{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,4,10]],"date-time":"2024-04-10T05:16:38Z","timestamp":1712726198032},"reference-count":23,"publisher":"American Society for Microbiology","issue":"18","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Bacteriol."],"published-print":{"date-parts":[[2012,9,15]]},"abstract":"<jats:title>ABSTRACT<\/jats:title><jats:p>Many of the developing countries of the Southeast Asian region are significantly affected by endemic typhoid fever, possibly as a result of marginal living standards. It is an important public health problem in countries such as Papua New Guinea, which is geographically close to some of the foci of endemicity in Asia. The severity of the disease varies in different regions, and this may be attributable to genetic diversity among the native strains. Genome sequence data on strains from different countries are needed to clearly understand their genetic makeup and virulence potential. We describe the genomes of two<jats:named-content xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" content-type=\"genus-species\" xlink:type=\"simple\">Salmonella<\/jats:named-content>Typhi isolates from patients with fatal and nonfatal cases of typhoid fever in Papua New Guinea. We discuss in brief the underlying sequencing methodology, assembly, genome statistics, and important features of the two draft genomes, which form an essential step in our functional molecular infection epidemiology program centering on typhoid fever. The comparative genomics of these and other isolates would enable us to identify genetic rearrangements and mechanisms responsible for endemicity and the differential severity of pathogenic salmonellae in Papua New Guinea and elsewhere.<\/jats:p>","DOI":"10.1128\/jb.01051-12","type":"journal-article","created":{"date-parts":[[2012,8,28]],"date-time":"2012-08-28T21:46:33Z","timestamp":1346190393000},"page":"5122-5123","source":"Crossref","is-referenced-by-count":12,"title":["Whole-Genome Sequences and Comparative Genomics of Salmonella enterica Serovar Typhi Isolates from Patients with Fatal and Nonfatal Typhoid Fever in Papua New Guinea"],"prefix":"10.1128","volume":"194","author":[{"given":"Ramani","family":"Baddam","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kwai-Lin","family":"Thong","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tiruvayipati Suma","family":"Avasthi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sabiha","family":"Shaik","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kien-Pong","family":"Yap","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cindy Shuan Ju","family":"Teh","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lay-Ching","family":"Chai","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Narender","family":"Kumar","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Niyaz","family":"Ahmed","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"235","published-online":{"date-parts":[[2012,8,28]]},"reference":[{"key":"key20180919081050_B1","doi-asserted-by":"crossref","first-page":"3385","DOI":"10.1128\/JB.05006-11","article-title":"Genomes of two chronological isolates (Helicobacter pylori 2017 and 2018) of the West African Helicobacter pylori strain 908 obtained from a single patient","volume":"193","author":"Avasthi","year":"2011","journal-title":"J. Bacteriol."},{"key":"key20180919081050_B2","doi-asserted-by":"crossref","first-page":"4272","DOI":"10.1128\/JB.05413-11","article-title":"Genome of multidrug-resistant uropathogenic Escherichia coli strain NA114 from India","volume":"193","author":"Avasthi","year":"2011","journal-title":"J. Bacteriol."},{"key":"key20180919081050_B3","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1186\/1471-2164-9-75","article-title":"The RAST server: rapid annotations using subsystems technology","volume":"9","author":"Aziz","year":"2008","journal-title":"BMC Genomics"},{"key":"key20180919081050_B4","doi-asserted-by":"crossref","first-page":"3565","DOI":"10.1128\/JB.00581-12","article-title":"Genetic fine structure of a Salmonella enterica serovar Typhi strain associated with the 2005 outbreak of typhoid fever in Kelantan, Malaysia","volume":"194","author":"Baddam","year":"2012","journal-title":"J. Bacteriol."},{"key":"key20180919081050_B5","doi-asserted-by":"crossref","first-page":"578","DOI":"10.1093\/bioinformatics\/btq683","article-title":"Scaffolding pre-assembled contigs using SSPACE","volume":"27","author":"Boetzer","year":"2011","journal-title":"Bioinformatics"},{"key":"key20180919081050_B6","first-page":"158","article-title":"Ribotyping of Salmonella enterica serovar Typhi isolates from Papua New Guinea over the period 1977 to 1996","volume":"48","author":"Combs","year":"2005","journal-title":"P. N. G. Med. J."},{"key":"key20180919081050_B7","doi-asserted-by":"crossref","first-page":"4636","DOI":"10.1093\/nar\/27.23.4636","article-title":"Improved microbial gene identification with GLIMMER","volume":"27","author":"Delcher","year":"1999","journal-title":"Nucleic Acids Res."},{"key":"key20180919081050_B8","doi-asserted-by":"crossref","first-page":"6488","DOI":"10.1128\/JB.01110-10","article-title":"Genome of Helicobacter pylori strain 908","volume":"192","author":"Devi","year":"2010","journal-title":"J. Bacteriol."