Article
Biotechnology & Applied Microbiology
Samuel J. Bloomfield, Aldert L. Zomer, Justin O'Grady, Gemma L. Kay, John Wain, Nicol Janecko, Raphaelle Palau, Alison E. Mather
Summary: Food products can carry various bacteria, including pathogenic, commensal, and spoilage bacteria, some of which may be resistant to antimicrobials. Current methods for detecting bacteria on food are time-consuming or can only identify different taxa without genetic content. This study optimized the depletion of host DNA to increase the efficiency of sequencing food microbiota.
Article
Food Science & Technology
Adrian Alvarez-Molina, Jose F. Cobo-Diaz, Elena A. Alexa, Fiona Crispie, Miguel Prieto, Mercedes Lopez, Paul D. Cotter, Avelino Alvarez-Ordonez
Summary: In recent years, advances in high throughput sequencing technologies have opened up new possibilities for environmental monitoring in the food processing industry. This study used whole metagenome sequencing to assess the microbiome and resistome of food processing environments from slaughterhouses, dairy processing plants, and meat processing plants. The results showed that slaughterhouses had more diverse microbiomes and resistomes, while dairy processing plants had the highest variability. Different predominant bacterial genera were found in each industry type. The study also identified the most abundant antimicrobial resistance genes, which were associated with resistance to aminoglycosides, tetracyclines, and quaternary ammonium compounds. The findings have important implications for food safety management systems.
FOOD RESEARCH INTERNATIONAL
(2023)
Article
Environmental Sciences
Andrea Di Cesare, Raffaella Sabatino, Tomasa Sbaffi, Diego Fontaneto, Diego Brambilla, Andrea Beghi, Franca Pandolfi, Cristina Borlandelli, Davide Fortino, Giovanni Biccai, Pietro Genoni, Gianluca Corno
Summary: This study analyzed the fate of antibiotic resistance genes (ARGs) in a lake-river-lake system in Northern Italy. The results showed that anthropogenic pressure promotes the spread of specific ARGs but also leads to a rapid decline in other ARGs.
Article
Engineering, Environmental
Jangwoo Lee, Feng Ju, Ayella Maile-Moskowitz, Karin Beck, Andreas Maccagnan, Christa S. McArdell, Marco Dal Molin, Fabrizio Fenicia, Peter J. Vikesland, Amy Pruden, Christian Stamm, Helmut Buergmann
Summary: This study tracked the fate of the resistome in treated wastewater in two Swiss rivers using a comprehensive analysis and found that wastewater-origin ARG did not persist in rivers after 5-6.8 km downstream. The potential for direct human exposure to the resistome of wastewater-origin appeared to typically abate rapidly in the studied rivers.
Article
Microbiology
Karen Leth Nielsen, Markus Harboe Olsen, Albert Palleja, Soren Roddik Ebdrup, Nikolaj Sorensen, Oksana Lukjancenko, Rasmus L. Marvig, Kirsten Moller, Niels Frimodt-Moller, Frederik Boetius Hertz
Summary: This study investigated the effects of antibiotics on the gut microbiome and resistome of antibiotic-naive patients during neurointensive care. It was found that narrow-spectrum antibiotic treatment increased microbial richness, while broad-spectrum treatment had diverse effects on different patients. Additionally, post-treatment broad-spectrum treatment resulted in higher abundance of antibiotic resistance genes.
Article
Gastroenterology & Hepatology
Achal Dhariwal, Lars Christian Haugli Braten, Kjersti Sturod, Gabriela Salvadori, Ahmed Bargheet, Heidi amdal, Roger Junges, Dag Berild, John-Anker Zwart, Kjersti Storheim, Fernanda Cristina Petersen
Summary: Long-term exposure to amoxicillin has a persistent impact on the gut resistome, leading to an increase in antimicrobial resistance genes. However, changes in microbiome composition are transient and recover within 9 months.
Article
Microbiology
Devin B. Holman, Katherine E. Gzyl, Kathy T. Mou, Heather K. Allen
Summary: Research reveals that the gut microbiome of piglets undergoes significant changes postweaning, with the weaning age having only a temporary effect on the microbiome. Within 7 days postweaning, the gut microbiome of pigs tends to stabilize, showcasing a predictable shift in microbial composition.
