Application of OrthoANI combined with MALDI-TOF MS in identification and typing of Campylobacter fetus / 中华检验医学杂志

Objective@#Establishing the mass spectrum library of a new Campylobacter- " C.fetus subsp.testudinum" for rapid species identification in clinical microbiology laboratory.@*Methods@#Illumina second generation sequencing platform 2000/miSeq was used to carry out high flux genome sequencing for the strains which were collected to establish mass spectrum library.The analysis oforthologous average nucleotide identity (OrthoANI) between collected strains and reference strains was performed at JAVA 8 operation environment. Then, the mass spectrums ofcollected strains andreference strains were acquired using MALDI-TOF MS. And the mass spectrum library of C. fetus subsp.testudinum. were established and verified.@*Results@#The OrthoANI analysis showed that the OrthoANI value of the collected strains and the reference strain C. fetus subsp.testudinum03-427 was 99.30%-99.96%, while the OrthoANI values of collected strains and C. fetus subsp.venerealisNCTC10354 orC.fetus subsp.fetus82-40 were 91.05%-92.26%. With reference to OrthoANI ≥ 95% as the basis for the determination of the same strain, the strains which collected to establish mass spectrum library was finally identified as " C. fetus subsp.testudinum" . The identification accuracy rate of the mass spectrum library was 100% (consistent with gene sequencing), and the confidence interval was 82.3%-99.9%, identification of the same strain is 100% reproducible.@*Conclusions@#The new" gold standard" based on high throughput sequencing and total genome analysis has provided the ideal reference value for the establishment of mass spectrum library.And the accurate and objective reference spectrum of the" C.fetus subsp.testudinum" provides a new platform for the rapid diagnosis of fetal Campylobacter infection. (Chin J Lab Med, 2018, 41: 583-588)

Identification and classification of non-tuberculosis Mycobacterium by matrix-assisted laser desorption ionization-time of flight mass spectrometry / 中华检验医学杂志

Objective Reference standard of the RPOB(rifampin resistance)gene recommended by CLSI-MM18A(Interpretive Criteria for Identification of Bacteria and Fungi by DNA Target Sequencing) was used to evaluate the ability of MALDI-TOFMS techniques for the identification and classification of non-tuberculous Mycobacterium.Methods Fifty five clinicalstrains were collected from 2012 to 2016 with different sources.The RPOB gene was sequenced, and results were applied to phylogenetics analysis. MALDI-TOF MS technology was implemented to identify the strains, and cluster analysis was conducted based on protein fingerprint.The consistency of two methods for NTM identification and typing was evaluated.Results The RPOB gene method showed a good ability of identification(similarity>99.0%) and subtyping(to subspeciesof the complex level).The French BioMérieux MALDI-TOF MS identified 89.1% of 55 strains to genus level and 78.2% to species level.The phylogeneticsanalysis of protein fingerprint by SARAMS Premium software also showed good typing ability.Conclusions MALDI-TOF MS technology can identify and classify non-tuberculous Mycobacterium effectively,which is rapid and easy.It is complementary to RPOB gene method in laboratory application.