title: Analysis of Salmonella enterica serotype paratyphi A gene expression in the blood of bacteremic patients in Bangladesh.
abstract: BACKGROUND
  Salmonella enterica serotype Paratyphi A is a human-restricted cause of paratyphoid fever, accounting for up to a fifth of all cases of enteric fever in Asia.
  
  
  RESULTS
  In this work, we applied an RNA analysis method, Selective Capture of Transcribed Sequences (SCOTS), and cDNA hybridization-microarray technology to identify S. Paratyphi A transcripts expressed by bacteria in the blood of three patients in Bangladesh. In total, we detected 1,798 S. Paratyphi A mRNAs expressed in the blood of infected humans (43.9% of the ORFeome). Of these, we identified 868 in at least two patients, and 315 in all three patients. S. Paratyphi A transcripts identified in at least two patients encode proteins involved in energy metabolism, nutrient and iron acquisition, vitamin biosynthesis, stress responses, oxidative stress resistance, and pathogenesis. A number of detected transcripts are expressed from PhoP and SlyA-regulated genes associated with intra-macrophage survival, genes contained within Salmonella Pathogenicity Islands (SPIs) 1-4, 6, 10, 13, and 16, as well as RpoS-regulated genes. The largest category of identified transcripts is that of encoding proteins with unknown function. When comparing levels of bacterial mRNA using in vivo samples collected from infected patients to samples from in vitro grown organisms, we found significant differences for 347, 391, and 456 S. Paratyphi A transcripts in each of three individual patients (approximately 9.7% of the ORFeome). Of these, expression of 194 transcripts (4.7% of ORFs) was concordant in two or more patients, and 41 in all patients. Genes encoding these transcripts are contained within SPI-1, 3, 6 and 10, PhoP-regulated genes, involved in energy metabolism, nutrient acquisition, drug resistance, or uncharacterized genes. Using quantitative RT-PCR, we confirmed increased gene expression in vivo for a subset of these genes.
  
  
  CONCLUSIONS
  To our knowledge, we describe the first microarray-based transcriptional analysis of a pathogen in the blood of naturally infected humans.
authors.affiliation: International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh. alaullah@icddrb.org
authors.forename: Alaullah
authors.initials: A
authors.lastname: Sheikh
authors.forename: Richelle C
authors.initials: RC
authors.lastname: Charles
authors.forename: Sean M
authors.initials: SM
authors.lastname: Rollins
authors.forename: Jason B
authors.initials: JB
authors.lastname: Harris
authors.forename: Md Saruar
authors.initials: MS
authors.lastname: Bhuiyan
authors.forename: Farhana
authors.initials: F
authors.lastname: Khanam
authors.forename: Archana
authors.initials: A
authors.lastname: Bukka
authors.forename: Anuj
authors.initials: A
authors.lastname: Kalsy
authors.forename: Steffen
authors.initials: S
authors.lastname: Porwollik
authors.forename: W Abdullah
authors.initials: WA
authors.lastname: Brooks
authors.forename: Regina C
authors.initials: RC
authors.lastname: LaRocque
authors.forename: Elizabeth L
authors.initials: EL
authors.lastname: Hohmann
authors.forename: Alejandro
authors.initials: A
authors.lastname: Cravioto
authors.forename: Tanya
authors.initials: T
authors.lastname: Logvinenko
authors.forename: Stephen B
authors.initials: SB
authors.lastname: Calderwood
authors.forename: Michael
authors.initials: M
authors.lastname: McClelland
authors.forename: James E
authors.initials: JE
authors.lastname: Graham
authors.forename: Firdausi
authors.initials: F
authors.lastname: Qadri
authors.forename: Edward T
authors.initials: ET
authors.lastname: Ryan
mesh_terms: D000293:Adolescent; D000328:Adult; D016470:Bacteremia / Q000382:microbiology*; D001459:Bangladesh; D001769:Blood / Q000382:microbiology*; D002648:Child; D002675:Child, Preschool; D018076:DNA, Complementary / Q000235:genetics; D020869:Gene Expression Profiling; D006801:Humans; D046228:Microarray Analysis; D008875:Middle Aged; D010284:Paratyphoid Fever / Q000382:microbiology*; D012329:RNA, Bacterial / Q000235:genetics / Q000302:isolation & purification; D012333:RNA, Messenger / Q000235:genetics / Q000302:isolation & purification; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012482:Salmonella paratyphi A / Q000235:genetics* / Q000302:isolation & purification; D055815:Young Adult
chemical_list: D018076:DNA, Complementary; D012329:RNA, Bacterial; D012333:RNA, Messenger