Rapid Identification and Subtyping of Enterobacter cloacae Clinical Isolates Using Peptide Mass Fingerprinting.

OBJECTIVE: To establish a domestic database of Enterobacteria cloacae (E. cloacae), and improve the identification efficiency using peptide mass fingerprinting. METHODS: Peptide mass fingerprinting was used for the identification and subtyping of E. cloacae. Eighty-seven strains, identified based on hsp60 genotyping, were used to construct and evaluate a new reference database. RESULTS: Compared with the original reference database, the identification efficiency and accuracy of the new reference database was greatly improved at the species level. The first super reference database for E. cloacae identification was also constructed and evaluated. Based on the super reference database and the main spectra projection dendrogram, E. cloacae strains were divided into two clades. CONCLUSION: Peptide mass fingerprinting is a powerful method to identify and subtype E. cloacae, and the use of this method will allow us to obtain more information to understand the heterogeneous organism E. cloacae.

Establishment and comparison of pulsed-field gel electrophoresis, multiple-locus variable number tandem repeat analysis and automated ribotyping methods for subtyping of Citrobacter strains.

OBJECTIVE: To establish and compare the pulsed-field gel electrophoresis (PFGE), multiple-locus variable number tandem repeat analysis (MLVA) and automated ribotyping for subtyping of Citrobacter strains. METHODS: PFGE protocol was optimized in terms of plug preparation procedure, restriction enzymes and configuration of electrophoretic parameters. MLVA method was evaluated by finding variable number tandem repeats in two genomes of Citrobacter strains. The ribotyping was performed by using the automated RiboPrinter system. RESULTS: We optimized the plug preparation procedure, focused on the cell suspension concentration (turbidity of 2.5 to 3.5), SDS addition (no SDS needed) and lysis time (1 h), and selected the appropriate restriction enzyme (XbaI) and the electrophoretic parameters (1.0 s-20.0 s for 19 h) of PFGE. There was nearly no discriminatory power of MLVA between Citrobacter strains. For 51 Citrobacter strains, automated ribotyping gave a D-value of 0.9945, while PFGE gave a D-value of 0.9969. Both PFGE and automated ribotyping clustered strains from the same sources (with the same species from the same place at the same time identified as the same source) and divided strains from different sources (from different years, places and hosts) into different subtypes. CONCLUSION: PFGE protocol established in this paper and automated ribotyping are suitable for application in Citrobacter subtyping.

[Gene detection of Neisseria spp. isolated from male patients with genitourinary tract infections].

OBJECTIVE: To detect the genes of Neisseria spp. isolated from patients with male genitourinary tract infections, and to study the pathogenicity of non-gonococcal strains of Neisseria and the laboratory diagnosis for the infections caused by Neisseria spp. METHODS: Using polymerase chain reaction and nucleotide sequencing, we amplified and sequenced 4 genes of Neisseria spp. isolated from patients with male genitourinary tract infections, including 16S rRNA, orfl, cppB and nspA. RESULTS: Fourteen Neisseria strains were identified through analysis of the 16S rRNA gene, including 3 N. mucosa strains, 3 N. cinerea strains, 2 N. gonorrhoea strains, 2 N. sicca strains, 2 N. subflava strains, 1 N. lactamica strain, and 1 N. polysaccharea strain. Among them, 9 showed positive results in gonococcal fluorescence-labeled multiplex-PCR detection, 1 in cppB gene reaction, 5 in orfl gene reaction, and 3 in nspA gene reaction. The consistency rate was 85.7% between the above results from our gene detection and those from the routine bacteriological methods. CONCLUSION: The cppB gene is absent in the non-gonococcal strains of Neisseria spp. that can cause male genitourinary tract infection. Most of the strains not only lack virulence-associated orfl and nspA genes, but also show positive results in gonococcal fluorescence-labeled multiplex-PCR detection, which is one of the important reasons for the misdiagnosis and missed diagnosis of gonorrhea infection. The combination of routine bacteriological methods and gene detection in laboratory examinations may help improve the accuracy rates of Neisseria species identification and clinical diagnosis of the infections caused by Neisseria spp.

Analysis of synonymous codon usage in Shigella flexneri 2a strain 301 and other Shigella and Escherichia coli strains.

