Article
Cell Biology
Martine C. Holst Sorensen, Amira Vitt, Horst Neve, Matteo Soverini, Stephen James Ahern, Jochen Klumpp, Lone Brondsted
Summary: Phase variation is a common mechanism for creating phenotypic heterogeneity in bacteria, and studies show that phages can adapt to phase-variable hosts by mimicking their hosts and encoding hypermutable polyG tracts to generate diverse phage populations. This phenomenon promotes co-existence of phages and hosts in a shared niche, suggesting that phase variation may be a widespread strategy for creating phenotypically diverse phage populations.
Article
Microbiology
Yuanyuan Niu, Xiaobo Yang, Shang Wang, Yutong Yang, Hongrui Zhou, Chenyu Li, Bin Xue, Xi Zhang, Chen Zhao, Zhiqiang Shen, Jingfeng Wang, Yun Ling, Pingfeng Yu, Zhigang Qiu
Summary: In this study, two phages PPAT and PPAY that infect Pseudomonas aeruginosa PAO1 were isolated and characterized. These phages showed growth inhibitory effects on bacteria and can be used for research and clinical purposes.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biology
Qingqing Fang, Yu Feng, Alan McNally, Zhiyong Zong
Summary: Fang et al. identified two previously unidentified phages that can inhibit the growth and decrease the virulence of carbapenem-resistant Klebsiella pneumoniae (CRKP). They also found that CRKP can develop phage resistance but can still be eliminated in a mouse intestinal colonization model, highlighting the potential of phage therapy as a treatment against drug-resistant pathogens.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Shengjian Yuan, Juan Shi, Jianrong Jiang, Yingfei Ma
Summary: The CRISPR/Cas9-based iterative phage genome reduction (CiPGr) approach was used to reduce the genomes of four distinct phages, resulting in heterogeneous genome-reduced mutants. Loss of non-essential genes for phage propagation was identified, although it had detrimental effects on phage fitness. However, some mutants showed higher infectious efficiency than their parental strains, indicating a trade-off between genome reduction and infectious fitness for phages. This study provides a foundation for future phage synthetic biology research leveraging CiPGr.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Microbiology
Ola H. Moghnia, Nourah A. Al-Sweih
Summary: The spread of carbapenem-resistant E. coli and K. pneumoniae is a global concern. This study aimed to investigate the genetic characteristics and variations of multidrug resistant isolates. Whole genome sequencing was carried out on eight carbapenem-resistant isolates, and various resistance genes were detected. This research is important for understanding and combating antimicrobial resistance.
Article
Multidisciplinary Sciences
Chandrasekar Karthika, Nambiraman Malligarjunan, Ravi Jothi, Thirupathi Kasthuri, Rajaiah Alexpandi, Arumugam Veera Ravi, Shunmugiah Karutha Pandian, Shanmugaraj Gowrishankar
Summary: The study explores the potential of phage therapy as an alternative antimicrobial treatment for multidrug-resistant Pseudomonas aeruginosa infection. Two novel virulent phages PSPa and APPa were investigated and shown to have therapeutic potential against P. aeruginosa. Both phages exhibited host specificity and significantly improved the survival rate of bacterial-infected zebrafish in vivo.
SCIENTIFIC REPORTS
(2023)
Article
Ecology
Mujie Zhang, Yali Hao, Yi Yi, Shunzhang Liu, Qingyang Sun, Xiaoli Tan, Shan Tang, Xiang Xiao, Huahua Jian
Summary: Phages, including transposable phages (TBPs), are widely distributed and play important roles in diverse environments. We established a TBP genome dataset by mining microbial genomes and viromes, expanding the accessible TBP genomes 384-fold. TBPs are prevalent and genetically diverse, and can infect a wider range of hosts than non-TBPs. We identified diverse auxiliary metabolic genes (AMGs) in TBP genomes, including genes related to glycoside hydrolases and pyrimidine deoxyribonucleotide biosynthesis. Our findings greatly expand the genetic diversity of TBPs and reveal their potential influences in various ecosystems.
