Article
Microbiology
Deyan Donchev, Ivan N. N. Ivanov, Ivan Stoikov, Stefana Sabtcheva, Yordan Kalchev, Marianna Murdjeva, Elina Dobreva, Rumyana Hristova
Summary: The study improved and extended the multi-locus VNTR analysis (MLVA) for strain-level differentiation of Klebsiella pneumoniae species complex. The modified scheme (MLVA8+) showed high concordance with classic MLST and provided greater differentiation capability. MLVA8+ also demonstrated its applicability in investigating the intra-hospital spread of carbapenem-resistant producers. It offers improved typing accuracy and extended typing scope for Klebsiella pneumoniae.
Article
Environmental Sciences
Markus Hoffmann, Martin A. Fischer, Bernd Neumann, Katja Kiesewetter, Ines Hoffmann, Guido Werner, Yvonne Pfeifer, Christoph Luebbert
Summary: A study in a German metropolitan area found carbapenemase-producing bacteria in hospital wastewater, wastewater treatment plants, and surface waters, including Klebsiella pneumoniae and Escherichia coli. These bacteria, carrying resistance genes, may pose a risk to human health and are potentially spreading through the urban water cycle.
SCIENCE OF THE TOTAL ENVIRONMENT
(2023)
Article
Public, Environmental & Occupational Health
C. Legouge, P. Bidet, M. Gits-Muselli, A. Cointe, C. Courroux, A. Birgy, S. Bonacorsi
Summary: This study evaluated a simple and rapid method of multi-locus variable number tandem repeat analysis (MLVA) as a screening tool to determine the relatedness of Klebsiella pneumoniae strains. The results showed that MLVA had a high discriminatory power and could be used for epidemiological investigation.
JOURNAL OF HOSPITAL INFECTION
(2023)
Article
Immunology
Morgane Nennig, Ann-Katrin Llarena, Malte Herold, Joel Mossong, Christian Penny, Serge Losch, Odile Tresse, Catherine Ragimbeau
Summary: A study on Campylobacter jejuni in Luxembourg revealed an unexpected endemic pattern in the genetic profiles, and tested the hypothesis of stable lineages occurrence by implementing whole genome sequencing (WGS). Results showed that regardless of the typing scheme used, epidemic or endemic signals were detected in the lineages, supporting the clonal expansion of stable genomes in the Campylobacter population.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Article
Microbiology
Chien-Shun Chiou, Ying-Shu Liao, Bo-Han Chen, Min-Chi Lu, Yu-Ping Hong, You-Wun Wang, Ru-Hsiou Teng
Summary: This study presents the demographic and genetic characteristics of invasive meningococcal disease (IMD) in Taiwan. The results show that IMD is rare in Taiwan, with NmB being the predominant serogroup responsible for the majority of cases. The study also highlights the effectiveness of cgMLST in comparing genetic relatedness among a large number of isolates.
MICROBIOLOGY SPECTRUM
(2022)
Article
Microbiology
Mostafa Y. Abdel-Glil, Prasad Thomas, Christian Brandt, Falk Melzer, Anbazhagan Subbaiyan, Pallab Chaudhuri, Dag Harmsen, Keith A. Jolley, Anna Janowicz, Giuliano Garofolo, Heinrich Neubauer, Mathias W. Pletz
Summary: This study describes a novel Brucella-wide cgMLST scheme that is applicable in Brucella molecular epidemiology and helps in accurately tracking and thus controlling the sources of infection.
JOURNAL OF CLINICAL MICROBIOLOGY
(2022)
Article
Food Science & Technology
Dan Wang, Graham C. Fletcher, Stephen L. W. On, Jon S. Palmer, Dragana Gagic, Steve H. Flint
Summary: This study evaluated the biofilm formation ability of Vibrio parahaemolyticus isolated from seafood related environments and found that biofilm cells were less susceptible to sodium hypochlorite. Polysaccharide production was found to be possibly correlated with sodium hypochlorite resistance. Genetic diversity played a role in the variation of biofilm formation between isolates.
INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY
(2023)
Article
Infectious Diseases
Katarina Pomorska, Vladislav Jakubu, Lucia Malisova, Marta Fridrichova, Martin Musilek, Helena Zemlickova
Summary: This study aimed to characterize methicillin-resistant Staphylococcus aureus (MRSA) isolates from the blood of hospitalized patients in the Czech Republic between 2016 and 2018. The majority of MRSA strains were found to be resistant to several antibiotics, with 52 different spa types identified in the analyzed strains. The CC5 clonal complex was predominant in this study, with other CCs such as CC398, CC22, CC8, CC45, and CC97 also present.