In this study, we analysed synonymous codon usage in Shigella flexneri 2a strain 301 (Sf301) and performed a comparative analysis of synonymous codon usage patterns in Sf301 and other strains of Shigella and Escherichia coli. Although there was a significant variety in codon usage bias among different Sf301 genes, there was a slight but observable codon usage bias that could primarily be attributable to mutational pressure and translational selection. In addition, the relative abundance of dinucleotides in Sf301 was observed to be independent of the overall base composition but was still caused by differential mutational pressure; this also shaped codon usage. By comparing the relative synonymous codon usage values across different Shigella and E. coli strains, we suggested that the synonymous codon usage pattern in the Shigella genomes was strain specific. This study represents a comprehensive analysis of Shigella codon usage patterns and provides a basic understanding of the mechanisms underlying codon usage bias.

Rapid and Sensitive Isothermal Detection of Nucleic-acid Sequence by Multiple Cross Displacement Amplification.

We have devised a novel amplification strategy based on isothermal strand-displacement polymerization reaction, which was termed multiple cross displacement amplification (MCDA). The approach employed a set of ten specially designed primers spanning ten distinct regions of target sequence and was preceded at a constant temperature (61-65 °C). At the assay temperature, the double-stranded DNAs were at dynamic reaction environment of primer-template hybrid, thus the high concentration of primers annealed to the template strands without a denaturing step to initiate the synthesis. For the subsequent isothermal amplification step, a series of primer binding and extension events yielded several single-stranded DNAs and single-stranded single stem-loop DNA structures. Then, these DNA products enabled the strand-displacement reaction to enter into the exponential amplification. Three mainstream methods, including colorimetric indicators, agarose gel electrophoresis and real-time turbidity, were selected for monitoring the MCDA reaction. Moreover, the practical application of the MCDA assay was successfully evaluated by detecting the target pathogen nucleic acid in pork samples, which offered advantages on quick results, modest equipment requirements, easiness in operation, and high specificity and sensitivity. Here we expounded the basic MCDA mechanism and also provided details on an alternative (Single-MCDA assay, S-MCDA) to MCDA technique.

[Study on the integration site and arrangement of SfII and SfX prophages in Shigella flexneri serotype 2b strains].

OBJECTIVE: To study the integration site and arrangement of SfII and SfX prophages in Shigella flexneri serotype 2b strains. METHODS: A series of primers were designed based on potential integration site of SfII and SfX prophages in Shigella flexneri serotype 2b strains, and PCR were performed for 50 serotype 2b strains to amplify special genes located in host and prophages. PCR products were sequenced to identify integration sites and arrangement of SfII and SfX. RESULTS: In all the serotype 2b strains, prophage SfII and SfX were adjacent to each other, and integrated into the thrW tRNA gene of the host, which were located between genes proA and yaiC of host. Prophage SfX was located immediately upstream of prophage SfII in all the detected 50 serotype 2b strains exception for strain 51251. CONCLUSION: This was the first report on the integration site and arrangement of serotype-converting prophages SfII and SfX in Shigella flexneri 2b strains.

[Secretion expression of cholera toxin B subunit in food-grading Lactococcus lactis expression system].

OBJECTIVE: To clone and secretion express cholera toxin B subunit (CTB) in food-grading Lactococcus lactis expression systems. METHODS: ctB fragment that encoding CTB was amplified by polymerase chain reaction (PCR) using the genomic DNA of Vibrio cholera strain 569B as template and was inserted into two secretion expression vector pSQZ and pSQ to construct food-grading expression system L.lactis MBP71/pSQZ-ctB and L.lactis MBP71/pSQ-ctB. The expressed CTB was detected by Western-blot assay. RESULTS: The ctB fragment was successfully amplified from Vibrio cholera strain 569B and inserted into two secretion expression vectors pSQZ and pSQ to construct food-grading expression system L. lactis MBP71/pSQZ-ctB and L. lactis MBP71/pSQ-ctB. Western-blot assay demonstrated that CTB was secretion and expressed from L.lactis MBP71 harboring vectors pSQZ-ctB and pSQ-ctB, and the quantity of CTB secreted by L. lactis MBP71/pSQ-ctB was about 2 microg/ml, higher than that of L. lactis MBP71/pSQZ-ctB. CONCLUSION: CTB was successfully secreted and expressed by food-grading L. lactis expression systems.

