Article
Microbiology
Hanako Fukano, Yuko Kazumi, Nobuya Sakagami, Nagatoshi Fujiwara, Manabu Ato, Satoshi Mitarai, Yoshihiko Hoshino
Summary: In this study, a novel species of slow-growing mycobacteria related to the Mycobacterium gordonae complex was discovered from respiratory samples of patients in Japan. The genomic and phenotypic characteristics of the isolates were analyzed, and it was proposed that they represent a new species named 'Mycobacterium kiyosense sp. nov.'
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2023)
Article
Microbiology
Guan Liu, Xia Yu, Jingjing Luo, Yanjie Hu, Lingling Dong, Guanglu Jiang, Fengmin Huo, Fen Wang, Qian Liang, Hairong Huang
Summary: A novel slow-growing scotochromogenic mycobacterial strain (24(T)) isolated from a Chinese male human's sputum was identified through phylogenetic analysis and genomic comparisons, and proposed to be named as Mycobacterium vicinigordonae sp. nov. based on its distinct phylogenetic, phenotypic, and chemotaxonomic features.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2021)
Article
Microbiology
Yuko Abe, Kiyoharu Fukushima, Yuki Matsumoto, Takayuki Niitsu, Hiroshi Nabeshima, Yasuharu Nagahama, Eri Akiba, Kako Haduki, Haruko Saito, Tadayoshi Nitta, Akira Kawano, Michio Tanaka, Takanori Matsuki, Daisuke Motooka, Kazuyuki Tsujino, Keisuke Miki, Shota Nakamura, Tetsuya Iida, Hiroshi Kida
Summary: A slowly growing mycobacteria, named Mycobacterium senriense sp. nov., was isolated from a patient with pneumonia, which is a novel species closely related to Mycobacterium avium complex.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2022)
Article
Microbiology
Yoshiaki Kawamura, Yuko Fujimoto, Ryo Kutsuna, Junko Tomida, Kei-ichi Yamamoto, Tohru Miyoshi-Akiyama, Miki Okuno, Yoshitoshi Ogura, Masao Matsuoka, Tatusya Kawaguchi, Hiroyasu Tsutsuki, Tomohiro Sawa
Summary: A novel species of spiral bacterium, Helicobacter kumamotonensis sp. nov., was isolated from the blood of a patient with diffuse large B-cell lymphoma. It is phylogenetically closely related to Helicobacter equorum but forms a distinct lineage. The human isolates can be distinguished from H. equorum by flagella type and biochemical characteristics.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2023)
Article
Microbiology
Peter Kuhnert, Isabelle Brodard, Lutz Schonecker, Hatice Akarsu, Henrik Christensen, Magne Bisgaard
Summary: 270 isolates identified as Taxon 39 of Bisgaard were obtained from veal calves at 11 independent Swiss fattening farms over 1 year. Genetic and phenotypic characterization placed the isolates into a new species within the genus Mannheimia, named Mannheimia pernigra sp. nov. based on whole genome sequences and biochemical markers.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2021)
Article
Microbiology
Lutz Schonecker, Philipp Schnydrig, Isabelle Brodard, Andreas Thomann, Andrew Hemphill, Sabrina Rodriguez-Campos, Vincent Perreten, Joerg Jores, Sonja Kittl
Summary: A novel Gram-stain-positive bacterium was isolated from different animals and tissues in Switzerland, and its genomes were obtained by sequencing. The bacteria were named as Trueperella pecoris sp. nov. based on their characteristics and presence in different livestock species.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2021)
Article
Microbiology
Moriyuki Hamada, Narumi Enomoto, Tomonari Yamashita, Masahiro Shimojima, Daiki Tanno, Noboru Ohana, Masahiro Toyokawa, Hiroki Takahashi, Takashi Yaguchi
Summary: Two novel actinobacteria were isolated from clinical specimens in Japan and their taxonomic positions were determined using various methods. The findings showed that these bacteria were closely related to members of the genus Nocardia, but had some phenotypic differences, indicating that they represent a new species within the genus Nocardia, named Nocardia sputorum sp. nov.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2023)
Article
Microbiology
Emma Allen-Vercoe, Michelle C. Daigneault, Sarah J. Vancuren, Kyla Cochrane, Lindsey L. O'Neal, Krithivasan Sankaranarayanan, Paul A. Lawson
Summary: The diversity of bacteria in biopsy material from colorectal cancer patients was studied. A new bacterium, strain CC70AT, was isolated from tissue samples and identified as a Gram-positive, strictly anaerobic, motile, rod-shaped bacterium. It was able to ferment formate but not acetate. Based on DNA analysis and 16S rRNA gene sequencing, strain CC70AT belongs to the Bacillota phylum and is closely related to Cellulosilyticum lentocellum and Cellulosilyticum ruminicola. This study proposes the name Holtiella tumoricola gen. nov., sp. nov. for this novel bacterium. The type strain is CC70AT (=DSM 27931T= JCM 30568T).
