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Genome Announc. 2017 March; 5(10): e01764-16.
Published online 2017 March 9. doi:  10.1128/genomeA.01764-16
PMCID: PMC5347255

Draft Genome Sequence of a Multidrug-Resistant Nosocomial Serratia marcescens Strain That Persisted in a Hospital in Kemerovo, Russian Federation

ABSTRACT

Serratia marcescens is a frequent cause of health care-associated infections and has led to multiple outbreaks. Here, we report the draft genome of a multidrug-resistant S. marcescens strain 189 which was isolated in 2012 as a predominant clone in a neonatal hospital in Kemerovo.

GENOME ANNOUNCEMENT

Serratia marcescens is now recognized as an important nosocomial pathogen capable of causing health care-associated infections such as urinary tract infections, respiratory tract infections, bloodstream infection, and meningitis (1). Many clinical isolates of this organism display intrinsic or acquired resistance to a wide range of antibiotics due to the acquisition of chromosomal and plasmid-encoded genetic determinants (2).

Serratia marcescens strain 189 is one of the isolates belonging to a single clone that persisted in a neonatal hospital in Kemerovo (Russian Federation). This strain was isolated in 2012 from feces of a colonized newborn patient. A pure culture was obtained by growing the isolates on blood agar plates at 37°C. Bacteria from each individual colony were grown overnight in tryptic soy broth, pelleted by centrifugation at 5,000 g for 10 min, followed by phenol-chloroform genomic DNA extraction. Genomic DNA was used to construct a sequencing library employing a NEBNext Ultra DNA library prep kit (New England BioLabs, Ipswich, MA). Sequencing was performed on an Illumina MiSeq with the 301-cycle MiSeq reagent kit version 2, to achieve 50× average genome coverage. The quality of the raw sequence data was checked using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The raw data were prepared before assembly, including reads with low quality, high proportions of N, and adapter contamination, using Trimmomatic 0.33 (3). The resulting nucleotide sequences were assembled de novo using the SPAdes 3.7.0 software. One hundred one contigs with 5,149,784-bp total length were obtained. The N50 contig length was 30,882 bp and the largest contig assembled was 323,253 bp. The mean G+C content was 59.97%.

Genomic analysis was done using the RAST annotation server (4). The results obtained with RAST showed that there are 574 subsystems denoted in the chromosome, which represent only 58% of the assigned sequences. A total of 4,691 coding sequences (CDSs) and 103 structural RNAs (76 tRNAs) were predicted.

Genes related to antimicrobial resistance were identified, including variants of an aac(6′)-Ic variant, and those encoding an extended spectrum-β-lactamase blaCTX-M-15, blaTEM-1A, blaOXA-9, blaOXA-1, and dfrA14, linked with class I integrons.

Accession number(s).

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. MQRJ00000000. The version described in this paper is version MQRJ00000000.1.

ACKNOWLEDGMENTS

This work was supported by a grant of the Russian Federation fund of basic research (RFBR grant 16-34-01060 to D. Azarov).

The funders had no role in the study design, data collection, and interpretation, or the decision to submit the work for publication.

Footnotes

Citation Azarov D, Goncharov A, Karaseva A, Brodina T, Lebedeva E, Taranenko I, Feting A, Bakaev M, Brusina E, Zueva L. 2017. Draft genome sequence of a multidrug-resistant nosocomial Serratia marcescens strain that persisted in a hospital in Kemerovo, Russian Federation. Genome Announc 5:e01764-16. https://doi.org/10.1128/genomeA.01764-16.

REFERENCES

1. Rodrigues AP, Holanda AR, Lustosa GP, Nóbrega SM, Santana WJ, Souza LB, Coutinho HD 2006. Virulence factors and resistance mechanisms of Serratia marcescens. A short review. Acta Microbiol Immunol Hung 53:89–93. doi:.10.1556/AMicr.53.2006.1.6 [PubMed] [Cross Ref]
2. Iguchi A, Nagaya Y, Pradel E, Ooka T, Ogura Y, Katsura K, Kurokawa K, Oshima K, Hattori M, Parkhill J, Sebaihia M, Coulthurst SJ, Gotoh N, Thomson NR, Ewbank JJ, Hayashi T 2014. Genome evolution and plasticity of Serratia marcescens, an important multidrug-resistant nosocomial pathogen. Genome Biol Evol 6:2096–2110. doi:.10.1093/gbe/evu160 [PMC free article] [PubMed] [Cross Ref]
3. Bolger AM, Lohse M, Usadel B 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120. doi:.10.1093/bioinformatics/btu170 [PMC free article] [PubMed] [Cross Ref]
4. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O 2008. The RAST server: Rapid Annotations using Subsystems Technology. BMC Genomics 9:75. doi:.10.1186/1471-2164-9-75 [PMC free article] [PubMed] [Cross Ref]

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