Evaluation of restriction enzymes for standardizing pulsed-field gel electrophoresis protocol for rapid subtyping of Vibrio parahaemolyticus

We evaluated the cost-effectiveness of the restriction enzymes with rare-cutting sites in the genome of Vibrio parahaemolyticus RIMD 2210633 for pulsed-field gel electrophoresis (PFGE) analysis. The evaluation indicated that PFGE with both NotI and SfiI was discriminatory, but NotI was more cost-effective. Based on the results of this study, we suggest using NotI and SfiI as the 1st and the 2nd restriction enzyme for standardizing the PulseNet PFGE protocol for molecular subtyping and global surveillance of V. parahaemolyticus.     

Candidemia due to Candida tropicalis: clinical, epidemiologic, and microbiologic characteristics of 188 episodes occurring in tertiary care hospitals

Candida tropicalis is the 2nd most frequent agent of candidemia in Brazil (20-24%). We attempted to characterize the epidemiology, microbiology, and outcome of candidemia due to C. tropicalis by comparing patients with candidemia due to C. tropicalis with those with candidemia due to Candida albicans. Among the 924 episodes of candidemia, 188 (20%) were caused by C. tropicalis. These cases were compared with 384 candidemias due to C. albicans. C. tropicalis was the 2nd most frequent species in adults (21.6%) and elderly patients (23.2%), and 3rd in neonates (11.9%) and children (18.5%). Cancer was the most frequent underlying disease, and in adults and elderly patients, diabetes was the 2nd most frequent underlying disease. The only difference between C. tropicalis and C. albicans candidemia was a higher proportion of neutropenic patients in C. tropicalis candidemia. C. tropicalis is a leading cause of candidemia in Brazil, and its epidemiology is similar to that of C. albicans.     

Invasive infection in an acute myeloblastic leukemia patient due to triazole-resistant Candida tropicalis

Non-albicans Candida species are being increasingly reported as causes of nosocomial fungal infections. For example, invasive candidiasis caused by C. tropicalis has been associated with hematologic malignancies. In this study, we report a fatal case of fungemia and a possible urinary and pulmonary infection in a leukemia patient that was due to a strain of C. tropicalis resistant to 2 triazole antifungals.     

The suitable restriction enzymes for pulsed-field gel electrophoresis analysis of Bordetella pertussis

We searched the restriction enzymes with rare cutting sites on the genome of Bordetella pertussis strain Tohama I using the Restriction Digest Tool software provided in the Institute for Genomic Research web site. The usefulness of 5 enzymes for pulsed-field gel electrophoresis (PFGE) analysis was evaluated with 68 B. pertussis isolates. The results indicated that AflII, DraI, SpeI, and XbaI were useful enzymes, and AflII was the best one for PFGE analysis of B. pertussis isolates.     

Comparison of multilocus variable-number tandem repeat analysis and pulsed-field gel electrophoresis in molecular subtyping of Salmonella enterica serovars Paratyphi A

Salmonella enterica serotype Paratyphi A is a highly clonal organism; pulsed-field gel electrophoresis (PFGE) is insufficient in discriminating isolates. A multilocus variable-number tandem repeat analysis (MLVA) was developed, and its usefulness in discriminating isolates was compared. PFGE analysis with XbaI and BlnI discriminated 55 isolates into 14 types, with a discriminatory index (DI) of 0.741 (confidence interval [CI], 0.635-0.847). MLVA divided the isolates into 23 types, with a DI of 0.937 (CI, 0.909-0.964), which was significantly higher than that for PFGE. Clustering analysis of PFGE and MLVA patterns indicated that S. Paratyphi A isolates recovered from 2000 to 2010 in South and Southeast Asia were highly clonal. Although MLVA is not sufficiently powerful in discriminating epidemiologically unrelated isolates, it can complement PFGE for epidemiologic investigation of S. Paratyphi A infections.     

