# | Rank | Similarity | Title + Abs. | Year | PMID |
|---|---|---|---|---|---|
| 0 | 1 | 2 | 3 | 4 | 5 |
| 7711 | 0 | 0.9954 | Beyond the desert sands: decoding the relationship between camels, gut microbiota, and antibiotic resistance through metagenomics. BACKGROUND: Camels, known as the enduring "ships of the desert," host a complex gut microbiota that plays a crucial role in their survival in extreme environments. However, amidst the fascinating discoveries about the camel gut microbiota, concerns about antibiotic resistance have emerged as a significant global challenge affecting both human and animal populations. Indeed, the continued use of antibiotics in veterinary medicine has led to the widespread emergence of antibiotic-resistant bacteria, which has worsened through gene transfer. METHODS: This study offers a deeper examination of this pressing issue by harnessing the potent tools of metagenomics to explore the intricate interplay between the camel (Camelus ferus) gut microbiota and antibiotic resistance. RESULTS: Samples from wild camels yielded varying amounts of raw and clean data, generating scaftigs and open reading frames. The camel fecal microbiome was dominated by bacteria (mainly Bacillota and Bacteriodota), followed by viruses, archaea, and eukaryota. The most abundant genera were the Bacteroides, Ruminococcus, and Clostridium. Functional annotation revealed enriched pathways in metabolism, genetic information processing, and cellular processes, with key pathways involving carbohydrate transport and metabolism, replication, and amino acid transport. CAZy database analysis showed high abundances of glycoside hydrolases and glycosyl transferases. Antibiotic resistance gene (ARG) analysis identified Bacillota and Bacteroidota as the main reservoirs, with vancomycin resistance genes being the most prevalent. This study identified three major resistance mechanisms: antibiotic target alteration, antibiotic target protection, and antibiotic efflux. CONCLUSION: These findings contribute to a broader understanding of antibiotic resistance within animal microbiomes and provide a foundation for further investigations of strategies to manage and mitigate antibiotic resistance. | 2024 | 39763640 |
| 6669 | 1 | 0.9954 | ANTIBIOTIC RESISTANT BACTERIA IN WILDLIFE: PERSPECTIVES ON TRENDS, ACQUISITION AND DISSEMINATION, DATA GAPS, AND FUTURE DIRECTIONS. The proliferation of antibiotic-resistant bacteria in the environment has potential negative economic and health consequences. Thus, previous investigations have targeted wild animals to understand the occurrence of antibiotic resistance in diverse environmental sources. In this critical review and synthesis, we summarized important concepts learned through the sampling of wildlife for antibiotic-resistant indicator bacteria. These concepts are helpful for understanding dissemination of resistance through environmental pathways and helping to guide future research efforts. Our review begins by briefly introducing antibiotic resistance as it pertains to bacteria harbored in environmental sources such as wild animals. Next, we differentiate wildlife from other animals in the context of how diverse taxa provide different information on antibiotic resistance in the environment. In the third section of our review, we identify representative research and seminal works that illustrate important associations between the occurrence of antibiotic-resistant bacteria in wildlife and anthropogenic inputs into the environment. For example, we highlight numerous investigations that support the premise that anthropogenic inputs into the environment drive the occurrence of antibiotic resistance in bacteria harbored by free-ranging wildlife. Additionally, we summarize previous research demonstrating foraging as a mechanism by which wildlife may be exposed to anthropogenic antibiotic resistance contamination in the environment. In the fourth section of our review, we summarize molecular evidence for the acquisition and dissemination of resistance among bacteria harbored by wildlife. In the fifth section, we identify what we believe to be important data gaps and potential future directions that other researchers may find useful toward the development of efficient, informative, and impactful investigations of antibiotic-resistant bacteria in wildlife. Finally, we conclude our review by highlighting the need to move from surveys that simply identify antibiotic-resistant bacteria in wildlife toward hypothesis-driven investigations that: 1) identify point sources of antibiotic resistance; 2) provide information on risk to human and animal health; 3) identify interventions that may interrupt environmentally mediated pathways of antibiotic resistance acquisition and transmission; and 4) evaluate whether management practices are leading to desirable outcomes. | 2020 | 31567035 |
