Multiplex PCR protocol for the diagnosis of staphylococcal infection

Cloning and expression of two plant proteins: similar antimicrobial activity of native and recombinant form

Antimicrobial peptides and proteins are being studied with increasing interest because of their broad range antimicrobial activity. Among plant antimicrobial proteins, the wheat seed polypeptides, puroindoline a and puroindoline b, are particularly interesting because of their established antibacterial activity. In this paper we describe different strategies used to clone His tagged and GST tagged puroindolines obtaining 1.5 mg recombinant protein from 1 l culture. The antimicrobial activity of recombinant and native puroindolines was comparable.

Guidelines for the laboratory diagnosis and susceptibility testing of methicillin-resistant Staphylococcus aureus (MRSA)

These evidence-based guidelines have been produced after a literature review of the laboratory diagnosis and susceptibility testing of methicillin-resistant Staphylococcus aureus (MRSA). We have considered the detection of MRSA in screening samples and the detection of reduced susceptibility to glycopeptides in S. aureus. Recommendations are given for the identification of S. aureus and for suitable methods of susceptibility testing and screening for MRSA and for S. aureus with reduced susceptibility to glycopeptides. These guidelines indicate what tests should be used but not when the tests are applicable, as aspects of this are dealt with in guidelines on control of MRSA. There are currently several developments in screening media and molecular methods. It is likely that some of our recommendations will require modification as the new methods become available.

Design and application of a Staphylococcus-specific single strand conformation polymorphism-PCR analysis to monitor Staphylococcus populations diversity and dynamics during production of raw milk cheese

AIM

Development of a nested-PCR single strand conformation polymorphism (SSCP) assay targeting the 16S rRNA genes of the Staphylococcus genus, to monitor staphylococci in cheese.

METHODS AND RESULTS

New primer sets to specifically amplify 16S rDNA of staphylococci were designed to be used in a nested-PCR SSCP assay. The method was efficient in discriminating the staphylococcal species most frequently found in cheese. It was validated by monitoring Staphylococcus populations in three productions of raw milk cheese. Analysis of milk samples revealed dominant SSCP peaks corresponding to Staphylococcus aureus, Staphylococcus equorum and Staphylococcus saprophyticus. After 12 h, the S. aureus peak became dominant.

CONCLUSIONS

The combination of specific Staphylococcus nested-PCR and SSCP allows rapid and direct monitoring of staphylococci diversity and dynamics in milk and cheese. In the core of the cheeses studied, S. aureus may have ecological advantages against other Staphylococcus populations.

SIGNIFICANCE AND IMPACT OF THE STUDY

This approach is a promising tool to study the ecology of staphylococci in cheeses and in other food samples.

Fluorescent amplified fragment length polymorphism (FAFLP) based molecular epidemiology of hospital infections in a tertiary care setting in Hyderabad, India

Bacterial isolates from respiratory and urinary tract infections in an Indian hospital setting were genotyped using FAFLP analysis. The 77 different isolates analyzed belonged to five genera namely Escherichia, Staphylococcus, Pseudomonas, Enterobacter and Pantoea. Before carrying out FAFLP analysis all the isolates were subjected to16S-23S ribosomal RNA-based species identification. Cluster analysis of FAFLP profiles of 77 isolates generated five groups corresponding to five bacterial genera that are used in the study. Further analyses of the dendrograms revealed efficient species and strain differentiation. Cluster analysis identified genetically distant clones among the clinical isolates of Staphylococcus aureus, two distinct genetic lineages among the Escherichia coli strains and a single cluster of closely related Pseudomonas aeruginosa isolates. Ribosomal spacer region amplification identified different species accurately but intraspecies discrimination could not be accomplished completely. Comparison of FAFLP profiles of our isolates, with a pilot database of validated strains, was very useful in identification and worked better in conjunction with dendrogram analysis.

