Article
Biochemistry & Molecular Biology
Anastasiya A. Kasimova, Sarah M. Cahill, Anna M. Shpirt, Aleksandra G. Dudnik, Mikhail M. Shneider, Anastasiya Popova, Andrey A. Shelenkov, Yuliya Mikhailova, Alexander O. Chizhov, Johanna J. Kenyon, Yuriy A. Knirel
Summary: The identification of a novel CPS biosynthesis gene cluster, KL139, in a multiply antibiotic resistant clinical isolate of A. baumannii provides insights for tailored treatment strategies. The CPS material from A. baumannii MAR-17-1041 was found to contain neutral carbohydrates, resembling K14 CPS but with distinct differences in the repeating unit structure.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Biochemistry & Molecular Biology
Anastasiya A. Kasimova, Aleksandra G. Dudnik, Alexander S. Shashkov, Mikhail M. Shneider, Alex Christofferson, Andrey A. Shelenkov, Yuliya V. Mikhailova, Johanna J. Kenyon, Yuriy A. Knirel
Summary: This study identified two acylated forms of a higher sugar called pseudaminic acid in the capsular polysaccharide (CPS) types of the pathogen Acinetobacter baumannii. The presence of a specific gene module determined the type of variant produced. The researchers discovered a novel gene module associated with a specific variant and determined the structure of the CPS. This study provides important insights into the pathogenic mechanism of A. baumannii.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Biochemistry & Molecular Biology
Anastasiya A. Kasimova, Nikolay P. Arbatsky, Jacob Tickner, Johanna J. Kenyon, Ruth M. Hall, Michael M. Shneider, Alina A. Dzhaparova, Alexander S. Shashkov, Alexander O. Chizhov, Anastasiya V. Popova, Yuriy A. Knirel
Summary: The whole genome sequences of two Acinetobacter baumannii clinical isolates, 48-1789 and MAR24, revealed that they carry different capsular polysaccharide biosynthesis gene clusters, KL106 and KL112 respectively. Both clusters are related to previously described ones and share certain genes. The structures of CPS material from both isolates are different, with the K112 unit containing an α-l-rhamnose side chain not found in the K106 structure.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Johanna J. Kenyon, Nikolay P. Arbatsky, Emma L. Sweeney, Yang Zhang, Sofya N. Senchenkova, Anastasiya Popova, Mikhail M. Shneider, Alexander S. Shashkov, Bin Liu, Ruth M. Hall, Yuriy A. Knirel
Summary: The KL55, KL74, and KL85 capsular polysaccharide biosynthesis loci in Acinetobacter baumannii are related and contain genes for L-Rhap and n-GlopA synthesis. Structural analysis revealed that K55 and K74 CPSs have similar core structures with differences in linkage patterns, while K85 CPS differs in the number of L-Rhap residues in the side chain. Additionally, each K locus includes fewer glycosyltransferase genes than necessary, suggesting some glycosyltransferases may have multifunctional roles in forming linkages.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Immunology
Jia-Ling Yang, Chia-Jui Yang, Yu-Chung Chuang, Wang-Huei Sheng, Yee-Chun Chen, Shan-Chwen Chang
Summary: This study found that KL2-type A. baumannii infection is associated with longer hospital stays, higher risk of pneumonia, and lower white blood cell counts. KL2 infection predicts higher mortality rate independently of other factors. Thrombocytopenia contributes to the effect of KL2 on mortality in bacteraemia.
EMERGING MICROBES & INFECTIONS
(2022)
Article
Microbiology
Nikolay P. Arbatsky, Anastasiya A. Kasimova, Alexander S. Shashkov, Mikhail M. Shneider, Anastasiya Popova, Dmitry A. Shagin, Andrey A. Shelenkov, Yuliya Mikhailova, Yurii G. Yanushevich, Ruth M. Hall, Yuriy A. Knirel, Johanna J. Kenyon
Summary: Bacteriophage therapy is an attractive innovative treatment for extensively drug resistant Acinetobacter baumannii infections, requiring knowledge of the chemical structures of CPS produced by the species to identify suitable phages for therapeutic cocktails.
MICROBIOLOGY SPECTRUM
(2022)
Article
Microbiology
Olga Y. Timoshina, Anastasiya A. Kasimova, Mikhail M. Shneider, Nikolay P. Arbatsky, Alexander S. Shashkov, Andrey A. Shelenkov, Yuliya V. Mikhailova, Anastasiya V. Popova, Ruth M. Hall, Yuriy A. Knirel, Johanna J. Kenyon
Summary: This article reports the isolation of a phage on an extensively antibiotic resistant A. baumannii isolate AB5001 that carries the KL3 CPS biosynthesis gene cluster predicting a K3-type CPS. The structure of the CPS isolated from AB5001 was determined to be a variant CPS form, K3-v1, lacking a specific sugar side chain. The presence of this sugar profoundly restricts the ability of the phage to digest the CPS.