Comparison of automated repetitive-sequence-based polymerase chain reaction and spa typing versus pulsed-field gel electrophoresis for molecular typing of methicillin-resistant Staphylococcus aureus

Automated repetitive polymerase chain reaction (PCR) (DiversiLab, bioMérieux, St. Laurent, Quebec, Canada) and single locus sequence typing of the Staphylococcus protein A (spa) gene with spa-type assignment by StaphType RIDOM software were compared to pulsed-field gel electrophoresis (PFGE) as the "gold standard" method for methicillin-resistant Staphylococcus aureus (MRSA) typing. Fifty-four MRSA isolates were typed by all methods: 10 of known PFGE CMRSA type and 44 clinical isolates. Correct assignment of CMRSA type or cluster occurred for 47 of 54 (87%) of the isolates when using a rep-PCR similarity index (SI) of ≥95%. Rep-PCR gave 7 discordant results [CMRSA1 (3), CMRSA2 (1), CMRSA4 (1), and CMRSA10 (2)], and some CMRSA clusters were not distinguished (CMRSA10/5/9, CMRSA 7/8, and CMRSA3/6). Several spa types occurred within a single PFGE or repetitive PCR types among the 19 different spa types found. spa type t037 was shared by CMRSA3 and CMRSA6 strains, and CMRSA9 and most CMRSA10 strains shared spa type t008. Time to results for PFGE, repetitive PCR, and spa typing was 3-4 days, 24 h, and 48 h, respectively. The annual costs of using spa or repetitive PCR were 2.4× and 1.9× higher, respectively, than PFGE but routine use of spa typing would lower annual labor costs by 0.10 full-time equivalents compared to PFGE. Repetitive PCR is a good method for rapid outbreak screening, but MRSA isolates that share the same repetitive PCR or PFGE patterns can be distinguished by spa typing.     

Molecular characterization of Italian Candida parapsilosis isolates reveals the cryptic presence of the newly described species Candida orthopsilosis in blood cultures from newborns

The authors report the molecular characterization of Candida parapsilosis isolates recovered from the blood and venous central catheter tips of patients admitted to different care units of the Polyclinic Hospital, University of Messina, Italy. Among 97 presumed C. parapsilosis isolates examined, 94 were identified as C. parapsilosis sensu stricto and the remaining 3 isolates were found to belong to the cryptic species Candida orthopsilosis which was recovered only from blood cultures of neonates (<30 days old) born prematurely. No C. metapsilosis was found in this study. This study emphasizes the role of C. parapsilosis as an important nosocomial pathogen, and it also describes, for the first time, the occurrence of C. orthopsilosis in newborns.     

A simple xylose-based agar medium for the differentiation of Candida dubliniensis and Candida albicans

The utility of xylose-based agar medium for differentiation of Candida dubliniensis from Candida albicans is evaluated. All C. dubliniensis isolates failed to grow on this medium, while C. albicans isolates yielded good growth. This simple in-house medium offers an inexpensive alternative to commercial yeast identification systems for resource poor settings.     

Rapid discrimination between Candida albicans and Candida dubliniensis by using real-time polymerase chain reaction

Several phenotypic methods have been used for the differentiation of Candida albicans and Candida dubliniensis, but molecular investigations are considered most reliable in their diagnostic value. Here, we suggest a rapid real-time polymerase chain reaction assay where the discrimination was achieved through melting point analysis with the help of the nonspecific fluorescent dye SybrGreen.     

Application of hypertonic Sabouraud glucose agar for differentiation of Candida dubliniensis from Candida albicans

An evaluation of hypertonic Sabouraud glucose agar (SGA) with 6.5% NaCl for phenotypic differentiation of Candida dubliniensis from Candida albicans is reported. Identity of the test fungi (C. albicans, 84; C. dubliniensis, 18) was based on their typical phenotypic characteristics and confirmed by a diagnostic polymerase chain reaction that targets the novel C. dubliniensis group I intron in the large ribosomal subunit. At 96 h of incubation at 28 °C, all of the 84 C. albicans isolates showed growth on hypertonic SGA contrary to the consistently negative results with the 20 C. dubliniensis isolates. In strong contrast, chlamydospore formation on Staib agar yielded 10 (11.9%) false-positive results and 74 (88%) of the test C. albicans isolates showed false-negative results at 45 °C. We conclude that hypertonic SGA with 6.5% NaCl can be recommended for wider application as a reliable and inexpensive medium for routine differentiation of C. dubliniensis from C. albicans.     