| 8416 | 2 | 0.9953 | Protective role of the vulture facial skin and gut microbiomes aid adaptation to scavenging. BACKGROUND: Vultures have adapted the remarkable ability to feed on carcasses that may contain microorganisms that would be pathogenic to most other animals. The holobiont concept suggests that the genetic basis of such adaptation may not only lie within their genomes, but additionally in their associated microbes. To explore this, we generated shotgun DNA sequencing datasets of the facial skin and large intestine microbiomes of the black vulture (Coragyps atratus) and the turkey vulture (Cathartes aura). We characterized the functional potential and taxonomic diversity of their microbiomes, the potential pathogenic challenges confronted by vultures, and the microbial taxa and genes that could play a protective role on the facial skin and in the gut. RESULTS: We found microbial taxa and genes involved in diseases, such as dermatitis and pneumonia (more abundant on the facial skin), and gas gangrene and food poisoning (more abundant in the gut). Interestingly, we found taxa and functions with potential for playing beneficial roles, such as antilisterial bacteria in the gut, and genes for the production of antiparasitics and insecticides on the facial skin. Based on the identified phages, we suggest that phages aid in the control and possibly elimination, as in phage therapy, of microbes reported as pathogenic to a variety of species. Interestingly, we identified Adineta vaga in the gut, an invertebrate that feeds on dead bacteria and protozoans, suggesting a defensive predatory mechanism. Finally, we suggest a colonization resistance role through biofilm formation played by Fusobacteria and Clostridia in the gut. CONCLUSIONS: Our results highlight the importance of complementing genomic analyses with metagenomics in order to obtain a clearer understanding of the host-microbial alliance and show the importance of microbiome-mediated health protection for adaptation to extreme diets, such as scavenging. | 2018 | 30309375 |
| 8418 | 3 | 0.9953 | The megaplasmid pCER270 of Bacillus cereus emetic strain affects the timing of the sporulation process, spore resistance properties, and germination. The Bacillus cereus group includes closely related spore-forming Gram-positive bacteria. In this group, plasmids play a crucial role in species differentiation and are essential for pathogenesis and adaptation to ecological niches. The B. cereus emetic strains are characterized by the presence of the pCER270 megaplasmid, which encodes the non-ribosomal peptide synthetase for the production of cereulide, the emetic toxin. This plasmid carries several genes that may be involved in the sporulation process. Furthermore, a transcriptomic analysis has revealed that pCER270 influences the expression of chromosome genes, particularly under sporulation conditions. In this study, we investigated the role of pCER270 on spore properties in different species of the B. cereus group. We showed that pCER270 plays a role in spore wet heat resistance and germination, with varying degrees of impact depending on the genetic background. In addition, pCER270 ensures that sporulation occurs at the appropriate time by delaying the expression of sporulation genes. This regulation of sporulation timing is controlled by the pCER270-borne Rap-Phr system, which likely regulates the phosphorylation state of Spo0A. Acquisition of the pCER270 plasmid by new strains could give them an advantage in adapting to new environments and lead to the emergence of new pathogenic strains. IMPORTANCE: The acquisition of new mobile genetic elements, such as plasmids, is essential for the pathogenesis and adaptation of bacteria belonging to the Bacillus cereus group. This can confer new phenotypic traits and beneficial functions that enable bacteria to adapt to changing environments and colonize new ecological niches. Emetic B. cereus strains cause food poisoning linked to the production of cereulide, the emetic toxin whose synthesis is due to the presence of plasmid pCER270. In the environment, cereulide provides a competitive advantage in producing bacteria against various competitors or predators. This study demonstrates that pCER270 also regulates the sporulation process, resulting in spores with improved heat resistance and germination capacity. The transfer of plasmid pCER270 among different strains of the B. cereus group may enhance their adaptation to new environments. This raises the question of the emergence of new pathogenic strains, which could pose a serious threat to human health. | 2024 | 39158315 |
