Draft Genome Sequence of Serratia fonticola LMG 7882T Isolated from Freshwater.

Serratia fonticola is a Gram-negative bacterium with a wide distribution in aquatic environments. On some occasions, it has also been regarded as a significant human pathogen. In this work, we report the first draft genome sequence of an S. fonticola strain (LMG 7882(T)), which was isolated from freshwater.

GENOME ANNOUNCEMENT

The genus Serratia comprises Gram-negative, rod-shaped, facultative anaerobes in the family Enterobacteriaceae. Members of this genus have been associated with a variety of habitats, such as water, soil, insects, plants, and humans (1). The genus includes strains that cause important infections in humans and other animals, particularly strains belonging to the species Serratia marcescens and the so-called Serratia liquefaciens-like species (1). Serratia fonticola was described in 1979 by Gavini et al. and is a ubiquitous inhabitant of aquatic environments, particularly freshwater. This species differs considerably from other Serratia species in terms of its DNA G+C content and also because most strains ferment d-dulcitol and do not produce DNase and gelatinase. For these reasons, its classification within the Serratia genus has been questioned (2). However, using 16S rRNA gene sequence analysis, S. fonticola has been found to belong to this genus (1). The first human infection caused by S. fonticola was reported in 1989 in a patient who had been involved in a car accident (3). On that occasion, the bacterium was recovered in pure culture from a purulent leg abscess and from a blood culture bottle. Since then, S. fonticola has been regarded as a significant human pathogen to which a variety of infections have been attributed (4–7). To our knowledge, there is no record of an S. fonticola genome sequence in the public databases.

S. fonticola LMG 7882 (ATCC 29814) is the type strain of the species and was isolated from freshwater (8). The draft genome sequence of this strain is presented here.

Genome sequencing was carried out using the Genome Sequencer FLX 454 (Roche) with a fragment library, and 72,753,131 bp was produced. The sequences were extracted from the .sff file with the script “sff_extract_0_2_13” (http://bioinf.comav.upv.es/sff_extract/). The reads were evaluated using Quality Assessment Long Reads (9) to remove low-quality reads using an average Phred score of 20. After this process, a total of 249,830 reads (69,827,222 bp) remained, representing a coverage of ~12×.

A de novo assembly approach was conducted using the software MIRA (10) and produced 427 contigs. This set of sequences was reassembled using SeqMan NGen version 11 to identify and remove redundant sequences, curate conflicts between the alignments, and extend the sequences that present similarities in their ends. The final draft assembly contained 363 contigs. The estimated size of the genome is 5,895,861 bp, with an N50 of 49 kb and a G+C content of 54%. Annotation using the Rapid Annotations using Subsystems Technology (RAST) server (11) predicted 5,214 coding sequences (CDSs), 74 tRNAs, and 5 rRNAs.

The draft genome sequence of S. fonticola LMG 7882T will enable further studies with the aim of understanding the ecology, virulence potential, and antibiotic resistance of this species.

Nucleotide sequence accession numbers.

The S. fonticola LMG 7882T draft genome sequence has been deposited in GenBank under the accession no. AVAH00000000. The version described in this paper is version AVAH01000000.