title: Employment of 16 S rDNA gene sequencing techniques to identify culturable environmental eubacteria in a tertiary referral hospital.
abstract: Universal or 'broad-range' eubacterial polymerase chain reaction (PCR) was performed on 53 isolates from environmental water-associated sites in a haematology unit (N = 22) and the outer surfaces of cleaning lotion containers sited throughout a tertiary referral hospital (N = 31) 16 S rDNA PCR was performed using two sets of universal primers, including the novel reverse primer, XB4, to generate a composite amplicon of 1068 bp, which was sequenced to obtain each isolate's identity. Sequence analysis was able to identify 51 isolates. Most (75% from the haematology unit and 81% from cleaner containers) were Gram-positive. Nine different genera were identified from the haematology unit and 13 from the cleaning lotion containers. This study provides the first reports of Terrabacter spp. and Brachybacterium paraconglomeratum isolated from a hospital environment. As unusual and difficult-to-identify environmental organisms are unlikely to be clinically significant, and molecular identification is costly and labour-intensive, we recommend that molecular methods are only used as an adjunct to first-line phenotypic identification schemes where a definitive identification is required. Where molecular identification methods are justified, partial 16 S rDNA PCR and sequencing employing the novel universal primer XB4, is a valuable and reliable technique.
authors.affiliation: Northern Ireland Public Health Laboratory, Department of Bacteriology, Belfast City Hospital, Northern Ireland, UK.
authors.forename: J
authors.initials: J
authors.lastname: Xu
authors.forename: C L
authors.initials: CL
authors.lastname: Smyth
authors.forename: J A
authors.initials: JA
authors.lastname: Buchanan
authors.forename: A
authors.initials: A
authors.lastname: Dolan
authors.forename: P J
authors.initials: PJ
authors.lastname: Rooney
authors.forename: B C
authors.initials: BC
authors.lastname: Millar
authors.forename: C E
authors.initials: CE
authors.lastname: Goldsmith
authors.forename: J S
authors.initials: JS
authors.lastname: Elborn
authors.forename: J E
authors.initials: JE
authors.lastname: Moore
mesh_terms: D000192:Actinomycetales / Q000235:genetics / Q000302:isolation & purification; D001419:Bacteria / Q000235:genetics* / Q000302:isolation & purification; D004269:DNA, Bacterial / Q000235:genetics*; D004866:Equipment Contamination / Q000706:statistics & numerical data*; D004865:Equipment and Supplies, Hospital / Q000382:microbiology*; D006094:Gram-Positive Bacteria / Q000235:genetics / Q000302:isolation & purification; D006405:Hematology; D006757:Hospital Units; D006773:Hospitals, Municipal; D006801:Humans; D009660:Northern Ireland; D016133:Polymerase Chain Reaction; D012336:RNA, Ribosomal, 16S / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D014871:Water Microbiology
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S