BACKGROUND: Recently, the iNtRON VRE vanA/vanB real-time PCR (iNtRON; iNtRON Biotechnology, Korea) assay, a multiplex real-time PCR method, was introduced. In this prospective study, we compared the iNtRON assay with the Seeplex VRE ACE detection kit (Seeplex; Seegene, Korea), a conventional multiplex PCR assay. METHODS: A chromogenic agar-based culture, in which pre-selected vancomycin-resistant enterococci (VRE) was grown and subsequently plated on blood agar with vancomycin disks, was regarded as the reference method. A total of 304 consecutive rectal swab specimens were tested for VRE by culture and by iNtRON and Seeplex PCR assays. For the PCR assays, specimens were enriched for 16-24 hr before PCR. RESULTS: VRE were isolated from 44 (14.5%) specimens by chromogenic agar-based culture. The clinical sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of the iNtRON assay were 100% (95% confidence interval: 89.8%-100%), 99.2% (96.9%-99.9%), 95.6% (83.6%-99.2%), and 100% (98.2%-100%), respectively, while those of the Seeplex assay were 97.7% (86.2%-99.9%), 99.6% (97.5%-99.9%), 97.7% (86.2%-99.9%), and 99.6% (97.5%-99.9%), respectively. The iNtRON assay had a detection limit of 3,159 copies/microL and 13,702 copies/microL for the vanA and vanB genes, respectively. No cross-reactivity was observed in 11 non-VRE bacterial culture isolates. CONCLUSIONS: The overall performance of the iNtRON assay was comparable to that of a chromogenic agar-based culture method for prompt identification of VRE-colonized patients in hospitals. This assay could be an alternative or supportive method for the effective control of nosocomial VRE infection.
Bacterial Proteins/*genetics ; Bacterial Typing Techniques/*methods/standards ; Carbon-Oxygen Ligases/*genetics ; DNA, Bacterial/*metabolism ; Gram-Positive Bacterial Infections/microbiology ; Humans ; Reagent Kits, Diagnostic ; *Real-Time Polymerase Chain Reaction ; Vancomycin Resistance/genetics ; Vancomycin-Resistant Enterococci/*genetics/isolation & purification

BACKGROUND: By conventional methods, the identification of anaerobic bacteria is more time consuming and requires more expertise than the identification of aerobic bacteria. Although the matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) systems are relatively less studied, they have been reported to be a promising method for the identification of anaerobes. We evaluated the performance of the VITEK MS in vitro diagnostic (IVD; 1.1 database; bioMerieux, France) in the identification of anaerobes. METHODS: We used 274 anaerobic bacteria isolated from various clinical specimens. The results for the identification of the bacteria by VITEK MS were compared to those obtained by phenotypic methods and 16S rRNA gene sequencing. RESULTS: Among the 249 isolates included in the IVD database, the VITEK MS correctly identified 209 (83.9%) isolates to the species level and an additional 18 (7.2%) at the genus level. In particular, the VITEK MS correctly identified clinically relevant and frequently isolated anaerobic bacteria to the species level. The remaining 22 isolates (8.8%) were either not identified or misidentified. The VITEK MS could not identify the 25 isolates absent from the IVD database to the species level. CONCLUSIONS: The VITEK MS showed reliable identifications for clinically relevant anaerobic bacteria.
Bacteria, Anaerobic/*genetics/isolation & purification ; Bacterial Typing Techniques/*instrumentation/*methods ; Body Fluids/microbiology ; Databases, Genetic ; Humans ; RNA, Ribosomal, 16S/*analysis/metabolism ; Sequence Analysis, DNA ; *Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization

