Article
Biochemistry & Molecular Biology
Luis Pineiro, Laura Villa, Paula Salmeron, Maria Dolores Macia, Luis Otero, Marti Vall-Mayans, Ana Milagro, Samuel Bernal, Ayla Manzanal, Inigo Ansa, Gustavo Cilla
Summary: This study assessed the dynamics of Chlamydia trachomatis infection transmission in Spain and its association with clinical and epidemiological variables. Genotype and sequence type distribution varied according to sex, sexual behavior, and geographical area. Sexual behavior was found to be an important factor in the transmission dynamics of C. trachomatis.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Microbiology
Shlomo Pilo, Gal Zizelski Valenci, Mor Rubinstein, Lea Pichadze, Yael Scharf, Zeev Dveyrin, Efrat Rorman, Israel Nissan
Summary: This study improved Bom's MLST scheme by using newly designed primers and stringent conditions, enhancing the detection performance for samples with low concentrations of Chlamydia DNA. A simple scoring scheme and flow chart were developed based on Real-Time PCR analysis values to identify reaction inhibitors and predict amplification success. The new MLST version showed great results in patients attending an STI clinic.
Article
Microbiology
Valentina A. Feodorova, Yury V. Saltykov, Anna A. Kolosova, Liudmila V. Rubanik, Nikolay N. Poleshchuk, Vladimir L. Motin
Summary: The study identified 12 different Chlamydia trachomatis sequence types (STs) among heterosexual chlamydia patients in seven regions of Belarus. The most common ST was ST4, followed by several other known and novel STs. The distribution of these STs varied across different regions. All detected CT strains were clustered into two groups characteristic of urogenital strains, and no STs specific to LGV strains were found.
Article
Immunology
Pao-Yu Chen, Yu-Chung Chuang, Jann-Tay Wang, Wang-Huei Sheng, Yee-Chun Chen, Shan-Chwen Chang
Summary: The study revealed the increasing prevalence of ST8/USA300 MRSA bacteremia in Asia, primarily in community settings. Patients with ST8/USA300 bacteremia had higher rates of diabetes, were more likely to come from long-term care facilities, and often had skin and soft tissue infections as their primary focus. Long-term surveillance is recommended to monitor the dissemination and pathogenicity of ST8/USA300 MRSA.
EMERGING MICROBES & INFECTIONS
(2021)
Article
Agriculture, Dairy & Animal Science
Chuncai Liang, Huan Cui, Ligong Chen, Hailong Zhang, Cheng Zhang, Juxiang Liu
Summary: This study investigated the antimicrobial resistance and prevalence of Escherichia coli (E. coli) in broiler chickens in Hebei Province. The results showed that ampicillin resistance was the highest, while meropenem resistance was the lowest. There was a serious problem of multidrug resistance in both types of broiler farms.
Article
Microbiology
Alicia C. Bertolotti, Eva Forsgren, Marc O. Schaefer, Fabrice Sircoulomb, Nicolas Gaiani, Magali Ribiere-Chabert, Laurianne Paris, Pierrick Lucas, Claire de Boisseson, Joakim Skarin, Marie-Pierre Riviere
Summary: This study introduces a standardized and robust cgMLST scheme for typing P. larvae, which allows for high-resolution differentiation and successful outbreak tracking. Compared to traditional MLST methods, cgMLST can provide finer differentiation of samples and maintains high stability and standardization for sharing results and methods across different laboratories.
ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Infectious Diseases
Cindy Shuan Ju Teh, Polly Soo Xi Yap, Noorfatin Jihan Zulkefli, Prasanna Subramaniam, Pik San Sit, Zhi Xian Kong, Chun Wie Chong, Kumutha Malar Vellasamy, Vanitha Mariappan, Sasheela Ponnampalavanar, Jamuna Vadivelu
Summary: The study conducted MLST analysis on B. pseudomallei strains in Malaysia, revealing a high diversity of sequence types and indicating localized evolution giving rise to new STs, with host and environmental factors playing a crucial role in the evolutionary changes of B. pseudomallei.
