CTX-M-3 extended-spectrum beta-lactamase in a Shigella sonnei clinical isolate: First report from Turkey

A Shigella sonnei strain resistant to cefotaxime and aztreonam (but not ceftazidime) was isolated from the stool sample of a 7-y-old outpatient. Double disk synergy test, isoelectric focusing, polymerase chain reaction and sequence analysis confirmed that the isolate produced CTX-M-3, an extended-spectrum beta-lactamase (ESBL). This is the first report from Turkey of Shigella spp. producing an ESBL, and of CTX-M type enzyme

The Identification of Acinetobacter baumannii Blood Isolates by MALDI-TOF MS, ARDRA and bla(OXA-51-like) Gene-Specific Real-Time PCR

The Acinetobacter cakoaceticus-Acinetobacter baumannii (Acb) complex consists of phenotypically very similar nosocomial species; A.baumannii, Acinetobacter nosocomialis, Acinetobacter pittii, Acinetobacter seifertii and Acinetobacter djikshoorniae and one environmental species Acakoaceticus. The rapid and accurate identification of the members of Acb complex is critical as these nosocomial pathogens can show differences in antimicrobial susceptibility and clinical outcomes. The conventional phenotypic methods are slow, unreliable and less efficient for the differentiation of Acb complex species, including the A.baumannii species within the Acb complex. Although various molecular methods are available, such as amplified ribosomal DNA restriction analysis (ARDRA) and bla(OXA-51-like), gene specific PCR, they are usually inconvenient for the routine diagnostic laboratories. Recently, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) offers an opportunity for rapid, cost-effective and convenient bacterial identification in routine diagnostic procedures conducted in clinical laboratory. In this study, we aimed to evaluate the diagnosis performance of MALDI-TOF MS system to identify blood isolates of A.baumannii. A total of 180 nonduplicate carbapenem resistant Acb complex (strain numbers; TR1-TR60) and A.baumannii (TR61-TR180) blood isolates were collected from the intensive care units of the three university hospitals in Turkey from January 2016 to December 2016. All isolates were evaluated by using bla(OXA-51-like) gene specific real time (Rt-PCR) analysis, ARDRA (restriction enzymes-AIM, Cfol, Mbol, Mspl, Rsal) method and MALDI-TOF MS (VITEK (R) MS, bioMerieux, France) system. All the strains except TRIO, TR31, TR35 and TR52 were identified as A.baumannii by ARDRA method. Out of 177 of all the isolates, presence of bla(OXA-51-like) gene was found except for TR10, TR31 and TR52 isolates. However, TR31 without the presence of bla(OXA-51-like) gene was identified as A.pittii using the ARDRA. Totally 176 isolates which were identified as A. baumannii by both of the methods, ARDRA and Rt-PCR-bla(OXA-51-like) ,were accepted as a reference for the evaluation of the diagnosis performance capacity of the MALDI-TOF MS. Overall, for all 176 isolates tested, the sensitivity obtained with the MALDI-TOF MS were 99.4% with 75% specificity. The accuracy value of the method was determined as 98.9% for the identification of A.baumannii to the species level. MALDI-TOF MS is increasingly used in diagnostic microbiology for the routine identification of bacteria to the genus, species or subspecies level with high rates of sensitivity and specificity. In future, by expanding the database, MALDI-TOF MS system would possibly become the ideal method for routine diagnostic laboratories that could potentially identify more species and even determine some characteristics of antimicrobial resistance and virulence determinants

Molecular Characterization of Carbapenem-Resistant Acinetobacter baumannii Blood Culture Isolates from Three Hospitals in Turkey

We aimed to investigate the clonal relationships, common sequence types, and carbapenemase genes in 177 non-repetitive blood culture isolates of Acinetobacter baumannii collected from patients at three university hospitals in Turkey in 2016. Molecular epidemiological characteristics of the isolates were examined using pulsed-field gel electrophoresis (PFGE), and multilocus sequence typing (MLST) (Pasteur scheme-cpn60, fusA, gltA, pyrG, recA, rplB, and rpoB). Multiplex PCR was used to investigate the carbapenemase genes, including bla(OXA-23-like),bla(OXA-24-like), bla(OXA-48-like), bla(OXA-58-like), bla(IMP), bla(VIM) and bla(NDm). PFGE genotyping yielded 92 pulsotypes with a clustering ratio of 69.7%. As per a >= 85% similarity coefficient, 159 (90.9%) isolates were found to be clonally related. The bla(OXA-)(23-like) and bla(OXA-)(58)-like genes were identified in 100% and 28.2% of the isolates, respectively. The bla(NDM) gene was identified in two isolates. The MLST analysis included 54 isolates with different pulsotypes, and 29 sequence types (STs). Most of the isolates (n = 36) belonged to the clonal complex (CC)2, one isolate belonged to CC1, and one isolate belonged to CC164. Sixteen new STs (ST1235-ST1250) were identified. Identifying both global ST2 and a large number of new STs, revealed high genetic diversity in A. baumannii isolates in the study population