Review
Microbiology
Ana Abad-Fau, Eloisa Sevilla, Inmaculada Martin-Burriel, Bernardino Moreno, Rosa Bolea
Summary: This review provides a comprehensive overview of the current molecular typing techniques used in research and medical communities for Clostridioides difficile. The main objectives are to describe the key methods and highlight the epidemiological characteristics of prevalent strains worldwide. Geographically distinct regions exhibit different strain types, with notable consistency among different typing methods. Next-generation sequencing offers unprecedented opportunities for genomic analyses and understanding the transmission of C. difficile.
Article
Microbiology
Mariana Meneguzzi, Caroline Pissetti, Raquel Rebelatto, Julian Trachsel, Suzana Satomi Kuchiishi, Adrienny Trindade Reis, Roberto Mauricio Carvalho Guedes, Joice Aparecida Leao, Caroline Reichen, Jalusa Deon Kich
Summary: Clinical salmonellosis has been increasing significantly in Brazil, with a majority of strains demonstrating high rates of multi-drug resistance. The identification of a major Choleraesuis clonal group in several Brazilian states suggests closely related strains. This highlights the endemic nature of salmonellosis in key pig-producing regions in Brazil.
Article
Immunology
Jing-Jing Huang, Xin-Fei Chen, Clement K. M. Tsui, Chong-Jie Pang, Zhi-Dong Hu, Yi Shi, Wei-Ping Wang, Lan-Ying Cui, Yu-Ling Xiao, Jie Gong, Xin Fan, Ying-Xing Li, Ge Zhang, Meng Xiao, Ying-Chun Xu
Summary: In this study, we conducted molecular epidemiology and resistance analysis of multi-drug resistant R. mucilaginosa. The results showed the presence of an epidemic cluster strain that may be an opportunistic pathogen, as well as a possible clonal transmission phenomenon.
EMERGING MICROBES & INFECTIONS
(2022)
Article
Infectious Diseases
Frank Hansen, Lone Jannok Porsbo, Tove Havnhoj Frandsen, Ayse Nur San Kaygisiz, Louise Roer, Anna E. Henius, Barbara Juliane Holzknecht, Lillian Soes, Kristian Schonning, Bent L. Roder, Ulrik S. Justesen, Claus ostergaard, Esad Dzajic, Mikala Wang, Nina Ank, Paul G. Higgins, Henrik Hasman, Anette M. Hammerum
Summary: This study used whole genome sequencing (WGS) to characterize carbapenemase-producing Acinetobacter baumannii isolates from Danish patients. The study compared typing and epidemiological data to investigate the spread and origin of these isolates. The results showed that most of the isolates belonged to the international clone IC2 and the most prevalent carbapenemase gene was bla OXA-23. The study confirmed sporadic and travel-related introductions of these isolates to Danish hospitals, highlighting the need for continued vigilance.
INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS
(2023)
Article
Microbiology
Mini Kamboj, Tracy McMillen, Mustafa Syed, Hoi Yan Chow, Krupa Jani, Anoshe Aslam, Jennifer Brite, Brian Fanelli, Nur A. Hasan, Manoj Dadlani, Lars Westblade, Ahmet Zehir, Matthew Simon, N. Esther Babady
Summary: The study evaluated the potential of combining MLST with WGS for cost-saving routine C. difficile typing, showing high agreement between MLST and WGS. A two-step algorithm for routine typing yields significantly lower cost compared to routine use of WGS.
JOURNAL OF CLINICAL MICROBIOLOGY
(2021)
Article
Microbiology
I-Chen Li, Rayean Wu, Chung-Wen Hu, Keh-Ming Wu, Zeng-Weng Chen, Chung-Hsi Chou
Summary: Studies have shown that whole genome sequencing (WGS) has the highest resolution in distinguishing Salmonella enterica serovar Schwarzengrund strains compared to traditional methods like pulsed-field gel electrophoresis (PFGE), clustered regular interspaced short palindromic repeats (CRISPR), and multilocus sequence typing (MLST).
Article
Microbiology
Jose Paulo H. Sato, Amanda G. S. Daniel, Carlos A. G. Leal, David E. S. N. Barcellos, Roberto M. C. Guedes
Summary: This study evaluated the genetic diversity, distribution, evolution, and population structure of Brazilian Brachyspira hyodysenteriae strains. The results showed genetic relationships between the strains from different regions in Brazil and their relation to global isolates.
