Article
Microbiology
Manisha Goyal, Andreu Coello Pelegrin, Magali Jaillard, Yulia Rosa Saharman, Corne H. W. Klaassen, Henri A. Verbrugh, Juliette A. Severin, Alex van Belkum
Summary: This study demonstrates the importance of detailed whole genome sequencing analysis for highly refined epidemiological analysis of carbapenem non-susceptible Pseudomonas aeruginosa. The analysis revealed variations in transmission and acquisition of CNPA strains among patients, as well as the correlation between genomic sequence changes and the distribution of antibiotic resistance and virulence genes.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Public, Environmental & Occupational Health
P. Bidet, A. Birgy, B. Brethon, J. H. Dalle, P. Mariani-Kurkdjian, C. Courroux, A. Monjault, M. Gits-Muselli, S. Bonacorsi
Summary: This study designed and evaluated a rapid and simple typing method for Pseudomonas aeruginosa compared to whole genome sequencing (WGS). The simplified and inexpensive method called MLVA could exclude most unrelated isolates in a short time and focus investigations on a small number of cases. Sequential use of both methods was identified as the optimal strategy to investigate clustered cases of P. aeruginosa infections.
JOURNAL OF HOSPITAL INFECTION
(2022)
Article
Immunology
Alexander J. Sundermann, Jieshi Chen, James K. Miller, Melissa Saul, Kathleen A. Shutt, Marissa P. Griffith, Mustapha M. Mustapha, Chinelo Ezeonwuka, Kady Waggle, Vatsala Srinivasa, Praveen Kumar, A. William Pasculle, Ashley M. Ayres, Graham M. Snyder, Vaughn S. Cooper, Daria Van Tyne, Jane W. Marsh, Artur W. Dubrawski, Lee H. Harrison
Summary: This study utilized WGS surveillance and machine learning algorithms to retrospectively detect an outbreak of previously unknown gastroscope-associated P. aeruginosa infections, highlighting the value of these methods in enhancing outbreak detection and preventing serious infections in hospitals.
CLINICAL INFECTIOUS DISEASES
(2021)
Article
Infectious Diseases
Omar Ahmed
Summary: This study evaluated the presence of antibiotic resistance genes in clinical strains of P. aeruginosa using whole-genome sequencing. The results showed that resistant strains had multiple antibiotic resistance genes and exhibited resistance to different types of antibiotics. These findings contribute to the understanding of the development of multidrug-resistant P. aeruginosa.
INFECTION AND DRUG RESISTANCE
(2022)
Article
Microbiology
Cong Shen, Jinxiang Zeng, Dexiang Zheng, Yinglun Xiao, Jieying Pu, Li Luo, Hongyun Zhou, Yimei Cai, Liling Zhang, Meina Wu, Xuan Zhang, Guangyuan Deng, Song Li, Qiwei Li, Jianming Zeng, Zhaohui Sun, Bin Huang, Cha Chen
Summary: Pseudomonas aeruginosa (P. aeruginosa) is a leading cause of chronic infections, and relapse infections are more common in carbapenem-resistant strains. This study identified relapse infections in a tertiary hospital in China and found that they were not caused by specific lineages. Genomic changes, including antimicrobial resistance and gene mutations, were observed during relapse episodes. A specific mutation in the fptA gene could be a potential target for the diagnosis and treatment of relapse P. aeruginosa infection.
MICROBIOLOGY SPECTRUM
(2023)
Article
Microbiology
Cong Shen, Jinxiang Zeng, Dexiang Zheng, Yinglun Xiao, Jieying Pu, Li Luo, Hongyun Zhou, Yimei Cai, Liling Zhang, Meina Wu, Xuan Zhang, Guangyuan Deng, Song Li, Qiwei Li, Jianming Zeng, Zhaohui Sun, Bin Huang, Cha Chen
Summary: Pseudomonas aeruginosa is a leading cause of chronic infections, especially in cystic fibrosis patients. In this study, we observed a high incidence of relapse P. aeruginosa infection in China, with carbapenem-resistant strains being more prevalent. Whole-genome sequencing revealed the dynamic changes and evolution of this pathogen during relapse episodes. A convergent non-synonymous mutation in a virulence gene could be a potential target for diagnosis and treatment. Integrated utilization of WGS and medical records provides opportunities for improved diagnostics of relapse infections.
