Identification of acinetobacter species and genotyping of Acinetobacter baumannii by multilocus PCR and mass spectrometry

Joseph A. Ecker, Christian Massire, Thomas A. Hall, Raymond Ranken, Thuy Trang D. Pennella, Cristina Agasino Ivy, Lawrence B. Blyn, Steven A. Hofstadler, Timothy P. Endy, Paul T. Scott, Luther Lindler, Tacita Hamilton, Charla Gaddy, Kerry Snow, Marie Pe, Joel Fishbain, David Craft, Gregory Deye, Scott Riddell, Eric MilstreyBruno Petruccelli, Sylvain Brisse, Vanessa Harpin, Amy Schink, David J. Ecker, Rangarajan Sampath, Mark W. Eshoo

Research output: Contribution to journalArticle

138 Citations (Scopus)

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 genomo-species 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.

Original languageEnglish (US)
Pages (from-to)2921-2932
Number of pages12
JournalJournal of clinical microbiology
Volume44
Issue number8
DOIs
StatePublished - Aug 1 2006

Fingerprint

Acinetobacter baumannii
Acinetobacter
Mass Spectrometry
Polymerase Chain Reaction
Genotype
Electrospray Ionization Mass Spectrometry
Disease Outbreaks
Iraq
Essential Genes
Military Personnel
Base Composition
Infection Control
Cross Infection
Electrophoresis
Epidemiology
Soil
Gels
Genome
Delivery of Health Care
Water

All Science Journal Classification (ASJC) codes

  • Microbiology (medical)

Cite this

Ecker, J. A., Massire, C., Hall, T. A., Ranken, R., Pennella, T. T. D., Ivy, C. A., ... Eshoo, M. W. (2006). Identification of acinetobacter species and genotyping of Acinetobacter baumannii by multilocus PCR and mass spectrometry. Journal of clinical microbiology, 44(8), 2921-2932. https://doi.org/10.1128/JCM.00619-06
Ecker, Joseph A. ; Massire, Christian ; Hall, Thomas A. ; Ranken, Raymond ; Pennella, Thuy Trang D. ; Ivy, Cristina Agasino ; Blyn, Lawrence B. ; Hofstadler, Steven A. ; Endy, Timothy P. ; Scott, Paul T. ; Lindler, Luther ; Hamilton, Tacita ; Gaddy, Charla ; Snow, Kerry ; Pe, Marie ; Fishbain, Joel ; Craft, David ; Deye, Gregory ; Riddell, Scott ; Milstrey, Eric ; Petruccelli, Bruno ; Brisse, Sylvain ; Harpin, Vanessa ; Schink, Amy ; Ecker, David J. ; Sampath, Rangarajan ; Eshoo, Mark W. / Identification of acinetobacter species and genotyping of Acinetobacter baumannii by multilocus PCR and mass spectrometry. In: Journal of clinical microbiology. 2006 ; Vol. 44, No. 8. pp. 2921-2932.
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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 genomo-species 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.",
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Ecker, JA, Massire, C, Hall, TA, Ranken, R, Pennella, TTD, Ivy, CA, Blyn, LB, Hofstadler, SA, Endy, TP, Scott, PT, Lindler, L, Hamilton, T, Gaddy, C, Snow, K, Pe, M, Fishbain, J, Craft, D, Deye, G, Riddell, S, Milstrey, E, Petruccelli, B, Brisse, S, Harpin, V, Schink, A, Ecker, DJ, Sampath, R & Eshoo, MW 2006, 'Identification of acinetobacter species and genotyping of Acinetobacter baumannii by multilocus PCR and mass spectrometry', Journal of clinical microbiology, vol. 44, no. 8, pp. 2921-2932. https://doi.org/10.1128/JCM.00619-06

Identification of acinetobacter species and genotyping of Acinetobacter baumannii by multilocus PCR and mass spectrometry. / Ecker, Joseph A.; Massire, Christian; Hall, Thomas A.; Ranken, Raymond; Pennella, Thuy Trang D.; Ivy, Cristina Agasino; Blyn, Lawrence B.; Hofstadler, Steven A.; Endy, Timothy P.; Scott, Paul T.; Lindler, Luther; Hamilton, Tacita; Gaddy, Charla; Snow, Kerry; Pe, Marie; Fishbain, Joel; Craft, David; Deye, Gregory; Riddell, Scott; Milstrey, Eric; Petruccelli, Bruno; Brisse, Sylvain; Harpin, Vanessa; Schink, Amy; Ecker, David J.; Sampath, Rangarajan; Eshoo, Mark W.

In: Journal of clinical microbiology, Vol. 44, No. 8, 01.08.2006, p. 2921-2932.

Research output: Contribution to journalArticle

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T1 - Identification of acinetobacter species and genotyping of Acinetobacter baumannii by multilocus PCR and mass spectrometry

AU - Ecker, Joseph A.

AU - Massire, Christian

AU - Hall, Thomas A.

AU - Ranken, Raymond

AU - Pennella, Thuy Trang D.

AU - Ivy, Cristina Agasino

AU - Blyn, Lawrence B.

AU - Hofstadler, Steven A.

AU - Endy, Timothy P.

AU - Scott, Paul T.

AU - Lindler, Luther

AU - Hamilton, Tacita

AU - Gaddy, Charla

AU - Snow, Kerry

AU - Pe, Marie

AU - Fishbain, Joel

AU - Craft, David

AU - Deye, Gregory

AU - Riddell, Scott

AU - Milstrey, Eric

AU - Petruccelli, Bruno

AU - Brisse, Sylvain

AU - Harpin, Vanessa

AU - Schink, Amy

AU - Ecker, David J.

AU - Sampath, Rangarajan

AU - Eshoo, Mark W.

PY - 2006/8/1

Y1 - 2006/8/1

N2 - 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 genomo-species 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.

AB - 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 genomo-species 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.

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