Article
Biochemistry & Molecular Biology
Brett Trost, Bhooma Thiruvahindrapuram, Ada J. S. Chan, Worrawat Engchuan, Edward J. Higginbotham, Jennifer L. Howe, Livia O. Loureiro, Miriam S. Reuter, Delnaz Roshandel, Joe Whitney, Mehdi Zarrei, Matthew Bookman, Cherith Somerville, Rulan Shaath, Mona Abdi, Elbay Aliyev, Rohan Patel, Thomas Nalpathamkalam, Giovanna Pellecchia, Omar Hamdan, Gaganjot Kaur, Zhuozhi Wang, Jeffrey R. MacDonald, John Wei, Wilson W. L. Sung, Sylvia Lamoureux, Ny Hoang, Thanuja Selvanayagam, Nicole Deflaux, Melissa Geng, Siavash Ghaffari, John Bates, Edwin J. Young, Qiliang Ding, Carole Shum, Lia D'Abate, Clarrisa A. Bradley, Annabel Rutherford, Vernie Aguda, Beverly Apresto, Nan Chen, Sachin Desai, Xiaoyan Du, Matthew L. Y. Fong, Sanjeev Pullenayegum, Kozue Samler, Ting Wang, Karen Ho, Tara Paton, Sergio L. Pereira, Jo-Anne Herbrick, Richard F. Wintle, Jonathan Fuerth, Juti Noppornpitak, Heather Ward, Patrick Magee, Ayman Al Baz, Usanthan Kajendirarajah, Sharvari Kapadia, Jim Vlasblom, Monica Valluri, Joseph Green, Vicki Seifer, Morgan Quirbach, Olivia Rennie, Elizabeth Kelley, Nina Masjedi, Catherine Lord, Michael J. Szego, Ma'n H. Zawati, Michael Lang, Lisa J. Strug, Christian R. Marshall, Gregory Costain, Kristina Calli, Alana Iaboni, Afiqah Yusuf, Patricia Ambrozewicz, Louise Gallagher, David G. Amaral, Jessica Brian, Mayada Elsabbagh, Stelios Georgiades, Daniel S. Messinger, Sally Ozonoff, Jonathan Sebat, Calvin Sjaarda, Isabel M. Smith, Peter Szatmari, Lonnie Zwaigenbaum, Azadeh Kushki, Thomas W. Frazier, Jacob A. S. Vorstman, Khalid A. Fakhro, Bridget A. Fernandez, M. E. Suzanne Lewis, Rosanna Weksberg, Marc Fiume, Ryan K. C. Yuen, Evdokia Anagnostou, Neal Sondheimer, David Glazer, Dean M. Hartley, Stephen W. Scherer
Summary: This study identifies rare variants associated with autism spectrum disorder (ASD) through whole-genome sequencing (WGS) and provides a research guide to explore genotype-phenotype correlations in families carrying these rare variants.
Article
Biochemistry & Molecular Biology
Anders Norgaard Sorensen, Cedric Woudstra, Martine C. Holst Sorensen, Lone Brondsted
Summary: In this study, the diversity of tail spike proteins (TSPs) in Ackermannviridae phages was analyzed through comprehensive in silico methods, revealing specific associations between TSP subtypes and different genera within the family. The research also demonstrated the genetic diversity and potential interchangeability of TSPs in Kuttervirus phages, influencing host recognition.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Biology
Dina El-Sayed, Tarek Elsayed, Nadia Amin, Ahmad Al-Shahaby, Hanan Goda
Summary: Shiga toxin-producing Escherichia coli (STEC) is a significant global public health and food safety concern. This study evaluated the applicability of phages as potential food bio-preservatives. The findings demonstrated that two promising phages exhibited strong lytic competence and varied survival rates in different environmental conditions.
Article
Biology
Martial Marbouty, Agnes Thierry, Gael A. Millot, Romain Koszul
Summary: The study applied metagenomic Hi-C approach to analyze healthy human gut samples, revealing a large infection network of bacteriophages in the gut microbiota, with over 6000 interactions identified. Results showed that 5% of the phages may be actively replicating, and 17 members of the crAss-like phage family were successfully identified with their bacterial hosts.
Article
Biochemistry & Molecular Biology
Sander Witte, Lea V. Zinsli, Rafael Gonzalez-Serrano, Cassandra I. Matter, Martin J. Loessner, Joel T. van Mierlo, Matthew Dunne
Summary: Bacteriophages are widely used as biocontrol agents in food production and surface treatment. Their infectivity is determined by the receptor binding proteins on the tail fibers, which also dictate their suitability as antibacterial agents. Phages EP75 and EP335 exhibit broad infectivity towards certain strains of bacteria.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Igor Babkin, Artem Tikunov, Vera Morozova, Andrey Matveev, Vitaliy V. Morozov, Nina Tikunova
Summary: In this study, a unique phage genome was discovered during the analysis of the human gut virome. Comparative analysis identified two similar phage genomes, indicating the presence of a new species within the proposed Phassvirus genus. Furthermore, a group of divergent phage genomes including the proposed Phassvirus genus was identified in metagenome data. These findings highlight the importance of using different translation tables when depositing phage genomes in GenBank.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Pauline C. Goeller, Tabea Elsener, Dominic Lorge, Natasa Radulovic, Viona Bernardi, Annika Naumann, Nesrine Amri, Ekaterina Khatchatourova, Felipe Hernandes Coutinho, Martin J. Loessner, Elena Gomez-Sanz
Summary: The study reveals that staphylococcal phages have a predominant multi-species host range, facilitating horizontal gene transfer. Additionally, there is potential for antibiotic resistance gene transfer among phages sharing common hosts.