VETERINARY MICROBIOLOGY
(2022)
Letter
Rheumatology
Sindhu R. Johnson, Martin Aringer
ANNALS OF THE RHEUMATIC DISEASES
(2023)
Review
Biology
Ramon C. Hermida, Artemio Mojon, Jose R. Fernandez, Ramon G. Hermida-Ayala, Juan J. Crespo, Maria T. Rios, Manuel Dominguez-Sardina, Alfonso Otero, Michael H. Smolensky
Summary: Elevated asleep blood pressure and blunted sleep-time relative systolic blood pressure decline are significant prognostic markers of cardiovascular disease risk. Current hypertension guidelines overlook the importance of asleep blood pressure and recommend diagnosis based on office blood pressure measurements. Studies have shown that taking blood pressure-lowering medications at bedtime results in greater reduction of blood pressure and improved cardiovascular outcomes compared to morning intake.
CHRONOBIOLOGY INTERNATIONAL
(2023)
Article
Environmental Sciences
Jun Wu, David Danko, Ebrahim Afshinnekoo, Daniela Bezdan, Malay Bhattacharyya, Eduardo Castro-Nallar, Agnieszka Chmielarczyk, Nur Hazlin Hazrin-Chong, Youping Deng, Emmanuel Dias-Neto, Alina Frolova, Gabriella Mason-Buck, Gregorio Iraola, Soojin Jang, Pawel Labaj, Patrick K. H. Lee, Marina Nieto-Caballero, Olayinka O. Osuolale, Christos A. Ouzounis, Michael H. Perlin, Bharath Prithiviraj, Nicolas Rascovan, Anna Rozanska, Lynn M. Schriml, Torsten Semmler, Haruo Suzuki, Juan A. Ugalde, Ben Young, Johannes Werner, Maria Mercedes Zambrano, Yongxiang Zhao, Christopher Mason, Tieliu Shi
Summary: Microbes play a crucial role in maintaining ecological functions that support human health and city life in urban ecosystems. However, knowledge about the species and functions in urban environments is limited. In this study, we identified 732 novel bacterial species from 4728 samples collected from the mass transit system in 60 cities. The number of novel species was positively correlated with city population, and more species were found in skin-associated samples. We also discovered an increased presence of biosynthetic gene clusters in novel species.
ENVIRONMENTAL RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Roberto Del Amparo, Luis Daniel Gonzalez-Vazquez, Laura Rodriguez-Moure, Ugo Bastolla, Miguel Arenas
Summary: Genetic recombination is a common evolutionary mechanism that contributes to molecular diversity. However, its impact on protein folding stability has been less studied compared to point mutations. This study found that although recombination can affect multiple protein sites, it does not significantly increase the elimination of proteins due to insufficient stability compared to mutation events. Recombination disrupts epistatic interactions but does not reduce the overall stability of recombinant proteins. Instead, it amplifies the difference in stability between recombined proteins, leading to phenotypic diversity.
JOURNAL OF MOLECULAR EVOLUTION
(2023)
Article
Biochemistry & Molecular Biology
Filipa Moreira, Miguel Arenas, Arnaldo Videira, Filipe Pereira
Summary: Type IB topoisomerases are important targets for anticancer drugs as they relax the torsional stress associated with DNA metabolism. TOP1 and TOP1MT are two types of topoisomerases specific to the nucleus and mitochondria respectively, and their origin and evolution in chordates remain unknown.
JOURNAL OF MOLECULAR EVOLUTION
(2023)
Review
Genetics & Heredity
Luis Daniel Gonzalez-Vazquez, Miguel Arenas
Summary: SARS-CoV-2 has produced various molecular variants during its expansion in humans, leading to different transmissibility, disease severity, and resistance to treatments. Recent studies have investigated the molecular evolution of the virus and found that it evolves at a moderate rate with fluctuations over time. Recombination events between related coronaviruses were infrequent, and molecular adaptation varied among SARS-CoV-2 genes. Monitoring the molecular evolution of the virus is crucial for predicting phenotypic consequences and designing effective treatments.
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
Genetics & Heredity
Roberto Del Amparo, Miguel Arenas
Summary: Probabilistic phylogenetic tree reconstruction has traditionally been performed by selecting the best-fitting substitution model of molecular evolution. Recent studies have proposed that this step is unnecessary, leading to a debate in the field. However, in the case of protein sequences, the selection of a substitution model has a significant influence on phylogenetic tree reconstruction. Our analysis of real and simulated data shows that phylogenetic trees reconstructed using the best-fitting substitution model of protein evolution are the most accurate in terms of topology and branch lengths.
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)
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)