Article
Microbiology
Raffaella Sabatino, Tomasa Sbaffi, Periyasamy Sivalingam, Gianluca Corno, Diego Fontaneto, Andrea Di Cesare
Summary: This study characterized the bacteriophage community and associated antimicrobial resistance genes (ARGs) in wastewater treatment plants. The results showed that bacteriophages have limited contribution to the overall antimicrobial resistome, but further investigation is needed to fully understand their role in microbial communities.
MICROBIOLOGY SPECTRUM
(2023)
Article
Microbiology
Jose F. Cobo-Diaz, Adrian Alvarez-Molina, Elena A. Alexa, Calum J. Walsh, Oscar Mencia-Ares, Paula Puente-Gomez, Eleni Likotrafiti, Paula Fernandez-Gomez, Bernardo Prieto, Fiona Crispie, Lorena Ruiz, Montserrat Gonzalez-Raurich, Mercedes Lopez, Miguel Prieto, Paul Cotter, Avelino Alvarez-Ordonez
Summary: The study found that pig carcasses were a source of resistant bacteria that colonized the food processing environment, with drains and certain food-contact surfaces serving as reservoirs for the spread of antibiotic resistance genes (ARGs). Over time, there was an increase in abundance and diversity of ARGs, mainly assigned to Acinetobacter and associated with resistance to antimicrobials frequently used in the region. The presence of mobile genetic elements and lateral gene transfer events were mainly detected in drains at a later sampling time.
Article
Genetics & Heredity
Devin B. Holman, Katherine E. Gzyl, Arun Kommadath
Summary: Conventional swine production involves indoor, high-density farming, while pasture-raised pigs are reared outdoors with lower stocking densities. The use of antimicrobials differs between these two production systems, with conventionally raised pigs being exposed to antimicrobials to control and prevent infectious diseases. This study used shotgun metagenomic sequencing to compare the gut microbiomes and resistomes of pigs raised in these two systems. The results showed significant differences in microbial compositions, resistomes, and functional profiles between the two groups of pigs. The findings provide insights into the impact of different production systems on pig gut microbiomes and antimicrobial resistance.
MICROBIAL GENOMICS
(2023)
Article
Environmental Sciences
Rachel A. Kaiser, Jason S. Polk, Tania Datta, Scott P. Keely, Nichole E. Brinkman, Rohan R. Parekh, Getahun E. Agga
Summary: Antimicrobial resistance (AMR) is a global crisis threatening human, animal, and environmental health. This study focused on an urban karst aquifer system in Bowling Green, KY, and used high-throughput qPCR to determine the occurrence and relative abundance of antimicrobial resistant genes (ARG) in the groundwater. The results showed a high prevalence of ARGs throughout the aquifer, with a prominent human influence detected.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Public, Environmental & Occupational Health
Priyanka Kumari, Binu Mani Tripathi, Ke Dong, Kyung Yeon Eo, Woo-Shin Lee, Junpei Kimura, Naomichi Yamamoto
Summary: This study investigates the risks and ecology of antimicrobial resistance genes (ARGs) in the environment by analyzing the feces of wildlife. The study finds significant differences in bacterial taxonomy composition and resistomes between different animal hosts, as well as selective correlations between certain ARGs and bacteria. This research provides important baseline information for conservation efforts and assessing health risks posed by ARGs and bacterial pathogens from wildlife.
Article
Environmental Sciences
Thi Thuy Do, Stephen Nolan, Nicky Hayes, Vincent O'Flaherty, Catherine Burgess, Fiona Brennan, Fiona Walsh
Summary: The study compared the effects of storage, composting, and anaerobic digestion on pig slurry microbiome, resistome, and nutrient content. Each treatment method has advantages and disadvantages, with composting being the most effective at reducing risks to human health and the environment.
