Complete Genome Sequencing of a Multidrug-Resistant and Human-Invasive Salmonella enterica Serovar Typhimurium Strain of the Emerging Sequence Type 213 Genotype

Abstract

Salmonella enterica subsp. enterica serovar Typhimurium strain YU39 was isolated in 2005 in the state of Yucatán, Mexico, from a human systemic infection. The YU39 strain is representative of the multidrug-resistant emergent sequence type 213 (ST213) genotype. The YU39 complete genome is composed of a chromosome and seven plasmids.

GENOME ANNOUNCEMENT

An epidemiological surveillance program in Mexico showed that Salmonella enterica serovar Typhimurium was the most frequently isolated serovar from human infections (1). The multilocus sequence type 213 (ST213) was assigned to more than half of the Typhimurium population. This genotype was associated with food animal samples, lacked the Salmonella virulence plasmid, and carried multidrug resistance IncA/C plasmids (2, 3). Most of the systemic infections recorded during the surveillance period were caused by ST213 strains. Strain YU39 was isolated from the blood culture of an 8-year-old child displaying hepatomegaly and thrombocytopenia (3). This strain was studied for its capacity for conjugative transfer of the resistance bla_CMY-2 gene through interactions between IncA/C and IncX1 plasmids (4).

Genomic DNA was extracted by standard protocols (5) and sheared into ~10-kb fragments for RSII-PacBio library preparation and P5-C3 sequencing. The continuous long read (CLR) data were assembled using the HGAP/Quiver protocol (SMRT portal version 2.2.0) (6). This resulted in an assembly containing eight contigs with ~70× genome coverage. A final polishing step was performed by remapping quality-filtered (7), 72-bp-long Illumina reads (n = 9,857,489, originating from a 200-bp paired-end library sequenced in a GAII instrument) and 454 GS FLX+ single-end reads (n = 58,117; mean length, 418.04) onto the assembly using BWA (8), increasing its coverage to >150×. The aligned reads were converted to BAM format with SAMtools (9), and passed down to Pilon (10) to correct for small indels and SNPs. SMRTview analysis of CLRs mapped at the contig ends in the SMRT portal revealed their circular structure. Terminal repeats were trimmed with Minimus2 (11). The total size of the resulting genome assembly is 5,190,370 bp, with a G+C content of 51.94%, consisting of a 4.89-Mb chromosome and seven plasmids (156.3, 88.9, 42.2, 5.1, 4.8, 4.2, and 2.7 kb). Gene calling and annotation was performed with a modified version of the Prokka annotation pipeline (12). A total of 5,216 genes were identified, including 89 tRNAs, 22 rRNAs, 1 transfer-messenger RNA (tmRNA), 174 noncoding RNAs (ncRNAs), and 4,930 coding sequences (CDSs). Three CRISPR-CAS repeats and 453 signal peptides were annotated. The annotation was manually curated and enriched with predictions from the PHAST server (13) to annotate prophages, and IslandViewer to annotate genomic islands (14).

Five complete prophages were located on the chromosome: ST104, Gifsy-2, P88-like, ST64B, and Gifsy-2, as well as several phage remnants. The three large plasmids of 156.3, 88.9, and 42.2 kb were assigned to the multidrug resistance pIncA/C, a phage-like plasmid, and the conjugative pIncX1, respectively. This is the first complete genome sequence of a Mexican pathogenic and multidrug-resistant Salmonella Typhimurium strain.

Nucleotide sequence accession numbers.

The complete genome sequences for the chromosome and the seven plasmids of Salmonella Typhimurium strain YU39 are available in GenBank under the accession numbers CP011428, CP011429, CP011430, CP011431, CP011432, CP011433, CP011434, and CP011435.