Article
Infectious Diseases
Gabriel Cabot, Paula Lara-Esbri, Xavier Mulet, Antonio Oliver
Summary: The study developed a highly efficient PCR detection method for direct detection of the widely distributed high-risk clone ST175 in clinical samples, which may be of significant importance for guiding infection control and treatment strategies.
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
(2021)
Article
Microbiology
Angela Sun, Paul M. Mirzayans, Andrew M. Piggott, Jo-Ann L. Stanton, Anwar Sunna
Summary: This work builds on a previously developed workflow for rapid and sensitive pathogen detection. It establishes a sample treatment strategy that consistently produces quantification efficiencies (QEs) for Campylobacter jejuni against a complex and highly variable sample matrix from a suburban river. The most effective treatments at minimizing the inhibitory effects of the sample matrix were pH buffering with HEPES and addition of the surfactant Tween 20. The workflow's consistency and scalability make it a suitable alternative to culture-based ISO methods for detecting Campylobacter spp. in environmental water.
FEMS MICROBIOLOGY ECOLOGY
(2023)
Article
Biochemical Research Methods
Dongze He, Mohsen Zakeri, Hirak Sarkar, Charlotte Soneson, Avi Srivastava, Rob Patro
Summary: Alevin-fry is a framework that accurately and efficiently quantifies single-cell and single-nucleus RNA-seq data. It is faster and more memory efficient than other methods, and addresses the memory scalability and false-positive expression issues exhibited by lightweight tools. This framework can be effectively used to quantify and analyze sc/snRNA-seq data.
Article
Microbiology
Martin Barbosa-Amezcua, Betzaida Cuevas-Cordoba, Cristobal Fresno, Joshua Haase-Hernandez, Karol Carrillo-Sanchez, Minerva Mata-Rocha, Marcela Munoz-Torrico, Claudia Backer, Vanessa Gonzalez-Covarrubias, Carmen Alaez-Verson, Xavier Soberon
Summary: The COVID-19 pandemic has had a negative impact on the diagnosis and treatment of Tuberculosis (TB) cases. In this study, a proof-of-concept protocol was developed to detect drug resistance and classify the phylogeny of Mycobacterium Tuberculosis (Mtb) from sputum samples. The results showed that the protocol could provide a complete drug resistance profile and phylogeny of Mtb, which could be useful for personalized and effective treatments.
MICROBIOLOGY SPECTRUM
(2022)
Article
Microbiology
Yanfeng Lin, Yan Dai, Yuqi Liu, Zhuli Ren, Hao Guo, Zhenzhong Li, Jinhui Li, Kaiying Wang, Lang Yang, Shuang Zhang, Hongbo Liu, Leili Jia, Ming Ni, Peng Li, Hongbin Song
Summary: This study evaluated the performance of adaptive sequencing for viral genome enrichment in clinical respiratory samples. It found that PCR-based nanopore adaptive sequencing can increase the relative abundance and data yield of samples, and has higher sensitivity and shorter sequencing time for detecting SARS-CoV-2.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Veterinary Sciences
Jacqueline King, Anne Pohlmann, Kamila Dziadek, Martin Beer, Kerstin Wernike
Summary: Bovine viral diarrhea virus (BVDV) is a significant pathogen causing economic losses globally. The genetic variability of BVDV highlights the importance of whole-genome sequencing for identifying novel strains and supplementing missing sequence information in public repositories. The proposed amplicon-based sequencing protocol allows rapid, inexpensive, and accessible obtainment of complete BVDV genomes.
BMC VETERINARY RESEARCH
(2021)
Article
Infectious Diseases
Sonia Quddus, Zainab Liaqat, Sadiq Azam, Mahboob Ul Haq, Sajjad Ahmad, Metab Alharbi, Ibrar Khan
Summary: This study examined the expression of MexAB-OprM and MexCD-OprJ efflux pump genes in antibiotic-resistant Pseudomonas aeruginosa. A total of 200 samples were collected from two hospitals in Peshawar, Pakistan. The presence of antibiotic-resistant efflux pump genes was detected in 178 amoxicillin-clavulanic acid-resistant isolates, and mutations in these genes were found to potentially increase structural stability.
