title: Identification of Acinetobacter species and genotyping of Acinetobacter baumannii by multilocus PCR and mass spectrometry.
abstract: Members of the genus Acinetobacter are ubiquitous in soil and water and are an important cause of nosocomial infections. A rapid method is needed to genotype Acinetobacter isolates to determine epidemiology and clonality during infectious outbreaks. Multilocus PCR followed by electrospray ionization mass spectrometry (PCR/ESI-MS) is a method that uses the amplicon base compositions to genotype bacterial species. In order to identify regions of the Acinetobacter genome useful for this method, we sequenced regions of six housekeeping genes (trpE, adk, efp, mutY, fumC, and ppa) from 267 isolates of Acinetobacter. Isolates were collected from infected and colonized soldiers and civilians involved in an outbreak in the military health care system associated with the conflict in Iraq, from previously characterized outbreaks in European hospitals, and from culture collections. Most of the isolates from the Iraqi conflict were Acinetobacter baumannii (189 of 216 isolates). Among these, 111 isolates had genotypes identical or very similar to those associated with well-characterized A. baumannii isolates from European hospitals. Twenty-seven isolates from the conflict were found to have genotypes representing different Acinetobacter species, including 8 representatives of Acinetobacter genomospecies 13TU and 13 representatives of Acinetobacter genomospecies 3. Analysis by the PCR/ESI-MS method using nine primer pairs targeting the most information-rich regions of the trpE, adk, mutY, fumC, and ppa genes distinguished 47 of the 48 A. baumannii genotypes identified by sequencing and identified at the species level at least 18 Acinetobacter species. Results obtained with our genotyping method were essentially in agreement with those obtained by pulse-field gel electrophoresis analysis. The PCR/ESI-MS genotyping method required 4 h of analysis time to first answer with additional samples subsequently analyzed every 10 min. This rapid analysis allows tracking of transmission for the implementation of appropriate infection control measures on a time scale previously not achievable.
authors.affiliation: Ibis Biosciences, Isis Pharmaceuticals, Inc., 1891 Rutherford Road, Carlsbad, CA 92008, USA.
authors.forename: Joseph A
authors.initials: JA
authors.lastname: Ecker
authors.forename: Christian
authors.initials: C
authors.lastname: Massire
authors.forename: Thomas A
authors.initials: TA
authors.lastname: Hall
authors.forename: Raymond
authors.initials: R
authors.lastname: Ranken
authors.forename: Thuy-Trang D
authors.initials: TT
authors.lastname: Pennella
authors.forename: Cristina
authors.initials: C
authors.lastname: Agasino Ivy
authors.forename: Lawrence B
authors.initials: LB
authors.lastname: Blyn
authors.forename: Steven A
authors.initials: SA
authors.lastname: Hofstadler
authors.forename: Timothy P
authors.initials: TP
authors.lastname: Endy
authors.forename: Paul T
authors.initials: PT
authors.lastname: Scott
authors.forename: Luther
authors.initials: L
authors.lastname: Lindler
authors.forename: Tacita
authors.initials: T
authors.lastname: Hamilton
authors.forename: Charla
authors.initials: C
authors.lastname: Gaddy
authors.forename: Kerry
authors.initials: K
authors.lastname: Snow
authors.forename: Marie
authors.initials: M
authors.lastname: Pe
authors.forename: Joel
authors.initials: J
authors.lastname: Fishbain
authors.forename: David
authors.initials: D
authors.lastname: Craft
authors.forename: Gregory
authors.initials: G
authors.lastname: Deye
authors.forename: Scott
authors.initials: S
authors.lastname: Riddell
authors.forename: Eric
authors.initials: E
authors.lastname: Milstrey
authors.forename: Bruno
authors.initials: B
authors.lastname: Petruccelli
authors.forename: Sylvain
authors.initials: S
authors.lastname: Brisse
authors.forename: Vanessa
authors.initials: V
authors.lastname: Harpin
authors.forename: Amy
authors.initials: A
authors.lastname: Schink
authors.forename: David J
authors.initials: DJ
authors.lastname: Ecker
authors.forename: Rangarajan
authors.initials: R
authors.lastname: Sampath
authors.forename: Mark W
authors.initials: MW
authors.lastname: Eshoo
mesh_terms: D000150:Acinetobacter / Q000145:classification* / Q000235:genetics; D000151:Acinetobacter Infections / Q000453:epidemiology / Q000382:microbiology*; D040981:Acinetobacter baumannii / Q000145:classification* / Q000235:genetics*; D015373:Bacterial Typing Techniques; D016000:Cluster Analysis; D017931:DNA Primers; D004269:DNA, Bacterial / Q000032:analysis / Q000235:genetics; D004196:Disease Outbreaks; D005798:Genes, Bacterial; D005838:Genotype; D006801:Humans; D013058:Mass Spectrometry; D017720:Molecular Epidemiology / Q000379:methods; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D017385:Sequence Homology
chemical_list: D017931:DNA Primers; D004269:DNA, Bacterial