TRANSBOUNDARY AND EMERGING DISEASES
(2022)
Article
Microbiology
Kiyoharu Fukushima, Yuki Matsumoto, Takanori Matsuki, Haruko Saito, Daisuke Motooka, Sho Komukai, Eriko Fukui, June Yamuchi, Tadayoshi Nitta, Takayuki Niitsu, Yuko Abe, Hiroshi Nabeshima, Yasuharu Nagahama, Takuro Nii, Kazuyuki Tsujino, Keisuke Miki, Seigo Kitada, Atsushi Kumanogoh, Shizuo Akira, Shota Nakamura, Hiroshi Kida
Summary: To determine the treatment strategy for nontuberculous mycobacterial pulmonary disease, a simplified workflow involving direct sequencing of mycobacterial cultures was developed. The direct MGIT-seq method achieved accurate identification of species and subspecies as well as detection of drug resistance, making it a valuable tool for clinical practice.
JOURNAL OF CLINICAL MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Stefano Ravaioli, Davide Campoccia, Werner Ruppitsch, Franz Allerberger, Alessandro Poggi, Emanuele Chisari, Lucio Montanaro, Carla Renata Arciola
Summary: This study evaluated the usefulness of automated ribotyping as a screening tool for identifying S. aureus genetic lineages. Results showed that automated ribotyping can predict spa and MLST clonal complexes, but its high cost and lower discriminatory power could be obstacles for fine genotyping analysis. However, automated ribotyping has advantages such as automation, ease of execution, stability, typeability, and reproducibility, making it a reliable method to be used alongside gold standard methods.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Agriculture, Dairy & Animal Science
Jianfei Zhao, Rui Liu, Yanpeng Sun, Xiaojun Yang, Junhu Yao
Summary: This study revealed the potential safety hazards of commercial probiotic enterococci in China, particularly the presence of vancomycin-resistant Enterococcus (VRE). It also showed that there is a risk of horizontal transmission of VRE from feed to food.
Article
Cell Biology
Benshak J. Audu, Strachan Norval, Lopes Bruno, Ramjee Meenakshi, Macrae Marion, Ken J. Forbes
Summary: This study in Nigeria investigated the genomic diversity and antimicrobial resistance profile of Campylobacter in humans and livestock, finding a higher prevalence of resistance in Campylobacter isolated from livestock compared to humans. The results contribute to the understanding of the epidemiology of thermophilic Campylobacter in Nigeria.
JOURNAL OF BIOMEDICAL SCIENCE
(2022)
Article
Food Science & Technology
Fuat Aydin, Tuba Kayman, Secil Abay, Harun Hizlisoy, Izzet Burcin Saticioglu, Emre Karakaya, Orhan Sahin
Summary: This study investigated the genetic diversity, prevalence, and mechanisms of resistance to quinolone antibiotics in 178 Campylobacter jejuni isolates from humans, cattle, dogs, and chickens in Turkey. The results showed that there were 21 clonal complexes (CCs) and 78 different sequence types (STs) among the isolates, with CC21, CC353, CC206, and CC257 being the predominant clones. Quinolone resistance was detected in 41% of the isolates, and all resistant isolates had a specific mutation in the gyrA gene. The study provided important insights into the transmission pathways of C. jejuni in Turkey, suggesting that broiler meat and dogs may be the most important sources of human campylobacteriosis in the country.
INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY
(2023)
Article
Infectious Diseases
Pamela Barbadoro, Daniela Bencardino, Elisa Carloni, Enrica Omiccioli, Elisa Ponzio, Rebecca Micheletti, Giorgia Acquaviva, Aurora Luciani, Annamaria Masucci, Antonella Pocognoli, Francesca Orecchioni, Marcello Mario D'Errico, Mauro Magnani, Francesca Andreoni
Summary: This study found a high prevalence of CPE in patients upon their admission, with over 50% of the strains being multidrug-resistant. The most prevalent plasmid profile was FIIK, FIB KQ (33%) and the most common sequence type was ST512.
Article
Agriculture, Dairy & Animal Science
Xinyuan Zhao, Wei Li, Shaopeng Hou, Yanjun Wang, Shuyang Wang, Jing Gao, Ruihua Zhang, Shijin Jiang, Yanli Zhu
Summary: In this study, an epidemiological investigation was conducted on drug resistance of 110 Salmonella strains isolated from multiple duck farms in Shandong Province and surrounding areas, China. The study found high rates of multidrug resistance and detected multiple drug resistance genes. The results also revealed the important role of class I integrons and plasmids in the transmission of drug resistance genes.