ENVIRONMENTAL POLLUTION
(2022)
Article
Agriculture, Dairy & Animal Science
Tatiana R. Vieira, Esther F. Cavinatto de Oliveira, Samuel P. Cibulski, Nubia M. V. Silva, Mauro R. Borba, Celso J. B. Oliveira, Marisa Cardoso
Summary: This study investigated the microbial composition, abundance of antimicrobial resistance genes (ARGs), and mobile genetic elements (MGEs) in retail chicken carcasses from different production systems. Although there were no differences in microbial diversity, certain taxa, including spoilage-associated organisms, showed significant differences across the groups. The co-resistome comprised 29 shared ARGs, and their abundance was lower in chicken carcasses from certified antimicrobial-free intensive production systems (AF) and certified organic production systems with restricted antimicrobial use (OR) compared to conventional intensive production systems (CO). Transposases were the most abundant MGEs, with a higher abundance in CO compared to OR.
Article
Microbiology
Ana Sofia Ribeiro Duarte, Timo Roder, Liese Van Gompel, Thomas Nordahl Petersen, Rasmus Borup Hansen, Inge Marianne Hansen, Alex Bossers, Frank M. Aarestrup, Jaap A. Wagenaar, Tine Hald
Summary: Metagenomics can reveal the genetic content of microbiota in different environments, with great potential for investigating the transmission of foodborne hazards. This study demonstrates the application of metagenomics in attributing antimicrobial resistance sources, showing a potential relationship between fecal resistome components and specific reservoirs.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Rheumatology
Magali Berland, Victoria Meslier, Samar Berreira Ibraim, Emmanuelle Le Chatelier, Nicolas Pons, Nicolas Maziers, Florence Thirion, Franck Gauthier, Florian Plaza Onate, Jean-Pierre Furet, Ariane Leboime, Roula Said-Nahal, Florence Levenez, Nathalie Galleron, Benoit Quinquis, Philippe Langella, Stanislav Dusko Ehrlich, Maxime Breban
Summary: This study further characterized the gut microbiota in patients with SpA and found dysbiosis compared to healthy controls. Disease activity and genetic background were shown to influence the composition of the gut microbiota in SpA patients.
ARTHRITIS & RHEUMATOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Lucia Trilla-Fuertes, Angelo Gamez-Pozo, Guillermo Prado-Vazquez, Rocio Lopez-Vacas, Andrea Zapater-Moros, Elena Lopez-Camacho, Maria Lumbreras-Herrera, Virtudes Soriano, Fernando Garicano, Ma Jose Lecumberri, Maria Rodriguez de la Borbolla, Margarita Majem, Elisabeth Perez-Ruiz, Maria Gonzalez-Cao, Juana Oramas, Alejandra Magdaleno, Joaquin Fra, Alfonso Martin-Carnicero, Monica Corral, Teresa Puertolas, Ricardo Ramos, Juan Angel Fresno Vara, Enrique Espinosa
Summary: Immunotherapy based on anti-PD1 antibodies has improved outcomes in advanced melanoma, but predicting response to treatment remains a challenge. This study used probabilistic graphical models and classificatory algorithms to classify melanoma samples, and found that gene expression data can be grouped into immune and molecular layers of information. The immune layer classification was able to distinguish responders from non-responders to immunotherapy in a new cohort, indicating its potential as a useful tool for clinicians in identifying patients who will benefit from immunotherapy.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Oncology
Lucia Trilla-Fuertes, Angelo Gamez-Pozo, Miguel Nogue, Isabel Busquier, Fernando Arias, Fernando Lopez-Campos, Ana Fernandez-Montes, Ana Ruiz, Concepcion Velazquez, Celia Martin-Bravo, Elisabeth Perez-Ruiz, Elena Asensio, Xavier Hernandez-Yague, Aline Rodrigues, Ismael Ghanem, Rocio Lopez-Vacas, Ahmed Hafez, Pedro Arias, Irene Dapia, Mario Solis, Antje Dittmann, Ricardo Ramos, Carlos Llorens, Joan Maurel, Angel Campos-Barros, Juan Angel Fresno Vara, Jaime Feliu
Summary: This study aimed to identify biomarkers for personalized treatments and improvement of therapeutic outcomes in anal squamous cell carcinoma (ASCC). The researchers analyzed tumor samples from ASCC patients through whole-exome sequencing and identified genes associated with disease-free survival. The presence of duplications in the CYP2D6 gene was found to be a biomarker of worse disease-free survival. Proteomics analysis also suggested mitochondria and mitochondrial cell-cycle genes as potential therapeutic targets.