[Immunoproteomic assay of secretive proteins from Streptococcus suis type 2 strain SC84].

OBJECTIVE: To identify antigenic proteins secreted by Streptococcus suis (S. suis) type 2 strain SC84. METHODS: Two-dimensional electrophoresis (2-DE), western-blot assay and matrix-assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS) analysis were performed to search and identify antigenic proteins secreted by S. suis strain SC84, which triggered an outbreak of the disease in Sichuan province,China, in 2005. RESULTS: A total number of 14 western blot spots were found on PVDF membrane. 11 spots which could be found the existence of matching protein on coomassie G-250-stained 2-DE gel were identified by MALDI-TOF MS. The 11 proteins, all located at extra-cellular or cell wall, were classified into 8 kinds of proteins. Among of them, muramidase-released protein (MRP), suilysin (Sly) and extra-cellular factor (EF) were the known antigenic proteins, but several proteins such as putative 5'-nucleotidase, ribo-nucleases G and E, and predicted metal-loendo-peptidase were newly found antigenic proteins. All the identified protein were found to have had the coding gene in genomic of S. suis strain 05ZYH33, isolated from patients in Sichuan province, China in 2005. CONCLUSION: The newly found proteins could be used as voluntary antigens for detection and vaccination of S. suis.

[Development of a protocol on pulsed field gel electrophoresis analysis for Streptococcus suis].

OBJECTIVE: To develop a PFGE protocol for Streptococcus suis. METHODS: We developed and optimized a PFGE protocol for S. suis, in terms of plug preparation, choice of restriction endonucleases and optimized electrophoresis parameters. By analyzing the genome sequences of S. suis P1/7 with Mapdraw of DNAStar, we found three restriction enzymes, Swa I, Sma I and Apa I, were more suitable than others. RESULTS: Analysis of 100 isolates of S. suis including 34 of 35 serotypes identified, 59, 53 and 43 patterns were obtained from Swa I, Sma I and Apa I restriction, respectively. The enzyme Swa I had the greatest power for discrimination ability. CONCLUSION: By optimization of the protocol at various conditions, a rapid, reproducible, economic and practical PFGE method for S. suis was developed.

[Molecular epidemiology of enterohaemorrhagic Esacherichia coli O157 in some areas in China].

OBJECTIVE: To understand the epidemiological characteristics of enterohaemorrhagic Escherichia coli (EHEC) O157 and to determine the degree of its genetic relations. METHODS: Polymerase chain reaction (PCR) techniques and chromosomal DNA digested by restriction enzyme Xba I according to PulseNet directions by pulsed field gel electrophoresis (PFGE) method were applied to 300 E. coli O157 strains isolated from patients and animal sources from 1988 to 2005 from Henan, Jiangsu and Anhui provinces. RESULTS: Very high prevalence of stx2 gene in EHEC O157:H7 strains isolated from some provinces of China was found and variation existed in some strains. We got 161 PFGE patterns from 300 strains. The stx2-producing strains could be clearly separated from stx2 variation-producing strains. CONCLUSION: The variability of restriction enzyme-digestion patterns of O157 genomes suggested that the presence of some genomic diversity among the strains did exist.

[Identification of harboring stx2::IS1203 Escherichia coli O157:H7 strains isolated in China].

OBJECTIVE: To understand the variation of Shiga toxin (stx) genes of Escherichia coli O157:H7 strains isolated in China. METHODS: Polymerase chain reaction (PCR) was used to identity the types of stx genes and the nucleotide sequences of the amplified stex variants genes were determined. Compare to the cytotoxicity of Stx,variants were tested by HeLa cell assay. RESULTS: We found novel stx2 genes in 3 of 289 strains of Shiga toxin-producing E. coli O157:H7 isolated from 1999 to 2002 in China. The novel stx2 genes were inserted by a 1.3-kb insertion sequence (IS) and the nucleotide sequences of IS showed 100% homology with that of IS1203 variant (IS1203v). The IS1203v inserted in the stx2 genes of three E. coli O157:H7 strains at different sites and the direction of the open reading frames (ORFs) of IS1203v of each strain was different. In addition to the above mentioned findings, the nucleotide sequences of three stx2 genes were completely identical and the type of the three Stx2 was Stx2 prototype. Compare to the cytotoxicity of Stx2 prototype, the novel Stx2 was found to be obviously lower. CONCLUSION: E. coli O157:H7 strains harboring stx2::IS1203v genes were isolated in China. Consequently, the results of HeLa cell assay showed that the insertion of IS1203v could lead to low cytotoxicity of Stx2.

