Using Next-Generation Sequencing Technology to Confirm the HLA Rare Alleles Detected by PCR-SSOP / 中国实验血液学杂志

OBJECTIVE@#To confirm the HLA genotypes of the samples including 4 cases of magnetic bead probe HLA genotyping result pattern abnormality and 3 cases of ambiguous result detected by PCR sequence-specific oligonudeotide probe (SSOP) method.@*METHODS@#All samples derived from HLA high-resolution typing laboratory were detected by PCR-SSOP. A total of 4 samples of magnetic bead probe HLA genotyping result pattern abnormality and 3 samples of ambiguous result were further confirmed by PCR sequence-based typing (SBT) technology and next-generation sequencing (NGS) technology.@*RESULTS@#A total of 4 samples of magnetic bead probe HLA genotyping result pattern abnormality were detected by PCR-SSOP method. The results of SBT and NGS showed that the HLA-A genotype of sample 1 did not match any known genotypes. NGS analysis revealed that the novel allele was different from the closest matching allele A*31:01:02:01at position 154 with G>A in exon 2, which resulting in one amino acid substitution at codon 28 from Valine to Methionine (p.Val28Met). The HLA-C genotype of sample 2 was C*03:119, 06:02, sample 3 was C*03:03, 07:137, and sample 4 was B*55:02, 55:12. A total of 3 samples with ambiguous result were initially detected by PCR-SSOP method. The re-examination results of SBT and NGS showed that the HLA-B genotype of sample 5 was B*15:58, 38:02, sample 6 was DRB1*04:05, 14:101, and sample 7 was DQB1*03:34, 05:02. Among them, alleles C*03:119, C*07:137 and DRB1*14:101 were not included in the Common and Well-documented Alleles (CWD) v2.4 of the Chinese Hematopoietic Stem Cell Donor Database.@*CONCLUSION@#The abnormal pattern of HLA genotyping results of magnetic probe by PCR-SSOP method suggests that it may be a rare allele or a novel allele, which needs to be verified by sequencing.

Polymorphism of KIR2DL4 gene among northern Chinese Han population / 中国输血杂志

【Objective】 To investigate the polymorphism of KIR2DL4 gene in northern Chinese Han population. 【Methods】 A total of 327 DNA samples were isolated by magnetic beads from unrelated individuals of northern Chinese Han population. The coding sequence (CDS) of KIR2DL4 were amplified using four pairs of KIR2DL4-specific PCR primers developed by our own KIR sequencing-based typing patent, and each exon of KIR2DL4 carried by the four PCR amplicons was then subjected to DNA Sanger sequencing in both directions. The genotype of each sample was assigned using the Assign 4.7 software. 【Results】 Among 327 individuals, 8 different kinds of KIR2DL4 alleles were detected, with observed frequencies ranked as KIR2DL4*00102 [77.1%(252/327)], *00501 [35.8%(117/327)], *011 [20.2%(66/327)], *00602 [12.5%(41/327)], *00801 [8.6%(28/327)], *00103 [4.9%(16/327)], *00503 [1.5%(5/327)] and *00504 [0.9%(3/327)]. In this study, the 10A type alleles which can encode a full membrane-bound receptor include 2DL4*00102, *00103, *00501, *00503, *00504 and *00602, whereas the 9A type alleles which produce truncated forms of receptor include 2DL4*00801 and *011. The observed frequencies for 10A and 9A type KIR2DL4 alleles were 97.6% (319/327) and 27.8% (91/327), respectively. The ratio of 10A to 9A type was 3.5: 1. The observed frequencies of KIR2DL4 alleles in northern Chinese Han population showed no significant difference compared with southern Chinese Han population (P>0.05). 【Conclusion】 The allelic diversity of KIR2DL4 elucidated in the present study can provide valuable data for KIR-associated disease studies and human evolution.