Article
Biochemistry & Molecular Biology
Roberta Genova, Pablo Laborda, Trinidad Cuesta, Jose Luis Martinez, Fernando Sanz-Garcia
Summary: Understanding the consequences of drug resistance in bacterial physiology is crucial for exploiting its weaknesses. Collateral sensitivity, a potentially exploitable phenotype, may not be conserved among different isolates. Identifying robust and conserved collateral sensitivity patterns is important for translating this knowledge into clinical practice.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Microbiology
Fernando Sanz-Garcia, Teresa Gil-Gil, Pablo Laborda, Paula Blanco, Luz-Edith Ochoa-Sanchez, Fernando Baquero, Jose Luis Martinez, Sara Hernando-Amado
Summary: In this Review, the authors discuss how eco-evolutionary-based approaches can contribute to the development of successful antibiotic therapies. They explore the exploitation of evolutionary trade-offs, targeting bacterial metabolism, and studying the ancestral functions of antibiotic resistance determinants. These approaches are crucial for tackling the urgent problem of antibiotic resistance and preserving the efficacy of current antibiotics.
NATURE REVIEWS MICROBIOLOGY
(2023)
Article
Multidisciplinary Sciences
Sara Hernando-Amado, Pablo Laborda, Jose Luis Martinez
Summary: In this study, the authors induced ciprofloxacin resistance in clinical isolates of Pseudomonas aeruginosa and found transient collateral sensitivity to tobramycin. This non-inherited induction of antibiotic resistance allows for the eradication of antibiotic-resistant strains when combined with tobramycin. These results suggest that transient collateral sensitivity could be a new evolutionary strategy to combat antibiotic-resistant infections.
NATURE COMMUNICATIONS
(2023)
Article
Biotechnology & Applied Microbiology
Ada Munoz-Cazalla, Jose L. Martinez, Pablo Laborda
Summary: Efflux pumps are important determinants of antibiotic resistance in Pseudomonas aeruginosa, and they are also involved in other bacterial activities such as quorum sensing-mediated regulation of virulence. However, the interconnection between efflux pumps and bacterial metabolism remains unclear. This study found that phenylethylamine acts as both an inducer and substrate of the MexCD-OprJ efflux pump, which is involved in antibiotic resistance and extrusion of quorum-sensing signal precursors in P. aeruginosa. While phenylethylamine did not increase antibiotic resistance, it reduced the virulence potential by suppressing the production of toxins and inhibiting swarming motility through the downregulation of quorum sensing signaling molecules.
MICROBIAL BIOTECHNOLOGY
(2023)
Article
Genetics & Heredity
Gregory E. McCallum, Amanda E. Rossiter, Mohammed Nabil Quraishi, Tariq H. Iqbal, Sarah A. Kuehne, Willem van Schaik
Summary: The gut microbiota serves as a reservoir for antimicrobial resistance genes. Recent advancements in metagenomic chromosome conformation capture methods have made it possible to link bacterial genes to phylogenetic markers, allowing for the identification of antimicrobial resistance genes and their hosts within the microbiome. By filtering out noise-causing repetitive element mapping and using spike-in controls, 87 antimicrobial resistance genes were successfully assigned to their bacterial hosts.
MICROBIAL GENOMICS
(2023)
Article
Microbiology
Robert A. Moran, Baomo Liu, Emma L. Doughty, Yingyi Guo, Xiaoliang Ba, Willem van Schaik, Chao Zhuo, Alan McNally
Summary: ESBL resistance has a significant impact on the clinical management of E. coli infections in hospitals worldwide. This study aimed to understand the structures and dynamics of ESBL-EC populations in a Guangzhou ICU. The results revealed distinct populations of ESBL-EC strains in patients, staff, and clinical environments, with bla(CTX-M) genes playing a major role in conferring ESBL resistance.
