We have sequenced 21 new genomes which encompass the phylogenetic diversity of salmonella, including strains of the previously unsequenced subspecies arizonae, diarizonae, houtenae, salamae, and indica as well as new diverse strains of subspecies enterica. The multiple genome sequence alignments of 17 global salmonella i 4,5,12. Whole genome sequence analysis of salmonella typhi. Typhimurium strain for which the complete genomic sequence has been determined. Complete genome sequence of salmonella enterica serovar typhimurium lt2 article pdf available in nature 46858. Salmonella enterica serovar typhimurium definitive phage type 104 dt104 has caused significant morbidity and mortality in humans and animals for almost three decades. The comparative studies of matched pairs included genomic microarray hybridizations using salmonella serovar typhimurium lt2 as a reference. Dublin have been reported in several countries including highincome countries. An indepth genomic comparison between the st3 isolate d23580 and the wellcharacterized st19 isolate 474 that causes gastroenteritis across the globe. The gene contains 1404 bases and encodes a 468 amino acid polypeptide, which is the same as for escherichia coli k12. Typhimurium strains stm00170 and stm05705 were generated by the online tool realphy using s. Jun 25, 2002 the presence of homologues of salmonella enterica sv. Sequencing the ends of a sample of these lambda clones ensures the correct melding of the genomic sequence by confirming linkage over many kilobases while also contributing information towards complete sequence of the genome.
Genome of salmonella enterica serovar typhi clinical. A phylogenetic tree based on homologue content, relative to lt2, was largely concordant with previous studies using. Oct 25, 2001 lateral transfer of genes is frequent, with 11% of the s. Differences in gene content among salmonella enterica serovar. A phylogenetic tree based on homologue content, relative to lt2, was largely. Chitinases are glycosyl hydrolases that catalyze the hydrolysis of the.
Frontiers salmonella serotyping using whole genome. Sequence searching and alignment for salmonella enterica and other microbial. Here, we present the complete 47,393bp genome sequence of the siphophage skate, which was isolated against s. The complete nucleotide sequence of the salmonella strain lt2 gnd gene for 6phosphogluconate dehydrogenase was determined. Draft genome sequences of salmonella enterica serovar. St3 and st19 vary by just 856 core genome singlenucleotide polymorphisms snps. Salmonella enterica lt2 type strain dsm 17058, atcc. This is the release of four single chitinase deletion mutants in salmonella enterica serovar. We sequenced the whole genomes of 103 salmonella isolates sampled between 1988 and 2003 from wildlife and exotic pet cases that were submitted to.
Genes of salmonella enterica serovar typhimurium lt2 expected to be specifically present in salmonella were selected using the basic local alignment search tool blast program. Genome sequencing and analysis of salmonella enterica subsp. Typhimurium, but important gaps in our knowledge remain. Differences in gene content among salmonella enterica. The ancestral strain st474 was originally isolated from the bowel of a calf with salmonellosis and used by bruce stocker to generate a histidine auxotroph named sl44. It is clear that a precise choreography of gene expression is required for salmonella infection, but basic genetic information such as the global locations of transcription start. Genes acquired by salmonella enterica during its evolution may have important roles in human infection. Until recently, traditional serology and the kauffmann white scheme kws have been the gold standard for salmonella serotyping. We sequenced the whole genomes of 103 salmonella isolates sampled between 1988 and 2003. Complete genomic sequence of the virulent salmonella 2003. Whole genome sequence analysis of salmonella typhi isolated. Salmonella serotyping using whole genome sequencing frontiers.
Sty ct18 is a multipledrugresistant isolate recovered from a typhoid fever patient from vietnam in 1993 18. Outbreaks of serovar virchow are a significant public health risk in many european, asian and oceanic countries 3, 58. The invasome of salmonella dublin as revealed by whole. Typhimurium bacteria isolated from humans exhibit wideranging virulence phenotypes in inbred mice, leading to speculation that some strains are more virulent in nature. Rabaa 3,5, phat voong vinh 3, tuyen ha thanh 3, guy e.
