GENOME ANNOUNCEMENT {#h0.0}
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Here, the complete genome sequence of *Salmonella enterica* subsp. *enterica* serovar Typhimurium strain 33676 is presented. It was isolated in 2011 in Mexico City, Mexico, from a blood culture taken from a 15-year-old woman suffering a febrile illness with invasive severe pancolitis, which was refractory to therapy with extended-spectrum cephalosporins (M. Wiesner, J. J. Calva, V. H. Bustamante, D. Pérez-Morales, M. Fernández-Mora, E. Calva, and C. Silva, unpublished data). Strain 33676 was assigned to sequence type 213 (ST213), which is the predominant genotype recovered in Mexico since 2001 ([@B1], [@B2]), and it is multidrug resistant, expresses FljB H2-phase flagella, and displays attenuated virulence on mice (Wiesner et al., unpublished data).

Genomic DNA was extracted by standard protocols ([@B3]) and sheared into \~10-kb fragments for PacBio library preparation and P5-C3 sequencing on two SMRT cells. The continuous long reads were assembled using the HGAP/Quiver-protocol in SMRT Portal version 2.3.0.140936.p4 ([@B4]), resulting in an assembly with 4 contigs. These were circularized by trimming the terminal repeats with Minimus2 ([@B5]) and subjected to two consecutive rounds of read remapping with the RS_Resequencing.1 module for sequence polishing, resulting in a final assembly with a mean coverage of \~119×. The size of the assembled genome is 5,088,186 bp, with a G+C content of 52.13%, comprising a 4.81-Mb chromosome and three plasmids: a multidrug resistance pIncA/C (161.5 kb), a pIncF carrying the *bla*~CMY-2~ gene (112.6 kb), and a small plasmid (4.5 kb).

Gene calling and annotation were performed with a modified version of Prokka ([@B6]). A total of 5,032 genes, 4,767 coding sequences (CDSs), and 30 pseudogenes were identified, which is \~4× more pseudogenes than those found (*n* = 7) in the previously sequenced ST213 genome of strain YU39 ([@B1]). Additionally, genes for 85 tRNAs, 22 rRNAs, and 1 transfer-messenger RNA (tmRNA) were annotated, plus 127 noncoding RNAs (ncRNAs), 3 clustered regularly interspaced short palindromic repeat (CRISPR) arrays, 3 riboswitches, and 444 signal peptides. The annotation was manually curated, adding prophage predictions made by the PHAST server ([@B7]), and genomic islands were detected by IslandViewer 3 ([@B8]).

Four complete prophages were located on the chromosome: ST104, Gifsy-2, ST64B, and Gifsy-1, plus several phage remnants. Two class 1 integrons were found on the pIncA/C plasmid that contribute to the multidrug-resistant phenotype: integron In27 (*dfrA12*, *gcuF*, and *aadA12*), which was previously reported for other ST213 strains ([@B1], [@B2], [@B9]), is widespread in *Enterobacteriaceae* plasmids; and In1003 (*estX-3*, *psp*, *aadA2*, and *qacH2*), which is reported for *Escherichia coli* plasmids in the INTEGRALL database ([@B10]), was detected in this study for the first time in *Salmonella*. A third resistance region on the pIncA/C plasmid contains the *floR*, *tetA*, *tetR*, *strB*, *strA*, and *sul2* genes linked to an IS*CR2* element (SE15cs_04884) ([@B11]). Additionally, several efflux pumps were identified, including the resistance-nodulation-division (RND) multidrug efflux pump (OqxAB) found in the YU39 pIncA/C and other *Enterobacteriaceae* plasmids ([@B12]). The extended-spectrum cephalosporinase gene *bla*~CMY-2~ was confirmed to be located on the pIncF plasmid. The orientation of the invertible H segment containing the promoter of the *fljBA* operon explains H2 phase flagellin expression ([@B13]).

Nucleotide sequence accession numbers. {#s1}
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The complete sequences of the chromosome and the three plasmids of *Salmonella* Typhimurium strain 33676 are available in GenBank under accession numbers [CP012681](CP012681), [CP012682](CP012682), [CP012683](CP012683), and [CP012684](CP012684).

**Citation** Silva C, Calva E, Calva JJ, Wiesner M, Fernández-Mora M, Puente JL, Vinuesa P. 2015. Complete genome sequence of a human-invasive *Salmonella enterica* serovar Typhimurium strain of the emerging sequence type 213 harboring a multidrug resistance IncA/C plasmid and a *bla*~CMY-2~-carrying IncF plasmid. Genome Announc 3(6):e01323-15. doi:10.1128/genomeA.01323-15.

This study was supported by grants from CONACyT (179946 to E.C. and 179133 to P.V.) and DGAPA/UNAM (IN201513 to E.C. and IN211814 to P.V.).

We thank Francisco Javier Santana Estrada and Lucía Perezgasga Ciscomani for technical support; Guilin Wang from the Yale Center for Genome Analysis, Yale University, for skillfully performing the PacBio sequencing; and Eugenio López, Santiago Becerra, Paul Gaytán, and Jorge Yáñez from the Unidad de Síntesis y Secuenciación of the Instituto de Biotecnología, UNAM. We gratefully acknowledge Alfredo Hernández Álvarez from the Centro de Ciencias Genómicas, UNAM for help with server system administration.

[^1]: Present address: Magdalena Wiesner, Subdirección de Innovación, Dirección de Investigación en Salud Pública, Instituto Nacional de Salud, Bogotá, Colombia.
