Preliminary application experience of disk microfluidic chip for detecting CALR gene mutation in patients with cerebral infarction / 中华检验医学杂志

Objective:To establish a disk (CD) microfluidic chip detection platform for the rapid detection of CALR-1 and CALR-2 mutations in patients with cerebral infarction, and summarize its clinical application value.Methods:Based on microfluidic technology and loop mediated isothermal amplification technology, a CD microfluidic chip detection platform for simultaneous detection of CALR-1 and CALR-2 gene mutations were established, and the sensitivity, specificity, repeatability and accuracy of the platform were verified. A total of 124 patients with cerebral infarction treated in Huashan Hospital, Shanghai Medical College, Fudan University from November 2019 to March 2021 were prospectively selected into the experimental group; and 80 healthy subjects were included in the control group. The CALR-1 and CALR-2 gene mutations in anticoagulant peripheral blood samples were detected by the CD microfluidic chip. Each chip could detect 4 samples at the same time and synchronously detect 3 indexes of each sample. The detection results could be obtained after isothermal amplification for 40 min. At the same time, sequencing method was used to verify the test results, and the consistency of the results of the two detection methods was compared.Results:Using this CD microfluidic chip platform, the synchronous amplification of 3 indexes in the sample could be completed within 40 min without the need of thermal circulation, and the whole detection process of the sample could be completed within 60 min. For samples with a high concentration of target nucleic acid, typical positive signals could be visualized after amplification for 10 min, and the test results would be available within 30 minutes after receiving the samples. The detection sensitivity of CD microfluidic chip method for CALR-1 and CALR-2 mutation load concentration was 1.0% and 0.5% respectively. Nonspecific amplification was not observed for the non-target nucleic acid samples, indicating the high specificity of this method. The coincidence rates of intra and inter batch repeatability were 100% (20/20) respectively. Two samples with CALR gene mutation were found in the cerebral infarction group, both of which were CALR-1 mutations (L367fs*46). There was no CALR-1 or CALR-2 mutation in the control group. The detection results of CD microfluidic chip method were completely consistent with the sequencing verification results (100% [204/204]).Conclusions:The CD microfluidic chip method could be used for the detection of CALR-1 and CALR-2 gene mutations in clinical samples of patients with cerebral infarction. This method has the advantages of high detection sensitivity, good detection specificity, fast detection speed and high detection flux, which is helpful to clarify the etiology of patients with cerebral infarction.

The challenge of MALDI-TOF MS technique in clinical microbiological diagnosis and application / 中华检验医学杂志

MALDI-TOF MS is a revolutionary and innovative technologyin clinical microbiological diagnosis. Due to its advantages of speed, specificity and ease of operation, MALDI-TOF MS has been rapidly accepted and approved by clinical laboratory. However, many challenges appeared when applied in clinical application. For example, sample preparation needs to be further optimized. Identification techniques have limitations. The quality improvement of database and the diversity of microbial species are still under discussion.The application of antimicrobial susceptibility testing is still controversial.The way ofrare identification resultstransmitting into clinical treatment is still being explored. But the application of MALDI-TOF MS in clinical microbiological diagnosis still needs to be improved.(Chin J Lab Med, 2018, 41: 559-562)

Mechanisms of carbapenem and fosfomycin resistance in an Escherichia coli strain isolated from bloodstream infection / 中国感染与化疗杂志

