No abstract

Acinetobacter baumannii has emerged as an important pathogen leading to multiple nosocomial outbreaks. Here, we describe the genomic sequence of a multidrug-resistant Acinetobacter baumannii sequence type 164 (ST164) isolate from a hospital patient in Sudan. To our knowledge, this is the first reported draft genome of an A. baumannii strain isolated from Sudan.

Pseudomonas aeruginosa is a common nosocomial pathogen often associated with a high mortality rate in vulnerable populations. Here, we describe the genomic sequence of a pan-resistant, high-risk clone of P. aeruginosa sequence type 111 (ST111) isolated from a hospital patient in Sudan.

Klebsiella pneumoniae is an opportunistic pathogen that accounts for a significant proportion of hospital-acquired infections and is a leading cause of nosocomial outbreaks. Here, we describe the genomic sequence of a highly resistant K. pneumoniae sequence type 14 (ST14) strain isolated from Sudan.

We report here the whole-genome sequence of Escherichia coli NUBRI-E, a representative of E. coli clone O25:H4 sequence type 131 with bla CTX-M-15 , which was obtained from a Sudanese patient with a urinary tract infection. E scherichia coli is the most common uropathogen associated with urinary tract infections globally, including Sudan (1-3). Uropathogenic E. coli (UPEC) strains harbor virulence factors, which are usually encoded on pathogenicity islands, providing a mechanism for coordinated horizontal transfer of virulence genes (4, 5). Furthermore, the presence of multidrug-resistant UPEC strains harboring several virulence factors is a major risk factor for inpatients (6). Here, we report the draft genome sequence of E. coli clone O25:H4 sequence type 131 (ST131) (NUBRI-E), which was isolated in Sudan.A urine sample was collected, via the clean-catch method, from a 22-year-old male patient who had been admitted to the Omdurman Teaching Hospital in Khartoum, Sudan, with a urinary tract infection. The specimen was inoculated directly onto MacConkey agar and then incubated overnight at 37°C under aerobic conditions. The colony was identified using Gram staining and biochemical tests, including the oxidase test, catalase test, Kligler's iron agar test, sulfide indole motility test, citrate agar test, and urea test. The Analytical Profile Index was used to confirm the species (7).The genomic DNA was extracted using a QIAamp DNA minikit (Qiagen, Germany). Paired-end libraries were prepared using the Nextera DNA Flex library preparation kit, followed by sequencing (2 ϫ 300 bp) on a MiSeq platform (Illumina, Inc., USA). The sequenced reads were quality trimmed using Sickle version 1.33 (https://github.com/ najoshi/sickle). Sickle was run using the following parameters: t sanger, q 20, and l 75. De novo assembly was performed using SPAdes version 3.11.1 (8). SPAdes was run using the parameter only-error-correction. All resultant contigs were then submitted to GenBank, where gene annotation was implemented using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) version 4.8 (9). Serotyping (O-antigen and flagellin genes) was performed with SerotypeFinder version 2.0 (10), multilocus sequence typing (MLST) with mlst (https://github.com/tseemann/mlst), and antibiotic resistance gene determination with ResFinder version 3.2 (11).A total of 1,777,192 sequencing reads were obtained. The assembled genome was composed of 156 contigs (55.6-fold coverage), all of which were longer than 200 bp (the longest contig was 511,930 bp), covering 5,239,013 bp, with a GC content of 50.7% and N 50 value of 182,864 bp. The NUBRI-E genome was found to harbor 5,050 proteincoding genes, 89 RNA genes, and 176 pseudogenes, as predicted by the NCBI PGAP. The O-and H-antigen types of NUBRI-E are O25 and H4, respectively. MLST based on the seven-allele scheme (E. coli scheme 1) indicated ST131. ResFinder was used to identify acquired antimicrobial resistance genes, with default parameter settings. Mul-Citation Mohamed SB, Hassan MM, Kambal S...