Virchow is one of most prevalent salmonella serovars in. The genome of a multidrugresistant mdr salmonella enterica subsp. Among the 21 new genomes, two strains were selected from each of the five previously unsequenced subspecies. The selected 152 genes of salmonella serovar typhimurium lt2 were compared using blast with each genomic sequence of 11 salmonella strains including s.
Genome analysis and crispr typing of salmonella enterica. The generation of complete genome sequences provides a blueprint that facilitates the genetic. Genetic boundaries to delineate the typhoid agent and other. Salmonella enterica is a common cause of minor and large food borne outbreaks. Pdf complete genome sequence of salmonella enterica serovar. Salmonella typhimurium strain lt2 sgsc1412 atcc 700720. Subsequently, suppression subtractive hybridization ssh libraries were constructed using salmonella serovar typhimurium lt2 as the driver and epidemic strains as the tester sequences. Complete genome sequence of salmonella enterica serovar. Analyze gene expression, metabolomics, and chipchip data sequence searching and alignment for salmonella enterica and other microbial genomes. Cerro isolates, including 16 from cattle operations in new york ny state, 2 from human clinical cases from ny in 2008, and 8 from diverse animal sources 7 from washington state and 1 from florida.
The 152 selected genes were compared with 11 genomic sequences of salmonella serovars, including salmonella enterica subsp. Groisman,2 and howard ochman1 department of chemistry and biochemistry, university of arizona, tucson, arizona,1 and howard hughes medical institute. These enzymes are considered emerging virulence factors during infection because the host glycan changes. Complete genome sequence of salmonella enterica serovar ncbi. Genome of salmonella enterica serovar typhi clinical infectious. Whole genome sequencing wgs has now emerged as an alternative in this field. We have deduced possible evolutionary paths traversed by this very important zoonotic pathogen and. The main causative agent is a pathovariant of salmonella typhimurium called st3, which is closely related to the wellcharacterized st19 sequence type of salmonella that causes gastroenteritis globally. The presence of homologues of salmonella enterica sv. Complete genome sequence of multidrugresistant salmonella. To achieve successful and nearly realtime monitoring and identification of outbreaks, reliable subtyping is essential. The incidence of nontyphoid salmonellosis is increasing worldwide, causing. Salmonella typhi is a humanspecific pathogen causing the systemic febrile illness typhoid fever. This proteome is part of the salmonella typhimurium strain lt2 sgsc1412 atcc 700720.
Typhimurium causes a large proportion of nontyphoidal salmonella nts infections, accounting for a quarter of infections, second only to s. Serotype information remains a cornerstone in food safety and public health activities to reduce the burden of salmonellosis. Salmonella enterica serovar dublin is a zoonotic infection that can be transmitted from cattle to humans through consumption of contaminated milk and milk products. The core genome of 35 sequenced salmonella is 2,811 gene families, and the pan genome is 10,015. In addition, 11 genomes were selected from 305 strains within subspecies enterica i that lacked many genes found in s. Comparison of salmonella enterica serovar typhimurium lt2 and. Typhimurium lt2 genes was assessed in 22 other salmonella including members of all seven subspecies and salmonella bongori. Stanley is a pathogen that contaminates food, and is related to salmonella outbreaks in a variety of hosts such as humans and farm animals through products like dairy items and vegetables.
Differences in gene content between paratyphi a and typhi. Genome variation and molecular epidemiology of salmonella. Comparison of salmonella enterica serovar typhimurium lt2. A library of salmonella typhimurium lt2 genomic sequences was. Evaluation of whole genome sequencing for outbreak detection of salmonella enterica pimlapas leekitcharoenphon1,2, eva m. Pdf complete genome sequence of salmonella enterica. Whole genome sequencing the total set of fortyseven salmonella enterica genomes was selected for multiplexed, pairedend sequencing on the illumina gaiix genome analyzer illumina, inc. Draft genome sequences of salmonella enterica serovar typhimurium lt2 with deleted chitinases that are emerging virulence factors narine arabyan, bihua c. The assembled genome sequence is in agreement with the physical map of the s. During completion of this manuscript, the genome sequence of a second s. Mcclelland m1, sanderson ke, spieth j, clifton sw, latreille. Oct 25, 2001 the assembled genome sequence is in agreement with the physical map of the s.