Objective This study was designed to determine the mechanisms of carbapenem and fosfomycin resistance in an Escherichia coli strain isolated from bloodstream infection in Huashan Hospital,Shanghai in 2010 and the mode of transmission of resistance genes.Methods The Escherichia coli isolate was characterized by antibiotic susceptibility testing,multilocus sequence typing (MLST),molecular identification of resistance genes,plasmid typing and the resistant genetic environment analysis.Results It was found that the isolate was resistant to carbapenem,fosfomycin and produced extended-spectrum β-1actamases.MLST genotyping showed it belonged to ST46.The carbapenem-resistant gene blaKPC-2 and fosfomycin resistant genefosA3 co-located on the same conjugative plasmid (～ 70 kb).The β-lactamases gene blaTEM and blaCTX-M located on another conjugative plasmid (～ 150 kb).PCR mapping showed that blaKPC-2 gene located in the structure Tn1721-blaKPC-2-Tn3 andfosA3 gene located between two IS26 elements.Conclusions This Escherichia coli strain isolated from bloodstream infection carried multiple antibiotic resistant genes,including blaKPC-2,fosA3,blaTEM,and blaCTX-M.More attention should be paid to the mechanisms of antibiotic resistance and transmission of resistance genes in Escherichia coli isolates for better control of hospital infections.

Molecular characteristics of Streptococcus pneumoniae in Shanghai, China / 中华检验医学杂志

Objective Toinvestigate the molecular characteristics including antibiotic resistance,strain type,serotype,virulence,biofilm formation of Streptococcus pneumoniae isolated from Shanghai adult patients.Methods A total of 37 non-repetitive S.pneumoniae isolates causing community acquired and hospital acquired infections of adults were collected from Shanghai Huashan Hospital from January 2011 to December 2013.The inhibitory zone diameter or minimum inhibitory concentrations (MICs) of 9 antimicrobial agents (penicillin,vancomycin,erythromycin,clindamycin,levofloxacin,cefprozi,ceftriaxone,cefotaxime and linezolid) were determined by Kirby-bauer (K-B) method or Etest method;Serotypes were tested by polymerase chain reaction (PCR) and S.pneumoniae antisera agglutination;Genomic characteristics of different serotype strains were determined by pulsed field gel electrophoresis (PFGE)method;Multilocus sequence types (MLST) was used for strain type;Semi quantitative biofilm formation test was used for the biological membrane formation.Ten main pneumococcal virulence genes (cbpA,pspA,cps2A,lytA,nana,pavA,piaA,ply,psaA and spxB) were detected by PCR and gel electrophoresis.Statistical analysis was performed using Stata software and association statistics were tested using Fisher's exact test.Results The most frequent serotypes were 19F (13.5％),23 F (13.5％),14 (10.8％),19A (10.8％).The penicillin resistance rate was 64.9％.Serotypes 19 F,19A and 23 F were significantly associated with penicillin resistance (x2 =5.89,P =0.015) and the isolates belonged to these serotypes were all multi-drug resistant (MDR).ST81 and ST271 showed high resistance rates to several antibiotics including penicillin (x2 =4.57,P =0.033).Biofilm formation was significantly associated with serotypes 19A (x2 =5.55,P =0.018) and strain type ST320 (x2 =4.33,P =0.037),but not associated with penicillin resistance (x2 =0.16,P =0.686).Virulence gene lytA,pavA,ply,psaA,spxB were found in all isolates.Conclusions Penicillin resistance rate of S.pneumoniae in adult is rising.Specific serotype,epidemic clone and antibiotic resistance are closely related,and can provide the basis for the infection control.The virulence factors such as PspA will be the new targets for vaccine development to reduce S.pneumoniae infection in the future.

Distribution of the novel cell wall anchored protein-encoding gene sasX in Staphylococcus aureus strains / 中华检验医学杂志