MICROBIOLOGY SPECTRUM
(2023)
Editorial Material
Microbiology
Sara Hernando-Amado, Jose Luis Martinez
Article
Biochemistry & Molecular Biology
Teresa Gil-Gil, Trinidad Cuesta, Sara Hernando-Amado, Jose Antonio Reales-Calderon, Fernando Corona, Juan F. Linares, Jose L. Martinez
Summary: Pseudomonas aeruginosa is a widespread nosocomial opportunistic pathogen with many virulence determinants. The lack of Crc in Pseudomonas aeruginosa leads to a defective Type III Secretion System (T3SS) activity, which is caused by reduced expression of T3SS genes and impaired protein secretion.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Petros Andrikopoulos, Judith Aron-Wisnewsky, Rima Chakaroun, Antonis Myridakis, Sofia K. Forslund, Trine Nielsen, Solia Adriouch, Bridget Holmes, Julien Chilloux, Sara Vieira-Silva, Gwen Falony, Joe-Elie Salem, Fabrizio Andreelli, Eugeni Belda, Julius Kieswich, Kanta Chechi, Francesc Puig-Castellvi, Mickael Chevalier, Emmanuelle Le Chatelier, Michael T. Olanipekun, Lesley Hoyles, Renato Alves, Gerard Helft, Richard Isnard, Lars Kober, Luis Pedro Coelho, Christine Rouault, Dominique Gauguier, Jens Peter Gotze, Edi Prifti, Philippe Froguel, Jean-Daniel Zucker, Fredrik Backhed, Henrik Vestergaard, Torben Hansen, Jean-Michel Oppert, Matthias Bluher, Jens Nielsen, Jeroen Raes, Peer Bork, Muhammad M. Yaqoob, Michael Stumvoll, Oluf Pedersen, S. Dusko Ehrlich, Karine Clement, Marc-Emmanuel Dumas
Summary: The study reveals that kidney function is the main determinant of circulating TMAO levels, while microbiota composition and diet play minor but significant roles. Mediation analysis suggests a causal relationship between TMAO and kidney function, which is supported by preclinical models. The study also finds that anti-diabetic drugs with reno-protective properties can lower TMAO levels.
NATURE COMMUNICATIONS
(2023)
Article
Microbiology
Sarah J. J. Element, Robert A. A. Moran, Emilie Beattie, Rebecca J. J. Hall, Willem van Schaik, Michelle M. C. Buckner
Summary: Antimicrobial resistance, especially in Gram-negative Enterobacteriaceae like Klebsiella pneumoniae, is a growing problem. Conjugative plasmids play a role in the dissemination of AMR genes. In this study, the transfer of a multi-drug resistance plasmid in planktonic and biofilm populations of K. pneumoniae was examined. The transfer frequency of the plasmid was found to be significantly higher in biofilm conditions compared to planktonic cells, with minimal impact on growth and gene expression.
Article
Biochemistry & Molecular Biology
Victoria Meslier, Elisa Menozzi, Aymeric David, Christian Morabito, Sara Lucas Del Pozo, Alexandre Famechon, Janet North, Benoit Quinquis, Sofia Koletsi, Jane Macnaughtan, Roxana Mezabrovschi, S. Dusko Ehrlich, Anthony H. V. Schapira, Mathieu Almeida
Summary: Recent attention has highlighted the importance of oral microbiota in human health and disease, especially in Parkinson's disease. It has been found that a semi-automated DNA extraction protocol can improve sample processing efficiency without compromising the structure of the oral microbiome.
Article
Biochemistry & Molecular Biology
Meritxell Llorens-Revull, Brenda Martinez-Gonzalez, Josep Quer, Juan Ignacio Esteban, Gonzalo Nunez-Moreno, Pablo Minguez, Idoia Burgui, Ricardo Ramos-Ruiz, Maria Eugenia Soria, Angie Rico, Mar Riveiro-Barciela, Silvia Sauleda, Maria Piron, Irene Corrales, Francesc E. Borras, Francisco Rodriguez-Frias, Ariadna Rando, Clara Ramirez-Serra, Silvia Camos, Esteban Domingo, Marta Bes, Celia Perales, Maria Isabel Costafreda
Summary: MicroRNAs (miRNAs) encapsulated in extracellular vesicles (EVs) have potential as diagnostic and prognostic biomarkers. This study aimed to find a reliable EV isolation method for miRNA sequencing, suitable for clinical applications. Results showed that SEC yielded the highest amount of EVs with good reproducibility, while GRAD and SEC+GRAD resulted in purer EV preparations. The NEBNext library exhibited the highest reproducibility in miRNA recovery and diversity. Therefore, combining GRAD EV isolation with NEBNext library preparation is suitable for miRNA detection using plasma samples.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)