| 4776 | 4 | 0.9953 | Integrate genome-based assessment of safety for probiotic strains: Bacillus coagulans GBI-30, 6086 as a case study. Probiotics are microorganisms that confer beneficial effects on the host; nevertheless, before being allowed for human consumption, their safety must be verified with accurate protocols. In the genomic era, such procedures should take into account the genomic-based approaches. This study aims at assessing the safety traits of Bacillus coagulans GBI-30, 6086 integrating the most updated genomics-based procedures and conventional phenotypic assays. Special attention was paid to putative virulence factors (VF), antibiotic resistance (AR) genes and genes encoding enzymes responsible for harmful metabolites (i.e. biogenic amines, BAs). This probiotic strain was phenotypically resistant to streptomycin and kanamycin, although the genome analysis suggested that the AR-related genes were not easily transferrable to other bacteria, and no other genes with potential safety risks, such as those related to VF or BA production, were retrieved. Furthermore, no unstable elements that could potentially lead to genomic rearrangements were detected. Moreover, a workflow is proposed to allow the proper taxonomic identification of a microbial strain and the accurate evaluation of risk-related gene traits, combining whole genome sequencing analysis with updated bioinformatics tools and standard phenotypic assays. The workflow presented can be generalized as a guideline for the safety investigation of novel probiotic strains to help stakeholders (from scientists to manufacturers and consumers) to meet regulatory requirements and avoid misleading information. | 2016 | 26952108 |
| 6606 | 5 | 0.9953 | Comprehensive analysis of antimicrobial resistance in the Southwest Indian Ocean: focus on WHO critical and high priority pathogens. The spread of antimicrobial resistance (AMR) is a major global concern, and the islands of the Southwest Indian Ocean (SWIO) are not exempt from this phenomenon. As strategic crossroads between Southern Africa and the Indian subcontinent, these islands are constantly threatened by the importation of multidrug-resistant bacteria from these regions. In this systematic review, our aim was to assess the epidemiological situation of AMR in humans in the SWIO islands, focusing on bacterial species listed as priority by the World Health Organization. Specifically, we examined Enterobacterales, Acinetobacter spp., Pseudomonas spp. resistant to carbapenems, and Enterococcus spp. resistant to vancomycin. Our main objectives were to map the distribution of these resistant bacteria in the SWIO islands and identify the genes involved in their resistance mechanisms. We conducted literature review focusing on Comoros, Madagascar, Maldives, Mauritius, Mayotte, Reunion Island, Seychelles, Sri Lanka, and Zanzibar. Our findings revealed a growing interest in the investigation of these pathogens and provided evidence of their active circulation in many of the territories investigated. However, we also identified disparities in terms of data availability between the targeted bacteria and among the different territories, emphasizing the need to strengthen collaborative efforts to establish an efficient regional surveillance network. | 2024 | 38628847 |
| 3918 | 6 | 0.9952 | Update on antibiotic resistance in foodborne Lactobacillus and Lactococcus species. Lactobacilli represent a major Lactic Acid Bacteria (LAB) component within the complex microbiota of fermented foods obtained from meat, dairy, and vegetable sources. Lactococci, on the other hand, are typical of milk and fermented dairy products, which in turn represent the vast majority of fermented foods. As is the case for all species originating from the environment, foodborne lactobacilli and lactococci consist of natural, uncharacterized strains, whose biodiversity depends on geographical origin, seasonality, animal feeding/plant growth conditions. Although a few species of opportunistic pathogens have been described, lactobacilli and lactococci are mostly non-pathogenic, Gram-positive bacteria displaying probiotic features. Since antibiotic resistant (AR) strains do not constitute an immediate threat to human health, scientific interest for detailed studies on AR genes in these species has been greatly hindered. However, increasing evidence points