Identification of two novel weak D alleles by sequence-based typing / 中国输血杂志

【Objective】 To study the molecular basis of D variant and explore the molecular genetic mechanism of novel weak D alleles. 【Methods】 Blood samples were screened for D variants by serological method. The nucleotide sequences of coding region were amplified by PCR and sequenced directly, and RHD gene heterozygosity was detected. 【Results】 Weak D phenotype was confirmed by serological test, and two novel alleles were detected by DNA sequencing. The first was novel weak D 1102A allele, 1102G>A mutation in exon 8, resulting in a 368Glu>Arg substitution in two samples. The second was novel weak D 399C allele, carried a 399G>C mutation in exon 3, which led to a 133Lys>Asn substitution. 【Conclusion】 In this study, D variants were detected by sequence-based typing, and two new alleles were identified.

Analysis of full-length sequence and 18 point mutations of HLA-B in a leukemia patient and her family / 中国组织工程研究

BACKGROUND: The human leukocyte antigen (HLA) has undergone long-term evolution to form diverse polymorphisms. In recent years, due to the increase in the number of examinees and the rapid development of HLA typing technology, novel HLA alleles have been discovered constantly. OBJECTIVE: To analyze the full-length sequence and 18 point mutations of HLA-B gene in a leukemia patient and her family using the next-generation sequencing technology. METHODS: Polymerase chain reaction and sequence-specific oligonucleotide probes (PCR-SSOP) and polymerase chain reaction-sequence based typing (PCR-SBT) revealed abnormalities in the patient’s HLA-B. To identify the genotype, we sequenced the full length of the gene by next-generation sequencing technology and collected blood samples from the patient’s father, mother and two sisters for genetic analysis of HLA genes. RESULTS AND CONCLUSION: Both PCR-SSOP and PCR-SBT indicated that the HLA-B sample had no perfectly matched genotype. Further detection using the next-generation sequencing technology revealed that the novel allele had 18 base mutations in the exon, intron and 3’UTR compared to the most homologous allele B*15:09:01. Five exon base mutations were located in the exons 3 and 4, which were: 486G→C, 583T→C, 636T→C, 652A→G, 756C→T, resulting in changes in the five corresponding codons, including 171 tyrosine (Tyr) → histidine (His) and 194 isoleucine (Ile) → valine (Val). A pedigree survey found that the patient’s novel HLA B allele was inherited from her father. The novel allele sequence was submitted to the Genbank database (MG595995). A novel HLA-B allele was confirmed by the next-generation sequencing, which was officially named HLA-B*15:435 by the World Health Organization HLA Factor Nomenclature Committee in December 2017.

A protective effect conferred by KIR3DL1 and its cognate ligand against cervical cancer among ethnic Han Chinese population and its potential mechanism / 中华医学遗传学杂志

Objective@#To explore the role of inhibitory KIR (iKIR) and its cognate HLA ligand in the occurrence and development of cervical cancer among ethnic Han Chinese and its potential mechanism.@*Methods@#Peripheral blood samples from 265 Han Chinese patients with cervical intraepithelial neoplasia (CIN)/cervical cancer and 200 ethnically matched healthy controls were collected. The results of KIR PCR-SSP, HLA PCR-rSSO and KIR3DL1 PCR-SBT, together with cervical cancer data from the TCGA database, were used to assess the association of iKIR genes, receptor-ligand gene combinations, iKIR transcription level in the tumor tissue and the KIR3DL1 alleles with the occurrence and development of cervical cancer.@*Results@#Among the four iKIR genes (KIR2DL1, 2DL2/3, 3DL1 and 3DL2), the frequencies of KIR3DL1 and KIR3DL1-HLA-Bw4 genes among controls were significantly higher than those of the cervical cancer group (96.5% vs. 87.0%, P = 0.018; 81.5% vs. 64.8%, P=0.009). The survival rate of cervical cancer patients with a high transcription level of KIR3DL1 in tumor tissues was significantly higher than those with a low/medium transcription level (P = 0.028). The frequency of strong-inhibitory and high-expression KIR3DL1*01502 allele among the healthy population was significantly higher than that of the cervical cancer group (76.0% vs. 59.3%, P = 0.015).@*Conclusion@#Combined KIR3DL1 and KIR3DL1-HLA-Bw4 can confer a protective effect against the development of cervical cancer, which may be attributed to the strong-inhibitory and high-expression allele of KIR3DL1*01502.