ObjectiveTo investigate the distribution and effect on antibiotic resistance of the novel cell wall anchored protein-encoding gene sasX.MethodsA total of 300 S.aureus isolates were randomly collected from inpatients with S.aureusinfection in ShanghaiHuashanhospitalin 2004, 2007and 2010.Meanwhile,170 S.aureus isolates from the nasal swabs of healthy people were collected as part of a population-based community prevalence study.Typing of S.aureus isolates were identified by using multilocus sequence typing (MLST) and S.aureus-specific staphylococcal protein A typing (spa typing).Determination of oxacillin MICs was used to screen MRSA.PCR and sequencing were used to analyze sasX gene.The effect on antibiotic resistance of sasX gene was detect by disc agar diffusion drug sensitive test.ResultsThe major clonal types of the 300 S.aureus isolates collected from inpatients with S.aureus infection were ST239 ( 110,36.7％) and ST5 (122,40.7％).From 2004 to 2010,the percentage of isolates from inpatients with S.aureus infection was increased from 17％ to 39％,but sasX was only found in 0.59％ of the S.aureus isolates from the nasal swabs of healthy people.The percentage of sasX positive was increased from 47.2％ to 83.8％ in ST239.The percentage of sasX positive MRSA was increased from 26.4％ to 50.8％,but the percentage of sasX positive MSSA was about 10％.Antibiotic resistance of sasX positive strains were higher than that of sasX negative strains.Conclusions SasX gene is mainly detected in nosocomial pathogenic S.aureus and it is a possible virulence factor of S.aureus in hosptal setting.The presence of sasX gene is related to antibiotic resistance.For better understanding the real function of this novel gene,further studies such as expression of the encoded protein should be carried out.

Molecular characterization of Staphylococcus aureus collected from 2004 to 2010 in patients with blood stream infection / 中华检验医学杂志

Objective To investigate the clonal types of Staphylococcus aureus collected from 2004to 2010 in patients with blood stream infection from a Grade A tertiary care hospital in Shanghai as well as the dynamic changes and to detect the variation in antimicrobial resistance and virulence-gene content in different strain types.Methods A total of 103 nonduplicate S.aureus isolates were collected from 2004 to 2010 from inpatients with S.aureus blood stream infection from Shanghai Huashan hospital.Determination of oxacillin MICs and the type of SCCmec gene were used to screen MRSA.Typing of S.aureus isolates was identified by using multilocus sequence typing(MLST) and S.aureus-specific staphylococcal protein A typing(spa typing),PCR was used to detect the antimicrobial resistance and virulence-gene.Results Sixtysix isolates(64.1%) MRSA were detected in 103 nonduplicate S.aureus isolates,and 35 isolates were MRSA with SCCmec type Ⅱ ,Twenty-nine isolates were MRSA with SCCmec type Ⅱ,two isolates were MRSA with SCCmec type Ⅳ,Thirty-seven isolates(35.9%) were MSSA.Thirty-three MRSA isolates were ST5,Twenty-nine MRSA isolates were ST239,two MRSA isolates were ST59,one MRSA isolates was ST641 and one MRSA isolates was ST6.All of the other clones belonged to MSSA.The percentage of ST5 and ST239 were decreased significantly after 2009(ST5 was decreased from 52.9% to 15.4%; ST239 was decreased from 61.1% to 15.4%),and new clonal types MSSA increased significantly(in 2009,the percentage of ST7 was 41.7%; new clonal types such as ST188 and ST15 were detected in 2010).In 2010,it was shown that 84.6% of MSSA were isolated from S.aureus blood stream infection,nineteen isolates(18.4%) harbored mupA gene and 41 isolates(39.8%) harbored qacA/B gene in 103 nonduplicate S.aureus isolates.It was shown that 70.6% ST239 harbored qacA/B gene.Four isolates of ST398 and 1 isolates of ST9were detected which were originally from animal.There was no significant difference of the virulence gene presence in the same strain types except sasX、lukSF and arcA genes,but there were a lot of genes which were restricted to different genomic background.Conclusions The percentage of ST5 and ST239 were decreased and new clonal types of MSSA were increased significantly in S.aureus blood stream infection,antimicrobial resistance and virulence-gene were restricted to different clonal types.