Therapy and outcome of Candida glabrata versus Candida albicans bloodstream infection

Candida glabrata is a common cause of bloodstream infection (BSI) and exhibits reduced susceptibility to antifungal agents. Those with C. glabrata BSI may therefore be at increased risk for a delay in receiving appropriate therapy and poor treatment outcome. We compared treatment and outcome of patients with C. glabrata to controls with Candida albicans BSI. Each patient with C. glabrata BSI from July 1997 through December 2004 was matched with a control patient infected with C. albicans. Appropriateness of therapy was defined using current guidelines, and the mortality end point was 30 days following the initial positive blood culture. Overall, 78% of patients received appropriate therapy (39/54 [72%] for C. glabrata versus 45/54 [83%] for C. albicans, P = 0.2). Crude 30-day mortality was high for both groups (41% for C. glabrata versus 44% for C. albicans, P = 0.7). There was no trend in mortality according to time of therapy initiation, but mortality was lower for those who received appropriate therapy (35% versus 71% for inappropriate therapy, P = 0.002). Twelve percent of patients received no antifungal therapy and contributed disproportionately to overall crude mortality. Strategies to decrease the incidence of untreated candidemia may favorably impact outcome.     

应用脉冲场凝胶电泳分型技术对江西省伤寒菌株的分析

目的 分析江西省1986年以来伤寒爆发疫情菌株的分子分型特征.方法 对所收集的伤寒沙门菌株利用脉冲场凝胶电泳(PFGE)技术进行菌株的分子分型.结果 40株伤寒菌株分离自1986、1987、2000和2003年的伤寒患者和带菌者,利用PFGE可分为16个型.不同年份、不同地点爆发的伤寒菌株带型不同,同一年份同一地点爆发的伤寒菌株带型也有差异.结论 基于PFGE的分子分型能很好地应用于菌株特征的分析,伤寒杆菌在不同年份变异较大.常规的疫苗是否能应对不同PFGE型菌株的流行值得关注.     

Evaluation of automated repetitive-sequence-based PCR (DiversiLab) compared to PCR ribotyping for rapid molecular typing of community- and nosocomial-acquired Clostridium difficile

Automated repetitive PCR (rep-PCR; DiversiLab) was compared to PCR ribotyping of the 16S-23S RNA intergenic spacer of Clostridium difficile (CD) as the "gold standard" method for CD typing. PCR products were separated on DiversiLab LabChips (bioMérieux, St. Laurent, Quebec, Canada) utilizing a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) operating the DiversiLab v1.4 assay. Bioanalyzer data were exported to a secure DiversiLab website and analyzed with DiversiLab v3.4 software. Replicability of each method was verified by confirming that the 5 CD reference strains (RS) formed distinct clusters (CD4, CD6, VL0047, VL0013 [ribotype 027], VL0018 [ribotype 001]) by both typing methods. Ninety randomly selected clinical isolates (CS) were analyzed by both methods: 49 from community-acquired and 41 from hospital-acquired cases. A similarity index (SI) of ≥90% was used to define clusters when comparing the known RS cluster to the PCR ribotyping and rep-PCR patterns of CS. Fourteen different PCR-ribotype clusters were identified, but most CS formed 4 major clusters (i.e., CD4 [15/90; 17%], CD6 [17%], 027 [12%], and 001 [9%]). A total of 7 rep-PCR types were identified, but most CS formed 2 major rep-PCR clusters (i.e., CD4 [29/90; 32%] and CD6 [23%]); several PCR ribotypes occurred within a single rep-PCR cluster. Rep-PCR did not distinguish 027 or 001 isolates; i) 027 RS strain did not cluster, ii) eleven 027 CS strains clustered as CD4, iii) no 027 CS strains clustered with the 027 RS, and iv) only 2 001 CS clustered with the RS. Agreement between the PCR-ribotype and rep-PCR clusters only occurred for 35/90 (39%) of the CS using a rep-PCR SI of ≥90%. Rep-PCR time to results was similar, but the annual costs of routinely using this method are 32% higher than PCR ribotyping. Routine use of rep-PCR for CD typing is limited by its lack of definitive separation of the hypertoxigenic 027 or 001 outbreak CD strains.     