at a crucial role for foodborne LAB as reservoir of potentially transmissible AR genes, underlining the need for further, more detailed studies aimed at identifying possible strategies to avoid AR spread to pathogens through fermented food consumption. The availability of a growing number of sequenced bacterial genomes has been very helpful in identifying the presence/distribution of mobile elements associated with AR genes, but open questions and knowledge gaps still need to be filled, highlighting the need for systematic and datasharing approaches to implement both surveillance and mechanistic studies on transferability of AR genes. In the present review we report an update of the recent literature on AR in lactobacilli and lactococci following the 2006 EU-wide ban of the use of antibiotics as feed additives in animal farming, and we discuss the limits of the present knowledge in evaluating possible risks for human health. | 2013 | 24115946 |
| 3972 | 7 | 0.9952 | Characterization of the resistome and antibiotic-resistant bacteria in top soil improvers and irrigation waters devoted to food production: a case study from Italy. Biosolids and reclaimed waters are valuable resources for reintroducing organic matter into agricultural soils and reducing the water footprint of intensive agricultural food system. While the circular economy is a sustainable practice, it may introduce vulnerabilities in the food chain, by exposing crops to zoonotic agents and antimicrobial resistance determinants. This option is far from being a speculation and evidence start to accumulate indicating that the risk is tangible. This study provides further evidence that the circular economy practices of reusing biomass and reclaimed waters in agricultural setting may be vectors for the spreading of antibiotic resistance genes (ARGs) targeting molecules used to treat human bacterial infections. We screened biosolid and water samples for ARGs presence using shotgun metagenomic sequencing. We demonstrated that the identified ARGs are present in live bacterial organisms, harbouring multidrug-resistant gene clusters, confirmed through phenotypic testing and whole-genome sequencing of isolated bacteria. Additionally, we observed that most of the antibiotic-resistant bacteria identified belonged to environmentally widespread species, which were not expected to be exposed to the antimicrobials, suggesting that inter-species transfer of resistance genes. | 2025 | 40439791 |
| 3762 | 8 | 0.9952 | The epidemiology of antimicrobial resistance and transmission of cutaneous bacterial pathogens in domestic animals. As the primary agents of skin and soft tissue infections in animals, Staphylococcus spp and Pseudomonas aeruginosa are among the most formidable bacterial pathogens encountered by veterinarians. Staphylococci are commensal inhabitants of the surfaces of healthy skin and mucous membranes, which may gain access to deeper cutaneous tissues by circumventing the stratum corneum's barrier function. Compromised barrier function occurs in highly prevalent conditions such as atopic dermatitis, endocrinopathies, and skin trauma. P aeruginosa is an environmental saprophyte that constitutively expresses virulence and antimicrobial resistance genes that promote its success as an animal pathogen. For both organisms, infections of the urinary tract, respiratory tract, joints, central nervous system, and body cavities may occur through ascension along epithelial tracts, penetrating injuries, or hematogenous spread. When treating infections caused by these pathogens, veterinarians now face greater therapeutic challenges and more guarded outcomes for our animal patients because of high rates of predisposing factors for infection and the broad dissemination of antimicrobial resistance genes within these bacterial species. This review considers the history of the rise and expansion of multidrug resistance in staphylococci and P aeruginosa and the current state of knowledge regarding the epidemiologic factors that underly the dissemination of these pathogens across companion animal populations. Given the potential for cross-species and zoonotic transmission of pathogenic strains of these bacteria, and the clear role played by environmental reservoirs and fomites, a one-health perspective is emphasized. | 2023 | 36917615 |