Dublin cases in humans are associated with invasive disease. Oct 25, 2001 the drugresistant strain has a genome of 4. Salmonella enterica subspecies i, serovar typhimurium s. Citeseerx document details isaac councill, lee giles, pradeep teregowda. Complete genome sequence of salmonella enterica serovar typhimurium lt2. Is there a package in r where i can load in a whole genome of salmonella typhimurium lt2, and then say e. Evaluation of whole genome sequencing for outbreak detection. Most of these homologues were previously unknown, and 50 may be. Seqsero is a pipeline for salmonella serotype determination from raw sequencing reads or genome assemblies.
Single nucleotide polymorphisms snps in 21 sara strains. The gene content and organization clearly place sp6 in the coliphage t7 group of phages, but. At the same time, recent advances in wgs have improved the. Adding function to the genome of african salmonella. Single nucleotide polymorphisms snps in 21 sara strains ranged from 46 to 11,916 snps, with an average.
Defining the core genome of salmonella enterica serovar. We have completed the genome sequence of the wellstudied strain ty2, and compared it with that of the recently isolated typhi strain ct18, sequenced at the sanger centre. Proteincoding and noncoding genes, splice variants, cdna and protein sequences, noncoding rnas. Despite the fact that several vaccines of salmonella strains had been constructed, none of them were developed according. Typhimurium strain for which the complete genomic sequence has been determined is the avirulent lt2 strain. Characterization of the genomes of a diverse collection of.
The genome contains 43,769 bp, including a 174bp direct terminal repeat. Whole genome sequencing wgs shows great promises for using as a routine epidemiological typing tool. As part of a project to complete the genomic sequence of salmonella typhimurium lt2 we have constructed a bacteriophage lambda library. Dyson 1,2, duy pham thanh 3, ladaporn bodhidatta 4, carl jeffries mason 4, apichai srijan4, maia a. The complete nucleotide sequence of usda15wa1 is 5,031,277 bp, including salmonella genomic island 4 encoding tolerance to multiple metals and an mdr module inserted in the fljb region. Identification of specific gene sequences conserved in. Nov 21, 2017 the aim of this study was to generate a reference set of salmonella enterica genomes isolated from wildlife from the united states and to determine the antimicrobial resistance and virulence gene profile of the isolates from the genome sequence data. Sequencing the ends of a sample of these lambda clones ensures the correct melding of the genomic sequence by confirming linkage over many kilobases while also contributing information towards complete. An unrooted phylogenomic tree was inferred by approximatelymaximum likelihood method via fasttreemp software. Typhimurium strains from salmonella reference collection a sara were analyzed using illumina highthroughput genome sequencing. We completed the full dna sequence of one dt104 strain, nctc348, and showed that significant differences between the genome of this isolate and the genome of the previously sequenced strain salmonella serovar typhimurium lt2. The aim of this study was to generate a reference set of salmonella enterica genomes isolated from wildlife from the united states and to determine the antimicrobial resistance and virulence gene profile of the isolates from the genome sequence data.
Shortterm signatures of evolutionary change in the. Typhi isolates from around the world indicates that they are highly related clonal and that they emerged from a single point of origin. The core genome of 35 sequenced salmonella is 2,811 gene families, and the pangenome is 10,015. Whole genome sequence analysis of salmonella typhi isolated in thailand before and after the introduction of a national immunization program zoe a. This study presents results of genome sequencing and analysis on our s.