MICROBIOLOGY SPECTRUM
(2023)
Article
Virology
Olga Yu Timoshina, Mikhail M. Shneider, Peter Evseev, Anastasia S. Shchurova, Andrey A. Shelenkov, Yulia Mikhaylova, Olga S. Sokolova, Anastasia A. Kasimova, Nikolay P. Arbatsky, Andrey S. Dmitrenok, Yuriy A. Knirel, Konstantin A. Miroshnikov, Anastasia Popova
Summary: The study focused on a novel pathogenic bacteriophage Aristophanes which can affect the sugar polysaccharide structure of A.baumannii strains, belonging to a new genus of the subfamily Beijerinckvirinae of the family Autographiviridae.
Article
Genetics & Heredity
Sarah M. Cahill, Ruth M. Hall, Johanna J. Kenyon
Summary: In this study, the authors provide an update to the reference sequence database for CPS typing in Acinetobacter baumannii, a critical bacterial pathogen. They also introduce a new version of the Kaptive code that enables prediction of CPS type based on specific gene combinations. The authors validate the updated database against publicly available genome assemblies and find that the majority of genomes can be accurately typed. However, poor sequence quality or the presence of insertion sequences can affect the confidence level of the typing result.
MICROBIAL GENOMICS
(2022)
Article
Biochemistry & Molecular Biology
Nikolay P. Arbatsky, Anastasiya Popova, Mikhail M. Shneider, Alexander S. Shashkov, Ruth M. Hall, Johanna J. Kenyon, Yuriy A. Knirel
Summary: The K87 capsular polysaccharide (CPS) isolated from Acinetobacter baumannii isolate LUH5547 consists of a branched heptasaccharide repeat containing various sugar residues. The structure of CPS, including a minor O-acetyl group, was determined through sugar analysis, chemical cleavages, and NMR spectroscopy. Enzyme functions coded by genes in the KL87 gene cluster were found to be consistent with the CPS structure.
CARBOHYDRATE RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Alena Y. Drobiazko, Anastasia A. Kasimova, Peter V. Evseev, Mikhail M. Shneider, Evgeniy I. Klimuk, Alexander S. Shashkov, Andrei S. Dmitrenok, Alexander O. Chizhov, Pavel V. Slukin, Yuriy P. Skryabin, Nikolay V. Volozhantsev, Konstantin A. Miroshnikov, Yuriy A. Knirel, Anastasia V. Popova
Summary: This study bioinformatically predicted and recombinantly produced several depolymerases encoded in the prophage regions of Acinetobacter baumannii genomes. These identified depolymerases showed multi-domain structures and were similar or identical to proteins in other A. baumannii genomes. The study also determined the specificity of two depolymerases to capsular polysaccharides (CPSs) of A. baumannii, and showed their potential as antibacterials against corresponding A. baumannii K types.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Organic
Diksha Rai, Suvarn S. Kulkarni
Summary: In this study, we successfully synthesized the tetrasaccharide repeating units of Acinetobacter baumannii strain 34 and O5, which have a common disaccharide motif [alpha-l-FucpNAc-(1 -> 4)-alpha-d-GalpNAcA], using a 2-azido-d-galacturonic acid derivative as the donor for the installation of 1,2-cis linkages. The total synthesis was achieved through relatively long linear sequences of 19 and 21 steps, with overall yields of 9.8% and 8.4%, respectively.