Article
Microbiology
Antonella Migliaccio, James Bray, Michele Intoccia, Maria Stabile, Giovanni Scala, Keith A. Jolley, Sylvain Brisse, Raffaele Zarrilli
Summary: This study evaluated the classification consistency and discriminatory power of different typing methods using a large database of non-baumannii Acinetobacter genomes.
FRONTIERS IN MICROBIOLOGY
(2023)
Correction
Multidisciplinary Sciences
Julia Bespyatykh, Egor Shitikov, Andrei Guliaev, Alexander Smolyakov, Ksenia Klimina, Vladimir Veselovsky, Maya Malakhova, Georgij Arapidi, Marine Dogonadze, Olga Manicheva, Dmitry Bespiatykh, Igor Mokrousov, Viacheslav Zhuravlev, Elena Ilina, Vadim Govorun
SCIENTIFIC REPORTS
(2020)
Article
Biochemical Research Methods
Elizaveta V. Starikova, Polina O. Tikhonova, Nikita A. Prianichnikov, Chris M. Rands, Evgeny M. Zdobnov, Elena N. Ilina, Vadim M. Govorun
Article
Medicine, General & Internal
I. Maev, D. N. Andreev, V. M. Govorun, E. N. Ilina, Yu A. Kucheryavyy, T. S. Oganesian, E. Melnikova, O. Zayratyants, T. Parfenova, L. Dzhedzheia, N. Kirillova, E. A. Maevskaya, A. K. Fomenko, E. G. Lobanova, A. Zaborovskii, K. A. Kriukov
TERAPEVTICHESKII ARKHIV
(2020)
Article
Infectious Diseases
Fermin Acosta, Anders Norman, Dilcia Sambrano, Victoria Batista, Igor Mokrousov, Egor Shitikov, Julio Jurado, Maritza Mayrena, Odemaris Luque, Maybis Garay, Laura Solis, Patricia Munoz, Dorte B. Folkvardsen, Troels Lillebaek, Laura Perez-Lago, Amador Goodridge, Dario Garcia de Viedma
Summary: This study identified a specific Beijing strain in the Panamanian province of Colon, showing increased virulence and resistance, likely introduced from Vietnam between 2000 and 2012. The strain is predominant in the province, but has low number of cases caused by recent transmission.
TRANSBOUNDARY AND EMERGING DISEASES
(2021)
Article
Biochemical Research Methods
Alexander Manolov, Dmitry Konanov, Dmitry Fedorov, Ivan Osmolovsky, Rinat Vereshchagin, Elena Ilina
PLOS COMPUTATIONAL BIOLOGY
(2020)
Article
Infectious Diseases
Julia Bespyatykh, Dmitry Bespiatykh, Maja Malakhova, Ksenia Klimina, Andrey Bespyatykh, Anna Varizhuk, Anna Tevyashova, Tatiana Nikolenko, Galina Pozmogova, Elena Ilina, Egor Shitikov
Article
Virology
Maria Kornienko, Gleb Fisunov, Dmitry Bespiatykh, Nikita Kuptsov, Roman Gorodnichev, Ksenia Klimina, Eugene Kulikov, Elena Ilina, Andrey Letarov, Egor Shitikov
Article
Immunology
Vladimir A. Veselovsky, Marina S. Dyachkova, Egor A. Menyaylo, Polina S. Polyaeva, Evgenii Olekhnovich, Egor A. Shitikov, Dmitry A. Bespiatykh, Tatiana A. Semashko, Artem S. Kasianov, Elena N. Ilina, Valeriy N. Danilenko, Ksenia M. Klimina
FRONTIERS IN IMMUNOLOGY
(2020)
Article
Microbiology
D. Bespiatykh, J. Bespyatykh, I. Mokrousov, E. Shitikov
Summary: This study identified 79 regions with specificity at the species, lineage, or sublineage level within the MTBC through a thorough search for deletions in whole-genome sequencing data collection. Additionally, a new workflow called RDscan was developed to detect deletions and correlate the results with high-specificity RDs. The study contributes to a better understanding of species differentiation within the MTBC and provides valuable insights into the evolution of individual clusters within different MTBC species.