Rapid identification and susceptibility testing of positive blood culture caused by gram negative bacteria / 中华微生物学和免疫学杂志

Objective To reduce the turnaround time for laboratory diagnosis of bacteremia, the feasibility of rapid identification and susceptibility testing using samples taken directly from positive blood culture bottles was evaluated. Methods The growth of microorganisms in blood culture bottles was screened by the BACTEC 9000 blood culture system. 65 positive blood culture bottles containing gram-negative bacteria were adopted to test. Culture fluid was injected into BD SST vacutainer and centrifuged to pellet blood cells. After collecting required McFarland units, they were cultured on Phoenix 100 NMIC/ID-4(identification-gram-negative bacteria and susceptibility testing) cards using 0.25 McF and 0.5 McF methods respectively. They were also evaluated by the standard method, involving subculture tests from positive blood culture bottles. Results 63 of 65 gram-negative bacteria (96. 9% ) were correctly identified with 0. 25 McF method. 59 of 65 gram-negative bacteria(90.8% ) were correctly identified with 0.5 McF method. For antimicrobial susceptibility testing, the 0.25 McF direct method had an agreement rate more than 94% , the 0.5 McF method was more than 85.7% and direct blood sample KB method was more than 93.8% compared to the standard method. But the overall minor error rate in susceptibility testing of direct blood sample KB method is higher than other methods. Conclusion Applying 0. 25 McF and 0. 5 McF rapid identification and susceptibility test was practical. During to possessing more prominent advantages, laboratory put the 0. 25 McF direct method into practice had a timely, remarkable significance.

Analysis of cefoxitin-sensitive, penicillin-resistant Staphylococcus tested by disk diffusion method / 中华检验医学杂志

Objective To evalue the ability of detecting the resistance of cefoxitin-sensitive,penicillin-resistant Staphylococcus by different methods and analyze the antibiotic susceptibility spectrum of coagulase-negative Staphylococcus which are non-mecA-mediated oxacillin resistance. Methods All the isolates were collected from Huashan hospital between 2007 and 2009. The isolates were recovered from various clinical sources, including respiratory tract, urine, secretion and sterile fluids samples. The oxacillin susceptibility of Staphylococcus aureus was determined by cefoxitin disk diffusion test, cefoxitin MIC test,oxacillin disk diffusion test and oxacillin MIC test Likewise, the oxacillin susceptibility of coagulasenegative Staphylococcus was determined by cefoxitin disk diffusion test and oxacillin MIC test. All the isolates with sensitive to cefoxitin were screened for the mec A gene by PCR Finally, the MIC of non-mecA-mediated oxacillin-resistant Staphylococcus were determined. Results Among 255 cefoxitin disk diffusion test sensitive and penicillin-resistant Staphylococcus aureus, 6 isolates were intermediated to oxacillin and 4 were resistant by oxacillin disk diffusion test, but all the isolates were sensitive by the cefoxitin disk diffusion test,cefoxitin MIC test and oxacillin MIC test. Among 75 cefoxitin disk diffusion test sensitive and penicillin-resistant coagulase-negative Staphylococcus, 16 isolates were resistant to oxacillin by oxacillin MIC method and 4 carried mecA gene. Among 12 non-mecA-mediated oxacillin-resistant Staphylococcus, the susceptible isolates of gentamicin is 10, clindamycin is 8, ciprofloxacin is 11, erythrornycin is 6, trimethoprim/sulfamethoxazo]e is 11 ,and cephalosporins, teicoplaninl, vancomycin, piperacillin/tazobactam, tetracycline are all 12. Conclusions The cefoxitin disk diffusion test can reliably predict mecA-mediated oxacillin resistant Staphylococcus aureus. It would be best to combine cefoxitin disk diffusion test and oxacillin MIC test to improve accuracy of detection of mecA-mediated oxacillin resistant coagulase-negative Staphylococcus.Furthermore, infections due to the non-mecA-mediated oxacillin resistant coagulase-negative Staphylococcus can be treated by penicillinase-stable penicillins, β-lactam/β-lactam inhibitor combinations, relevant cephems and carbapenems.