NATURE COMMUNICATIONS
(2021)
Article
Microbiology
Dustin A. Therrien, Kranti Konganti, Jason J. Gill, Brian W. Davis, Andrew E. Hillhouse, Jordyn Michalik, H. Russell Cross, Gary C. Smith, Thomas M. Taylor, Penny K. Riggs
Summary: This study involved sequencing the genomes of E. coli surrogates using two different platforms and found that combining long-read, short-read, and combined sequences can yield more accurate completed genomes. These data provide valuable insights for the adoption of WGS in the food industry and offer guidance for researchers and regulators in implementing related workflows.
Article
Immunology
Valeria Michelacci, Rosangela Tozzoli, Silvia Arancia, Alfio D'Angelo, Arianna Boni, Arnold Knijn, Gianni Prosseda, David R. Greig, Claire Jenkins, Teresa Camou, Alfredo Sirok, Armando Navarro, Felipe Schelotto, Gustavo Varela, Stefano Morabito
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2020)
Article
Microbiology
Michele Zuppi, Rosangela Tozzoli, Paola Chiani, Pablo Quiros, Adan Martinez-Velazquez, Valeria Michelacci, Maite Muniesa, Stefano Morabito
FRONTIERS IN MICROBIOLOGY
(2020)
Article
Food Science & Technology
Frank Boelaert, Anca Stoicescu, Giusi Amore, Winy Messens, Michaela Hempen, Valentina Rizzi, Sotiria-Eleni Antoniou, Francesca Baldinelli, Elisabeth Dorbek-Kolin, Yves Van der Stede, Taina Niskanen, Joana Haussig, Marlena Kaczmarek, Joana Gomes Dias, Lisa Barco, Marzia Mancin, Claudio Mantovani, Angelo Sardella, Pietro Antonelli, Marta Leati, Antonia Anna Lettini, Carmen Losasso, Stefano Morabito, Gaia Scavia, Arnold Knijn, Rosangela Tozzoli, Francesca Iacoponi, Ornella Moro, Michele Luca D'Errico, Antonietta Gattuso, Elisabetta Suffredini, Ilaria Di Bartolo, Elisabetta Delibato, Fabrizio Anniballi, Giovanni Ianiro, Ilaria Altieri, Maria Angeles Gomez Morales, Adriano Casulli, Simone Caccio, Corinne Danan, Benjamin Felix
Summary: The report presents the results of zoonoses monitoring activities in 36 European countries in 2019, highlighting the high incidence of campylobacteriosis and salmonellosis in humans, as well as the implementation of Salmonella control programs and monitoring of other pathogens.
Article
Infectious Diseases
Stefania Lauzi, Camilla Luzzago, Paola Chiani, Valeria Michelacci, Arnold Knijn, Luca Pedrotti, Luca Corlatti, Clelia Buccheri Pederzoli, Gaia Scavia, Stefano Morabito, Rosangela Tozzoli
Summary: This study found the presence of STEC infection in free-ranging red deer living in areas with different levels of anthropisation, highlighting the potential zoonotic risk posed to humans. Particularly, red deer were carriers of STEC strains with zoonotic potential and may contaminate the environment with STEC, affecting soil and water sources. Special attention should be paid to these findings in the handling and preparation of game meat.