Whole genome sequencingbased detection of antimicrobial. The procedures for dna and library preparation including sequencing in this study have been described previously and according to hendriksen. Jan 18, 2006 sequence comparison of selected genes with various salmonella genome sequences. Comparison of genome degradation in paratyphi a and typhi. Weimer genome announcements aug 2017, 5 31 e0065917. Genome sequencing and analysis of salmonella enterica. How do i access and query entire genome sequences salmonella. Salmonella enterica serovar typhimurium is a gramnegative pathogen that causes gastroenteritis in humans and a typhoidlike disease in mice and is often used as a model for the disease promoted by the humanadapted s. Analyze gene expression, metabolomics, and chipchip data. After the reannotation, lt2 and 14028s had 5078 and 5081 genes, respectively, and, most importantly. The wellcome trust sanger insitute pathogen genomics group was funded to sequence salmonella typhi strain ct18 in. Sequence comparison of selected genes with various salmonella genome sequences. As a control, we tested the growth of salmonella enterica serovar typhimurium lt2, which has a defect in rpos that increases its sensitivity to reactive oxygen species.
The salmonella enterica serovar typhimurium lt2 genome. In 2015, plasmidmediated colistin resistance was reported to be caused by a mobilized phosphoethanolamine transferase gene mcr1 in enterobacteriaceae here, we announce the complete genome sequence of the earliest dtartratefermenting salmonella enterica subsp. After exclusion of contigs fewer than 200 bp, the total length of the s. Typhimurium lt2 as a reference to be compared with. Genomic characterization of salmonella cerro st367, an. We completed the full dna sequence of one dt104 strain, nctc348, and showed that significant differences between the genome of this isolate and the genome of the previously sequenced. Genomes were hybridized to a microarray of over 97% of the 4,596 annotated orfs in the lt2 genome. We report the complete genome sequence of enterobacteriophage sp6, which infects salmonella enterica serovar typhimurium. Aarestrup1 1division for epidemiology and microbial genomics, national food institute, technical university of denmark, kgs. Analyze gene expression, metabolomics, and chipchip data sequence searching and alignment for salmonella enterica and. Evaluation of whole genome sequencing for outbreak. Salmonella enterica serovar typhimurium is one of approximately 2,500 distinct serovars of the genus salmonella but is exceptional in its wide distribution in the environment, livestock, and wild animals.
The transcriptional landscape and small rnas of salmonella. Genomic characterization of endemic salmonella enterica. Shortterm signatures of evolutionary change in the salmonella enterica serovar typhimurium 14028 genome tyler jarvik, 1chris smillie, eduardo a. Evolutionary genomics of salmonella enterica subspecies mbio. Cerro fsl r80235 has a genome size of approximately 4. This proteome is part of the salmonella typhimurium strain lt2 sgsc1412. Salmonella enterica serovar typhimurium is one of the most common s. Salmonella enterica serovar typhimurium is the most common salmonella serovar causing foodborne infections in australia and many other countries. Typhimurium strain sl44 has played an important role in the analysis of salmonella infection, starting with its use as a virulent salmonella strain for vaccine research. The relatively high sequence similarity of strain lt2 isolated in the 1940s with strain t000240 isolated in 2000 led izumiya and colleagues to suggest that progeny of lt2 might be reemerging. A library of salmonella typhimurium lt2 genomic sequences.
Stanley upm 517 strain taken from fecal swabs of 21dayold healthy commercial chickens in perak, malaysia and used salmonella enterica subsp. Mcclelland m1, sanderson ke, spieth j, clifton sw, latreille p, courtney l, porwollik s, ali j, dante m, du f, hou s, layman d, leonard s, nguyen c, scott k, holmes a, grewal n, mulvaney e, ryan e, sun h, florea l, miller w, stoneking t, nhan m, waterston r, wilson rk. Salmonella enterica serovar typhimurium atcc 14028s is. However, it is unclear whether increased virulence in humans is related to organism. May 15, 2012 more than 50 y of research have provided great insight into the physiology, metabolism, and molecular biology of salmonella enterica serovar typhimurium s. They are more likely to be from genes that are integrated in the genome of lt2 such as the fels prophage 6,7 but are related to genes found on phage or plasmids in other bacteria. Evolutionary genomics of salmonella genome biology. Sample sequencing of a salmonella typhimurium lt2 lambda.
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