Use of sequence-based typing and multiplex PCR to identify clonal lineages of outbreak strains of Acinetobacter baumannii J.F. Turton, S.N. Gabriel,

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Use of sequence-based typing and multiplex PCR to identify clonal lineages of outbreak strains of Acinetobacter baumannii J.F. Turton, S.N. Gabriel, C. Valderrey, M.E. Kaufrnann, T.L. Pitt Clinical Microbiology and Infection Volume 13, Issue 8, Pages 807-815 (August 2007) DOI: 10.1111/j.1469-0691.2007.01759.x Copyright © 2007 European Society of Clinical Infectious Diseases Terms and Conditions

Fig. 1 Pulsed-field gel electrophoresis (PFGE) profiles of ApaI-digested genomic DNA and allele designations (in the order ompA, csuE, blaOXA-51-like) for representative strains of Acinetobacter baumannii, including representatives of European clones I–III. Strains belonging to the same sequence type group (Groups 1–3) clustered at a level of 69% (indicated by the broken line) by PFGE with the parameters used. Circles, squares and diamonds indicate Groups 1, 2 and 3, respectively. Alleles within the Group 1 clonal complex labelled 1a or 1b have one or two nucleotide difference(s), respectively, from allele 1. 1a* indicates a distinct base-pair difference (G at nucleotide 499 of coding sequence) from allele 1a. Clinical Microbiology and Infection 2007 13, 807-815DOI: (10.1111/j.1469-0691.2007.01759.x) Copyright © 2007 European Society of Clinical Infectious Diseases Terms and Conditions

Fig. 2 Dendrograms showing percentage similarity between (a) csuE alleles (corresponding to nucleotides 230–678 of DQ648278) and (b) blaOXA-51-like alleles (corresponding to nucleotides 79–771 of AJ309734) by pairwise alignment. Circles, squares and diamonds indicate Group 1, 2 and 3 alleles, respectively. Clinical Microbiology and Infection 2007 13, 807-815DOI: (10.1111/j.1469-0691.2007.01759.x) Copyright © 2007 European Society of Clinical Infectious Diseases Terms and Conditions

Fig. 3 Partial amino-acid sequences translated from ompA alleles 1 and 2 (corresponding to nuelotides 39–724 of DQ648278 and nucleotides 108–784 of DQ648279, respectively). Residues that differ are highlighted. For clarity, only alleles 1 and 2 are compared here, but amino-acid substitutions were also associated with alleles 3 and 4 (found in sporadic isolates L4 and IR1), available under accession numbers DQ779967 and DQ779966. Clinical Microbiology and Infection 2007 13, 807-815DOI: (10.1111/j.1469-0691.2007.01759.x) Copyright © 2007 European Society of Clinical Infectious Diseases Terms and Conditions

Fig. 4 Examples of multiplex PCRs designed to selectively amplify ompA, csuE and blaOXA-51-like alleles of isolates belonging to (a) Group 1 and (b) Group 2. Genotypes and country of isolation were: lanes 1–6 (Group 1), Strain A (Israel), SE clone, 24AC-1, NW strain (UK), clone II (Spain), T strain (UK); lanes 7–9 (Group 2), AYE VEB-1 (France), OXA-23 clone 2, W strain (UK); lanes 10–12 (Group 3), Midlands 2 (UK), clone I, clone I (Spain). Strains in lanes 1, 3, 4, 5, 6, 7, 9, 10, 11 and 12 were Israel 1, 24, 33, 5/28, 4A, AYE VEB-1, 1, 4C, 5/5 and 9/46, respectively. Lanes labelled M contain a 123-bp size ladder; a negative (water) control is contained in lane 13. Clinical Microbiology and Infection 2007 13, 807-815DOI: (10.1111/j.1469-0691.2007.01759.x) Copyright © 2007 European Society of Clinical Infectious Diseases Terms and Conditions