Genotyping of Vibrio alginolyticus isolates from Daya Bay by infrequent-restriction-site PCR and pulsed-field gel electrophoresis

Vibrio alginolyticus is a serious bacterial pathogen that hampered the whole industry of fish farming in Guangdong, China. In order to facilitate epidemiologic studies and improve the control of disease, we developed a highly efficient method of genotyping for V. alginolyticus using infrequent-restriction-site PCR (IRS-PCR) technology. With the enzyme combination of NotI-HhaI, optimized, unique, and easy-to-interpret patterns were generated. Forty-five V. alginolyticus isolates from aquatic animals and the marine environment in Daya Bay in Guangdong were fingerprinted by IRS-PCR and pulsed-field gel electrophoresis (PFGE). The reproducibility of the IRS-PCR method was high (100%) in conformity with PFGE. When primer PN-T or PN-G was used, IRS-PCR obtained the identical clustering as PFGE, producing 24 different patterns, respectively. Moreover, IRS-PCR presented a high discriminatory power (D=0.953) identical to that of PFGE. In conclusion, the IRS-PCR fingerprinting method using NotI-HhaI can provide a potentially useful tool for epidemiologic investigations of V. alginolyticus isolates.     

环境水系分离嗜肺军团菌脉冲场凝胶电泳的分型研究

目的初步揭示中国环境水系嗜肺军团菌分离株的脉冲场凝胶电泳（PFGE）分型特征。方法分别以SfiI和AscI为限制性内切酶,使用PFGE对菌株进行分型和聚类分析。结果单独使用SfiI、AscI和联合使用两种内切酶分别将78株嗜肺军团菌分为47、48和60个型别,分型得到的Simpson差异指数分别为0.9833、0.9817和0.9933;同一水系中分离的菌株既有带型相同或者相似者,又有带型差异较大者;相同型别的菌株可在同一水系中跨年份存在。结论PFGE对嗜肺军团菌具有很好的分辨率;多个克隆系的菌株可以在同一水系中共存,某些克隆系的菌株可以跨年份存在;环境水系中存在优势克隆系,这些优势克隆系应该在今后军团菌的监测中引起注意。     

Molecular epidemiology and antifungal susceptibility of Candida parapsilosis sensu stricto, Candida orthopsilosis, and Candida metapsilosis in Taiwan

