title: Genomic Variability of Serial Human Isolates of Salmonella enterica Serovar Typhimurium Associated with Prolonged Carriage.
abstract: Salmonella enterica serovar Typhimurium is an important foodborne human pathogen that often causes self-limiting but severe gastroenteritis. Prolonged excretion of S. Typhimurium after the infection can lead to secondary transmissions. However, little is known about within-host genomic variation in bacteria associated with asymptomatic shedding. Genomes of 35 longitudinal isolates of S. Typhimurium recovered from 11 patients (children and adults) with culture-confirmed gastroenteritis were sequenced. There were three or four isolates obtained from each patient. Single nucleotide polymorphisms (SNPs) were analyzed in these isolates, which were recovered between 1 and 279 days after the initial diagnosis. Limited genomic variation (5 SNPs or fewer) was associated with short- and long-term carriage of S. Typhimurium. None of the isolates was shown to be due to reinfection. SNPs occurred randomly, and the majority of the SNPs were nonsynonymous. Two nonsense mutations were observed. A nonsense mutation in flhC rendered the isolate nonmotile, whereas the significance of a nonsense mutation in yihV is unknown. The estimated mutation rate is 1.49 × 10(-6) substitution per site per year. S. Typhimurium isolates excreted in stools following acute gastroenteritis in children and adults demonstrated limited genomic variability over time, regardless of the duration of carriage. These findings have important implications for the detection of possible transmission events suspected by public health genomic surveillance of S. Typhimurium infections.
authors: School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia.
authors: Sophie
authors: S
authors: Octavia
authors: Centre for Infectious Diseases and Microbiology-Public Health, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Sydney, New South Wales, Australia.
authors: Qinning
authors: Q
authors: Wang
authors: School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia.
authors: Mark M
authors: MM
authors: Tanaka
authors: Centre for Infectious Diseases and Microbiology-Public Health, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Sydney, New South Wales, Australia Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, New South Wales, Australia r.lan@unsw.edu.au vitali.sintchenko@sydney.edu.au.
authors: Vitali
authors: V
authors: Sintchenko
authors: School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia r.lan@unsw.edu.au vitali.sintchenko@sydney.edu.au.
authors: Ruiting
authors: R
authors: Lan
mesh_terms: D000328:Adult; D001315:Australia; D001483:Base Sequence; D002648:Child; D018389:Codon, Nonsense / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics; D005243:Feces / Q000382:microbiology; D005260:Female; D005759:Gastroenteritis / Q000175:diagnosis* / Q000382:microbiology; D016680:Genome, Bacterial / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008297:Male; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D039002:Prophages / Q000235:genetics; D012478:Salmonella Food Poisoning / Q000175:diagnosis* / Q000382:microbiology; D012480:Salmonella Infections / Q000175:diagnosis* / Q000382:microbiology; D012486:Salmonella typhimurium / Q000235:genetics* / Q000302:isolation & purification*; D017422:Sequence Analysis, DNA; D020080:Tandem Repeat Sequences / Q000235:genetics
chemical_list: D018389:Codon, Nonsense; D004269:DNA, Bacterial