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2023)
Article
Microbiology
Fuxiang Li, Wenhua Zhao, Pei Zhu, Zhanhong Li, Jianling Song, Jianbo Zhu, Huafeng Gao
Summary: A novel strain ZY190618(T) was isolated from the nasal cavity of a cow with respiratory disease. Phylogenetic and phylogenomic analyses indicated that the strain belonged to the genus Moraxella and represented a new species named Moraxella nasibovis sp. nov. The strain showed high similarity to Moraxella nasovis CCUG 75922(T) and had distinct characteristics in terms of fatty acid composition, DNA G+C content, growth conditions, and major polar lipids.
CURRENT MICROBIOLOGY
(2023)
Article
Microbiology
Ju Hye Baek, Dong Min Han, Jeong Min Kim, Baolei Jia, Ji Young Jung, Che Ok Jeon
Summary: Two Gram-stain-negative, facultative aerobic, catalase- and oxidase-positive, and non-motile rod bacteria, strains BLT and W38(T), were isolated from soil and freshwater, respectively. They belong to a novel genus Tahibacter and are named Tahibacter soli and Tahibacter amnicola.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2023)
Article
Microbiology
Maxime Descartes Mbogning Fonkou, Cheikh Ibrahima Lo, Zouina Mekhalif, Melhem Bilen, Enora Tomei, Edmond Kuete Yimagou, Gregory Dubourg, Didier Raoult, Florence Fenollar, Pierre-Edouard Fournier
Summary: Culturomics has enhanced research on human microbiota by isolating previously uncultured bacterial species. A new bacterial species, Gemella massiliensis, was successfully isolated from a sputum sample of a healthy French man. This strain exhibits unique characteristics and genetic differences compared to its closest known species, Gemella bergeri.
ARCHIVES OF MICROBIOLOGY
(2021)
Article
Microbiology
Junko Tomida, Toru Akiyama-Miyoshi, Kaori Tanaka, Masahiro Hayashi, Ryo Kutsuna, Nagatoshi Fujiwara, Yoshiaki Kawamura
Summary: The study isolated eight spindle-shaped bacteria from clinical samples in Japan and investigated their taxonomic position, revealing their relationship with Fusobacterium nucleatum and its closely related species. Through phylogenetic and genomic analysis, a new species, Fusobacterium watanabei, was proposed based on distinctive characteristics and differential phenotypic properties.
Article
Microbiology
Minji Bang, Myung Kyum Kim, Hee-Young Jung
Summary: Two novel bacterial strains, BT175(T) and BT728(T), belonging to the genus Hymenobacter, were isolated from soil in the Republic of Korea. They were found to possess distinct molecular and biological characteristics.
ARCHIVES OF MICROBIOLOGY
(2022)
Article
Microbiology
Babacar Mbaye, Cheikh Ibrahima Lo, Niokhor Dione, Sarah Benabdelkader, Maryam Tidjani Alou, Samy Brahimi, Nicholas Armstrong, Stephane Alibar, Didier Raoult, Valerie Moal, Matthieu Million, Pierre-Edouard Fournier, Florence Fenollar
Summary: The two bacterial strains examined in this study were isolated from the stool of a healthy volunteer and the urine of a kidney transplant recipient, respectively. Through analysis of their morphology, biochemistry, and genomic characteristics, they were identified as new members of the Peptoniphilus genus and named Peptoniphilus coli sp. nov. and Peptoniphilus urinae sp. nov.
ARCHIVES OF MICROBIOLOGY
(2022)
Article
Microbiology
Hyejin Oh, Hyang Burm Lee, Myung Kyum Kim
Summary: Two novel bacterial strains, Hymenobacter lucidus and Hymenobacter nitidus, were isolated from soil in Gyeonggi province, Republic of Korea.