Rapid identification of staphylococcal strains from positive-testing blood culture bottles by internal transcribed spacer PCR followed by microchip gel electrophoresis

PCR analysis of the 16S-23S rRNA gene internal transcribed spacer (ITS) followed by microchip gel electrophoresis (MGE) was evaluated for its usefulness in identification of staphylococci. Forty ITS PCR patterns were demonstrated among 228 isolated colonies of Staphylococcus aureus: 26 patterns for methicillin-susceptible S. aureus (MSSA; 91 strains), 11 patterns for methicillin-resistant S. aureus (MRSA; 99 strains), and 3 patterns for both MSSA and MRSA (38 strains). Thirty-seven control strains of coagulase-negative staphylococci (CNS) representing 16 species showed unique ITS PCR patterns (24 patterns) at the species and subspecies levels: two patterns for S. caprae, S. cohnii, S. haemolyticus, and S. saprophyticus; three patterns for S. lugdunensis; four patterns for S. capitis; and one pattern for each of the other CNS species. The combined PCR-MGE method was prospectively adapted to the positive blood culture bottles, and this method correctly identified MSSA and MRSA in 102 (89%) of 114 blood cultures positive for S. aureus on the basis of the ITS PCR patterns. Eight ITS PCR patterns were demonstrated from 166 blood culture bottles positive for CNS. The most frequent CNS species isolated from blood cultures were S. epidermidis (76%), S. capitis (11%), and S. hominis (8%). Overall, all 280 blood culture bottles shown to contain a single Staphylococcus species by routine phenotypic methods were correctly identified by the PCR-MGE method at the species level, whereas the organism failed to be identified in 8 culture bottles (3%) with mixed flora. The PCR-MGE method is useful not only for rapid identification ( approximately 1.5 h) of staphylococci in positive blood culture bottles, but also for strain delineation of S. aureus.

Comparative genomics of Staphylococcus aureus musculoskeletal isolates

Much of the research aimed at defining the pathogenesis of Staphylococcus aureus has been done with a limited number of strains, most notably the 8325-4 derivative RN6390. Several lines of evidence indicate that this strain is unique by comparison to clinical isolates of S. aureus. Based on this, we have focused our efforts on two clinical isolates (UAMS-1 and UAMS-601), both of which are hypervirulent in our animal models of musculoskeletal infection. In this study, we used comparative genomic hybridization to assess the genome content of these two isolates relative to RN6390 and each of seven sequenced S. aureus isolates. Our comparisons were done by using an amplicon-based microarray from the Pathogen Functional Genomics Resource Center and an Affymetrix GeneChip that collectively represent the genomes of all seven sequenced strains. Our results confirmed that UAMS-1 and UAMS-601 share specific attributes that distinguish them from RN6390. Potentially important differences included the presence of cna and the absence of isaB, sarT, sarU, and sasG in the UAMS isolates. Among the sequenced strains, the UAMS isolates were most closely related to the dominant European clone EMRSA-16. In contrast, RN6390, NCTC 8325, and COL formed a distinct cluster that, by comparison to the other four sequenced strains (Mu50, N315, MW2, and SANGER-476), was the most distantly related to the UAMS isolates and EMRSA-16.

Simultaneous detection of Staphylococcus aureus and coagulase-negative staphylococci in positive blood cultures by real-time PCR with two fluorescence resonance energy transfer probe sets

A real-time PCR assay that uses two fluorescence resonance energy transfer probe sets and targets the tuf gene of staphylococci is described here. One probe set detects the Staphylococcus genus, whereas the other probe set is specific for Staphylococcus aureus. One hundred thirty-eight cultured isolates, which contained 41 isolates of staphylococci representing at least nine species, and 100 positive blood cultures that contained gram-positive cocci in clusters were tested. This assay was 100% sensitive and 100% specific for the detection of the Staphylococcus genus and of S. aureus.

