An update to the database for Acinetobacter baumannii capsular polysaccharide locus typing extends the extensive and diverse repertoire of genes found at and outside the K locus
TLDR
A comprehensive update to the international CPS sequence typing database for A. baumannii is provided, increasing the utility of this resource for prediction of CPS type from WGS to assist with clinical surveillance, and/or the design and application of CPS-targeted therapies.Abstract:
Several novel non-antibiotic therapeutics for the critical priority bacterial pathogen, Acinetobacter baumannii, rely on specificity to the cell-surface capsular polysaccharide (CPS). Hence, prediction of CPS type deduced from genes in whole genome sequence data underpins the development and application of these therapies. In this study, we provide a comprehensive update to the A. baumannii K locus reference sequence database for CPS typing (available in Kaptive v. 2.0.1) to include 145 new KL, providing a total of 237 KL reference sequences. The database was also reconfigured for compatibility with the updated Kaptive v. 2.0.0 code that enables prediction of ‘K type’ from special logic parameters defined by detected combinations of KL and additional genes outside the K locus. Validation of the database against 8994 publicly available A. baumannii genome assemblies from NCBI databases identified the specific KL in 73.45% of genomes with perfect, very high or high confidence. Poor sequence quality or the presence of insertion sequences were the main reasons for lower confidence levels. Overall, 17 KL were overrepresented in available genomes, with KL2 the most common followed by the related KL3 and KL22. Substantial variation in gene content of the central portion of the K locus, that usually includes genes specific to the CPS type, included 34 distinct groups of genes for synthesis of various complex sugars and >400 genes for forming linkages between sugars or adding non-sugar substituents. A repertoire of 681 gene types were found across the 237 KL, with 88.4% found in <5% of KL. 3. Significance as a BioResource to the community New therapies that target the bacterial polysaccharide capsule (CPS) show promise as effective tools to curb the high mortality rates associated with extensively resistant A. baumannii; one of the world’s most troublesome Gram-negative pathogens. As important information about the CPS structure produced by an isolate can be extracted from Whole Genome Sequences (WGS), simple bioinformatic tools and definitive sequence databases are needed to facilitate robust prediction of CPS type from WGS data. Here, we provide a comprehensive update to the international CPS sequence typing database for A. baumannii, increasing the utility of this resource for prediction of CPS type from WGS to assist with clinical surveillance, and/or the design and application of CPS-targeted therapies. This study is expected to further inform epidemiological tracking efforts, as well as the design of therapeutics targeting the CPS, enhancing global efforts to identify, trace and treat infections caused by this pathogen. 4. Data summary The updated A. baumannii KL reference sequence database including 241 fully annotated gene clusters is available for download under Kaptive v. 2.0.1 at https://github.com/katholt/Kaptive. Genome assemblies, short read data, or GenBank records used as representative reference sequence for each K locus are listed in Supplementary Table S1, and are referenced within each entry in the A. baumannii KL reference sequence database. The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.read more
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Loss of a Branch Sugar in the Acinetobacter baumannii K3-Type Capsular Polysaccharide Due To Frameshifts in the gtr6 Glycosyltransferase Gene Leads To Susceptibility To Phage APK37.1
Olga Yu Timoshina,Anastasiya A. Kasimova,Mikhail N. 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 +10 more
TL;DR: In this paper , the authors reported the isolation of a phage on an extensively antibiotic resistant ST2 A. baumannii isolate AB5001 that carries the KL3 CPS biosynthesis gene cluster predicting a K3-type CPS.
Journal ArticleDOI
Phenotypic Characterization and Heterogeneity among Modern Clinical Isolates of Acinetobacter baumannii
Adam Valcek,Chantal Philippe,Clemence Whiteway,Etienne Robino,Kristina Nešporová,Mona Bové,Tom Coenye,Tim De Pooter,Wouter De Coster,Mojca Strazisar,Charles Van der Henst +10 more
TL;DR: A. baumannii is an opportunistic pathogenic bacterium prioritized by the WHO and CDC because of its increasing antibiotic resistance, leading to treatment failures as mentioned in this paper , and the hallmark of this pathogen is the high heterogeneity observed among isolates, due to a very dynamic genome.
Journal ArticleDOI
Complete chemical structure of the K135 capsular polysaccharide produced by Acinetobacter baumannii RES-546 that contains 5,7-di-N-acetyl-8-epipseudaminic acid.
Alexander S. Shashkov,Anastasiya A. Kasimova,Nikolay P. Arbatsky,Sof'ya N. Senchenkova,Andrei V. Perepelov,Andrey S. Dmitrenok,Alexander O. Chizhov,Yuriy A. Knirel,Mikhail N. Shneider,Anastasiya V. Popova,Johanna J. Kenyon +10 more
TL;DR: In this article , the complete chemical structure of this CPS, designated K135, was elucidated, and the CPS was found to have a branched tetrasaccharide K unit and to include the higher sugar as part of a 8ePse5Ac7Ac-(2 → 6)-α-Gal disaccharides branching from a →3)-α −D-GlcpNAc-(1 → 3)-β-D-glpcNAc(1→ main chain.
Journal ArticleDOI
Friunavirus Phage-Encoded Depolymerases Specific to Different Capsular Types of Acinetobacter baumannii
Olga Yu Timoshina,Anastasiya A. Kasimova,Mikhail N. Shneider,Ilya O. Matyuta,Alena Yu. 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,Anastasiya V. Popova +16 more
TL;DR: In this paper , the tailspike depolymerases (TSDs) encoded in genomes of six novel Friunaviruses, APK09, K14, K16, K37/K3-v1, K86, K127, and K128 were characterized.
Journal ArticleDOI
5,7-Diamino-3,5,7,9-tetradeoxynon-2-ulosonic Acids in the Capsular Polysaccharides of Acinetobacter baumannii
Yuriy A. Knirel,Anastasiya A. Kasimova,Nikolay P. Arbatsky,Mikhail N. Shneider,Anastasiya V. Popova,Fedor Brovko,Alexander S. Shashkov,S. N. Senchenkova,Andrei V. Perepelov,Anna M. Shpirt +9 more
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