Article
Chemistry, Multidisciplinary
Na Zhao, Jiabao Cao, Jiayue Xu, Beibei Liu, Bin Liu, Dingqiang Chen, Binbin Xia, Liang Chen, Wenhui Zhang, Yuqing Zhang, Xuan Zhang, Zhimei Duan, Kaifei Wang, Fei Xie, Kun Xiao, Wei Yan, Lixin Xie, Hongwei Zhou, Jun Wang
Summary: Utilizing RNA sequencing and third-generation sequencing technology for pathogen identification can improve the ratio of microbial reads and accelerate clinical diagnosis, showing significant potential.
Article
Microbiology
Ellen C. Carbo, Igor A. Sidorov, Anneloes L. Van Rijn-Klink, Nikos Pappas, Sander van Boheemen, Hailiang Mei, Pieter S. Hiemstra, Tomas M. Eagan, Eric C. J. Claas, Aloys C. M. Kroes, Jutte J. C. de Vries
Summary: This study compares the performance of five taxonomic classifiers in detecting respiratory viruses, showing that their sensitivity and specificity are within acceptable ranges for clinical diagnosis. Data preprocessing and classification level can impact the performance.
Article
Microbiology
Mari Tohya, Kanae Teramoto, Shin Watanabe, Tomomi Hishinuma, Masahito Shimojima, Miho Ogawa, Tatsuya Tada, Yoko Tabe, Teruo Kirikae
Summary: The study compared different methods to identify Pseudomonas species and found that many of the clinical isolates, initially identified as P. putida or P. fluorescens, were misidentified. Whole-genome sequencing (WGS) and MALDI-TOF MS analysis revealed that these isolates actually belonged to different Pseudomonas species, including 9 novel species. The study suggests that WGS is the optimal method for Pseudomonas species identification, and MALDI-TOF MS has the potential to complement WGS.
MICROBIOLOGY SPECTRUM
(2022)
Article
Medical Laboratory Technology
Dong Zhang, Jingjia Zhang, Juan Du, Yiwen Zhou, Pengfei Wu, Zidan Liu, Zhunzhun Sun, Jianghao Wang, Wenchao Ding, Junjie Chen, Jun Wang, Yingchun Xu, Chuan Ouyang, Qiwen Yang
Summary: This study introduces a rapid and real-time bioinformatics pathogen identification solution using optimized internal index adaptors and a real-time analysis pipeline, which enables accurate pathogen identification in a short period of time.
CLINICAL CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Tara N. Furstenau, Tsosie Schneider, Isaac Shaffer, Adam J. Vazquez, Jason Sahl, Viacheslav Fofanov
Summary: With the growth of sequence databases and sequencing datasets, traditional alignment methods are no longer suitable for taxonomic classification of metagenomic reads. Existing methods sacrifice either speed or accuracy. To address this issue, a flexible new method called MTSv has been designed to balance efficiency and accuracy.
Article
Infectious Diseases
Slawomir Kubik, Ana Claudia Marques, Xiaobin Xing, Janine Silvery, Claire Bertelli, Flavio De Maio, Spyros Pournaras, Tom Burr, Yannis Duffourd, Helena Siemens, Chakib Alloui, Lin Song, Yvan Wenger, Alexandra Saitta, Morgane Macheret, Ewan W. Smith, Philippe Menu, Marion Brayer, Lars M. Steinmetz, Ali Si-Mohammed, Josiane Chuisseu, Richard Stevens, Pantelis Constantoulakis, Michela Sali, Gilbert Greub, Carsten Tiemann, Vicent Pelechano, Adrian Willig, Zhenyu Xu
Summary: This study aimed to establish clear and broadly applicable recommendations for reliable virus genotyping of SARS-CoV-2, finding that at least 1000 viral genomes are necessary to confidently detect variants in the genome. The broad applicability of the recommendations was validated in over 200 clinical samples, where genotype clustering by sampling location and period was observed.
CLINICAL MICROBIOLOGY AND INFECTION
(2021)
Article
Infectious Diseases
Jie Xu, Peng Zhou, Jia Liu, Lina Zhao, Hailong Fu, Qingzhen Han, Lin Wang, Weiwei Wu, Qiuxiang Ou, Yutong Ma, Jun He
Summary: Clinical metagenomic next-generation sequencing (mNGS) is a powerful diagnostic tool in pathogen detection. In this study, mNGS showed high sensitivity and accuracy in detecting pathogens in samples from patients suspected of having acute or chronic infections.