BACKGROUND: Acinetobacter species are the leading cause of bloodstream infection (BSI), but their correct identification is challenging. We evaluated the matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS)-based VITEK MS (bioMerieux, France), and two automated systems, VITEK 2 (bioMerieux) and MicroScan (Siemens, USA) for identification of Acinetobacter BSI isolates. METHODS: A total of 187 BSI isolates recovered at a university hospital in Korea between 2010 and 2012 were analyzed. The identification results obtained using VITEK MS and two automated systems were compared with those of rpoB sequencing. RESULTS: Of 187 isolates analyzed, 176 were identified to the species level by rpoB sequencing: the Acinetobacter baumannii group (ABG; 101 A. baumannii, 43 A. nosocomialis, 10 A. pittii isolates) was most commonly identified (82.4%), followed by Acinetobacter genomic species 13BJ/14TU (5.3%), A. ursingii (2.1%), A. soli (2.1%), A. bereziniae (1.1%), and A. junii (1.1%). Correct identification rates to the species group (ABG) level or the species level was comparable among the three systems (VITEK MS, 90.3%; VITEK 2, 89.2%; MicroScan, 86.9%). However, VITEK MS generated fewer misidentifications (0.6%) than VITEK 2 (10.8%) and MicroScan (13.1%) (P<0.001). In addition, VITEK MS demonstrated higher specificity (100%) for discrimination between ABG and non-ABG isolates than the other systems (both, 31.8%) (P<0.001). CONCLUSIONS: The VITEK MS system is superior to the VITEK 2 and MicroScan systems for identification of Acinetobacter BSI isolates, with fewer misidentifications and better discrimination between the ABG and non-ABG isolates.
Acinetobacter/*genetics/isolation & purification ; Acinetobacter Infections/diagnosis/microbiology ; Bacterial Proteins/genetics ; Bacterial Typing Techniques/*instrumentation/*methods ; Blood/*microbiology ; DNA, Bacterial/*analysis/metabolism ; Databases, Genetic ; Humans ; *Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization

Bacterial Typing Techniques ; methods ; Brucella ; classification

OBJECTIVETo type the Chinese Anaplasma phagocytophilum isolates by Multispacer typing (MST).

METHODSBased on the genomes of the 4 published Anaplasma strains, 4 genomic sequences were analyzed by Mauve 2.3.1 software and variable spacer sequences were selected for designing primers with the bio-software Primer Premier 5.0. A total of 11 Chinese A. phagocytophilum isolates, obtained from different areas of China during 2009-2012 were assayed by the MST. Twenty two intergenic sequences for each isolate tested and the reference A. phagocytophilum strain Webster and A. phagocytophilum strain HZ were concatenated in the order of HGA-mst 1F/1R-mst 2F/2R, HGA-mst 22F/22R.

RESULTSTwenty two pairs of primers were successfully used for typing the Human granulocytic anaplasmosis (HGA) strains in the study. Those 22 intergenic sequences exhibited a great diversity among the strains tested and each of the strain tested was identified as unique genotype, according to the alignment analysis of the 22 concatenated intergenic sequences. Of these single nucleotide polymorphism (SNPs) identified in the study, the nucleotide transitions shared the highest percentage (60.2%, 251/417) and then the nucleotide transversion, accounted for 23.0% (96/417) and the indel events (insertion/deletion) were observed of 16.7% (70/417)SNPs. Phylogenetic analysis indicated that the 5 strains from patients (LZ-H1, LZ-H2, LZ-H3, LZ-H4, LZ-H5) from Laizhou areas, Shandong province and 1 tick strain (LZ-T1) from Haemaphysalis longicornis collected from the same areas where the patients lived were grouped in the same clan with the reference A. phagocytophilum strain Webster and strain HZ. Beijing isolates (BJ-H1) grouped with Xinjiang isolates (XJ-H1 and XJ-H3) while another tick isolates from Laizhou areas (LZ-T2) and another Xinjiang human isolate(XJ-H2)were in the same clan, which was closely related to the isolates from severe patients in Laizhou.

CONCLUSIONChinese HGA isolates exhibited a great diversity of intergenic regions. MST seemed a valuable tool for the detection and tracing for any endemic strains of Anaplasma during the outbreak investigations in the public health events.