Article
Chemistry, Organic
Tatyana N. Makarieva, Lyudmila A. Romanenko, Konstantin S. Mineev, Larisa K. Shubina, Elena B. Guglya, Natalia I. Kalinovskaya, Natalia V. Ivanchina, Alla G. Guzii, Olga A. Belozerova, Sergey I. Kovalchuk, Roman S. Popov, Vladimir A. Denisenko, Valery V. Mikhailov, Vladislav V. Babenko, Elena N. Ilina, Maja V. Malakhova, Stanislav S. Terekhov, Arsen M. Kudzhaev, Pavel S. Dmitrenok, Ilia V. Yampolsky, Valentin A. Stonik
Summary: This article describes a new structural class of highly chlorinated antibiotics, streptocinnamides A and B, produced by the bacterium Streptomyces sp. KMM 9044 isolated from a sample of marine sediment collected in the northwestern part of the Sea of Japan. The structures of streptocinnamides A and B were determined using nuclear magnetic resonance and mass spectrometry studies and their inhibitory activity against various bacteria was demonstrated.
Article
Endocrinology & Metabolism
Elena V. Pokrovskaya, Elena S. Zhgun, Ekaterina A. Shestakova, Igor A. Sklyanik, Irina V. Fedushkina, Evgeniy I. Olekhnovich, Dmitry N. Konanov, Dmitry A. Kardonsky, Yurly V. Kislun, Ekaterina A. Sorokina, Lubov I. Zilberman, Natalia V. Zaytseva, Elena N. Ilina, Vadim M. Govorun, Marina V. Shestakova
Summary: Obesity and metabolic diseases are associated with changes in the gut microbiota. Fecal microbiota transplantation (FMT) is an effective method for correcting intestinal microflora and has been used to treat infections and certain metabolic disorders. However, limited and contradictory data exist regarding the application of FMT for metabolic disorders.
Article
Ecology
Danil V. V. Krivonos, Dmitry N. N. Konanov, Elena N. N. Ilina
Summary: The study of individual fungi and their communities is important in modern biology as they can be both beneficial producers and harmful pathogens. Functional capabilities of fungi are determined by gene content, which is often obtained through whole genome sequencing. However, whole genome sequencing of fungi is not commonly done, and amplicon sequencing of ITS region does not provide functional annotation. Here, we introduce FunFun, a tool that evaluates gene content from ITS sequencing data using a modified K-nearest neighbors algorithm. FunFun can be used to compare and estimate functional capabilities of fungi and accurately predict the most variable functions.
ECOLOGY AND EVOLUTION
(2023)
Article
Microbiology
Evgenii I. I. Olekhnovich, Artem B. B. Ivanov, Anna A. A. Babkina, Arseniy A. A. Sokolov, Vladimir I. I. Ulyantsev, Dmitry E. E. Fedorov, Elena N. N. Ilina
Summary: In this study, a list of potentially beneficial bacteria associated with melanoma immunotherapy responsiveness was compiled. Functional biomarkers of immunotherapy responsiveness were also identified and found to be dispersed among different bacterial species. These findings contribute to understanding the relationship between gut microbiome composition and treatment response, and have implications for the development of diagnostic tests and recommendations for gut microbiome correction in cancer immunotherapy.
Article
Multidisciplinary Sciences
Maria Kornienko, Nikita Kuptsov, Roman Gorodnichev, Dmitry Bespiatykh, Andrei Guliaev, Maria Letarova, Eugene Kulikov, Vladimir Veselovsky, Maya Malakhova, Andrey Letarov, Elena Ilina, Egor Shitikov
SCIENTIFIC REPORTS
(2020)
Article
Urology & Nephrology
Elena S. Kotova, Yulia A. Savochkina, Yuriy Doludin, Alexander O. Vasilyev, Elena A. Prilepskay, Natalia Potoldykova, Konstantin A. Babalyan, Alexandra Kanygina, Andrey O. Morozov, Alexander Govorov, Dmitry Enikeev, Elena S. Kostryukova, Elena N. Ilina, Vadim M. Govorun, Dmitry Y. Pushkar, Elena Sharova
RESEARCH AND REPORTS IN UROLOGY
(2020)