Article
Biochemistry & Molecular Biology
Olga Y. Timoshina, Anastasia A. Kasimova, Mikhail M. Shneider, Ilya O. Matyuta, Alena Y. Nikolaeva, Peter V. Evseev, Nikolay P. Arbatsky, Alexander S. Shashkov, Alexander O. Chizhov, Andrey A. Shelenkov, Yulia V. Mikhaylova, Pavel V. Slukin, Nikolay V. Volozhantsev, Konstantin M. Boyko, Yuriy A. Knirel, Konstantin A. Miroshnikov, Anastasia V. Popova
Summary: In this study, tailspike depolymerases (TSDs) from seven different Friunavirus phages were characterized and their specific cleavage mechanism on Acinetobacter baumannii capsular polysaccharides (CPSs) was established. The crystal structures of three TSDs were determined, and oligosaccharide fragments from degradation of various CPS types were identified. One recombinant TSD, APK09_gp48, showed significant reduction in mortality of Galleria mellonella larvae infected with A. baumannii of K9 capsular type. These findings contribute to a better understanding of phage-bacterial host interactions and the rational usage of lytic phages and phage-derived enzymes as antibacterial agents.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Microbiology
Janardhanaachari Roshini, L. Ponoop Prasad Patro, Sruthi Sundaresan, Thenmalarchelvi Rathinavelan
Summary: This article summarizes the multi-drug resistance and structural diversity of capsular polysaccharides in Acinetobacter baumannii. The K-antigens of A. baumannii exploit a specific pathway for their assembly and transport onto the outer membrane. The article also presents a digital repository of K-antigens and analyzes the marker proteins involved in the assembly and transportation.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Anastasiya A. Kasimova, Mikhail M. Shneider, Mikhail V. Edelstein, Alina A. Dzhaparova, Alexander S. Shashkov, Yuriy A. Knirel, Johanna J. Kenyon
Summary: The K98 capsular polysaccharide from Acinetobacter baumannii REV-1184 was characterized and found to have linear tetrasaccharide repeats with a unique structure compared to the K4 capsular polysaccharide. This difference is attributed to variations in the sequence of the polymerase responsible for biosynthesis.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Microbiology
Rafael Nakamura-Silva, Louise Cerdeira, Mariana Oliveira-Silva, Karen Regina Carim da Costa, Elder Sano, Bruna Fuga, Quezia Moura, Fernanda Esposito, Nilton Lincopan, Kelly Wyres, Andre Pitondo-Silva
Summary: This article reports on the analysis of Klebsiella pneumoniae strains isolated from hospitalized patients in Manaus, Brazil. The study found the presence of multidrug-resistant and highly virulent strains, with a diverse distribution of genetic sequences and clones.
ARCHIVES OF MICROBIOLOGY
(2022)
Article
Microbiology
Ben Vezina, Louise M. Judd, Fiona K. McDougall, Wayne S. J. Boardman, Michelle L. Power, Jane Hawkey, Sylvain Brisse, Jonathan M. Monk, Kathryn E. Holt, Kelly L. Wyres
Summary: The study identified the dynamics of Klebsiella pneumoniae strain transmission clusters within grey-headed flying fox colonies, including both intra- and inter-colony transmission, and highlighted gene flow between human clinical and flying fox isolates. Additionally, inter-species horizontal plasmid transmission was observed. The metabolic models generated showed no distinction in metabolic capabilities, instead being consistent with population structure and lineage.
ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Jane Hawkey, Ben Vezina, Jonathan M. Monk, Louise M. Judd, Taylor Harshegyi, Sebastian Lopez-Fernandez, Carla Rodrigues, Sylvain Brisse, Kathryn E. Holt, Kelly L. Wyres
Summary: KpSC is a group of Klebsiella bacteria that can cause opportunistic healthcare-associated infections in humans. Researchers generated strain-specific genome-scale metabolic models (GEMs) for 37 isolates, representing all seven taxa. These models revealed strain-specific differences within and between species.
Article
Infectious Diseases
Uduak A. Okomo, Saffiatou Darboe, Saikou Y. Bah, Abigail Ayorinde, Sheikh Jarju, Abdul Karim Sesay, Ngange Kebbeh, Abdou Gai, Tida Dibbasey, Mary Grey-Johnson, Kirsty Le Doare, Kathryn E. Holt, Joy E. Lawn, Beate Kampmann
Summary: In this study, we found a low prevalence of vertical transmission of maternal genital tract colonization in maternal-newborn pairs for early-onset neonatal sepsis in the West African context.
CLINICAL MICROBIOLOGY AND INFECTION
(2023)
Article
Biochemistry & Molecular Biology
Anastasiya A. Kasimova, Mikhail M. Shneider, Mikhail V. Edelstein, Alina A. Dzhaparova, Alexander S. Shashkov, Yuriy A. Knirel, Johanna J. Kenyon
Summary: The K98 capsular polysaccharide from Acinetobacter baumannii REV-1184 was characterized and found to have linear tetrasaccharide repeats with a unique structure compared to the K4 capsular polysaccharide. This difference is attributed to variations in the sequence of the polymerase responsible for biosynthesis.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Biochemistry & Molecular Biology
Alexander S. Shashkov, Anastasiya A. Kasimova, Nikolay P. Arbatsky, Sof'ya N. Senchenkova, Andrei V. Perepelov, Andrei S. Dmitrenok, Alexander O. Chizhov, Yuriy A. Knirel, Mikhail M. Shneider, Anastasia V. Popova, Johanna J. Kenyon
Summary: A structurally diverse capsular polysaccharide in Acinetobacter baumannii has been found to include a novel isomer with a unique configuration. The complete chemical structure of this CPS, designated K135, has been elucidated, shedding light on the complexity of CPS structures in this bacterial pathogen.
