Objective Antimicrobial resistance(AMR)has become a global concern and is especially severe in China.To effectively and reliably provide AMR data,we developed a new high-throughput real-time PCR assay based on microfl...Objective Antimicrobial resistance(AMR)has become a global concern and is especially severe in China.To effectively and reliably provide AMR data,we developed a new high-throughput real-time PCR assay based on microfluidic dynamic technology,and screened multiple AMR genes in broiler fecal samples.Methods A high-throughput real-time PCR system with an new designed integrated fluidic circuit assay were performed AMR gene detection.A total of 273 broiler fecal samples collected from two geographically separated farms were screened AMR genes.Results The new assay with limits of detection ranging from 40.9 to 8,000 copies/reaction.The sensitivity rate,specificity rate,positive predictive value,negative predictive value and correct indices were 99.30%,98.08%,95.31%,99.79%,and 0.9755,respectively.Utilizing this assay,we demonstrate that AMR genes are widely spread,with positive detection rates ranging from 0 to 97.07%in 273 broiler fecal samples.bla CTX-M,bla TEM,mcr-1,fex A,cfr,optr A,and int I1 showed over 80%prevalence.The dissemination of AMR genes was distinct between the two farms.Conclusions We successfully established a new high-throughput real-time PCR assay applicable to AMR gene surveillance from fecal samples.The widespread existence of AMR genes detected in broiler farms highlights the current and severe problem of AMR.展开更多
Here,we report the identification of Histoplasma causing an unexplained disease cluster in Matthews Ridge,Guyana.In March 2019,14 employees of Chongqing Bosai Mining Company,China,working in a manganese mining of Guya...Here,we report the identification of Histoplasma causing an unexplained disease cluster in Matthews Ridge,Guyana.In March 2019,14 employees of Chongqing Bosai Mining Company,China,working in a manganese mining of Guyana,had unexplained fever,and two of them died.We obtained lung and brain tissues as well as the blood samples from the two deceased cases(patient No.1 and 2),and bronchoscopy lavages and cerebrospinal fluid samples from one severe case(patient No.3),respectively.All samples were tested by pathological examination,high-throughput sequencing,and real-time PCR.Pathological detection showed the presence of spore-like structures in the lung tissue of patient No.1,indicating a fungal infection in this patient.Nanopore sequencing identified the existing of H.capsulatum in the lung tissue sample within 13 h.Next-generation sequencing identified specific fragments of H.capsulatum in all of the samples tested(lung,brain and blood serum from the deceased cases,and plasma from the severe case).Real-time PCR assays did not reveal any viral infection related to transmission from bat feces.We conclude that H.capsulatum was the causative pathogen of this disease cluster based on epidemiologic,clinical,pathological and nucleic acid evidence.展开更多
基金supported by the National Natural Science Foundation of China [Grant agreement 31502124]the National Science and Technology Major Project of China [Grant agreement 2018ZX10733402]
文摘Objective Antimicrobial resistance(AMR)has become a global concern and is especially severe in China.To effectively and reliably provide AMR data,we developed a new high-throughput real-time PCR assay based on microfluidic dynamic technology,and screened multiple AMR genes in broiler fecal samples.Methods A high-throughput real-time PCR system with an new designed integrated fluidic circuit assay were performed AMR gene detection.A total of 273 broiler fecal samples collected from two geographically separated farms were screened AMR genes.Results The new assay with limits of detection ranging from 40.9 to 8,000 copies/reaction.The sensitivity rate,specificity rate,positive predictive value,negative predictive value and correct indices were 99.30%,98.08%,95.31%,99.79%,and 0.9755,respectively.Utilizing this assay,we demonstrate that AMR genes are widely spread,with positive detection rates ranging from 0 to 97.07%in 273 broiler fecal samples.bla CTX-M,bla TEM,mcr-1,fex A,cfr,optr A,and int I1 showed over 80%prevalence.The dissemination of AMR genes was distinct between the two farms.Conclusions We successfully established a new high-throughput real-time PCR assay applicable to AMR gene surveillance from fecal samples.The widespread existence of AMR genes detected in broiler farms highlights the current and severe problem of AMR.
基金This work was supported by grants from the China MegaProjects for Infectious Disease(2018ZX10713-002,2018ZX10711001,2017ZX10104001,and 2017ZX10302301-004-002).
文摘Here,we report the identification of Histoplasma causing an unexplained disease cluster in Matthews Ridge,Guyana.In March 2019,14 employees of Chongqing Bosai Mining Company,China,working in a manganese mining of Guyana,had unexplained fever,and two of them died.We obtained lung and brain tissues as well as the blood samples from the two deceased cases(patient No.1 and 2),and bronchoscopy lavages and cerebrospinal fluid samples from one severe case(patient No.3),respectively.All samples were tested by pathological examination,high-throughput sequencing,and real-time PCR.Pathological detection showed the presence of spore-like structures in the lung tissue of patient No.1,indicating a fungal infection in this patient.Nanopore sequencing identified the existing of H.capsulatum in the lung tissue sample within 13 h.Next-generation sequencing identified specific fragments of H.capsulatum in all of the samples tested(lung,brain and blood serum from the deceased cases,and plasma from the severe case).Real-time PCR assays did not reveal any viral infection related to transmission from bat feces.We conclude that H.capsulatum was the causative pathogen of this disease cluster based on epidemiologic,clinical,pathological and nucleic acid evidence.