Nature Reviews Methods Primers, Journal Year: 2025, Volume and Issue: 5(1)
Published: Jan. 23, 2025
Language: Английский
BioMedInformatics, Journal Year: 2023, Volume and Issue: 3(4), P. 1145 - 1177
Published: Dec. 7, 2023
Emerging infectious diseases (EIDs) pose an increasingly significant global burden, driven by urbanization, population explosion, travel, changes in human behavior, and inadequate public health systems. The recent SARS-CoV-2 pandemic highlights the urgent need for innovative robust technologies to effectively monitor newly emerging pathogens. Rapid identification, epidemiological surveillance, transmission mitigation are crucial challenges ensuring safety. Genomics has emerged as a pivotal tool during pandemics, enabling diagnosis, management, prediction of infections, well analysis identification cross-species interactions categorization agents. Recent advancements high-throughput DNA sequencing tools have facilitated rapid precise characterization This review article provides insights into latest advances various genomic techniques pathogen detection tracking their applications outbreak surveillance. We assess methods that leverage sequences explore role understanding epidemiology diseases. Additionally, we address technical limitations, ethical legal considerations, highlight opportunities integrating genomics with other surveillance approaches. By delving prospects obstacles genomics, can gain valuable its mitigating threats posed pathogens improving preparedness face future outbreaks.
Language: Английский
Citations
37
Frontiers in Microbiology, Journal Year: 2023, Volume and Issue: 14
Published: Nov. 23, 2023
The World Health Organization (WHO) estimated that pathogens like Escherichia coli, primarily linked to food and water contamination, are associated with 485,000 deaths from diarrheal diseases annually, translating a staggering worldwide economic loss of nearly 12 billion USD per annum. International organizations the WHO United Nations Children’s Fund (UNICEF) have established related guidelines criteria for pathogenic detection technologies driving search innovative efficient methods. This comprehensive review examines trajectory waterborne bacteria traditional techniques, i.e., culture-based methods, current methods including various forms polymerase chain reaction (PCR) techniques [qualitative real-time PCR, digital ELISA, loop-mediated isothermal amplification, next-generation sequencing (NGS)] emerging biosensors artificial intelligence (AI). scope paper focuses on recognized as human pathogens, posing tangible threats public health through waterborne. techniques’ merits, constraints, research gaps future perspectives critically discussed. Advancements in droplet NGS significantly improved sensitivity specificity, revolutionizing pathogen detection. Additionally, integration (AI) these has enhanced accuracy, enabling analysis large datasets. Molecular-based show promise quality monitoring, especially resource-constrained settings, but on-site practical implementation remains challenge. pairwise comparison metrics used this also offer valuable insights into quick evaluation advantages, limitations focusing their applicability field settings timely analyses. Future efforts should focus developing robust, cost-effective user-friendly routine ultimately safeguarding global supplies health, AI data playing crucial role advancing safer environment.
Language: Английский
Citations
36
Advanced Materials, Journal Year: 2023, Volume and Issue: 35(12)
Published: Jan. 10, 2023
Fast and accurate detection of microbial cells in clinical samples is highly valuable but remains a challenge. Here, simple, culture-free diagnostic system developed for direct pathogenic bacteria water, urine, serum using an optical colorimetric biosensor. It consists printed nanoarrays chemically conjugated with specific antibodies that exhibits distinct color changes after capturing target pathogens. By utilizing the internal capillarity inside evaporating droplet, preconcentration achieved within few minutes to enable rapid identification more efficient bacterial More importantly, scattering signals are significantly amplified by due strong near-field localization, which supports visualizable analysis growth, reproduction, cell activity at single-cell level. Finally, addition high selectivity, this nanoarray-based biosensor also capable quantification continuous monitoring load on food over broad linear range, limit 10 CFU mL-1 . This work provides accessible user-friendly tool point-of-care testing pathogens many environmental applications, possibly enables breakthrough early prevention treatment.
Language: Английский
Citations
31
BMC Genomics, Journal Year: 2023, Volume and Issue: 24(1)
Published: Aug. 4, 2023
Oxford Nanopore Technologies (ONT) offers an accessible platform for long-read sequencing, which improves the reconstruction of genomes and helps to resolve complex genomic contexts, especially in case metagenome analysis. To take best advantage DNA extraction methods must be able isolate pure high molecular weight (HMW) from metagenomics samples, without introducing any bias. New released on market, protocols developed at research level, were specifically designed this application need assessed.In study, with different bacterial cocktail mixes, analyzed as or spiked a synthetic fecal matrix, we evaluated performances 6 using various cells lysis purification techniques, quick easy, more time-consuming gentle protocols, including portable method on-site application. In addition comparison quality, quantity purity extracted DNA, performance obtained when doing sequencing MinION flow cell was also tested. From results, Quick-DNA HMW MagBead Kit (Zymo Research) selected producing yield DNA. Furthermore, kit allowed accurate detection, by almost all species present mock community.Amongst tested methods, considered most suitable would recommended studies technology.
