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An expectation–maximization algorithm for estimating proportions of deletions among bacterial populations with application to study antibiotic resistance gene transfer in Enterococcus faecalis

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Marine Life Science & Technology 2023年第1期5卷 28-43页

作者： Yu Zhang Cong Zhang Wenwen Huo Xinlei Wang Michael Zhang kelli palmer Min Chen School of Mathematical Sciences Ocean University of ChinaQingdao266000China Department of Mathematical Sciences University of Texas at DallasRichardsonTX75080USA Department of Biological Sciences University of Texas at DallasRichardsonTX75080USA Department of Statistical Science Southern Methodist UniversityDallasTX75205USA MOE Key Laboratory of Bioinformatics Tsinghua UniversityBeijing100084China Department of Population and Data Sciences UT Southwestern Medical CenterDallasTX75390USA

The emergence of antibiotic resistance in bacteria limits the availability of antibiotic choices for treatment and infection control,thereby representing a major threat to human *** de novo mutation of bacterial genomes is an essential mechanism by which bacteria acquire antibiotic ***,deletion mutations within bacterial immune systems,ranging from dozens to thousands of base pairs(bps)in length,have been associated with the spread of antibiotic *** current methods for evaluating genomic structural variations(SVs)have concentrated on detecting them,rather than estimating the proportions of populations that carry distinct SVs.A better understanding of the distribution of mutations and subpopulations dynamics in bacterial populations is needed to appreciate antibiotic resistance evolution and movement of resistance genes through ***,we propose a statistical model to estimate the proportions of genomic deletions in a mixed population based on Expectation–Maximization(EM)algorithms and next-generation sequencing(NGS)*** method integrates both insert size and split-read mapping information to iteratively update estimated *** proposed method was evaluated with three simulations that demonstrated the production of accurate *** proposed method was then applied to investigate the horizontal transfers of antibiotic resistance genes in concert with changes in the CRISPR-Cas system of ***.

关键词： Bacterial genomes CRISPR-Cas system Antibiotic resistance EM algorithm Proportion estimation

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Screening for arboviruses in healthy blood donors: Experience from Karachi, Pakistan

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Virologica Sinica 2022年第5期37卷 774-777页

作者： Moiz Ahmed Khan Kehkashan Imtiaz Humaira Shafaq Joveria Farooqi Mohammad Hassan Afia Zafar Maureen T.Long kelli L.Barr Erum Khan Clinical Microbiology Laboratory Department of Pathology&Lab MedicineAga Khan UniversityKarachi 74800Pakistan Blood Bank Haematology&Transfusion MedicineDepartment of Pathology&Lab MedicineAga Khan UniversityKarachi 74800Pakistan Comparative Diagnostic and Population Medicine University of FloridaGainesville FL32611USA Center for Global Health and Infectious Disease Research University of South FloridaTampa FL33620USA

Dear Editor,Arboviruses of medical importance are maintained in nature in enzootic cycles between haematogenous vectors and susceptible vertebrate hosts(Huang et al.,2019).The rapid increase in human populations around the globe and the associated urbanization are creating irreversible damage to the ecosystem,giving rise to many problems including emergence and intensification of the vector borne diseases(Sutherst,2004).Among vector borne diseases,mosquito-borne arboviruses including dengue virus(DENV),West Nile virus(WNV),Japanese Encephalitis virus(JEV)and Zika virus(ZIKV)are rapidly emerging in the affected regions of the world(palmer et al.,2011).

关键词： maintained irreversible Pakistan

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