Molecular analysis of Acinetobacter baumannii strains isolated in Lebanon using four different typing methods

• Published in: PloS one Vol. 9; no. 12; p. e115969
• Main Authors: Rafei, Rayane, Dabboussi, Fouad, Hamze, Monzer, Eveillard, Matthieu, Lemarié, Carole, Gaultier, Marie-Pierre, Mallat, Hassan, Moghnieh, Rima, Husni-Samaha, Rola, Joly-Guillou, Marie-Laure, Kempf, Marie
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 26-12-2014; Public Library of Science (PLoS)
• Subjects: Acinetobacter; Acinetobacter baumannii; Acinetobacter baumannii - drug effects; Acinetobacter baumannii - genetics; Acinetobacter baumannii - isolation & purification; Acinetobacter Infections - diagnosis; Acinetobacter Infections - epidemiology; Acinetobacter Infections - microbiology; Analysis; Anti-Bacterial Agents - pharmacology; Bacterial Typing Techniques; Biology and Life Sciences; Carbapenems - pharmacology; Cloning; Clustering; Collection; Drug Resistance, Bacterial; Electrophoresis, Gel, Pulsed-Field; Epidemics; Epidemiology; Gel electrophoresis; Genes; Hospitals; Humans; Identification; Lebanon - epidemiology; Life Sciences; Medicine and Health Sciences; Methods; Molecular Epidemiology; Multilocus Sequence Typing; Nosocomial infections; Outbreaks; Polymerase Chain Reaction; Population structure; Population studies; Research and Analysis Methods; Strains (organisms); Lebanon; France; United States > US
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0115969

This study analyzed 42 Acinetobacter baumannii strains collected between 2009-2012 from different hospitals in Beyrouth and North Lebanon to better understand the epidemiology and carbapenem resistance mechanisms in our collection and to compare the robustness of pulsed field gel electrophoresis (PFGE), multilocus sequence typing (MLST), repetitive sequence-based PCR (rep-PCR) and blaOXA-51 sequence-based typing (SBT). Among 31 carbapenem resistant strains, we have detected three carbapenem resistance genes: 28 carried the blaOXA-23 gene, 1 the blaOXA-24 gene and 2 strains the blaOXA-58 gene. This is the first detection of blaOXA-23 and blaOXA-24 in Lebanon. PFGE identified 11 types and was the most discriminating technique followed by rep-PCR (9 types), blaOXA-51 SBT (8 types) and MLST (7 types). The PFGE type A'/ST2 was the dominant genotype in our collection present in Beyrouth and North Lebanon. The clustering agreement between all techniques was measured by adjust Wallace coefficient. An overall agreement has been demonstrated. High values of adjust Wallace coefficient were found with followed combinations: PFGE to predict MLST types  = 100%, PFGE to predict blaOXA-51 SBT = 100%, blaOXA-51 SBT to predict MLST = 100%, MLST to predict blaOXA-51 SBT = 84.7%, rep-PCR to predict MLST = 81.5%, PFGE to predict rep-PCR = 69% and rep-PCR to predict blaOXA-51 SBT = 67.2%. PFGE and MLST are gold standard methods for outbreaks investigation and population structure studies respectively. Otherwise, these two techniques are technically, time and cost demanding. We recommend the use of blaOXA-51 SBT as first typing method to screen isolates and assign them to their corresponding clonal lineages. Repetitive sequence-based PCR is a rapid tool to access outbreaks but careful interpretation of results must be always performed.