[Study on molecular typing by pulsed-field gel electrophoresis of food Listeria monocytogenes isolates from eight province (municipalities) of China].

OBJECTIVE: To analyse the molecular types of Listeria (L.) monocytogenes, and to construct the standard China L. monocytogenes pulsed-field gel electrophoresis (PFGE) subtyping database, using the international standardized L. monocytogenes-PFGE protocol. METHODS: 118 L. monocytogenes strains isolated from 8 provinces or municipalities of China were subtyped according to L. monocytogenes-PFGE protocol. RESULTS: 118 strains of L. monocytogenes were divided into 39 subtypes. In the 39 subtypes, 37 strains (31.36%) were GX6A160004 pattern, showing it was the predominant Lm subtype in China. CONCLUSION: Data from molecular typing suggested that the predominant Lm strains were distributed in different regions of China. PulseNet China-Lm database was constructed which was valuable for the molecular subtyping-based surveillance of L. monocytogenes.

[An outbreak of human Streptococcus suis serotype 2 infections presenting with toxic shock syndrome in Sichuan, China].

OBJECTIVE: In mid-July 2005, five patients presented with septic shock to a hospital in Ziyang city in Sichuan, China, to identify the etiology of the unknown reason disease, an epidemiological, clinical, and laboratory study were conducted. METHODS: An enhanced surveillance program were established in Sichuan, the following activities were introduced: active case finding in Sichuan of (a) laboratory diagnosed Streptococcus suis infection and (b) clinically diagnosed probable cases with exposure history; supplemented by (c) monitoring reports on meningococcal meningitis. Streptococcus suis serotype 2 infection was confirmed by culture and biochemical reactions, followed by sequencing for specific genes for serotype and virulence factors. RESULTS: From June 10 to August 21, 2005, 68 laboratory confirmed cases of human Streptococcus suis infections were reported. All were villagers who gave a history of direct exposure to deceased or sick pigs in their backyards where slaughtering was performed. Twenty six (38%) presented with toxic shock syndrome of which 15 (58%) died. Other presentations were septicaemia or meningitis. All isolates were tested positive for genes for tuf, species-specific 16S rRNA, cps2J, mrp, ef and sly. There were 136 clinically diagnosed probable cases with similar exposure history but incomplete laboratory investigations. CONCLUSION: An outbreak of human Streptococcus suis serotype 2 infections occurred in villagers after direct exposure to deceased or sick pigs in Sichuan. Prohibition of slaughtering in backyards brought the outbreak to a halt. A virulent strain of the bacteria is speculated to be in circulation, and is responsible for the unusual presentation of toxic shock syndrome with high case fatality.

Influence of tat mutations on the ribose-binding protein translocation in Escherichia coli.

Proteins are exported across the bacterial cytoplasmic membrane either as unfolded precursors via the Sec machinery or in folded conformation via the Tat system. The ribose-binding protein (RBP) of Escherichia coli is a Sec-pathway substrate. Intriguingly, it exhibits fast folding kinetics and its export is independent of SecB, a general chaperone protein dedicated for protein secretion. In this study, we found that the quantity of RBP was significantly reduced in the periplasm of tat mutants, which was restored by in trans expression of the tatABC genes. Pulse-chase experiments showed that significant amount of wild-type RBP was processed in a secY mutant in the presence of azide (SecA inhibitor), whereas the processing of a slow folding RBP derivative was almost completely blocked under the same conditions. These results would suggest that under the Sec-defective conditions the export of a portion of folded RBP could be rescued by the Tat system.