Identification and Characterization of Clostridium difficile Sequence Type 37 Genotype by Matrix-Assisted Laser Desorption Ionization
            <b>–</b>
            Time of Flight Mass Spectrometry

Li, Ruxin; Xiao, Di; Yang, Jing; Sun, Suzhen; Kaplan, Samuel E.; Li, Zhirong; Niu, Yanan; Qiang, Cuixin; Zhai, Yu; Wang, Xiaoming; Zhao, Xinghui; Zhao, Bin; Welker, Martin; Pincus, David; Jin, Dazhi; Kamboj, Mini; Zheng, Guoan; Zhang, Guojun; Zhang, Jianzhong; Tang, Yi‐Wei; Zhao, Jianhong

doi:10.1128/jcm.01990-17

Cited by 21 publications

(14 citation statements)

References 38 publications

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“…In addition, according to Cooper et al [26], the animal call rate was also related to genotyping accuracy, the individual call rate ranged from 96-99% in our study. All the above results demonstrated that the genotyping data got in the present study was validated, and the method of MALDI-TOF MS could be a stable platform for genotyping those SNPs [27,28].…”

Section: Resultssupporting

confidence: 63%

Selection and implementation of SNP markers for parentage analysis in a Chinese crossbred cattle population

Hu¹,

Liu²,

Chu³

et al. 2020

Preprint

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Combining direct sequencing method in polymerase chain reaction (PCR) products of deoxyribonucleic acid (DNA) pooling and matrix-assisted laser desorption/ionisation time of flight mass spectrometry (MALDI-TOF MS) genotyping method in individuals, a panel consisting of 50 highly informative single nucleotide polymorphisms (SNPs) for parentage analysis was developed in a crossbred Chinese cattle population. The average minor allele frequency (MAF) was 0.43 and the cumulative exclusion probability for single-parent and both-parent inference met 0.99797 and 0.999999, respectively. The maker-set was then used for parentage verification in a group of 81 trios with the likelihood-based parentage-assignment program of Cervus software. Compared with on-farm records, the results showed that this 50-SNP system could provide sufficient and reliable information for parentage testing with the parental mistakes for mother-offspring and sire-offspring being 8.6% and 18.5%, respectively. Knowledge of these results, we provided one low-cost and efficient method of SNP assays for running paternity testing in crossbred cattle population of Simmental and Holstein in China.

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Section: Resultssupporting

confidence: 63%

Selection and implementation of SNP markers for parentage analysis in a Chinese crossbred cattle population

Hu¹,

Liu²,

Chu³

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…In addition, according to Cooper et al [21], the call rate of the animal was also related to genotyping accuracy, the individual call rate ranged from 96-99% in our study. All the above results revealed that the genotyping data got in the present study was validated, and the method of MALDI-TOF MS could be a stable platform for genotyping those SNPs [22,23].…”

Section: Discussionsupporting

confidence: 61%

Selection and implementation of SNP markers for parentage analysis in a Chinese crossbred cattle population

Liu

Chu

et al. 2020

Preprint

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Background: In China, the widespread crossbreeding between Simmental and Holstein is a universal way so as to better improve the comprehensive benefits, as well as decline the inbreeding coefficient. However, the wrong parentage appeared frequently in this population than others due to not only the reasons in pure breeds, but more importantly, the lack of enough attention, which caused the lower accuracy of genetic parameter estimation and genetic evaluation in breeding systems. Single nucleotide polymorphism (SNP) panel in a certain population as a powerful tool for parentage assignment has been reported in numerous studies, especially in cattle. Therefore, the aim of this study was to build an SNP panel with sufficient power for parentage testing in the crossbred population of Simmental and Holstein in China. Results: In the present study, combining direct sequencing method in polymerase chain reaction (PCR) products of deoxyribonucleic acid (DNA) pooling and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) genotyping method in individuals, a panel comprising 50 highly informative single nucleotide polymorphisms (SNPs) for parentage analysis was developed in a crossbred Chinese cattle population. The average minor allele frequency (MAF) was 0.43 and the cumulative exclusion probability for single-parent and both-parent inference met 0.99797 and 0.999999, respectively. The maker-set was then used for parentage verification in a group of 81 trios with the likelihood-based parentage-assignment program of Cervus software. Compared with on-farm records, the results showed that this 50-SNP system could provide sufficient and reliable information for parentage testing with the parental mistakes for mother-offspring and sire-offspring being 8.6% and 18.5%, respectively.Conclusion: Knowledge of these results, we provided one set of low-cost and efficient SNPs for running paternity testing in the crossbred cattle population of Simmental and Holstein in China. Keywords: Parentage analysis, Single nucleotide polymorphism (SNP), Chinese crossbred cattle

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“…A recent study in China reported that RT 017 can also be identified using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) with high sensitivity and specificity [45]. However, this study did not include other C. difficile strains from clade 4 and another Chinese study suggested that different clade 4 strains may not be distinguishable by this method [46].…”

Section: Characteristics Of C Difficile Rt 017mentioning

confidence: 99%

Clostridium difficile ribotype 017 – characterization, evolution and epidemiology of the dominant strain in Asia

Imwattana

Knight

Kullin

et al. 2019

Emerging Microbes & Infections

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Clostridium difficile ribotype (RT) 017 is an important toxigenic C. difficile RT which, due to a deletion in the repetitive region of the tcdA gene, only produces functional toxin B. Strains belonging to this RT were initially dismissed as nonpathogenic and circulated largely undetected for almost two decades until they rose to prominence following a series of outbreaks in the early 2000s. Despite lacking a functional toxin A, C. difficile RT 017 strains have been shown subsequently to be capable of causing disease as severe as that caused by strains producing both toxins A and B. While C. difficile RT 017 strains can be found in almost every continent today, epidemiological studies suggest that the RT is endemic in Asia and that the global spread of this MLST clade 4 lineage member is a relatively recent event. C. difficile RT 017 transmission appears to be mostly from human to human with only a handful of reports of isolations from animals. An important feature of C. difficile RT 017 strains is their resistance to several antimicrobials and this has been documented as a possible factor driving multiple outbreaks in different parts of the world. This review summarizes what is currently known regarding the emergence and evolution of strains belonging to C. difficile RT 017 as well as features that have allowed it to become an RT of global importance.

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Identification and Characterization of Clostridium difficile Sequence Type 37 Genotype by Matrix-Assisted Laser Desorption Ionization – Time of Flight Mass Spectrometry

Cited by 21 publications

References 38 publications

Selection and implementation of SNP markers for parentage analysis in a Chinese crossbred cattle population

Selection and implementation of SNP markers for parentage analysis in a Chinese crossbred cattle population

Selection and implementation of SNP markers for parentage analysis in a Chinese crossbred cattle population

Clostridium difficile ribotype 017 – characterization, evolution and epidemiology of the dominant strain in Asia

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