},{"key":"key20180919081050_B9","doi-asserted-by":"crossref","first-page":"4614","DOI":"10.1073\/pnas.0400932101","article-title":"Salmonella typhi encodes a functional cytolethal distending toxin that is delivered into host cells by a bacterial-internalization pathway","volume":"101","author":"Haghjoo","year":"2004","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"key20180919081050_B10","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1111\/j.1574-6968.1997.tb10251.x","article-title":"Survival of Vi-capsulated and Vi-deleted Salmonella typhi strains in cultured macrophage expressing different levels of CD14 antigen","volume":"147","author":"Hirose","year":"1997","journal-title":"FEMS Microbiol. Lett."},{"key":"key20180919081050_B11","doi-asserted-by":"crossref","first-page":"3100","DOI":"10.1093\/nar\/gkm160","article-title":"RNammer: consistent annotation of rRNA genes in genomic sequences","volume":"35","author":"Lagesen","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"key20180919081050_B12","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1186\/1471-2105-4-21","article-title":"EasyGene\u2014a prokaryotic gene finder that ranks ORFs by statistical significance","volume":"4","author":"Larsen","year":"2003","journal-title":"BMC Bioinformatics"},{"key":"key20180919081050_B13","doi-asserted-by":"crossref","first-page":"1018","DOI":"10.1073\/pnas.92.4.1018","article-title":"Rearrangements in the genome of the bacterium Salmonella typhi","volume":"92","author":"Liu","year":"1995","journal-title":"Proc. Natl. Acad. Sci. U. S. A."},{"key":"key20180919081050_B14","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1016\/S0167-7012(00)00148-2","article-title":"Genotypic characterization of Salmonella typhi by amplified fragment length polymorphism fingerprinting provides increased discrimination as compared to pulsed-field gel electrophoresis and ribotyping","volume":"41","author":"Nair","year":"2000","journal-title":"J. Microbiol. Methods"},{"key":"key20180919081050_B15","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1016\/S0966-842X(00)88937-4","article-title":"Typhoid fever and other salmonelloses: a continuing challenge","volume":"3","author":"Pang","year":"1995","journal-title":"Trends Microbiol."},{"key":"key20180919081050_B16","doi-asserted-by":"crossref","first-page":"848","DOI":"10.1038\/35101607","article-title":"Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18","volume":"413","author":"Parkhill","year":"2001","journal-title":"Nature"},{"key":"key20180919081050_B17","first-page":"83","article-title":"Highly endemic typhoid fever in Papua New Guinea","volume":"26","author":"Passey","year":"1995","journal-title":"Southeast Asian J. Trop. Med. Public Health"},{"key":"key20180919081050_B18","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1128\/IAI.74.1.19-27.2006","article-title":"Capsule-mediated immune evasion: a new hypothesis explaining aspects of typhoid fever pathogenesis","volume":"74","author":"Raffatellu","year":"2006","journal-title":"Infect. Immun."},{"key":"key20180919081050_B19","doi-asserted-by":"crossref","first-page":"5598","DOI":"10.1128\/JB.05667-11","article-title":"Genome of a novel isolate of Paracoccus denitrificans capable of degrading N,N-dimethylformamide","volume":"193","author":"Siddavattam","year":"2011","journal-title":"J. Bacteriol."},{"key":"key20180919081050_B20","doi-asserted-by":"crossref","first-page":"1938","DOI":"10.1128\/JCM.33.7.1938-1941.1995","article-title":"Analysis of Salmonella typhi isolates from Southeast Asia by pulsed-field gel electrophoresis","volume":"33","author":"Thong","year":"1995","journal-title":"J. Clin. Microbiol."},{"key":"key20180919081050_B21","doi-asserted-by":"crossref","first-page":"1029","DOI":"10.1128\/JCM.34.4.1029-1033.1996","article-title":"Molecular analysis of isolates of Salmonella typhi obtained from patients with fatal and nonfatal typhoid fever","volume":"34","author":"Thong","year":"1996","journal-title":"J. Clin. Microbiol."},{"key":"key20180919081050_B22","doi-asserted-by":"crossref","first-page":"4156","DOI":"10.1128\/JCM.40.11.4156-4160.2002","article-title":"Increasing genetic diversity of Salmonella enterica serovar Typhi isolates from Papua New Guinea over the period from 1992 to 1999","volume":"40","author":"Thong","year":"2002","journal-title":"J. Clin. Microbiol."},{"key":"key20180919081050_B23","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1101\/gr.074492.107","article-title":"Velvet: algorithms for de novo short read assembly using de Bruijn graphs","volume":"18","author":"Zerbino","year":"2008","journal-title":"Genome Res."}],"container-title":["Journal of Bacteriology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1128\/JB.01051-12","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,7,29]],"date-time":"2021-07-29T17:26:53Z","timestamp":1627579613000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/JB.01051-12"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,8,28]]},"references-count":23,"journal-issue":{"issue":"18","published-online":{"date-parts":[[2012,8,28]]},"published-print":{"date-parts":[[2012,9,15]]}},"alternative-id":["10.1128\/JB.01051-12"],"URL":"https:\/\/doi.org\/10.1128\/jb.01051-12","relation":{},"ISSN":["0021-9193","1098-5530"],"issn-type":[{"value":"0021-9193","type":"print"},{"value":"1098-5530","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012,8,28]]}}}