CARBOHYDRATE RESEARCH
(2023)
Article
Microbiology
Margaret M. C. Lam, Jonathan Koong, Kathryn E. Holt, Ruth M. Hall, Mehrad Hamidian
Summary: Plasmids in Acinetobacter species, which contribute to the spread of antibiotic resistance genes, were classified into 3 groups based on Rep protein domains, with 80 distinct types identified using nucleotide clustering. The study established a typing system that will aid in tracking plasmids and resistance genes, as well as identifying plasmids in other Acinetobacter species.
MICROBIOLOGY SPECTRUM
(2023)
Letter
Infectious Diseases
Margaret M. C. Lam, Kathryn E. Holt, Kelly L. Wyres
JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
(2023)
Article
Microbiology
Sydney L. L. Miles, Vincenzo Torraca, Zoe A. A. Dyson, Ana Teresa Lopez-Jimenez, Ebenezer Foster-Nyarko, Damian Lobato-Marquez, Claire Jenkins, Kathryn E. E. Holt, Serge Mostowy
Summary: By analyzing the genetic sequences of ST99 E. coli, we found that there are two subsets of strains, one with a virulence plasmid pINV and one without. The results of zebrafish infection experiments show that the virulence of ST99 E. coli is temperature-dependent. Furthermore, it was discovered that ST99 strains may have been virulent before the acquisition of pINV, indicating the importance of pINV in the dissemination of ST99 E. coli.
Article
Biochemical Research Methods
Ryan R. R. Wick, Louise M. M. Judd, Kathryn E. E. Holt
Summary: A perfect bacterial genome assembly requires improved long-read sequencing, assemblers, and polishers. By combining Oxford Nanopore Technologies long reads and Illumina short reads, we suggest using Trycycler long-read assembly, Medaka long-read polishing, Polypolish short-read polishing, and additional short-read polishing tools and manual curation. We also discuss potential challenges and provide an online tutorial for reference.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Genetics & Heredity
Ebenezer Foster-Nyarko, Hugh Cottingham, Ryan R. Wick, Louise M. Judd, Margaret M. C. Lam, Kelly L. Wyres, Thomas D. Stanton, Kara K. Tsang, Sophia David, David M. Aanensen, Sylvain Brisse, Kathryn E. Holt
Summary: Oxford Nanopore Technologies (ONT) sequencing has potential for genomic epidemiology and public health investigations of bacterial pathogens, but low base-call accuracy limits its reliability for critical tasks. In this study, we tested the accuracy of ONT-only assemblies for genotyping and cluster detection. We found that the SUP basecalling method performed the best, accurately identifying capsule type, multi-locus sequence type, and acquired antimicrobial resistance genes. However, cluster detection was challenging with ONT data.
MICROBIAL GENOMICS
(2023)
Article
Genetics & Heredity
Marit A. K. Hetland, Jane Hawkey, Eva Bernhoff, Ragna-Johanne Bakksjo, Hakon Kaspersen, Siren I. Rettedal, Arnfinn Sundsfjord, Kathryn E. Holt, Iren H. Lohr
Summary: Klebsiella pneumoniae ST17 is a globally disseminated clone that causes multidrug-resistant hospital infections. An outbreak of MDR ST17 occurred at a neonatal intensive care unit in Norway, with long-term colonization observed in the children even after discharge. The within-host evolution of ST17 during colonization showed stability with minimal genetic changes and persistent carriage of a specific plasmid. ST17 has diverse lineages with various AMR genes and virulence loci, but many strains do not acquire AMR. The non-human sources and human colonization may play a crucial role in severe infections.
MICROBIAL GENOMICS
(2023)
Article
Immunology
Vincenzo Torraca, Dominik Brokatzky, Sydney L. Miles, Charlotte E. Chong, P. Malaka De Silva, Stephen Baker, Claire Jenkins, Kathryn E. Holt, Kate S. Baker, Serge Mostowy
Summary: Shigella, including specific serotypes, can establish persistent infection in the zebrafish model. The O-antigen plays a crucial role in this process, and the serotype-associated effects observed in humans are also observed in zebrafish.
JOURNAL OF INFECTIOUS DISEASES
(2023)