ABSTRACT
We report here the draft genome sequence of Serratia marcescens ML2637, isolated from a South African pediatric patient in the intensive care unit with peritoneal cancer. The genome comprised 5,718,350 bp, with a 59.1% G+C content. There were 5,594 predicted genes, including 5,301 protein-coding genes, 199 pseudogenes, and 94 RNA genes.
GENOME ANNOUNCEMENT
Serratia marcescens is a motile, short, rod-shaped, Gram-negative, facultative anaerobic bacterium, classified in the large family Enterobacteriaceae. An Italian pharmacist discovered it on spoiled polenta in 1819 (1). Since then, S. marcescens is often found in the soil, water, and animals, as well as on plants (2, 3). Along with other opportunistic and nosocomial pathogens, S. marcescens is involved in hospital-acquired infections, particularly catheter-associated bacteremia and urinary tract and wound infections (4, 5). Here, we present the draft genome sequence of S. marcescens ML2637, recovered from a blood culture isolated from a 9-year-old patient with peritoneal cancer in the intensive care unit of an academic hospital in South Africa.
We sequenced the isolate because antimicrobial susceptibility testing showed that the isolate was phenotypically resistant to multiple classes of antibiotics. We therefore required confirmation with genotypic resistance.
Genomic DNA was extracted using the QIAamp DNA mini kit (QIAGEN, Germany). Paired-end libraries (2 × 300 bp) were prepared using the Nextera XT DNA sample preparation kit (Illumina, USA). Sequencing was performed on an Illumina MiSeq machine. The resulting paired-end reads (2,969,552 reads) were merged, quality trimmed, and de novo assembled using the Qiagen CLC Genomics Workbench version 10 (Qiagen, Netherlands). The assembly contains 224 contig sequences longer than 500 bp, comprising 5,718,350 bp with a G+C content of 59.1% and an N50 of 62,301 bp. All contigs were then submitted to GenBank, where gene annotation was implemented using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) (6). Among the 5,594 genes predicted by PGAP, 5,301 were protein-coding genes, 199 were pseudogenes, and 94 were RNAs (5 rRNAs [5S, 16S, and 23S], 74 tRNAs, and 15 ncRNAs). The annotation was further uploaded to the Rapid Annotations using Subsystems Technology (RAST) server for subsystems-based annotation (7–9). The RAST annotation assigned 4,117 genes (73.59%) into 591 subsystems, with the maximum number of genes associated with carbohydrates (14.84%), followed by metabolism of amino acids and derivatives (12.43%) and membrane transport (7.91%). By using ResFinder (10), several antibiotic resistance genes were found in this genome, including the beta-lactamase resistance genes blaSRT-2 and blaNDM-1, the tetracycline resistance genes tet(A) and tet(41), the aminoglycoside resistance genes rmtC and aac(6′)-Ic, the sulfonamide resistance gene (sul1), and the trimethoprim resistance gene (dfrA14).
Accession number(s).
This draft genome sequence has been deposited at NCBI GenBank under the accession number NDXU01000000.
ACKNOWLEDGMENTS
We thank Dr. Teena Thomas, Dr. Trusha Nana, Dr. Norma Bosman, and Dr. Vindana Chibabhai from the Infection Control Services Laboratory, Department of Clinical Microbiology and Infectious Diseases, Charlotte Maxeke Johannesburg Academic Hospital, and Dr. Warren Lowman from Vermaak and Partners Pathologists, Wits Donald Gordon Medical Centre, for submission of the isolate; Wilhelmina Strasheim, Cheryl Hamman, Ruth Mohlabeng, Rubeina Badat, Naseema Bulbulia, Rosah Mobokachaba, Marshagne Smith, Gloria Molaba, and Crystal Viljoen for assistance with the laboratory work; and Boniwe Makwakwa and Penny Crowther-Gibson for assistance with the database.
This work was funded by the National Institute for Communicable Diseases, and no external funding was obtained.
Footnotes
Citation Singh-Moodley A, Perovic O, Mtshali S, Ismail A, Allam M. 2017. Draft genome sequence of a multidrug-resistant Serratia marcescens strain, isolated from a patient with peritoneal cancer in South Africa. Genome Announc 5:e00580-17. https://doi.org/10.1128/genomeA.00580-17.
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