduates should cherish the opportunity to learn the new technology during the internship period and should master basic principle and operation. As internship teachers, it is necessary to introduce the new technology to students during the internship and encourage undergraduates to cultivate creative and innovative thinking of scientific research.
Topics: Humans; Bacteria; Internship and Residency; Laboratories; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; Lasers
PubMed: 37844040
DOI: 10.7754/Clin.Lab.2023.221127 -
Cureus Nov 2023Aortic valve replacement (AVR) successfully treats aortic valve stenosis and aortic regurgitation from aging or bicuspid aortic valves. The procedure intends to restore... (Review)
Review
Aortic valve replacement (AVR) successfully treats aortic valve stenosis and aortic regurgitation from aging or bicuspid aortic valves. The procedure intends to restore the obstructed left ventricular outflow tract (LVOT). AVR can be performed surgically (surgical aortic valve replacement (SAVR); open heart) or via transcatheter (transcatheter aortic valve replacement (TAVR)), typically done through a femoral approach as a minimally invasive procedure, allowing for quicker recovery and reduced hospital stays. AVR has many complications, including life-threatening ones, such as infective endocarditis (IE), retarding the recovery process and increasing mortality following surgery. IE is an uncommon and deadly condition that involves multiple organ systems and is caused by bacteremia stemming from a microorganism that enters the bloodstream. Many manifestations are involved in the development of IE, such as fevers, flu-like symptoms, splinter hemorrhages, Osler nodes, abscesses, and vegetations found on the valves at the leaflets. Vegetations and abscesses tend to create further complications, such as stroke and acute kidney injury, as emboli block blood flow, leading to ischemia and damage. This paper aims to evaluate the difference in SAVR- and TAVR-associated IE, as the goal is to elucidate a danger that diminishes the positive effects of either procedure despite its rarity. Studies have been inconclusive in determining whether or not there is a trend, let alone a difference in incident rates. Both procedures share similar risk factors, but SAVR-associated IE is usually caused by and studies indicate possibly in TAVR-associated IE. Incident rates of IE are much higher than they should be, whether or not they differ between procedures, and future research needs to consider the pathways and risk factors that can be used to reduce the occurrence of AVR-associated IE.
PubMed: 38116334
DOI: 10.7759/cureus.49048 -
BMC Medical Informatics and Decision... Dec 2023Invasive detection methods such as liver biopsy are currently the gold standard for diagnosing liver cirrhosis and can be used to determine the degree of liver fibrosis... (Meta-Analysis)
Meta-Analysis
BACKGROUND
Invasive detection methods such as liver biopsy are currently the gold standard for diagnosing liver cirrhosis and can be used to determine the degree of liver fibrosis and cirrhosis. In contrast, non-invasive diagnostic methods, such as ultrasonography, elastography, and clinical prediction scores, can prevent patients from invasiveness-related discomfort and risks and are often chosen as alternative or supplementary diagnostic methods for liver fibrosis or cirrhosis. However, these non-invasive methods cannot specify the pathological grading and early diagnosis of the lesions. Recent studies have revealed that gut microbiome-based machine learning can be utilized as a non-invasive diagnostic technique for liver cirrhosis or fibrosis, but there is no evidence-based support. Therefore, this study conducted a systematic review and meta-analysis for the first time to investigate the accuracy of machine learning based on the gut microbiota in the prediction of liver fibrosis and cirrhosis.
METHODS
A comprehensive and systematic search of publications published before April 2th, 2023 in PubMed, Cochrane Library, Embase, and Web of Science was conducted for relevant studies on the application of gut microbiome-based metagenomic sequencing modeling technology to the diagnostic prediction of liver cirrhosis or fibrosis. A bivariate mixed-effects model and Stata software 15.0 were adopted for the meta-analysis.
RESULTS
Ten studies were included in the present study, involving 11 prediction trials and 838 participants, 403 of whom were fibrotic and cirrhotic patients. Meta-analysis showed the pooled sensitivity (SEN) = 0.81 [0.75, 0.85], specificity (SEP) = 0.85 [0.77, 0.91], positive likelihood ratio (PLR) = 5.5 [3.6, 8.7], negative likelihood ratio (NLR) = 0.23 [0.18, 0.29], diagnostic odds ratio (DOR) = 24 [14, 41], and area under curve (AUC) = 0.86 [0.83-0.89]. The results demonstrated that machine learning methods had excellent potential to analyze gut microbiome data and could effectively predict liver cirrhosis or fibrosis. Machine learning provides a powerful tool for non-invasive prediction and diagnosis of liver cirrhosis or liver fibrosis, with broad clinical application prospects. However, these results need to be interpreted with caution due to limited clinical data.
CONCLUSION
Gut microbiome-based machine learning can be utilized as a practical, non-invasive technique for the diagnostic prediction of liver cirrhosis or fibrosis. However, most of the included studies applied the random forest algorithm in modeling, so a diversified prediction system based on microorganisms is needed to improve the non-invasive detection of liver cirrhosis or fibrosis.