Application of NASBA and RPA in detection of pathogenic bacteria / 中华流行病学杂志

Nucleic acid sequence-based amplification and recombinase polymerase amplification are the recently developed thermostatic amplification techniques based on PCR. This paper briefly summarizes the principle of reaction, design principle of primer and probe, advantage of these two techniques (simple, accurate, highly sensitive and rapid) and introduces the application of the techniques in the detection of pathogenic bacteria.

Biological and Genetic Characteristics of Clinically Isolated Enterobacter cloacae with Multidrug Resistance

BACKGROUND: From January 2014 to December 2015, 69 clones of Enterobacter cloacae showing multidrug resistance to six classes of antimicrobial agents were collected from two medical centers in Korea. METHODS: Minimum inhibitory concentrations were determined using the E-test method, and 17 genes were detected using polymerase chain reaction (PCR). The epidemiological relatedness of the strains was identified using repetitive element sequence-based PCR and multilocus sequence typing. RESULTS: The 69 E. cloacae clones produced extended spectrum β lactamase (ESBL) and AmpC and showed multidrug resistance to cefotaxime, ceftazidime, and aztreonam. We identified the following sequence types: ST56 of type VI for ESBL SHV (N=12, 17.4%); ST53, ST114, ST113, and ST550 of types I, IV, VI, and VII, respectively, for CTX-M (N=11, 15.9%); and ST668 of type III for the carbapenemase NDM gene (N=1, 1.5%). The AmpC DHA gene (N=2, 2.89%) was confirmed as ST134, although its type was not identified, whereas EBC (MIR/ACT; N=18, 26.1%) was identified as ST53, ST24, ST41, ST114, ST442, ST446, ST484, and ST550 of types V, I, III, IV, VII, and VI, respectively. The formed subclasses were bla CTX-M-3 and bla CTX-M-22 by CTX-M-1, bla CTX-M-9 and bla CTX-M-125 by CTX-M-9, bla DHA-1 by DHA, and bla MIR-7 and bla ACT-15,17,18,25,27,28 by EBC (MIR/ACT). CONCLUSIONS: There were no epidemiological relationships between the gene products and the occurrence of resistance among the strains.

Distribution of the bla OXA, bla VEB-1, and bla GES-1 genes and resistance patterns of ESBL-producing Pseudomonas aeruginosa isolated from hospitals in Tehran and Qazvin, Iran

Abstract INTRODUCTION: Pseudomonas aeruginosa is one of the most common nosocomial pathogens. The emergence of extended spectrum β-lactamases (ESBLs) has been increasingly reported as a major clinical concern worldwide. The main aim of the present study was to determine the distribution of bla OXA, bla PER-1, bla VEB-1, and bla GES-1 genes among ESBL-producing P. aeruginosa isolated from two distinct provinces in Iran. METHODS: In this study, a total of 75 (27.5%) ESBL-producing isolates were identified from 273 P. aeruginosa isolates collected from patients in Qazvin and Tehran. Phenotypic detection of ESBLs and antimicrobial susceptibility testing were performed according to the Clinical and Laboratory Standards Institute guidelines. PCR and sequencing were employed to detect bla OXA-1, bla OXA, bla GES-1, bla PER-1, and bla VEB-1 genes. Isolate genetic relationships were evaluated by repetitive extragenic palindromic sequence-based PCR (REP-PCR). RESULTS: In total, 59 (78.7%) of the ESBL-producing isolates showed multidrug resistance. The highest rates of susceptibility were observed against colistin (75 isolates, 100%) and polymyxin B (75, 100%) followed by amikacin (44, 58.7%), and piperacillin-tazobactam (40, 53.3%). The bla OXA-1 (37.3%) gene was the most common of the genes investigated, followed by bla OXA-4 (32%), bla GES-1 (16%), and bla VEB-1 (13.3%). REP-PCR identified three different genotypes: types A (89.3%), B (6.7%), and C (4%). CONCLUSIONS: We found a significant presence of bla OXA-1, bla OXA-4, bla GES-1, and bla VEB-1 genes among P. aeruginosa isolates, highlighting the need for suitable infection control strategies to effectively treat patients and prevent the further distribution of these resistant organisms.