| 6692 | 9 | 0.9952 | An omics-based framework for investigating the emerging antibiotic resistance gene: The case of estT. The escalating prevalence of antimicrobial resistance (AMR) constitutes a global public health crisis. This is exacerbated by the continuous emergence of new variants and the discovery of previously unrecognized antibiotic resistance genes (ARGs). While advanced AMR surveillance efforts include time-consuming epidemiological investigations and retrospective analyses, critical gaps often remain towards our understanding of the sources of newly identified ARGs. Here, we established a framework integrating omics-based epidemiological investigations, genomic feature analysis of ARGs-carrying bacteria and evolution analysis of novel ARGs. We took the novel resistance gene estT as an example and analyzed it following this framework. Our study revealed that the estT gene was widely prevalent, capable of cross-phyla transmission, and predominantly present in human- and animal-derived bacteria. We explored the genomic characteristics of estT-positive Escherichia coli, Bacillus spp., Mannheimia haemolytica, and Riemerella anatipestifer, uncovering their public health risks. Evolution analysis of estT homologs found historical connections between estTs and tet(X)s. This study provides a systematic strategy for the proactive surveillance of emerging ARGs, enabling omics-data-driven monitoring of ARG evolution and dissemination to mitigate the escalating crisis of AMR. | 2025 | 41160932 |
| 4053 | 10 | 0.9951 | Evidence for the circulation of antimicrobial-resistant strains and genes in nature and especially between humans and animals. The concern over antibiotic-resistant bacteria producing human infections that are difficult to treat has led to a proliferation of studies in recent years investigating resistance in livestock, food products, the environment and people, as well as in the mechanisms of transfer of the genetic elements of resistance between bacteria, and the routes, or risk pathways, by which the spread of resistance might occur. The possibility of transfer of resistant genetic elements between bacteria in mixed populations adds many additional and complex potential routes of spread. There is now considerable evidence that transfer of antimicrobial resistance from food-producing animals to humans directly via the food chain is a likely route of spread. The application of animal wastes to farmland and subsequent leaching into watercourses has also been shown to lead to many potential, but less well-documented, pathways for spread. Often, however, where contamination of water sources, processed foods, and other environmental sites is concerned, specific routes of circulation are unclear and may well involve human sources of contamination. Examination of water sources in particular may be difficult due to dilution and their natural flow. Also, as meat is comparatively easy to examine, and is frequently suspected of being a source of spread, there is some bias in favour of studying this vehicle. Such complexities mean that, with the evidence currently available, it is not possible to prioritise the importance of potential risk pathways and circulation routes. | 2012 | 22849279 |
| 3916 | 11 | 0.9951 | Antibiotic Resistance in Fermented Foods Chain: Evaluating the Risks of Emergence of Enterococci as an Emerging Pathogen in Raw Milk Cheese. Fermented foods, particularly fermented dairy products, offer significant health benefits but also present serious concerns. Probiotic bacteria, such as lactic acid bacteria (LAB), found in these foods have been strongly linked to the selection and dissemination of antibiotic resistance genes (ARGs). This study aims to examine the potential risks associated with fermented foods, despite their importance in human nutrition, by analyzing the entire production chain from raw material acquisition to storage. Focusing on cheese production as a key fermented food, the study will investigate various aspects, including dairy farm management, milk acquisition, milk handling, and the application of good manufacturing practices (GMP) and good hygiene practices (GHP) in cheese production. The findings of this review highlight that ARGs found in LAB are similar to those observed in hygiene indicator bacteria like E. coli and pathogens like S. aureus. The deliberate use of antibiotics in dairy farms and the incorrect use of disinfectants in cheese factories contribute to the prevalence of antibiotic-resistant bacteria in cheeses. Cheese factories, with their high frequency of horizontal gene transfer, are environments where the microbiological diversity of raw milk can enhance ARG transfer. The interaction between the raw milk microbiota and other environmental microbiotas, facilitated by cross-contamination, increases metabolic communication between bacteria, further promoting ARG transfer. Understanding these bacterial and ARG interactions is crucial to ensure food safety for consumers. | 2024 | 39749146 |