Topics: Humans; Gastrointestinal Microbiome; Liver Cirrhosis; Fibrosis; Machine Learning
PubMed: 38115019
DOI: 10.1186/s12911-023-02402-1 -
Annals of Intensive Care Apr 2024Drowning-associated pneumonia (DAP) is frequent in drowned patients, and possibly increases mortality. A better understanding of the microorganisms causing DAP could... (Review)
Review
BACKGROUND
Drowning-associated pneumonia (DAP) is frequent in drowned patients, and possibly increases mortality. A better understanding of the microorganisms causing DAP could improve the adequacy of empirical antimicrobial therapy. We aimed to describe the pooled prevalence of DAP, the microorganisms involved, and the impact of DAP on drowned patients.
METHODS
Systematic review and meta-analysis of studies published between 01/2000 and 07/2023 reporting on DAP occurrence and microorganisms involved.
RESULTS
Of 309 unique articles screened, 6 were included, involving 688 patients. All were retrospective cohort studies, with a number of patients ranging from 37 to 270. Studies were conducted in Europe (France N = 3 and Netherland N = 1), United States of America (N = 1) and French West Indies (N = 1). Mortality ranged between 18 to 81%. The pooled prevalence of DAP was 39% (95%CI 29-48), similarly following freshwater (pooled prevalence 44%, 95%CI 36-52) or seawater drowning (pooled prevalence 42%, 95%CI 32-53). DAP did not significantly impact mortality (pooled odds ratio 1.43, 95%CI 0.56-3.67) but this estimation was based on two studies only. Respiratory samplings isolated 171 microorganisms, mostly Gram negative (98/171, 57%) and mainly Aeromonas sp. (20/171, 12%). Gram positive microorganisms represented 38/171 (22%) isolates, mainly Staphylococcus aureus (21/171, 12%). Water salinity levels had a limited impact on the distribution of microorganisms, except for Aeromonas sp. who were exclusively found following freshwater drowning (19/106, 18%) and never following seawater drowning (0%) (p = 0.001). No studies reported multidrug-resistant organisms but nearly 30% of the isolated microorganisms were resistant to amoxicillin-clavulanate, the drug that was the most commonly prescribed empirically for DAP.
CONCLUSIONS
DAP are commonly caused by Gram-negative bacteria, especially Aeromonas sp. which is exclusively isolated following freshwater drowning. Empirical antimicrobial therapy should consider covering them, noting than amoxicillin-clavulanate may be inadequate in about one-third of the cases. The impact of DAP on patients' outcome is still unclear.
PubMed: 38641650
DOI: 10.1186/s13613-024-01287-1 -
Heliyon Nov 2023Essential oils (EOs) are natural products called volatile oils or aromatic and ethereal oils derived from various parts of plants. They possess antioxidant and... (Review)
Review
Essential oils (EOs) are natural products called volatile oils or aromatic and ethereal oils derived from various parts of plants. They possess antioxidant and antimicrobial properties, which offer natural protection against a variety of pathogens and spoilage microorganisms. Studies conducted in the last decade have demonstrated the unique applications of these compounds in the fields of the food industry, agriculture, and skin health. This systematic article provides a summary of recent data pertaining to the effectiveness of EOs and their constituents in combating fungal pathogens through diverse mechanisms. Antifungal investigations involving EOs were conducted on multiple academic platforms, including Google Scholar, Science Direct, Elsevier, Springer, Scopus, and PubMed, spanning from April 2000 to October 2023. Various combinations of keywords, such as "essential oil," "volatile oils," "antifungal," and " species," were used in the search. Numerous essential oils have demonstrated both and antifungal activity against different species of , including , , A. , A. , and A. ochraceus. They have also exhibited efficacy against other fungal species, such as species, , and Alternaria. The findings of this study offer novel insights into inhibitory pathways and suggest the potential of essential oils as promising agents with antifungal and anti-mycotoxigenic properties. These properties could make them viable alternatives to conventional preservatives, thereby enhancing the shelf life of various food products.
PubMed: 37954273
DOI: 10.1016/j.heliyon.2023.e21386 -
Microorganisms Nov 2023Antibiotic resistance is a significant threat to public health worldwide. Genome-wide association studies (GWAS) have emerged as a powerful tool to identify genetic... (Review)
Review
Antibiotic resistance is a significant threat to public health worldwide. Genome-wide association studies (GWAS) have emerged as a powerful tool to identify genetic variants associated with this antibiotic resistance. By analyzing large datasets of bacterial genomes, GWAS can provide valuable insights into the resistance mechanisms and facilitate the discovery of new drug targets. The present study aimed to undertake a systematic review of different GWAS approaches used for detecting genetic variants associated with antibiotic resistance. We comprehensively searched the PubMed and Scopus databases to identify relevant studies published from 2013 to February 2023. A total of 40 studies met our inclusion criteria. These studies explored a wide range of bacterial species, antibiotics, and study designs. Notably, most of the studies were centered around human pathogens such as , , , and . The review seeks to explore the several GWAS approaches utilized to investigate the genetic mechanisms associated with antibiotic resistance. Furthermore, it examines the contributions of GWAS approaches in identifying resistance-associated genetic variants through binary and continuous phenotypes. Overall, GWAS holds great potential to enhance our understanding of bacterial resistance and improve strategies to combat infectious diseases.
PubMed: 38138010
DOI: 10.3390/microorganisms11122866 -
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