MICROBIOLOGY SPECTRUM
(2023)
Article
Microbiology
Bing Liu, Jianpeng Gao, Xue Fei Liu, Guanhua Rao, Jiajie Luo, Peng Han, Weiting Hu, Ze Zhang, Qianqian Zhao, Lizhong Han, Zhi Jiang, Min Zhou
Summary: This study successfully achieved the direct prediction of carbapenem resistance in Pseudomonas aeruginosa through the selection of key gene features and construction of machine learning models. The prediction was validated in clinical samples using metagenomic sequencing technology, providing assistance in timely treatment and surveillance of carbapenem-resistant Pseudomonas aeruginosa.
JOURNAL OF CLINICAL MICROBIOLOGY
(2023)
Article
Immunology
Alexander J. Sundermann, Vatsala Rangachar Srinivasa, Emma G. Mills, Marissa P. Griffith, Kady D. Waggle, Ashley M. Ayres, Lora Pless, Graham M. Snyder, Lee H. Harrison, Daria Van Tyne
Summary: This article describes two cases of extensively drug-resistant Pseudomonas aeruginosa infection caused by a strain associated with contaminated artificial tears outbreak. The cases were detected through genome sequencing-based surveillance, and the genetic relatedness and antimicrobial resistance genes of the outbreak strain were analyzed using publicly available Pseudomonas aeruginosa genomes.
JOURNAL OF INFECTIOUS DISEASES
(2023)
Article
Microbiology
Richard A. Stanton, Davina Campbell, Gillian A. McAllister, Erin Breaker, Michelle Adamczyk, Jonathan B. Daniels, Joseph D. Lutgring, Maria Karlsson, Kyle Schutz, Jesse T. Jacob, Lucy E. Wilson, Elisabeth Vaeth, Linda Li, Ruth Lynfield, Paula M. Snippes Vagnone, Erin C. Phipps, Emily B. Hancock, Ghinwa Dumyati, Rebecca Tsay, P. Maureen Cassidy, Jacquelyn Mounsey, Julian E. Grass, Sandra N. Bulens, Maroya Spalding Walters, Alison Laufer Halpin
Summary: This study investigated carbapenem-resistant Pseudomonas aeruginosa (CRPA) in the United States through genetic sequencing and typing. The results revealed diverse sources of carbapenem resistance, including non-carbapenemase beta-lactamase genes. The study findings shed light on the genetic diversity and transmission mechanisms of carbapenem-resistant P. aeruginosa.
ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
(2022)
Article
Infectious Diseases
Raul Recio, Jennifer Villa, Sara Gonzalez-Bodi, Patricia Branas, Maria Angeles Orellana, Mikel Mancheno-Losa, Jaime Lora-Tamayo, Fernando Chaves, Esther Viedma
Summary: This study analyzed the phenotypic and genomic characteristics of ceftazidime/avibactam (CZA) resistance in different GES-producing Pseudomonas aeruginosa isolates. The results showed that all CZA-resistant isolates belonged to the ST235 clone and O11 serotype, and different mutations within the bla(GES)(-20) gene were associated with CZA resistance, suggesting the involvement of other resistance mechanisms.
Article
Microbiology
Rucha Datar, Andreu Coello Pelegrin, Sylvain Orenga, Valerie Chalansonnet, Caroline Mirande, Jill Dombrecht, John D. Perry, Audrey Perry, Herman Goossens, Alex van Belkum
Summary: The study found that cystic fibrosis (CF) patients suffer from chronic lung infections caused by Pseudomonas aeruginosa, leading to lung damage. There are phenotypic and genotypic differences among P. aeruginosa isolates from different CF patients, but isolates from the same patient have high similarity. Bacteria show varying levels of resistance to different antibiotics, and lung transplantation (LTx) does not change the type of infecting strains.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Megan O'Shaughnessy, Jasmine Hurley, Shane C. Dillon, Celine Herra, Pauraic McCarron, Malachy McCann, Michael Devereux, Orla Howe
Summary: Antimicrobial resistance (AMR) is a major global health challenge, and there is an urgent need to develop novel therapeutic agents to overcome it. Metal complexes incorporating 1,10-phenanthroline and various dicarboxylate ligands were found to have high antibacterial activity against AMR pathogens. The chelates incorporating both phen and the dianion of 3,6,9-trioxaundecanedioic acid were the most effective, and their activity varied depending on the metal center. Whole-genome sequencing of Pseudomonas aeruginosa exposed to these metal complexes revealed mutations in genes involved in cellular respiration, polyamine biosynthesis, and virulence mechanisms.
JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY
(2023)
Article
Microbiology
Hauke Toennies, Karola Prior, Dag Harmsen, Alexander Mellmann
Summary: A novel cgMLST scheme for P. aeruginosa was established using a Bayesian approach to determine different groups, incorporating 15 reference strains and 3867 target genes. The scheme was highly reproducible and was validated through comparisons with SNP results and other cgMLST schemes, demonstrating its accuracy in outbreak investigations.
JOURNAL OF CLINICAL MICROBIOLOGY
(2021)
Article
Immunology
Baharak Babouee Flury, Anja Bosch, Valentin Gisler, Adrian Egli, Salome N. Seiffert, Oliver Nolte, Jacqueline Findlay
Summary: This study aimed to determine the molecular mechanisms of CZA and IPM-resistance in clinical P. aeruginosa isolates obtained from Swiss hospitals. The results demonstrated that CZA-resistance in P. aeruginosa is likely multifactorial and could be caused by the interplay between different resistance mechanisms, including ESBL carriage, increased efflux, loss of permeability, and derepression of its intrinsic ampC.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2023)
Article
Agriculture, Dairy & Animal Science
Sophie Le Bouquin, Laetitia Bonifait, Amandine Thepault, Thomas Ledein, Francois Guillon, Sandra Rouxel, Rozenn Souillard, Marianne Chemaly
Summary: This study details a recurrent outbreak of pullorum disease on a quail farm in western France in 2019, where epidemiological and bacteriological investigations were used to identify the source of contamination and the possibility of pathogen persistence on the site was highlighted. Recommendations for disease control were proposed based on high-risk sanitary practices identified during the investigation.
Article
Biochemistry & Molecular Biology
Muhammad Yasir, Christopher Icke, Radwa Abdelwahab, James R. Haycocks, Rita E. Godfrey, Pavelas Sazinas, Mark J. Pallen, Ian R. Henderson, Stephen J. W. Busby, Douglas F. Browning
MOLECULAR MICROBIOLOGY
(2019)
Letter
Multidisciplinary Sciences
Rudolf I. Amann, Shakuntala Baichoo, Benjamin J. Blencowe, Peer Bork, Mark Borodovsky, Cath Brooksbank, Patrick S. G. Chain, Rita R. Colwell, Daniele G. Daffonchio, Antoine Danchin, Victor de Lorenzo, Pieter C. Dorrestein, Robert D. Finn, Claire M. Fraser, Jack A. Gilbert, Steven J. Hallam, Philip Hugenholtz, John P. A. Ioannidis, Janet K. Jansson, Jihyun F. Kim, Hans-Peter Klenk, Martin G. Klotz, Rob Knight, Konstantinos T. Konstantinidis, Nikos C. Kyrpides, Christopher E. Mason, Alice C. McHardy, Folker Meyer, Christos A. Ouzounis, Aristides A. N. Patrinos, Mircea Podar, Katherine S. Pollard, Jacques Ravel, Alejandro Reyes Munoz, Richard J. Roberts, Ramon Rossello-Mora, Susanna-Assunta Sansone, Patrick D. Schloss, Lynn M. Schriml, Joao C. Setubal, Rotem Sorek, Rick L. Stevens, James M. Tiedje, Adrian Turjanski, Gene W. Tyson, David W. Ussery, George M. Weinstock, Owen White, William B. Whitman, Ioannis Xenarios
Letter
Gastroenterology & Hepatology
Falk Hildebrand, Mark J. Pallen, Peer Bork
Article
Genetics & Heredity
Anuradha Ravi, Fenella D. Halstead, Amy Bamford, Anna Casey, Nicholas M. Thomson, Willem van Schaik, Catherine Snelson, Robert Goulden, Ebenezer Foster-Nyarko, George M. Savva, Tony Whitehouse, Mark J. Pallen, Beryl A. Oppenheim
MICROBIAL GENOMICS
(2019)
Article
Multidisciplinary Sciences
Madikay Senghore, Bassirou Diarra, Florian Gehre, Jacob Otu, Archibald Worwui, Abdul Khalie Muhammad, Brenda Kwambana-Adams, Gemma L. Kay, Moumine Sanogo, Bocar Baya, Susan Orsega, Seydou Doumbia, Souleymane Diallo, Bouke C. de Jong, Mark J. Pallen, Martin Antonio
SCIENTIFIC REPORTS
(2020)
Article
Biotechnology & Applied Microbiology
Nicholas M. Thomson, Chuanzhen Zhang, Eleftheria Trampari, Mark J. Pallen
Article
Genetics & Heredity
Ebenezer Foster-Nyarko, Nabil-Fareed Alikhan, Anuradha Ravi, Gaetan Thilliez, Nicholas M. Thomson, David Baker, Gemma Kay, Jennifer D. Cramer, Justin O'Grady, Martin Antonio, Mark J. Pallen
MICROBIAL GENOMICS
(2020)
Review
Biochemistry & Molecular Biology
Mark J. Pallen, Andrea Telatin, Aharon Oren
Summary: Latin binomials, popularized by Linnaeus in the 18th century, have provided a stable and clear system of nomenclature in biology. However, with the increasing exploration of the microbial world, there is a need for a large number of new names for Archaea and Bacteria. To address this issue, an automated approach using Latin and Greek roots for creating linguistically correct names has been proposed, demonstrating the potential for creating millions of new names for Bacteria and Archaea.