Language: Английский
Citations
28
Nature Food, Journal Year: 2023, Volume and Issue: 4(8), P. 707 - 720
Published: Aug. 10, 2023
China is the largest global consumer of antimicrobials and improving surveillance methods could help to reduce antimicrobial resistance (AMR) spread. Here we report ten large-scale chicken farms four connected abattoirs in three Chinese provinces over 2.5 years. Using a data mining approach based on machine learning, analysed 461 microbiomes from birds, carcasses environments, identifying 145 potentially mobile antibiotic genes (ARGs) shared between chickens environments across all farms. A core set 233 ARGs 186 microbial species extracted gut microbiome correlated with AMR profiles Escherichia coli colonizing same gut, including Arcobacter, Acinetobacter Sphingobacterium, clinically relevant for humans, 38 ARGs. Temperature humidity barns were also ARG presence. We reveal an intricate network correlations communities AMR, suggesting multiple routes livestock production.
Language: Английский
Citations
25
mLife, Journal Year: 2023, Volume and Issue: 2(4), P. 350 - 364
Published: Dec. 1, 2023
The emergence and rapid spread of antimicrobial resistance is global public health concern. gut microbiota harboring diverse commensal opportunistic bacteria that can acquire via horizontal vertical gene transfers considered an important reservoir sink antibiotic genes (ARGs). In this review, we describe the reservoirs ARGs their dynamics in both animals humans, use One Health perspective to track transmission ARG-containing between animals, environment, assess impact on human socioeconomic development. resistome evolve environment subject various selective pressures, including administration environmental lifestyle factors (e.g., diet, age, gender, living conditions), interventions through probiotics. Strategies reduce abundance clinically relevant antibiotic-resistant determinants niches are needed ensure mitigation acquired resistance. With help effective measures taken at national, local, personal, intestinal management, it will also result preventing or minimizing infectious diseases. This review aims improve our understanding correlations provide a basis for development management strategies mitigate crisis.
Language: Английский
Citations
25
Water Research, Journal Year: 2023, Volume and Issue: 235, P. 119875 - 119875
Published: March 14, 2023
Language: Английский
Citations
24
Advanced Science, Journal Year: 2023, Volume and Issue: 10(26)
Published: July 9, 2023
Abstract Antibiotic overuse and the subsequent environmental contamination of residual antibiotics poses a public health crisis via an acceleration in spread antibiotic resistance genes (ARGs) through horizontal gene transfer. Although occurrence, distribution, driving factors ARGs soils have been widely investigated, little is known about soilborne pathogens at global scale. To explore this gap, contigs from 1643 globally sourced metagnomes are assembled, yielding 407 ARG‐carrying (APs) with least one ARG; APs detected 1443 samples (sample detection rate 87.8%). The richness greater agricultural (with median 20) than non‐agricultural ecosystems. Agricultural possess high prevalence clinical affiliated Escherichia, Enterobacter, Streptococcus , Enterococcus . tend to coexist multidrug bacA A map soil AP generated, where anthropogenic climatic explained hot spots East Asia, South eastern United States. results herein advance understanding distribution determine regions prioritized control worldwide.
Language: Английский
Citations
23
Critical Reviews in Environmental Science and Technology, Journal Year: 2023, Volume and Issue: 54(4), P. 267 - 289
Published: July 22, 2023
Groundwater has been a relatively safe water source and associated with series of global pressing issues. It can, however, be vulnerable to pathogen contamination exhibit risks public health. While groundwater often considered closed ecosystem, it is important understand the transport pathogens into within groundwater-dependent ecosystems in context their physiological characteristics, soil/sediment texture, hydrogeological climatic conditions. The rapid progress monitoring modeling tools recent years facilitated detection prediction migration groundwater, which aids surveillance remediation health-related risks. This review aims provide an updated understanding about pathogens, impacts on human health, surveillance, risk assessment, strategies environment climate changes. challenges perspectives protecting biosafety are also discussed.
Language: Английский
Citations
23
Frontiers in Public Health, Journal Year: 2023, Volume and Issue: 11
Published: Nov. 23, 2023
The quality of the indoor environment significantly impacts human health and productivity, especially given amount time individuals spend indoors globally. While chemical pollutants have been a focus air research, microbial contaminants also significant bearing on quality. This review provides comprehensive overview contamination in built environments, covering sources, sampling strategies, analysis methods. Microbial has various origins, including occupants, pets, outdoor environment. Sampling strategies for include air, surface, dust sampling, methods are used to assess diversity complexity environments. discusses risks associated with contaminants, bacteria, fungi, viruses, their products highlighting need evidence-based studies that can relate specific conditions. importance is emphasized from perspective COVID-19 pandemic. A section highlights knowledge gap related microbiological burden environments developing countries, using India as representative example. Finally, potential mitigation improve briefly reviewed.
Language: Английский
Citations
23