| 4352 | 12 | 0.9951 | Genomic potential of crustose coralline algae-associated bacteria for the biosynthesis of novel antimicrobials. The global rise of antimicrobial resistance has intensified efforts in bioprospecting, with researchers increasingly exploring unique marine environments for novel antimicrobials. In line with this trend, our study focused on bacteria isolated from the unique microbiome of crustose coralline algae (CCA), which has yet to be investigated for antimicrobial discovery. In the present work, bacteria were isolated from a CCA collected from Varadero Reef located in Cartagena Bay, Colombia. After performing antimicrobial assays against antibiotic-resistant human and marine pathogens, three isolates were selected for genome sequencing using the Oxford Nanopore technology. Genome mining of the high-quality assemblies revealed 115 putative biosynthetic gene clusters (BGCs) and identified genes in relevant biosynthetic pathways across the three genomes. Nonetheless, we hypothesize that the biosynthesis of antimicrobial compounds results from the expression of undescribed BGCs. Further analysis revealed the absence of genes pertaining to the synthesis of coral larvae settling molecule tetrabromopyrrole, commonly produced by CCA-associated bacteria. We also discuss how differential representation of gene functions between the three isolates may be attributed to the distinct ecological niches they occupy within the CCA. This study provides valuable resources for future research aimed at the discovery of novel antimicrobials, particularly in the face of the antibiotic-resistance global crisis, and highlights the potential of specialized marine environments like CCA. | 2025 | 40711470 |
| 4080 | 13 | 0.9951 | Antibacterial resistance: an emerging 'zoonosis'? Antibacterial resistance is a worldwide threat, and concerns have arisen about the involvement of animal commensal and pathogenic bacteria in the maintenance and spread of resistance genes. However, beyond the facts related to the occurrence of resistant microorganisms in food, food-producing animals and companion animals and their transmission to humans, it is important to consider the vast environmental 'resistome', the selective pathways underlying the emergence of antibacterial resistance and how we can prepare answers for tomorrow. | 2014 | 25348154 |
| 3964 | 14 | 0.9951 | Working across the veterinary and human health sectors. Antibiotics are widely used in human and veterinary medicine for the prevention and treatment of infectious diseases. This practice has led to the emergence of antimicrobial-resistant bacteria in both humans and animals. The potential role that animals, particularly livestock, might play as potential reservoirs of antibiotic resistance genes has been recognized, and it is currently a cause of public health concern. The impact of animal and human antibiotic usage on the emergence and persistence of resistant bacteria and the precise transfer pathways for resistance genes between humans and animals are not currently fully understood. As part of the remit of the UK Advisory Committee on Antimicrobial Resistance and Healthcare-Associated Infection (ARHAI), two main areas were addressed, namely methicillin-resistant Staphylococcus aureus (MRSA) and multidrug-resistant Gram-negative bacteria, where both the human and veterinary health sectors share interests. We review the current knowledge of MRSA and resistant Gram-negative bacteria, and provide guidance on occupational risks for veterinary healthcare workers relating to animals infected or colonized with MRSA. Findings and recommendations for further work across disciplines and future research in multidrug-resistant Gram-negative bacteria are also presented. Working collaboratively across disciplines is essential in order to better understand and challenge an important human and animal health problem: antimicrobial resistance. | 2012 | 22855878 |