TRANSBOUNDARY AND EMERGING DISEASES
(2022)
Article
Immunology
Valeria Michelacci, Margherita Montalbano Di Filippo, Federica Gigliucci, Silvia Arancia, Paola Chiani, Fabio Minelli, Nancy H. C. Roosens, Sigrid C. J. De Keersmaecker, Bert Bogaerts, Kevin Vanneste, Stefano Morabito
Summary: O26 serogroup of Shiga toxin-producing Escherichia coli (STEC) is a significant cause of Hemolitic Uremic Syndrome (HUS) in children worldwide. The genomic characterization and population structure of O26 STEC strains in Italy reveal differences among different clones and suggest the influence of selective pressure and ecological niches on their evolution.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Infectious Diseases
Lena Manhique-Coutinho, Paola Chiani, Valeria Michelacci, Elisa Taviani, Adilson Fernando Loforte Bauhofer, Assucenio Chissaque, Idalecia Cossa-Moiane, Julia Sambo, Jorfelia Chilaule, Esperanca Lourenco Guimaraes, Judite Salencia, Marta Cassocera, Diocreciano Matias Bero, Jose Paulo Langa, Nilsa de Deus
Summary: This study analyzed the frequency and antimicrobial resistance profiles of diarrheagenic Escherichia coli (DEC) among children aged <15 years with diarrhea in four provinces of Mozambique. The results showed that enteroaggregative E. coli was the most common pathotype, and there was a high level of resistance to ampicillin and tetracycline among isolated DEC strains.
INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES
(2022)
Article
Public, Environmental & Occupational Health
Elina Tast Lahti, Nadja Karamehmedovic, Hilde Riedel, Linnea Blom, Jeppe Boel, Elisabetta Delibato, Martine Denis, Alieda van Essen-Zandbergen, Aurora Garcia-Fernandez, Rene Hendriksen, Anna Heydecke, Angela H. A. M. van Hoek, Tom Huby, Renata Kwit, Claudia Lucarelli, Karl Lundin, Valeria Michelacci, Slawomir Owczarek, Isaac Ring, Jette Sejer Kjeldgaard, Ingegerd Sjogren, Milena Skora, Mia Torpdahl, Maria Ugarte-Ruiz, Kees Veldman, Eleonora Ventola, Magdalena Zajac, Cecilia Jernberg
Summary: Several proficiency tests and external quality assessments are available for evaluating laboratories' ability to detect and characterize enteropathogenic bacteria, but they are usually targeting specific sectors. This study aimed to assess the cross-sectoral capability of European laboratories in detecting and characterizing foodborne pathogens and provide recommendations for future assessments. The results confirmed the feasibility of using a cross-sectoral approach for assessing the joint capacity to detect and characterize foodborne pathogens.
FRONTIERS IN PUBLIC HEALTH
(2023)
Review
Reproductive Biology
Antonella Maugliani, Francesca Baldi
Summary: Pregnancy is a crucial time for women to make changes in their diet and lifestyle, and ensuring food safety is important to avoid risks. Although there are recommendations for pregnant women, more evidence is needed to evaluate the effectiveness of these recommendations on food safety behavior. Surveys were used to investigate the knowledge and awareness of pregnant women, and this research analyzed the characteristics of surveys on PubMed. The findings provide valuable information for designing new surveys and improving existing ones.
REPRODUCTIVE TOXICOLOGY
(2023)
Article
Genetics & Heredity
Valeria Michelacci, Adrien Assere, Simone Caccio, Marina Cavaiuolo, Kirsten Mooijman, Stefano Morabito, Susanne Karlsmose Pedersen, Maroua Sayeb, Bo Segerman, Magnus Simonsson, Hanna Skarin, Rosangela Tozzoli, Angela van Hoek, Rene Sjogren Hendriksen
Summary: The Inter European Union Reference Laboratories (EURLs) Working Group on Next Generation Sequencing (NGS) has been working since 2017 to promote the adoption of NGS by the National Reference Laboratories (NRLs) in the European Union. By releasing guidance documents and working together, the EURLs have aimed to improve preparedness in the use of NGS for characterizing microbial hazards and tracing infection sources.
MICROBIAL GENOMICS
(2023)
Meeting Abstract
Pediatrics
Eleonora Ventola, Valeria Michelacci, Alessandra Gianviti, Carmine Pecoraro, Mattia Parolin, Mario Giordano, Rosangela Tozzoli, Paola Chiani, Fabio Minelli, Federica Gigliucci, Arnold Knijn, Stefano Morabito, Gaia Scavia
PEDIATRIC NEPHROLOGY
(2021)
Article
Immunology
Federica Gigliucci, Angela H. A. M. van Hoek, Paola Chiani, Arnold Knijn, Fabio Minelli, Gaia Scavia, Eelco Franz, Stefano Morabito, Valeria Michelacci
Summary: This study identified and characterized 53 STEC strains with ExPEC-associated virulence genes isolated in Italy and the Netherlands from 2000 to 2019. The strains were divided into two major populations, each carrying different plasmids and virulence genes, indicating that ExPEC-associated plasmids can be acquired and mobilized by STEC strains.
EMERGING INFECTIOUS DISEASES
(2021)