title: atpE gene as a new useful specific molecular target to quantify Mycobacterium in environmental samples.
abstract: BACKGROUND
  The environment is the likely source of many pathogenic mycobacterial species but detection of mycobacteria by bacteriological tools is generally difficult and time-consuming. Consequently, several molecular targets based on the sequences of housekeeping genes, non-functional RNA and structural ribosomal RNAs have been proposed for the detection and identification of mycobacteria in clinical or environmental samples. While certain of these targets were proposed as specific for this genus, most are prone to false positive results in complex environmental samples that include related, but distinct, bacterial genera. Nowadays the increased number of sequenced genomes and the availability of software for genomic comparison provide tools to develop novel, mycobacteria-specific targets, and the associated molecular probes and primers. Consequently, we conducted an in silico search for proteins exclusive to Mycobacterium spp. genomes in order to design sensitive and specific molecular targets.
  
  
  RESULTS
  Among the 3989 predicted proteins from M. tuberculosis H37Rv, only 11 proteins showed 80% to 100% of similarity with Mycobacterium spp. genomes, and less than 50% of similarity with genomes of closely related Corynebacterium, Nocardia and Rhodococcus genera. Based on DNA sequence alignments, we designed primer pairs and a probe that specifically detect the atpE gene of mycobacteria, as verified by quantitative real-time PCR on a collection of mycobacteria and non-mycobacterial species. The real-time PCR method we developed was successfully used to detect mycobacteria in tap water and lake samples.
  
  
  CONCLUSIONS
  The results indicate that this real-time PCR method targeting the atpE gene can serve for highly specific detection and precise quantification of Mycobacterium spp. in environmental samples.
authors.affiliation: Laboratoire Eau Environnement Systèmes Urbains (Leesu) UMR MA 102-AgroParisTech, Université Paris-Est, 6-8 avenue Blaise Pascal Cité, Descartes, FR 77455, Champs sur Marne, France. nicolas.radomski.phd@gmail.com.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Radomski
authors.forename: Adélaïde
authors.initials: A
authors.lastname: Roguet
authors.forename: Françoise S
authors.initials: FS
authors.lastname: Lucas
authors.forename: Frédéric J
authors.initials: FJ
authors.lastname: Veyrier
authors.forename: Emmanuelle
authors.initials: E
authors.lastname: Cambau
authors.forename: Héberte
authors.initials: H
authors.lastname: Accrombessi
authors.forename: Régis
authors.initials: R
authors.lastname: Moilleron
authors.forename: Marcel A
authors.initials: MA
authors.lastname: Behr
authors.forename: Laurent
authors.initials: L
authors.lastname: Moulin
mesh_terms: D058491:Bacterial Load / Q000379:methods*; D025243:Bacterial Proton-Translocating ATPases / Q000235:genetics*; D017931:DNA Primers / Q000235:genetics; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004783:Environmental Microbiology; D008969:Molecular Sequence Data; D009161:Mycobacterium / Q000235:genetics / Q000302:isolation & purification*; D015345:Oligonucleotide Probes / Q000235:genetics; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA
chemical_list: D017931:DNA Primers; D004269:DNA, Bacterial; D015345:Oligonucleotide Probes; D025243:Bacterial Proton-Translocating ATPases