RGAAT: A Reference-based Genome Assembly and Annotation Tool for New Genomes and Upgrade of Known Genomes

The rapid development of high-throughput sequencing technologies has led to a dramatic decrease in the money and time required for de novo genome sequencing or genome resequencing projects, with new genome sequences constantly released every week. Among such projects, the plethora of updated genome assemblies induces the requirement of versiondependent annotation files and other compatible public dataset for downstream analysis. To handlethese tasks in an efficient manner, we developed the reference-based genome assembly and annotation tool（RGAAT）, a flexible toolkit for resequencing-based consensus building and annotation update. RGAAT can detect sequence variants with comparable precision, specificity, and sensitivity to GATK and with higher precision and specificity than Freebayes and SAMtools on four DNAseq datasets tested in this study. RGAAT can also identify sequence variants based on cross-cultivar or cross-version genomic alignments. Unlike GATK and SAMtools/BCFtools, RGAAT builds the consensus sequence by taking into account the true allele frequency. Finally, RGAAT generates a coordinate conversion file between the reference and query genomes using sequence variants and supports annotation file transfer. Compared to the rapid annotation transfer tool（RATT）,RGAAT displays better performance characteristics for annotation transfer between different genome assemblies, strains, and species. In addition, RGAAT can be used for genome modification,genome comparison, and coordinate conversion. RGAAT is available at https://sourceforge.net/projects/rgaat/and https://github.com/wushyer/RGAAT;2 at no cost.

Epidemiological and comparative genomic analyses of Multidrug- Resistant Acinetobacter baumannii collected between 2020 and 2022 in Liaocheng City, Shandong Province, China

The emergence and prevalence of multidrug-resistant Acinetobacter baumannii(MRAB)poses a huge challenge to clinical treatment.To investigate the genetic and epidemiologic characteristics of MRAB in Liaocheng,China,and to explore potential resistance mechanisms,56 MRAB strains were collected from the clinical departments of seven hospitals in Liaocheng between 2020 and 2022.Molecular typing,antimicrobial resistance patterns,and epidemiological characteristics were determined by genome sequencing and comparative genome analysis.Sequence type(ST)540 was the most prevalent ST of the 56 MRAB in Liaocheng,and most strains(92.86%)were grouped into CC92.Core genome multilocus sequence typing subdivided the strains according to the number of allelic differences and could distinguish different outbreaks caused by ST540 isolates in the hospitals.All the isolates harbored blaOXA-23 and blaADC-25,and at least 92.86%of the isolates were resistant to 10 antibiotics.The major MRAB epidemic clone detected in Liaocheng was ST540,which was different from the results reported in other regions in China.Furthermore,several inter-hospital transmissions of ST540 isolates were observed.The findings highlight the urgent need for effective nosocomial infection control measures and the continuous surveillance of ST540 MRAB in Liaocheng.