Anaplasma phagocytophilum ; classification ; genetics ; Bacterial Typing Techniques ; methods ; China ; DNA, Ribosomal Spacer ; genetics ; Polymorphism, Single Nucleotide

BACKGROUND: We evaluated the performance of three chromogenic media (Brilliance agar I [Oxoid, UK], Brilliance agar II [Oxoid], and ChromID MRSA [Biomerieux, France]) combined with broth enrichment and the Xpert MRSA assay for screening of methicillin-resistant Staphylococcus aureus (MRSA). METHODS: We obtained 401 pairs of duplicate nasal swabs from 321 patients. One swab was suspended overnight in tryptic soy broth; 50-microL aliquots of suspension were inoculated on the three chromogenic media. Brilliance agar I and II were examined after 24 hr, and ChromID MRSA, after 24 and 48 hr. The paired swab was processed directly using real-time PCR-based Xpert MRSA assay. RESULTS: True positives, designated as MRSA growth in any of the culture media, were detected with the prevalence of 17% in our institution. We report the sensitivity, specificity, positive predictive value, and negative predictive value of MRSA growth as follows: 92.3%, 94.0%, 75.9%, and 98.4% in Brilliance agar I (24 hr); 92.7%, 97.9%, 90.0%, and 98.5% in Brilliance agar II (24 hr); 95.6%, 95.8%, 82.3%, and 99.1% in ChromID MRSA (24 hr); 100%, 92.5%, 73.1%, and 100% in ChromID MRSA (48 hr); 92.6%, 96.7%, 85.1%, and 98.5% in Xpert MRSA assay. The agreement between the enriched culture and Xpert MRSA assay was 96.0%. CONCLUSIONS: Three chromogenic culture media combined with enrichment and Xpert MRSA assay demonstrated similar capabilities in MRSA detection. The Xpert MRSA assay yielded results comparable to those of culture methods, saving 48-72 hr, thus facilitating earlier detection of MRSA in healthcare settings.
Bacterial Proteins/genetics ; Bacterial Typing Techniques/*methods ; Chromogenic Compounds/chemistry/*metabolism ; Culture Media/chemistry ; DNA, Bacterial/analysis ; Humans ; Methicillin-Resistant Staphylococcus aureus/*genetics/growth & development/*isolation & purification/metabolism ; Nasal Cavity/*microbiology ; Reagent Kits, Diagnostic ; *Real-Time Polymerase Chain Reaction ; *Staphylococcal Infections/diagnosis/microbiology

OBJECTIVESelecting variable-number tandem-repeat (VNTR) loci for different serogroups of Shigella spp to explore and establish multilocus variable-number tandem-repeat analysis (MLVA) method, in order to study the molecular characteristic of the isolated strains.

METHODSOf the Shigella strains found by dysentery surveillance in Beijing from 2001 to 2009, 180 strains were selected for this study, according to the number and serotypes of the surveillant strains, at the ratio of 15%; including 50 strains of Shigella sonnei and 130 strains of Shigella flexneri. After screening the polymorphism of the 18 VNTR loci, 10 VNTR loci (sh1-sh10) were retained and constructed three groups of multi-PCR methods to detect all he 180 strains and analyze MLVA molecular subtypes using capillary segments.

RESULTSA range of 2 to 11 alleles were found on the 10 VNTR loci among the 180 Shigella strains, with a diversity index value between 0.158 and 0.766. The 10 loci showed diversity in different serogroups, such as only one allele found in sh6 of Shigella flexneri, sh2 and sh3 of Shigella sonnei individually. The isolated 180 strains were divided into 84 MLVA subtypes, with a resolution ratio D value at 0.967 (95%CI: 0.956 - 0.978). The 130 strains of Shigella flexneri were divided into 63 subtypes, named as TF001-TF063; among which TF001, TF002 and TF 005 were the dominant subtypes, accounting to 17, 16 and 15 strains respectively. The 50 strains of Shigella sonnei were divided into 21 subtypes, named as TS001-TS021; among which TS002 (14 strains) and TS001 (7 strains) were the dominant subtypes.

CONCLUSIONMLVA subtyping method including 10 VNTR loci was preliminarily developed. The MLVA cluster analysis revealed that the subtypes of Shigella strains isolated in Beijing were diverse, and suggested the possibility of multiple-clone source.