ARCHIVES OF MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Matus Dohal, Vera Dvorakova, Miluse Sperkova, Martina Pinkova, Andrea Spitaleri, Anders Norman, Andrea Maurizio Cabibbe, Erik Michael Rasmussen, Igor Porvaznik, Maria Skerenova, Ivan Solovic, Daniela Maria Cirillo, Juraj Mokry
Summary: The emergence and spread of drug-resistant tuberculosis pose a threat to public health. This study used whole genome sequencing to analyze the diversity, drug resistance mechanisms, and transmission chains of multidrug-resistant tuberculosis strains in the Czech Republic. The majority of drug-resistant strains belonged to the Beijing lineage, with some strains belonging to the Euro-American lineage. Cluster analysis revealed several clusters, with a majority located in the Prague region.
SCIENTIFIC REPORTS
(2022)
Article
Infectious Diseases
Giovanni Lorenzin, Floriana Gona, Simone Battaglia, Andrea Spitaleri, Francesca Saluzzo, Alberto Trovato, Federico di Marco, Paola Cichero, Anna Biancardi, Paola Nizzero, Barbara Castiglione, Paolo Scarpellini, Matteo Moro, Daniela Maria Cirillo
Summary: In this study, a hybrid long-read sequencing approach was used to fully characterise four extensively drug-resistant hypervirulent Klebsiella pneumoniae isolates. One of the isolates, the first of its kind in Italy, expressed NDM-1/5 and OXA-48 carbapenemases. The results revealed the presence of new high-risk K. pneumoniae clones that co-produced OXA-48, NDM-1, and NDM-5, posing a significant challenge to public health.
JOURNAL OF GLOBAL ANTIMICROBIAL RESISTANCE
(2022)
Editorial Material
Infectious Diseases
Annelies Van Rie, Timothy Walker, Bouke de Jong, Praharshinie Rupasinghe, Emmanuel Riviere, Veronique Dartois, Lindsay Sonnenkalb, Diana Machado, Sebastien Gagneux, Philip Supply, Viola Dreyer, Stefan Niemann, Galo Goig, Conor Meehan, Elisa Tagliani, Daniela Maria Cirillo
LANCET INFECTIOUS DISEASES
(2022)
Letter
Pharmacology & Pharmacy
Clara Sciorati, Rebecca De Lorenzo, Nicola I. Lore, Cristina Tresoldi, Daniela M. Cirillo, Fabio Ciceri, Angelo Corti, Angelo A. Manfredi, Patrizia Rovere-Querini
PHARMACOLOGICAL RESEARCH
(2023)
Article
Immunology
Francesca Nicola, Daniela M. Cirillo, Nicola I. Lore
Summary: This article reviews the current murine models for M. abscessus lung infection and their application in studying new therapeutic approaches. The murine models can be used to validate new targets and drugs and study the combinatorial regimens and dosage and administration of existing antibiotics. Additionally, the murine models can be used to develop new therapeutic approaches to modulate the host immune response and limit immunopathological damage.
Article
Genetics & Heredity
Edoardo Luigi Draetta, Dejan Lazarevic, Paolo Provero, Davide Cittaro
Summary: Through high-throughput sequencing techniques, we discovered that genes with high frequency of somatic mutations in common cancers and ancient evolutionary age are most likely to be involved in abnormal phenotypes and diseases. This provides new insights into the common origin of cancer and genetic diseases and improves the identification of new disease genes.
FRONTIERS IN GENETICS
(2023)
Article
Microbiology
Mehri Haeili, Samaneh Barmudeh, Maryam Omrani, Narges Zeinalzadeh, Hossein Samadi Kafil, Virginia Batignani, Arash Ghodousi, Daniela Maria Cirillo
Summary: This study investigated the incidence of carbapenem resistance among 104 clinical isolates of Escherichia coli and the genomic features of carbapenem resistant isolates. Four isolates were identified as carbapenem resistant E. coli and exhibited high susceptibility to colistin, nitrofurantoin, fosfomycin, and tigecycline. Molecular analysis revealed different sequence types and the presence of NDM carbapenemase gene in all carbapenem resistant isolates. Various amino acid substitutions were found in a colistin-carbapenem resistant isolate.