INFECTIOUS DISEASES AND THERAPY
(2023)
Review
Infectious Diseases
Kristel C. Tjandra, Nikhil Ram-Mohan, Ryuichiro Abe, Marjan M. Hashemi, Jyong-Huei Lee, Siew Mei Chin, Manuel A. Roshardt, Joseph C. Liao, Pak Kin Wong, Samuel Yang
Summary: Bloodstream infections are a major cause of death worldwide, and the lack of timely and reliable diagnostic practices is an ongoing issue. The current blood culture practice is time-consuming and cannot provide timely results. Therefore, there is an urgent need for new technologies that can offer accurate and timely diagnosis and susceptibility testing.
Article
Microbiology
Manuel Aira, Marcos Perez-Losada, Keith A. Crandall, Jorge Dominguez
Summary: Earthworms heavily modify the soil microbiome as they pass through their guts, with unique bacterial populations present in the soil, gut, and casts. This study highlights the importance of understanding soil microbial communities and their dynamics in nutrient cycles.
Article
Virology
Seble G. Kassaye, Zehava Grossman, Priyanka Vengurlekar, William Chai, Megan Wallace, Soo-Yon Rhee, William A. Meyer, Harvey W. Kaufman, Amanda Castel, Jeanne Jordan, Keith A. Crandall, Alisa Kang, Princy Kumar, David A. Katzenstein, Robert W. Shafer, Frank Maldarelli
Summary: By analyzing HIV sequences, virus load, and zip-code location, the transmission dynamics of HIV can be determined. The study found that HIV-1 viruses were transmitted between different regions, and the combination of HIV-1 viral load data and phylogenetic inferences can serve as an enhanced tool for contact tracing and guiding HIV treatment and prevention services.
Article
Multidisciplinary Sciences
Andrea Hahn, Aszia Burrell, Hollis Chaney, Iman Sami, Anastassios C. Koumbourlis, Robert J. Freishtat, Keith A. Crandall, Edith T. Zemanick
Summary: This retrospective observational study found that sub-therapeutic and broad-spectrum antibiotic exposure leads to a decrease in microbial diversity, but did not find a long-term association with better recovery of lung function.
SCIENTIFIC REPORTS
(2023)
Article
Medicine, General & Internal
Gabriella Shumyatsky, Aszia Burrell, Hollis Chaney, Iman Sami, Anastassios C. Koumbourlis, Robert J. Freishtat, Keith A. Crandall, Edith T. Zemanick, Andrea Hahn
Summary: This study conducted a stratified functional analysis of bacterial genes at three distinct time points during the treatment of exacerbations in cystic fibrosis patients. The results showed that the metabolic potential of bacterial species provides more insight into changes across clinical states.
FRONTIERS IN MEDICINE
(2023)
Correction
Marine & Freshwater Biology
Patricio R. De Los Rios-Escalante, P. Jara-Seguel, A. Contreras, M. Latsague, G. Lara, E. Rudolph, K. A. Crandall
Article
Environmental Sciences
Yoelvis Sulbaran-Bracho, Matias Orellana-Saez, Juan Castro-Severyn, Cristobal Galban-Malagon, Eduardo Castro-Nallar, Ignacio Poblete-Castro
Summary: More than 21,000 tons of diesel oil were accidentally released into the environment in 2020, with water bodies being the most contaminated. Sustainable technologies are urgently needed to clean up rivers and oceans in order to protect wildlife and human health. Bacterial consortia, especially those from Antarctic microorganisms, show promise in diesel degradation, but their effectiveness at higher temperatures compared to their natural habitats remains uncertain.
ENVIRONMENTAL POLLUTION
(2023)
Article
Microbiology
Marcos Perez-Losada, Eduardo Castro-Nallar, Jose Laerte Boechat, Luis Delgado, Tiago Azenha Rama, Valentin Berrios-Farias, Manuela Oliveira
Summary: Allergic rhinitis and asthma lead to dysbiosis of nasal bacteriome, which can be potential biomarkers for diagnostics and therapeutics. This study provides insights into the distinct bacteriota in the nose during health and respiratory diseases.
