title: In vivo expression of Salmonella enterica serotype Typhi genes in the blood of patients with typhoid fever in Bangladesh.
abstract: BACKGROUND
  Salmonella enterica serotype Typhi is the cause of typhoid fever. It is a human-restricted pathogen, and few data exist on S. Typhi gene expression in humans.
  
  
  RESULTS
  We applied an RNA capture and amplification technique, Selective Capture of Transcribed Sequences (SCOTS), and microarray hybridization to identify S. Typhi transcripts expressed in the blood of five humans infected with S. Typhi in Bangladesh. In total, we detected the expression of mRNAs for 2,046 S. Typhi genes (44% of the S. Typhi genome) in human blood; expression of 912 genes was detected in all 5 patients, and expression of 1,100 genes was detected in 4 or more patients. Identified transcripts were associated with the virulence-associated PhoP regulon, Salmonella pathogenicity islands, the use of alternative carbon and energy sources, synthesis and transport of iron, thiamine, and biotin, and resistance to antimicrobial peptides and oxidative stress. The most highly represented group were genes currently annotated as encoding proteins designated as hypothetical, unknown, or unclassified. Of the 2,046 detected transcripts, 1,320 (29% of the S. Typhi genome) had significantly different levels of detection in human blood compared to in vitro cultures; detection of 141 transcripts was significantly different in all 5 patients, and detection of 331 transcripts varied in at least 4 patients. These mRNAs encode proteins of unknown function, those involved in energy metabolism, transport and binding, cell envelope, cellular processes, and pathogenesis. We confirmed increased expression of a subset of identified mRNAs by quantitative-PCR.
  
  
  CONCLUSIONS
  We report the first characterization of bacterial transcriptional profiles in the blood of patients with typhoid fever. S. Typhi is an important global pathogen whose restricted host range has greatly inhibited laboratory studies. Our results suggest that S. Typhi uses a largely uncharacterized genetic repertoire to survive within cells and utilize alternate energy sources during infection.
authors.affiliation: International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh.
authors.forename: Alaullah
authors.initials: A
authors.lastname: Sheikh
authors.forename: Richelle C
authors.initials: RC
authors.lastname: Charles
authors.forename: Nusrat
authors.initials: N
authors.lastname: Sharmeen
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: Mohammad
authors.initials: M
authors.lastname: Arifuzzaman
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: Daniel T
authors.initials: DT
authors.lastname: Leung
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; D001426:Bacterial Proteins / Q000145:classification / Q000235:genetics; D001459:Bangladesh; D002648:Child; D002675:Child, Preschool; D020869:Gene Expression Profiling; D006801:Humans; D007223:Infant; D008875:Middle Aged; D020411:Oligonucleotide Array Sequence Analysis; D012329:RNA, Bacterial / Q000097:blood* / Q000737:chemistry / Q000145:classification; D012333:RNA, Messenger / Q000097:blood / Q000737:chemistry / Q000145:classification; D060888:Real-Time Polymerase Chain Reaction; D012485:Salmonella typhi / Q000235:genetics* / Q000302:isolation & purification; D014435:Typhoid Fever / Q000097:blood / Q000382:microbiology*
chemical_list: D001426:Bacterial Proteins; D012329:RNA, Bacterial; D012333:RNA, Messenger