Candida parapsilosis was recently reclassified into 3 closely related species, C. parapsilosis sensu stricto, Candida orthopsilosis, and Candida metapsilosis. Variation in susceptibility characteristics and prevalence of the 3 genomic species could have therapeutic and epidemiologic implications. The aim of this study is to characterize the genetic and antifungal susceptibility profiles of 97 C. parapsilosis isolates from 71 patients. Among the 71 nonduplicate isolates, 85.9% (61/71) were identified as C. parapsilosis sensu stricto, 5.6% (4/71) as C. metapsilosis, and 8.5% (6/71) as C. orthopsilosis species based on sequences of the internal transcribed spacer (ITS) region. The delineation of these 3 species is concordant with that achieved by pulsed-field gel electrophoresis of BssHII restriction fragments at 75% similarity. Antifungal susceptibility tests showed that most isolates were susceptible to flucytosine, azoles, amphotericin B, and echinocandins, whereas 3 C. metapsilosis isolates from 1 patient showed resistance and susceptible-dose dependence to fluconazole. The C. metapsilosis isolates exhibited significantly higher MIC values to both fluconazole and voriconazole than those of C. parapsilosis sensu stricto and C. orthopsilosis. On the other hand, the C. metapsilosis isolates showed significantly lower MIC values on 24 h to caspofungin than those of C. parapsilosis sensu stricto and C. orthopsilosis. For micafungin, the isolates of C. parapsilosis sensu stricto had significantly higher MIC values on 24 h than those of C. orthopsilosis and C. metapsilosis. Compared to Candida albicans, mutations from proline to alanine were identified on the hot spot 1 of Fks1 in all these C. parapsilosis sensu lato isolates regardless of their MIC levels. Some of the C. orthopsilosis and C. metapsilosis isolates expressed the isoleucine to valine substitution on the hot spot 2 region. However, the amino acid variations in these isolates did not correlate to their MIC values of echinocandin.     

Screening of strains of the Candida parapsilosis group of the BCCM/IHEM collection by MALDI-TOF MS

One hundred sixty-three strains stored as Candida parapsilosis in the BCCM/IHEM collection were reidentified based on internal transcribed spacer sequencing: 92% were identified as true C. parapsilosis, while 4.3% and 3% belonged to the closely related species C. metapsilosis and C. orthopsilosis, respectively, providing important epidemiologic information. Furthermore, we showed that matrix-assisted laser desorption ionisation time-of-flight mass spectrometry is a fast method that can discriminate between these species.     

脉冲场电泳分析布鲁菌标准菌株

目的探索一种布鲁菌分型的快速、准确、可靠的分子生物学方法。方法建立脉冲场凝胶电泳(PF-GE)的分子生物学分型方法,比较染色体限制性内切酶图谱,确定菌株的亲缘关系。结果在分析的19株布鲁菌标准菌株中,6种布鲁菌的PFGE图谱各不相同,但猪种菌和犬种菌的PFGE图谱只有1条带不同。羊种菌和猪种菌内各生物型均可在各自种内被区别,但牛种菌各生物型被区分为3类。从系统发生的观点来看,羊、牛、猪种菌是从共同祖先进化来的,犬种菌可认为是猪种菌的主要株或是刚从该种布鲁菌进化而来的株。沙林鼠种菌与牛种菌关系密切,而绵羊附睾种菌与猪种5型菌遗传距离也较近。结论PFGE方法可用于布鲁菌的基因分型的研究,是对传统分型方法一种较好的补充。     

Significant differences in drug susceptibility among species in the Candida parapsilosis group

Candida parapsilosis family has 3 proposed species: C. parapsilosis sensu stricto, Candida orthopsilosis, and Candida metapsilosis. C. parapsilosis sensu stricto had significantly higher caspofungin (CAS) and anidulafungin MICs than C. orthopsilosis or C. metapsilosis; C. metapsilosis was least susceptible to fluconazole. C. parapsilosis sensu stricto more frequently displayed (37%) paradoxical growth in CAS (P < or = 0.02). These species susceptibility differences could affect therapeutic choices.     

Reliable identification of clinically prevalent species and subspecies of staphylococci by sodium dodecyl sulfate polyacrylamide gel electrophoresis analysis

We identified by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) 10 species and 5 subspecies of Staphylococcus among 139 clinical isolates and compared it with conventional tests. All isolates showed species-specific whole-cell protein profiles, even atypical strains, with up to 60% and at least 73.5% of interspecies and intraspecies similarity, respectively. Except for 5 isolates that presented biochemical profiles of Staphylococcus hominis subsp. hominis, but were identified as S. hominis subsp. novobiosepticus by SDS-PAGE, there was 100% accordance between the methods used. Comparison with the partial 16S-rDNA sequences confirmed by SDS-PAGE showed the high accuracy of this method to identify staphylococci subspecies and species.