Article
Microbiology
Sergio Guajardo-Leiva, Katterinne N. Mendez, Claudio Meneses, Beatriz Diez, Eduardo Castro-Nallar
Summary: While progress has been made in studying microbial and viral communities in the oceans, the coastal waters of Northern Patagonia, particularly the Comau Fjord, remain understudied despite high-density salmon farming and other disturbances. In this study, the researchers found that the microbial and viral communities in the Comau Fjord were distinct from global surveys but shared similarities with cosmopolitan marine microbes and known viral members from North America and the southern oceans. They also discovered functional enrichment of antibiotic resistance genes (ARGs), indicating the potential impact of salmon farming and anthropogenic activities. These findings highlight the importance of further research on the diversity, resilience, and resistance of these communities.
Article
Microbiology
Eduardo Castro-Nallar, Valentin Berrios-Farias, Beatriz Diez, Sergio Guajardo-Leiva
Summary: This study provides 48 viral metagenomes and 5,656 viral operational taxonomic units (vOTUs) from Comau Fjord, Patagonia (42 degrees S), to understand viral-mediated processes in coastal and estuarine waters.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Microbiology
Eduardo Castro-Nallar, Valentin Berrios-Farias, Beatriz Diez, Sergio Guajardo-Leiva
Summary: This article presents a study on 93 metagenomes and 677 metagenome-assembled genomes (MAGs) from Comau Fjord, Patagonia (42 degrees S) to explore the microbial dynamics and their response to anthropogenic disturbances.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Microbiology
Sergio Guajardo-Leiva, Valentin Berrios-Farias, Felipe G. Bermudez, Eduardo Castro-Nallar
Summary: Sentinel species can be used to monitor environmental disturbances. In this study, 30 temporally explicit metagenomes and 166 metagenome-assembled genomes (MAGs) from the gut of South American sea lions were analyzed to assess whether changes in gut microbiome composition and gene content could indicate environmental disturbances from salmon farming.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Biochemistry & Molecular Biology
James P. Bernot, Christopher L. Owen, Joanna M. Wolfe, Kenneth Meland, Jorgen Olesen, Keith A. Crandall
Summary: This study investigates the phylogeny of the clade Pancrustacea, particularly focusing on the impact of taxon sampling on phylogenetic estimation. The researchers discover that small changes in taxon sampling can significantly affect the resulting phylogenetic trees. By comparing their results with previous studies, the researchers propose new relationships between certain taxa.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Review
Environmental Sciences
Claudia Egas, Cristobal Galban-Malagon, Eduardo Castro-Nallar, Marco A. Molina-Montenegro
Summary: The Arctic and the Antarctic Continent are two eco-regions with extreme climatic conditions. Anthropogenic pollution by semi-volatile organic compounds (SVOCs) in these polar ecosystems has been well-documented since the 1960s and continues to pose a threat to biodiversity and the ecosystem. Microorganisms in polar environments have the potential for biodegradation of SVOCs through a variety of genes encoding enzymes, making bioremediation by native microorganisms a feasible strategy to mitigate SVOCs presence. A comprehensive approach at the molecular and ecological level is required to address the slow degradation and accumulation of SVOCs in polar ecosystems, with implications for the preservation of these ecosystems at a global level.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Microbiology
Marcos Perez-Losada, Keith A. Crandall
Summary: The bacterial communities of the human skin vary across different skin regions and microenvironments, impacting the physiology and homeostasis of the skin. In this study, we surveyed five skin regions of 129 healthy adults and found significant differences in bacterial diversity and functional profiles among these regions. However, no significant differences were observed among genders, ages, and ethnicities. Furthermore, the bacterial diversity within skin regions also varied significantly across different years.
FRONTIERS IN MICROBIOLOGY
(2023)
Meeting Abstract
Zoology
M. Leray, B. N. Nguyen, S. Connolly, N. Knight, A. H. Altieri, G. Paulay, R. M. Lasley, F. Michonneau, W. O. McMillan, K. A. Crandall, N. Knowlton
INTEGRATIVE AND COMPARATIVE BIOLOGY
(2023)