| 3865 | 15 | 0.9951 | Assessing Transmission of Antimicrobial-Resistant Escherichia coli in Wild Giraffe Contact Networks. There is growing evidence that anthropogenic sources of antibiotics and antimicrobial-resistant bacteria can spill over into natural ecosystems, raising questions about the role wild animals play in the emergence, maintenance, and dispersal of antibiotic resistance genes. In particular, we lack an understanding of how resistance genes circulate within wild animal populations, including whether specific host characteristics, such as social associations, promote interhost transmission of these genes. In this study, we used social network analysis to explore the forces shaping population-level patterns of resistant Escherichia coli in wild giraffe (Giraffa camelopardalis) and assess the relative importance of social contact for the dissemination of resistant E. coli between giraffe. Of 195 giraffe sampled, only 5.1% harbored E. coli isolates resistant to one or more tested antibiotics. Whole-genome sequencing on a subset of resistant isolates revealed a number of acquired resistance genes with linkages to mobile genetic elements. However, we found no evidence that the spread of resistance genes among giraffe was facilitated by interhost associations. Giraffe with lower social degree were more likely to harbor resistant E. coli, but this relationship was likely driven by a correlation between an individual's social connectedness and age. Indeed, resistant E. coli was most frequently detected in socially isolated neonates, indicating that resistant E. coli may have a selective advantage in the gastrointestinal tracts of neonates compared to other age classes. Taken together, these results suggest that the maintenance of antimicrobial-resistant bacteria in wild populations may, in part, be determined by host traits and microbial competition dynamics within the host.IMPORTANCE Antimicrobial resistance represents a significant threat to human health, food security, and the global economy. To fully understand the evolution and dissemination of resistance genes, a complete picture of antimicrobial resistance in all biological compartments, including natural ecosystems, is required. The environment and wild animals may act as reservoirs for anthropogenically derived resistance genes that could be transferrable to clinically relevant bacteria of humans and domestic animals. Our study investigated the possible transmission mechanisms for antimicrobial-resistant bacteria within a wild animal population and, more broadly, contributes to our understanding of how resistance genes are spread and maintained in natural ecosystems. | 2019 | 30413480 |
| 6700 | 16 | 0.9951 | Antimicrobial Resistance in Diverse Ecological Niches-One Health Perspective and Food Safety. Antimicrobial resistance (AMR) is a multi-sectoral, systemic, and global issue worldwide. Antimicrobial use (AMU) is a key factor in the selection of resistant bacteria within different ecological niches, from agriculture to food-producing animals to humans. There is a question regarding the extent to which the use of antibiotics in livestock production and the primary food production sector influences the selection and transmission of resistant bacteria and/or resistant genes throughout the food chain and thus contributes to the complexity in the development of AMR in humans. Although the trends in the prevalence of foodborne pathogens have changed over time, the burden of ecological niches with resistance genes, primarily in commensal microorganisms, is of concern. The implementation of the harmonized surveillance of AMU and AMR would provide comprehensive insights into the actual status of resistance and further interventions leading to its reduction. Tracking AMR in different ecological niches by applying advanced genome-based techniques and developing shared AMR data repositories would strengthen the One Health concept. | 2025 | 40426510 |
| 7677 | 17 | 0.9951 | Genomic evidence for flies as carriers of zoonotic pathogens on dairy farms. Dairy farms are major reservoirs of zoonotic bacterial pathogens, which harbor antimicrobial resistance genes (ARGs), and raise critical questions about their dissemination on and off the farm environment. Here, we investigated the role of coprophagous muscid flies (Diptera: Muscidae) as carriers of zoonotic pathogens and antimicrobial resistance. We collected cow manure and flies on a dairy farm and used shotgun metagenomics to identify the presence of clinically relevant bacteria, virulence factors, and ARGs in both environments. Our results reveal that, although the fly microbiome is largely composed of manure-associated taxa, they also harbor specific insect-associated bacteria, which may be involved in nutrient provisioning to the host. Furthermore, we identifed shared ARGs, virulence factors, and zoonotic pathogens enriched within the fly gastrointestinal tract (GIT). Our study illustrates the potential flow of pathogenic microorganisms from manure to coprophagous flies, suggesting that flies may pose an important zoonotic threat on dairy farms. | 2025 | 40537478 |