TRENDS IN MICROBIOLOGY
(2021)
Article
Multidisciplinary Sciences
Liang Tian, Xu-Wen Wang, Ang-Kun Wu, Yuhang Fan, Jonathan Friedman, Amber Dahlin, Matthew K. Waldor, George M. Weinstock, Scott T. Weiss, Yang-Yu Liu
NATURE COMMUNICATIONS
(2020)
Article
Multidisciplinary Sciences
Ebenezer Foster-Nyarko, Nabil-Fareed Alikhan, Usman N. Ikumapayi, Golam Sarwar, Catherine Okoi, Peggy-Estelle Maguiagueu Tientcheu, Marianne Defernez, Justin O'Grady, Martin Antonio, Mark J. Pallen
Summary: The study reveals the genomic diversity of Escherichia coli in asymptomatic children from rural Gambia, with 56 genotypes identified and an average of 2.7 genotypes per host. Most diversity is attributed to immigration events, while a minority arises from within-host evolution. Many isolates carry virulence factors and resistance genes, indicating a potential reservoir for these genes. The study also highlights the importance of immigration and strain establishment in generating diversity, with only a minor role played by within-host evolution.
Article
Genetics & Heredity
Ebenezer Foster-Nyarko, Nabil-Fareed Alikhan, Anuradha Ravi, Nicholas M. Thomson, Sheikh Jarju, Brenda A. Kwambana-Adams, Arss Secka, Justin O'Grady, Martin Antonio, Mark John Pallen
Summary: The study revealed that E. coli isolates from chickens and guinea fowl in Gambian homes harbor antimicrobial resistance genes, particularly the ST155 strain showing multidrug resistance to clinically relevant antibiotics, indicating potential pathogenicity. Moreover, close relatedness between Gambian poultry strains and human isolates suggests a risk of transmission.
MICROBIAL GENOMICS
(2021)
Article
Nutrition & Dietetics
Briana M. Nosal, Junichi R. Sakaki, Zachary Macdonald, Kyle Mahoney, Kijoon Kim, Matthew Madore, Staci Thornton, Thi Dong Binh Tran, George Weinstock, Elaine Choung-Hee Lee, Ock K. Chun
Summary: This study aimed to examine the dose-dependent effects of blackcurrant supplementation on preventing bone loss in adult women. The results showed that blackcurrant supplementation decreased the loss of whole-body bone mineral density and increased the marker of bone formation, P1NP. Further studies with larger samples and different skeletal conditions are needed to confirm these findings.
Article
Microbiology
Evgenia Jen Filatava, Zhongmao Liu, Jiaojiao Xie, Dong-Binh Tran, Kun Chen, Noura El Habbal, George Weinstock, Yanjiao Zhou, Katherine E. Gregory
Summary: Despite a growing recognition that the type of nutrition received by preterm infants influences their intestinal microbiome and health outcomes, the microbiota of mother's own milk (MOM), pasteurized donor human milk (PDHM), and infant formula remain poorly characterized. In our study, we found that the structure of microbial communities, bacterial diversity, and relative abundances of specific genera were significantly different between MOM, PDHM, and formula. Additionally, our results suggest that the microbiota of MOM changes as a function of time and maternal factors. Lastly, we identified three lactotypes within MOM that have distinct microbial compositions and described the maternal factors associated with them. These findings set the stage for future research aimed at advancing our knowledge of the microbiota of preterm infant nutrition and the specific influence it may have on health outcomes.
Correction
Biotechnology & Applied Microbiology
Laura Glendinning, Robert D. Stewart, Mark J. Pallen, Kellie A. Watson, Mick Watson
Summary: The amended version of this paper has been published and is accessible through the original article.
Article
Biotechnology & Applied Microbiology
Laura Glendinning, Robert D. Stewart, Mark J. Pallen, Kellie A. Watson, Mick Watson