Detection of nucleic acid sequence-based amplification products by gold nanoprobe-based solution hybridization for the diagnosis of invasive aspergillosis / 临床检验杂志

Objective To establish a method of gold nanoprobe-based solution hybridization (GNBSH) to detect nucleic acid sequence-based amplification (NASBA) products for the rapid diagnosis of invasive aspergillosis (IA).Methods The Aspergillus specific 18S rRNA was amplified by NASBA and then the amplified products were hybridized with the gold nanoprobes which were modified with thiol compounds at the 5'end.Serum samples from 106 patients,including 14 with a definite IA,32 with suspected IA and 60 without IA,were detected by the established method,and the obtained results were compared with that of galactomannan (GM) test to evaluate its accuracy.Results The gold nanoprobes only hybridized with Aspergillus NASBA products but not other non-Aspergillus strains.The sensitivity,specificity and the area under the ROC curve (AUCROC) of the established GNBSH method for detecting 106 clinical samples were 82.61％ (38/46),81.67％ (49/60) and 0.890,respectively.The sensitivity,specificity and AUCROC of GM test were 56.52％ (26/46),83.33％ (50/60) and 0.723,respectively.Conclusion The established GNBSH method to detect Aspergillus NASBA products has high sensitivity and specificity and simple operation,which may be used to detect the infection of Aspergillus by clinical laboratories.

Correlation between HLA-B~* 13:01 allele and liver dysfunction in patients with occupational medicamentosa-like dermatitis due to trichloroethylene / 中国职业医学

OBJECTIVE: To explore the correlation between human leukocyte antigen( HLA)-B~* 13 : 01 allele and liver dysfunction in patients with occupational medicamentosa-like dermatitis due to trichloroethylene( OMDT). METHODS: Twenty patients with OMDT were chosen as study subjects by using a convenient sampling method. The sequence-based genotyping method was used for detecting HLA-B~* 13 : 01 allele in the DNA samples from peripheral blood of all study subjects. The serum levels of total protein,albumin,total bilirubin,direct bilirubin and alanine aminotransferase,aspartate aminotransferase and alkaline phosphatase activities in patients were examined. The correlation between the number of HLA-B~* 13 : 01 alleles and the liver function indices was also analyzed. RESULTS: There were 16 patients carrying HLA-B~* 13: 01 allele. The serum total protein in the HLA-B~* 13: 01 carriers was higher than that of non-carriers( P < 0. 05). The serum total protein was positively correlated with the number of patients carrying HLA-B~* 13: 01 alleles( P < 0. 05). CONCLUSION: The degree of liver function damage in OMDT patients may be related to carrying the HLA-B~* 13: 01 allele.

Sequence Analysis and Identification of A Novel HLA-A* 2 4∶3 2 7 Allele Been Designated by the HLA Nomenclature Committee of WHO / 现代检验医学杂志

Objective To do analysis of sequence and identify a novel HLA-A allele in Chinese hematopoietic stem cell do-nors.Methods A rare HLA-A allele was initially detected by Luminex PCR-SSO typing,then the sample was sequenced by sequence-based typing (SBT)and the group-specific sequencing primer (GSSP)to confirm the mutation allele and locus.Re-sults The sequence of the sample results showed that the allele compared with the highest homologous allele HLA-A*24∶02∶01∶01 was the difference in the exon 3 at position 544 G>A,resulting in an amino acid sequence of HLA-A*24∶02∶01∶01 at position 158 change Ala to Thr.Conclusion This allele is a new HLA-A allele and has been designated as HLA-A*24∶327 by the HLA Nomenclature Committee of World Health Organization (WHO).