Article
Biochemistry & Molecular Biology
Giulia Unali, Giovanni Crivicich, Isabel Pagani, Monah Abou-Alezz, Filippo Folchini, Erika Valeri, Vittoria Matafora, Julie A. Reisz, Anna Maria Sole Giordano, Ivan Cuccovillo, Giacomo M. Butta, Lorena Donnici, Angelo D'Alessandro, Raffaele De Francesco, Lara Manganaro, Davide Cittaro, Ivan Merelli, Carolina Petrillo, Angela Bachi, Elisa Vicenzi, Anna Kajaste-Rudnitski
Summary: The interferon-induced transmembrane proteins (IFITM) inhibit endocytic viral entry by binding to phosphatidylinositol 3,4,5-trisphosphate (PIP3), which plays a key role in endosomal antiviral immunity. The level of PIP3 is closely correlated with the potency of endosomal IFITM restriction, and exogenous PIP3 enhances the inhibition of endocytic viruses. These findings elucidate cell-compartment-specific antiviral mechanisms and have potential relevance for the development of broadly acting antiviral strategies.
Article
Microbiology
Federico Di Marco, Andrea Spitaleri, Simone Battaglia, Virginia Batignani, Andrea Maurizio Cabibbe, Daniela Maria Cirillo
Summary: This study compared the performances of short-reads (SRS), long-reads (LRS), and hybrid-reads (HYBR) in various investigative tasks in Mycobacterium tuberculosis (MTB) genome analysis. The results showed that HYBR exhibited the best performance in genome coverage estimation and variant calling, and also had better assembly quality compared to SRS and LRS. Therefore, the use of HYBR technology can provide a comprehensive resolution of the MTB genome and achieve more accurate analysis results.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Immunology
Sophia B. Georghiou, Margaretha de Vos, Kavindhran Velen, Paolo Miotto, Rebecca E. Colman, Daniela Maria Cirillo, Nazir Ismail, Timothy C. Rodwell, Anita Suresh, Morten Ruhwald
Summary: Diagnostic development must be conducted alongside drug development to ensure the effectiveness of tuberculosis treatment. The lack of rapid molecular diagnostic options for certain drugs compromises the current treatment regimens. This article identifies the diagnostic gaps and proposes design priorities for next generation molecular assays to support appropriate treatment selection based on drug resistance and achieve End TB targets.
EMERGING MICROBES & INFECTIONS
(2023)
Article
Biochemical Research Methods
Davide Cittaro, Dejan Lazarevic, Giovanni Tonon, Francesca Giannese
Summary: scGET-seq is a method that profiles both euchromatin and heterochromatin simultaneously. It utilizes the combined action of transposase Tn5 and its hybrid form TnH, which specifically targets H3K9me3 domains. This article provides a step-by-step protocol for performing scGET-seq on single cells using a 103 Chromium Controller, including transposome preparation and validation, nuclei preparation and transposition, encapsulation, library preparation, sequencing, and data analysis.
Article
Microbiology
Michal Bar-Oz, Maria Carla Martini, Maria Natalia Alonso, Michal Meir, Nicola Ivan Lore, Paolo Miotto, Camilla Riva, Shiva K. Angala, Junpei Xiao, Catherine S. Masiello, Maria-Anna Misiakou, Huaming Sun, Justin K. Moy, Mary Jackson, Helle Krogh Johansen, Daniela Maria Cirillo, Scarlet S. Shell, Daniel Barkan
Summary: This study reveals that the sRNA B11 controls gene expression and virulence-associated phenotypes in Mycobacterium abscessus. Deletion of B11 increased pro-inflammatory signaling, virulence, and antibiotic resistance. Clinical isolates with B11 mutations or reduced expression were also identified. This is the first report on the role of sRNA in M. abscessus.
Article
Biology
Tommaso Lanciano, Aurora Savino, Francesca Porcu, Davide Cittaro, Francesco Bonchi, Paolo Provero
Summary: Biological networks are widely used in functional genomics to describe relationships between genes and proteins. Contrast subgraphs are an effective technique for comparing networks from different conditions or techniques. This study demonstrates the utility of contrast subgraphs in comparing gene and protein networks in breast cancer subtypes, transcriptomic and proteomic data, and protein-protein interaction networks in different cell lines.
Article
Respiratory System
Anca Vasiliu, Antonia Morita Iswari Saktiawati, Raquel Duarte, Christoph Lange, Daniela Maria Cirillo
Summary: Tuberculosis is one of the deadliest infectious diseases globally, and early and accurate diagnosis plays a crucial role in reducing its burden. However, the implementation of molecular diagnostic tests in resource-limited settings faces various challenges, which require innovative solutions.