| 4639 | 18 | 0.9951 | Genomic and Phenotypic Characterization of Mastitis-Causing Staphylococci and Probiotic Lactic Acid Bacteria Isolated from Raw Sheep's Milk. Dairy products play a crucial role in human nutrition as they provide essential nutrients. However, the presence of diverse microorganisms in these products can pose challenges to food safety and quality. Here, we provide a comprehensive molecular characterization of a diverse collection of lactic acid bacteria (LAB) and staphylococci isolated from raw sheep's milk. Whole-genome sequencing, phenotypic characterization, and bioinformatics were employed to gain insight into the genetic composition and functional attributes of these bacteria. Bioinformatics analysis revealed the presence of various genetic elements. Important toxin-related genes in staphylococci that contribute to their pathogenic potential were identified and confirmed using phenotypic assays, while adherence-related genes, which are essential for attachment to host tissues, surfaces in the dairy environment, and the creation of biofilms, were also present. Interestingly, the Staphylococcus aureus isolates belonged to sequence type 5, which largely consists of methicillin-susceptible isolates that have been involved in severe nosocomial infections. Although genes encoding methicillin resistance were not identified, multiple resistance genes (RGs) conferring resistance to aminoglycosides, macrolides, and fluroquinolones were found. In contrast, LAB had few inherently present RGs and no virulence genes, suggesting their likely safe status as food additives in dairy products. LAB were also richer in bacteriocins and carbohydrate-active enzymes, indicating their potential to suppress pathogens and effectively utilize carbohydrate substrates, respectively. Additionally, mobile genetic elements, present in both LAB and staphylococci, may facilitate the acquisition and dissemination of genetic traits, including RGs, virulence genes, and metabolic factors, with implications for food quality and public health. The molecular and phenotypic characterization presented herein contributes to the effort to mitigate risks and infections (e.g., mastitis) and enhance the safety and quality of milk and products thereof. | 2023 | 37762186 |
| 4357 | 19 | 0.9951 | Comparative genomic analysis of 255 Oenococcus oeni isolates from China: unveiling strain diversity and genotype-phenotype associations of acid resistance. Oenococcus oeni, the only species of lactic acid bacteria capable of fully completing malolactic fermentation under challenging wine conditions, continues to intrigue researchers owing to its remarkable adaptability, particularly in combating acid stress. However, the mechanism underlying its superior adaptation to wine stresses still remains elusive due to the lack of viable genetic manipulation tools for this species. In this study, we conducted genomic sequencing and acid resistance phenotype analysis of 255 O. oeni isolates derived from diverse wine regions across China, aiming to elucidate their strain diversity and genotype-phenotype associations of acid resistance through comparative genomics. A significant correlation between phenotypes and evolutionary relationships was observed. Notably, phylogroup B predominantly consisted of acid-resistant isolates, primarily originating from Shandong and Shaanxi wine regions. Furthermore, we uncovered a noteworthy linkage between prophage genomic islands and acid resistance phenotype. Using genome-wide association studies, we identified key genes correlated with acid resistance, primarily involved in carbohydrates and amino acid metabolism processes. This study offers profound insights into the genetic diversity and genetic basis underlying adaptation mechanisms to acid stress in O. oeni.IMPORTANCEThis study provides valuable insights into the genetic basis of acid resistance in Oenococcus oeni, a key lactic acid bacterium in winemaking. By analyzing 255 isolates from diverse wine regions in China, we identified significant correlations between strain diversity, genomic islands, and acid resistance phenotypes. Our findings reveal that certain prophage-related genomic islands and specific genes are closely linked to acid resistance, offering a deeper understanding of how O. oeni adapts to acidic environments. These discoveries not only advance our knowledge of microbial stress responses but also pave the way for selecting and engineering acid-resistant strains, enhancing malolactic fermentation efficiency and wine quality. This research underscores the importance of genomics in improving winemaking practices and addressing challenges posed by high-acidity wines. | 2025 | 40261018 |