Draft Genome Sequences of 19 Salmonella enterica Serovar Typhimurium [4,5:i:−] Strains Resistant to Nalidixic Acid from a Long-Term Outbreak in Italy

Abstract

Here, we present the draft genome sequences of 19 Salmonella enterica serovar Typhimurium monophasic variant [4,5:i:−] strains involved in a long-term salmonellosis outbreak that occurred in central Italy in 2013 to 2014.

Pediatric Epidemic of Salmonella enterica Serovar Typhimurium in the Area of L’Aquila, Italy, Four Years after a Catastrophic Earthquake

“…S. typhymurium strains were isolated from samples of surface waters and sewage plants, all obtained in the area of L’Aquila. Serotyping of the isolated strains showed that all of them could be identified as S. enterica serovar Typhimurium [4,5:i:-], monophasic variant [ 6 ]. As reported by Orsini et al , whole-genome sequencing was performed on 19 strains, which were chosen among clinical and environmental isolates because of their spatial-temporal distribution and familiar kinship, and three unrelated strains as outgroups.…”

“…As reported by Orsini et al , whole-genome sequencing was performed on 19 strains, which were chosen among clinical and environmental isolates because of their spatial-temporal distribution and familiar kinship, and three unrelated strains as outgroups. The genomic results, including numbers of coding sequences (CDSs), rRNAs, and tRNAs, N 50 values and GenBank accession numbers, have been published [ 6 ]. On the basis of the maximum-likelihood phylogenetic tree derived from the Single Nucleotide Polymorphism matrix of sequenced strains, a close relationship between the isolates of water sources and isolates from patients was suggested [ 11 ].…”

“…The strains were identified by multiplex polymerase chain reaction and typed by phage typing, pulsed-field gel electrophoresis (PFGE), and multiple-locus variable analysis (MLVA) following ECDC laboratory standard operating procedures [ 9 , 10 ]. Genomic DNA was extracted by Qiagen Easy Prep (Foster City, CA, USA), libraries were prepared using the Hi-Q sequencing kit, and sequencing was performed on a PGM Ion Torrent platform [ 6 ]. Raw reads were submitted to the SRA repository, and the samples were registered under the project ID PRJNA266093.…”

“…Raw reads were submitted to the SRA repository, and the samples were registered under the project ID PRJNA266093. Reads were trimmed and assembled using a de novo workflow under the Orione framework plus some specific python scripts [ 6 ].…”

“…The monophasic variant of S. typhimurium , S. 4,[5],12:i:-, characterized by the antimicrobial resistance to Ampicillin, Streptomycin, Sulphonamide, and Tetracycline (pattern ASSuT) is emerging and extensively circulating in Denmark, Italy, United Kingdom, and Greece [ 4 , 5 , 6 ]. In Italy, S. typhimurium 4,[5],12:i:-, showed a dramatic increase since 2003, both in humans and in animals farmed for food production, particularly pigs and bovines [ 7 ].…”