Comparison Analysis of HLA-B27 Detected by PCR-SBT and IMS-ELISA in AS Patients / 现代检验医学杂志

Objective To compare PCR-SBT to IMS-ELISA in the HLA-B27 detection in the ankylosing spondylitis (AS)pa-tients.Methods Simultaneously,PCR-SBT and IMS-ELISA were used to detect the HLA-B27 expression in peripheral blood samples which were suspected patients with AS from 120 cases.Chisquare test of paired design and the area under curve of receiver operating characteristics of SPSS17.0 software were used to evaluate the value of PCR-SBT and IMS-ELISA in HLA-B27 detection of AS patients.Results Among 120 cases of suspected patients with AS,the positive rates of HLA-B27 detected by PCR-SBT and IMS-ELISA were 45.83%(55/120)and 37.50% (45/120),respectively.There was statistical difference between the two methods in the HLA-B27 detection (χ2 =59.455,P =0.000).The sensibility and spe-cificity of PCR-SBT were 96.36% and 96.92%,respectively.While the sensibility and the specificity of IMS-ELISA were 69.09% and 89.23%,respectively.Area under the curve of two methods were 0.966 and 0.792,respectively.Conclusion In comparison with IMS-ELISA,the sensibility and the specificity of PCR-SBT in HLA-B27 detection were higher in AS diag-nosis,that is to say,PCR-SBT is better in HLA-B27 detection and AS diagnosis.

Contamination and homology of carbapenem-resistant Acinetobacter baumannii from hospital environmental object surface / 中国感染控制杂志

Objective To investigate the contamination of carbapenem-resistant Acinetobacter baumannii (CRAB) from object surface of key departments in a hospital,and identify whether these CRAB were homologous. Methods Environmental hygienic monitoring in intensive care unit (ICU),emergency intensive care unit(EICU), hemodialysis room and operating room was conducted.Acinetobacter baumannii (A.baumannii)isolated from ICU and EICU environmental specimens were amplified and typed by enterobacterial repetitive intergenic consensus-poly-merase chain reaction (ERIC-PCR).Results Except hand hygiene of health care workers in EICU was qualified, bacterial count of object surface of ICU and EICU were all unqualified;detection results of specimens from hemodi-alysis room and operating room were all qualified.A total of 53 specimens were taken from object surface of ICU and EICU,7 (13.21 %)A.baumannii isolates were isolated,and all were CRAB isolates,6 of which were of the same genotype and were identical with A.baumannii from patients’sputum.Conclusion CRAB isolated from object surface in key departments is homologous,cleaning and disinfection of environmental object surface should be inten-sified to reduce the occurrence of healthcare-associated infection.

The correlation between human leukocyte antigens-A, B, DRB1 high-resolution alleles and chronic renal failure caused by immunoglobulin-a nephropathy / 中华器官移植杂志

Objective To investigate the correlation between human leukocyte antigens-A,-B,-DRB1 (HLA-A,-B,-DRB1) high resolution alleles and chronic renal failure (CRF) caused by immunoglobulin-a nephropathy (IgAN).Method The polymerase chain reaction-sequence-based typing (PCR-SBT) method was used to investigate the genotypes of HLA-A,-B and-DRB1 high-resolution alleles in 191 cases of CRF caused by IgAN (experimental group) and 503 healthy blood donors (control group).The alleles frequencies between two groups were compared and the association between CRF caused by IgAN and the polyrnorphism of HLA was analyzed.Result (1) There were 25 alleles at A locus,48 alleles at B locus and 32 alleles at DRB1 locus in experimental group.(2) The genetic frequency of HLAA * 2901 [Pc =0.033,OR =10.738,95％ CI (1.193,96.691)],HLA DRB1 * 1106 [Pc =0.0001,OR =0.969,95％ CI (0.944,0.994)],HLA-DRB1 * 1202[Pc =0.002,OR =1.859,95％ CI (1.259,2.745)],HLA-DRB1 * 1401 [Pc =0.021,OR =0.984,95％ CI (0.967,0.998)],HLA-DRB1 * 1602[Pc=0.015,OR=1.915,95％ CI (1.157,3.17)] in experimental group was higher than in control group (P＜0.05).Conclusion There is susceptibility association of HLA-A * 2901,HLA-DRB1 * 1106,HLA-DRE * 1202,HLA-DRB1 * 1401,HLA-DRB1 * 1602 with CRF caused by IgAN.It is concluded that there is a close genetic and immunological correlation between HLA alleles and the pathogenesis of CRF caused by IgAN.

