Comprehensive Genome Analysis of Acinetobacter baumannii

We extracted genomic DNA from all the presumptively identified Acinetobacter baumannii complex isolates, prepared double-stranded genomic DNA libraries, and sequenced the libraries on an Illumina platform as previously described (7 (link)). After preliminary analyses of the short-read whole-genome sequencing (WGS) data, we selected representatives of the different A. baumannii lineages identified in our data set and carried out long-read whole-genome sequencing of these isolates using the Oxford Nanopore technology to obtain completely assembled genomes for comprehensive analyses. Genomic DNA was reextracted from the selected isolates using the A&A Genomic Mini AX Bacteria+ kit (A&A Biotechnology, Gdańsk, Poland) to obtain less fragmented DNA. Long-read sequencing libraries were then generated using the Rapid Barcoding Sequencing kit (SQK-RBK004) and sequenced on a MinION Flow Cell (R9.4.1) with MinKNOW version 22.08.9 (Oxford Nanopore Technologies, Inc., Oxford, United Kingdom). We then carried out superaccuracy base calling and demultiplexing on the generated reads using Guppy version 6.3.8.

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Odih E.E., Oaikhena A.O., Underwood A., Hounmanou Y.M., Oduyebo O.O., Fadeyi A., Aboderin A.O., Ogunleye V.O., Argimón S., Akpunonu V.N., Oshun P.O., Egwuenu A., Okwor T.J., Ihekweazu C., Aanensen D.M., Dalsgaard A, & Okeke I.N. (2023). High Genetic Diversity of Carbapenem-Resistant Acinetobacter baumannii Isolates Recovered in Nigerian Hospitals in 2016 to 2020. mSphere, 8(3), e00098-23.

Publication 2023

Rapid Barcoding Sequencing kit MinION Flow Cell (R9.4.1)

Acinetobacter baumannii Bacteria Cell Genomic Genomic dna libraries Guppy

Corresponding Organization : University of Copenhagen

Other organizations : University of Oxford, University of Lagos, University of Ilorin, Obafemi Awolowo University Teaching Hospitals Complex, University College Hospital, Ibadan, Lancet Laboratories, Nigeria Centre for Disease Control

Top 5 similar protocols

Variable analysis

independent variables

Extraction of genomic DNA from presumptively identified Acinetobacter baumannii complex isolates
Preparation of double-stranded genomic DNA libraries
Sequencing of the libraries on an Illumina platform
Selection of representatives of different A. baumannii lineages for long-read whole-genome sequencing using Oxford Nanopore technology
Reextraction of genomic DNA from selected isolates using the A&A Genomic Mini AX Bacteria+ kit
Generation of long-read sequencing libraries using the Rapid Barcoding Sequencing kit (SQK-RBK004)
Sequencing on a MinION Flow Cell (R9.4.1) with MinKNOW version 22.08.9
Superaccuracy base calling and demultiplexing of the generated reads using Guppy version 6.3.8

dependent variables

Completely assembled genomes for comprehensive analyses

control variables

Presumptively identified Acinetobacter baumannii complex isolates

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