Matrix-assisted laser desorption ionization-time of flight mass spectrometry assigns Escherichia coli to the phylogroups A,B1, B2 and D

Escherichia coli classification into phylogroups reflects the diversity of their pathogenicity and their ecological niche, B2 isolates being the most virulent among extra-intestinal strains. MALDI-TOF MS allows a quick, automated, simple and inexpensive bacterial identification. We evaluated the MALDI-TOF MS as a tool for E. coli phylogroup differentiation.We used 656 E. coli isolates, previously assigned to phylogroup A, B1, B2, and D by multiplex PCR, to constitute independent training and validation sets. We then defined two phylogrouping strategies, both validated on spectra obtained by the ‘direct transfer method’.The first strategy used the MALDI Biotyper software (Bruker Daltonik) that identified a single peak shift between isolates of phylogroup B2 and those of groups A, B1 and D. It accurately classified 89% of the isolates. The second strategy used the ClinProTools software (Bruker Daltonik) and was based on three successive models. The model 1 adequately differentiated 92% of phylogroup B2-isolates from those belonging to phylogroups A, B1, D. The model 2 adequately discriminated 87% of phylogroup D-isolates from those of phylogroups A and B1. The model 3 correctly sorted 69% of A and B1-isolates.We concluded that clinical laboratories could routinely and very quickly assign E. coli isolates to phylogroups with MALDI-TOF MS. These methods could (i) expedite the detection of the most virulent strains belonging to phylogroup B2 and (ii) be a first-line tool to monitor the epidemiology of extra-intestinal pathogenic E. coli.     

Investigation of the presence of carbapenemases in carbapenem-resistant Klebsiella pneumoniae strains by MALDI-TOF MS (matrix-assisted laser desorption ionization-time of flight mass spectrometry) and comparison with real-time PCR method

PurposeWe aimed to develop a new procedure for rapid detection of the carbapenemase activity using MALDI-TOF MS, and to determine the sensitivity and specificity of the method. Also, we aimed to determine the distribution of carbapenemase genes among the K.pneumoniae strains isolated in our hospital using real-time PCR.MethodBetween January 2017–February 2019; K. pneumoniae strains(n = 74) isolated from blood culture samples were included. Klebsiella pneumoniae NCTC 13438 was used as a positive control and Escherichia coli ATCC 25922 as a negative control. First, Imipenem, meropenem, and ertapenem MIC values of strains were determined. Then bla_KPC, bla_OXA-48, and/or bla_NDM genes were investigated with PCR. Carbapenemase activity was investigated in strains with the newly developed method using MALDI-TOF MS. The performance of the new method was evaluated for both the second and fourth hours of the incubation period.ResultsWhile 65 strains were found resistant to tested carbapenems, nine of them were susceptible. Of the 65 resistant strains, 57 had bla_OXA-48, 15 had bla_NDM, and four had bla_KPC genes. Bla_OXA-48 and bla_NDM genes were detected together in 11 strains. Bla_OXA-48, bla_NDM, and bla_KPC genes were not detected in any of the susceptible strains. The sensitivity and specificity of MALDI-TOF MS at the second hour were 83.1% and 100%, respectively. At the fourth hour, the sensitivity and specificity of MALDI-TOF MS were 100%. No false-positive results were observed.ConclusionThe sensitivity of the method at the fourth hour was better than the second hour. The false-negative results observed in the second hour disappeared when the incubation period was extended to 4 h. MALDI-TOF MS which is still under development is a fast, cost-effective, promising method for the detection of carbapenemase activity.     

应用多重PCR和MLPA技术检测DMD患者和携带者的基因突变及产前诊断

目的 应用多重PCR和多重连接依赖探针扩增(multiplex ligation-dependent probe amplification,MLPA)技术检测Duchenne/Becker肌营养不良症(Duchenne/Becker muscular dystrophy,DMD/BMD)患者、携带者并应用于产前诊断.方法 首先采用多重PCR对临床诊断为DMD/BMD的患者检测DMD基因的26个外显子,未查到缺失突变者和可能的携带者采用MLPA检测全部79个外显子是否有缺失或重复突变.对产前诊断病例,用PCR法检测缺失突变,用MLPA法检测重复突变.结果 多重PCR对22例患者的DMD基因的26个外显子检测.13例有缺失突变.未查到常见缺失突变的9例患者经MLPA检测DMD基因的全部79个外显子,3例为重复突变、1例为单个第18外显子缺失、其他5例未查到缺失和重复突变.16例携带者中,3例有家族史,其中2例检出突变;13例为检测到突变的散发病例患儿的母亲,有8例检测到突变.产前诊断9个胎儿(其中双胎1例),2例胎儿有突变,引产后核实无误;7例胎儿未检测到突变,现均已分娩.结论 多重PCR可检出92.86%的缺失突变并可用于缺失突变的产前诊断,因其简便、可靠、价廉可作为临床上DMD/BMD基因诊断的初选.MLPA可用于多重PCR未检测到缺失突变的患者及携带者的检查.     

Relative sensitivity of immunohistochemistry,multiple reaction monitoring mass spectrometry,in situ hybridization and PCR to detect Coxsackievirus B1 in A549 cells

BackgroundEnteroviruses (EVs) have been linked to the pathogenesis of several diseases and there is a collective need to develop improved methods for the detection of these viruses in tissue samples.ObjectivesThis study evaluates the relative sensitivity of immunohistochemistry (IHC), proteomics, in situ hybridization (ISH) and RT-PCR to detect one common EV, Coxsackievirus B1 (CVB1), in acutely infected human A549 cells in vitro.Study designA549 cells were infected with CVB1 and diluted with uninfected A549 cells to produce a limited dilution series in which the proportion of infected cells ranged from 10⁻¹ to 10⁻⁸. Analyses were carried out by several laboratories using IHC with different anti-EV antibodies, ISH with both ViewRNA and RNAScope systems, liquid chromatography multiple reaction monitoring mass spectrometry (LC/MRM/MS/MS), and two modifications of RT-PCR.ResultsRT-PCR was the most sensitive method for EV detection yielding positive signals in the most diluted sample (10⁻⁸). LC/MRM/MS/MS detected viral peptides at dilutions as high as 10⁻⁷. The sensitivity of IHC depended on the antibody used, and the most sensitive antibody (Dako clone 5D8/1) detected virus proteins at a dilution of 10⁻⁶, while ISH detected the virus at dilutions of 10⁻⁴.ConclusionsAll methods were able to detect CVB1 in infected A549 cells. RT-PCR was most sensitive followed by LC/MRM/MS/MS and then IHC. The results from this in vitro survey suggest that all methods are suitable tools for EV detection but that their differential sensitivities need to be considered when interpreting the results from such studies.