Resolution of Ambiguous HLA Genotyping in Korean by Multi-Group-Specific Sequence-Based Typing

PURPOSE: To evaluate a multi-group-specific sequence-based typing (SBT) method for resolving ambiguous results from human leukocyte antigen (HLA) genotyping. MATERIALS AND METHODS: A total of 50 samples that showed ambiguous genotypes for at least two HLA loci from HLA-A, -B, -C and -DRB1 by the conventional SBT assay were evaluated using a new SBT test, the AVITA plus assay. The most likely HLA genotypes for the respective samples considering allele frequencies in Korean were concordant between the AVITA and conventional SBT assays. RESULTS: An average of 3.3 loci among the HLA-A, -B, -C and -DRB1 loci per sample gave results with two or more possible allele combinations with the conventional SBT, and 48 (96.0%) out of 50 showed reduced numbers of possible genotypes for at least one HLA locus with the AVITA. A total of 41, 43, 42, and 38 cases among the 50 samples showed ambiguous results for HLA-A, -B, -C, and -DRB1 typing by the conventional SBT, respectively. The average numbers of possible allele combinations for the respective four HLA loci were 8.2, 6.7, 5.9, and 3.2, and they were reduced to 1.5, 2.2, 4.4, and 1.8, respectively, by the AVITA. Ambiguity was resolved by the AVITA in 33 (80.5%), 31 (72.1%), 17 (40.5%) and 28 (73.7%) samples among the ambiguous cases from the conventional SBT for HLA-A, -B, -C, and -DRB1 typing, respectively. CONCLUSION: The multi-group-specific SBT method considerably reduced the number of ambiguous results, and thus may be useful for accurate HLA typing in clinical laboratories.

Diagnostic value of immediate early antigen-mRNA in the diagnosis of cytomegalovirus infection after kidney transplantation / 中国综合临床

Objective To investigate the diagnostic value of the immediate early antigen(IE) mRNA by nucleic acid sequence-based amplification(NASBA) in peripheral blood cytomegalovirus (CMV) infection,and to establish and promote the diagnosis method for CMV.Methods Five to seven ml blood was taken from 32 patients at 3 week and 7 week after renal transplantation to detect serum cytomegalovirus antigen and antibody expression by NASBA,Real time-PCR and enzyme-linked immunosorbent assay (ELISA) sensitivity and specificity were compared.Results The results of CMV detection in 32 renal transplanted patients respectively showed that the positive rate of peripheral blood IE-mRNA by NASBA was 45.8％ (15/32) ;The positive rate of HCMV-DNA in blood by Real time-PCR was 45.8％ (15/32).Using ELISA,the positive rate of HCMV-(IgG +IgM) was 37.5％ (14/32).IE-mRNA and HCMV-DNA had higher sensitivity and specificity and lower false positive rate than HCMV-(IgG +IgM).The positive rates of IE-mRNA by NASBA,Real time-PCR and ELISA were 92.8％,71.5％ and 42.8％ respectively in the 14 cases.Conclusion The nucleic acid amplification method (NASBA based sequence) and Real time-PCR are sensitive,rapid diagnosis methods of HCMV infection,with higher sensitivity and specificity and lower false positive rate than traditional ELISA.And NASBA detection of IE-mRNA has good value for auxiliary clinical diagnosis.

Relationship between the density difference of microRNA binding and the evolution-ary conservation of 3′UTRs in housekeeping and non-housekeeping human genes / 军事医学

Objective To study the microRNA ( miRNA) regulation on the expression of housekeeping and non-house-keeping human genes from the systemic level , and to reveal the influence of conservation at 3′UTRs region for the density difference of miRNA regulatory between the two classes of genes .Methods We obtained miRNA regulation informations for the two classes of genes through the integration analysis of three sequence-based target gene prediction softwares and the conjoint analysis based on gene expression profile data .We also used phastCons-score based evolution analysis to study the conservation of 3′UTRs regions between the two classes of genes .Results Our results showed that housekeeping genes have a significantly higher density of miRNA binding sites and their 3′UTR are relatively conservative .Conclusion These findings highlight the importance of miRNA regulation in housekeeping genes , suggesting that investigating the roles of miR-NAs on the robustness of housekeeping genes expression is highly necessary .