Alleles ; Bacterial Typing Techniques ; methods ; China ; DNA, Bacterial ; genetics ; Genotype ; Minisatellite Repeats ; Polymorphism, Genetic ; Shigella ; classification ; genetics ; isolation & purification

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.
Bacterial Typing Techniques/*methods ; Clinical Laboratory Techniques/*methods ; DNA Fingerprinting ; DNA, Bacterial/*analysis ; Disease Outbreaks ; Electrophoresis, Gel, Pulsed-Field/methods ; Food Microbiology ; Humans ; Laboratories ; Molecular Typing/*methods ; Preventive Medicine ; *Public Health

BACKGROUND: Multiple-locus variable-number tandem-repeat fingerprinting (MLVF) is based on multiplex PCR, utilizing variable number tandem repeat. Our goal was to compare the performance of MLVF in distinguishing clinical Staphylococcus aureus isolates with that of pulsed-field gel electrophoresis (PFGE), which has traditionally been the gold standard. METHODS: Sixty-three clinically significant S. aureus isolates were tested using both PFGE and MLVF. Multiplex PCR for MLVF was performed using PCR primers for clfA, clfB, sdrCDE, sspA, and spa. PFGE was performed with genomic DNA fragments generated by SmaI endonuclease digestion. Banding patterns of MLVF or PFGE were analyzed using InfoQuestFP software. RESULTS: The hands-on time of our modified method was about 3 h, on average, for each of 18 isolates. PFGE (80% cutoff) or MLVF (75% cutoff) separated all of the 63 isolates into 13 and 12 types, respectively. Three types generated by PFGE were identical to those generated by MLVF. PFGE and MLVF yielded similar Simpson's diversity indices, indicating similar discriminatory power. The overall concordance between PFGE and MLVF was low, as represented by adjusted Rand indices (0.266-0.278). PFGE predicted MLVF type better than MLVF predicted PFGE type, as reflected by Wallace coefficients (PFGE cutoff 80% vs. MLVF cutoff 75%, 0.389 vs. 0.233). Analysis of the relationship between a pair of isolates showed 91.0% concordance between the PFGE (80% cutoff) and MLVF (75% cutoff). CONCLUSIONS: Our simple, low-cost, modified MLVF protocol can effectively discriminate between S. aureus clinical isolates. MLVF can replace PFGE for the hospital infection control of S. aureus.
Bacterial Typing Techniques/*methods ; *DNA Fingerprinting ; DNA, Bacterial/analysis ; *Electrophoresis, Gel, Pulsed-Field ; Genotype ; Humans ; Methicillin-Resistant Staphylococcus aureus/classification/genetics/isolation & purification ; Multiplex Polymerase Chain Reaction ; Staphylococcal Infections/*microbiology ; Staphylococcus aureus/*classification/*genetics/isolation & purification

OBJECTIVETo develop a pulsed field gel electrophoresis (PFGE) method for molecular typing of Lactobacillus and Streptococcus thermophilus (S. thermophilus) and to apply it in identification and characterization of both bacteria isolated from yoghurt collected from Beijing supermarket.

METHODSThe five most useful restriction enzymes including Apa I, Not I, Sfi I, Xba I and Sma I were chosen to cut DNA of 52 strains of Lactobacillus, S. thermophilus as well as associated standard bacteria strains. The endonucleases and electrophoresis conditions for PFGE analysis were optimized and applied in molecular typing of Lactobacillus and S.thermophilus isolates. Cluster analysis based on the PFGE data was conducted. The identification results of PFGE were compared with those obtained in biochemical and 16s ribosomal RNA PCR identification tests.

RESULTSNot I was suitable for L. bulgaricus, L. fermentum and L. delbrueckii digestion. While Apa I was an appropriate endonuclease for S. thermophilus, L. acidophilus and L. casei digestion. The results of molecular typing indicated that 24 strains of L.bulgaricus and 15 strains of S. thermophilus were grouped into 8 types by PFGE method, respectively. While 7 strains of L.acidophilus were grouped into 3 types and 2 strains of L. delbrueckii were grouped into 2 different PFGE types.

CONCLUSIONThe results of PFGE analysis are in compliance with those of 16s rRNA PCR and biochemical identification. The PFGE method developed in this study is suitable for molecular characterization of both Lactobacillus and S. thermophilus.

Bacterial Typing Techniques ; methods ; Electrophoresis, Gel, Pulsed-Field ; methods ; Lactobacillus ; classification ; isolation & purification ; Streptococcus thermophilus ; classification ; isolation & purification