Electronic Resource
Identification of Acinetobacter baumannii loci for capsular polysaccharide (KL) and lipooligosaccharide outer core (OCL) synthesis in genome assemblies using curated reference databases compatible with Kaptive
| العنوان: | Identification of Acinetobacter baumannii loci for capsular polysaccharide (KL) and lipooligosaccharide outer core (OCL) synthesis in genome assemblies using curated reference databases compatible with Kaptive |
|---|---|
| المؤلفون: | Wyres, KL, Cahill, SM, Holt, KE, Hall, RM, Kenyon, JJ |
| بيانات النشر: | MICROBIOLOGY SOC 2020-03 |
| نوع الوثيقة: | Electronic Resource |
| مستخلص: | Multiply antibiotic-resistant Acinetobacter baumannii infections are a global public health concern and accurate tracking of the spread of specific lineages is needed. Variation in the composition and structure of capsular polysaccharide (CPS), a critical determinant of virulence and phage susceptibility, makes it an attractive epidemiological marker. The outer core (OC) of lipooligosaccharide also exhibits variation. To take better advantage of the untapped information available in whole genome sequences, we have created a curated reference database of 92 publicly available gene clusters at the locus encoding proteins responsible for biosynthesis and export of CPS (K locus), and a second database for 12 gene clusters at the locus for outer core biosynthesis (OC locus). Each entry has been assigned a unique KL or OCL number, and is fully annotated using a simple, transparent and standardized nomenclature. These databases are compatible with Kaptive, a tool for in silico typing of bacterial surface polysaccharide loci, and their utility was validated using (a) >630 assembled A. baumannii draft genomes for which the KL and OCL regions had been previously typed manually, and (b) 3386 A. baumannii genome assemblies downloaded from NCBI. Among the previously typed genomes, Kaptive was able to confidently assign KL and OCL types with 100 % accuracy. Among the genomes retrieved from NCBI, Kaptive detected known KL and OCL in 87 and 90 % of genomes, respectively, indicating that the majority of common KL and OCL types are captured within the databases; 13 of the 92 KL in the database were not detected in any publicly available whole genome assembly. The failure to assign a KL or OCL type may indicate incomplete or poor-quality genomes. However, further novel variants may remain to be documented. Combining outputs with multilocus sequence typing (Institut Pasteur scheme) revealed multiple KL and OCL types in collections of a single sequence type (ST) representing each of the |
| مصطلحات الفهرس: | Journal Article |
| URL: | |
| الاتاحة: | Open access content. Open access content CC BY https://creativecommons.org/licenses/by/4.0 |
| Other Numbers: | UMV oai:jupiter.its.unimelb.edu.au:11343/245861 Wyres, K. L., Cahill, S. M., Holt, K. E., Hall, R. M. & Kenyon, J. J. (2020). Identification of Acinetobacter baumannii loci for capsular polysaccharide (KL) and lipooligosaccharide outer core (OCL) synthesis in genome assemblies using curated reference databases compatible with Kaptive. MICROBIAL GENOMICS, 6 (3), https://doi.org/10.1099/mgen.0.000339. 10.1099/mgen.0.000339 2057-5858 2057-5858 1315682243 |
| المصدر المساهم: | UNIV OF MELBOURNE From OAIster®, provided by the OCLC Cooperative. |
| رقم الانضمام: | edsoai.on1315682243 |
| قاعدة البيانات: | OAIster |
| الوصف غير متاح. |