Molecular Typing in Public Health Laboratories: From an Academic Indulgence to an Infection Control Imperative / 예방의학회지

Using three Austrian case studies, the variegated applications of molecular typing in today's public health laboratories are discussed to help illustrate preventive management strategies relying on DNA subtyping. DNA macrorestriction analysis by pulsed field gel electrophoresis has become the gold standard for subtyping of food borne pathogens like listeria, salmonella, campylobacter and Bacillus cereus. Using a Salmonella Mbandaka outbreak from the year 2010 as example, it is shown how the comparison of patterns from human isolates, food isolates, animal isolates and feed isolates can allow to identify and confirm a source of disease. An epidemiological connection between the simultaneous occurrence of tuberculosis in cattle and deer with cases of human tuberculosis due to Mycobacterium caprae in 2010 was excluded using mycobacterial interspersed repetitive units variable-number tandem repeats subtyping. Also in 2010, multilocus sequence typing with nonselective housekeeping genes, the so-called sequence based typing protocol, was used to elucidate connections between an environmental source (a hospital drinking water system) and a case of legionellosis. During the last decades, molecular typing has evolved to become a routine tool in the daily work of public health laboratories. The challenge is now no longer to simply type microorganisms, but to type them in a way that allows for data exchange between public health laboratories all over the world.

Real-Time Nucleic Acid Sequence-Based Amplification to Predict the Clinical Outcome of Invasive Aspergillosis

Monitoring the response to therapy for invasive aspergillosis (IA) is essential for the management of patients with hematologic diseases. We evaluated the correlation between the outcome of real-time nucleic acid sequence-based amplification (RTi-NASBA) for Aspergillus 18S rRNA and the clinical outcome of IA. A total of 157 serum samples from 29 patients with IA were tested for RTi-NASBA. The treatment response and mortality were compared with the NASBA outcome (whether the NASBA value was converted to negative or not) at 12 weeks after the start of antifungal therapy. At 12 weeks, there was a moderate correlation between the treatment failure and persistently positive NASBA (kappa = 0.482; P = 0.019). Deaths attributable to IA were more prevalent in patients without negative conversion of NASBA than in those with negative conversion (50% vs 5%; P = 0.013). Significant factors of treatment failure at 12 weeks were the status of hematologic disease (nonremission; P = 0.041) and the NASBA outcome (failure of negative conversion; P = 0.024). Survival was significantly better in patients with negative conversion of NASBA than those with persistently positive values (P = 0.036). This study suggests that the serial monitoring of RTi-NASBA could be useful for prediction of the clinical outcome in hematologic patients with IA.

Typing methods and DL MRSA Library database in study of MRSA causing nosocomial infection / 中华临床感染病杂志

Objective To investigate the drug resistance,source and molecular epidemiology of methicillin-resistant Staphyloccus aureus(MRSA)causing nosocomial infection. Methods Fifty-seven pathogenic MRSA strains were isolated from Beijing Tongren Hospital during 2007 and 2008.K-B method,MIC assay,multiple PCR,automatic repetitive element sequence-based PCR(REP-PCR)typing platform and DL MRSA Library were used to identify the resistant phenotypes,Panton-Valentine leukocidin gene (pvl)and REP-PCR types of the MRSA.Results All strains were classified as 6 antibiotic resistant phenotypes(a-f)based on the resistance to rifampin,clindamycin,levofloxacin and cotrimoxazole.The MRSAs with Staphylococcal cassette chromosome mec(SCCmec)Ⅲ and SCCmec Ⅱ accounted for 91.23% (52/57)and 5.26%(3/57)of all strains,respectively.Only one strain was pvl positive.All strains were typed as REP-A-F(6 types)and three single clones by automatic REP-PCR typing platform,in which REP-C was predominant(30/57,52.63%).Three out of 6 REP-D strains were from laryngology wards.The REP-C-SCCmec Ⅲ were genetically most close to the Brazilian clone-SCCmec Ⅲ in DL MRSA Library.Conclusion s REP-C-SCCmec Ⅲ-a type are the major epidemic hospital-associated MRSA and the REP-D-SCCmec Ⅲ-d is usually isolated from patients received laryngeal surgery. Automatic REP-PCR typingplatform combined with DL MRSA Library database is an effective approach to study the nosocomial infection.