Development of a multiplex PCR for the identification of Staphylococcus genus and four staphylococcal species isolated from food

AIMS

To develop a multiplex PCR that allows the identification of bacteria belonging to the Staphylococcus genus and in particular to the species Staphylococcus xylosus, S. saprophyticus, S. epidermidis and S. aureus isolated from food manufacturing plants.

METHODS AND RESULTS

Five primer pairs were used in the multiplex PCR, one specific to the Staphylococcus genus and four specific to S. xylosus, S. saprophyticus, S. epidermidis and S. aureus species. All the 31 Staphylococcus reference strains yielded a specific PCR product with the genus-specific primers. Staphylococcus xylosus, S. saprophyticus, S. epidermidis and S. aureus gave a specific PCR fragment with the corresponding species-specific primers. No amplification with the Kocuria, Macrococcus and Micrococcus strains was observed in our conditions. This multiplex PCR was performed on 30 strains of Gram-positive cocci isolated from different workshops and fermented sausages. Among them, 28 belonged to the Staphylococcus genus and 14 were identified to S. saprophyticus, four to S. xylosus, two to S. aureus and one to S. epidermidis.

CONCLUSIONS

This multiplex PCR provided reliable and repeatable PCR results. It allowed the identification of a major part of the isolates, highlighting the predominance of the S. saprophyticus species in the workshops studied.

SIGNIFICANCE AND IMPACT OF THE STUDY

This tool is a useful way to screen the strains isolated from foodstuff and food environment and to monitor these species during the food processing.

A multiplex PCR method for the detection of all five individual genes ofica locus inStaphylococcus epidermidis. A survey on 400 clinical isolates from prosthesis-associated infections

In Staphylococcus epidermidis, ica locus encodes for the synthesis of a polysaccharide intercellular adhesin (slime or biofilm). A multiplex polymerase chain reaction (PCR) for the detection of the five individual genes of ica locus was developed, with the aim to probe the set of genes in a large collection of Staphylococcus epidermidis clinical isolates. Single representative fragments for icaR, icaA, icaD, icaB, and icaC genes were selected. Multiplex PCR was applied to two reference Staphylococcus epidermidis strains [the non-biofilm-forming ATCC 12228 and the biofilm-forming ATCC 35984 (RP62A)] and to 400 clinical isolates of Staphylococcus epidermidis from orthopedic prosthesis associated infections. The gene profile was compared with the phenotypic biofilm-forming ability, evaluated by means of an optimized Congo red agar (CRA) plate test. Among the clinical isolates, 228 (57%) turned out completely ica positive and were biofilm producing. Among the 172 non-biofilm-forming strains (43%), 164 (41%) were completely ica negative and 8 strains (2%) harbored all five ica genes. The ica locus thus proves to be a cluster of strictly linked genes, without any evidence of single gene deletion.

Search for the insertion element IS256 within the ica locus of Staphylococcus epidermidis clinical isolates collected from biomaterial-associated infections

Staphylococcus epidermidis biofilm-forming strains produce a polysaccharide intercellular adhesin (PIA), which mediates bacterial cell aggregation and favours the colonisation on prosthetic implants. PIA synthesis is regulated by the icaADBC locus. In vitro, by repeated subcultures of a biofilm-producing strain, the loss of the ability to produce biofilm appears associated with the insertion of the IS256 element into the ica locus. This study was aimed (i) to investigate if the five genes of ica locus are always all present in different strains of S. epidermidis, and (ii) to search if IS256 insertion naturally occurs in ica locus without making recourse to the experimental procedure of repeated subcultures of strains. 120 S. epidermidis clinical isolates from peri-prosthesis infections were investigated both by an original multiplex PCR analysis of the ica genes and by PCR amplification of the IS256 element. Also two reference strains (the biofilm-negative S. epidermidis ATCC 12228 and the biofilm-forming ATCC 35984 [RP62A]) and two biofilm-negative RP62A-derived acriflavin mutants (D9 and HAM892) were analysed. D9 e HAM892 were for the first time shown to contain in ica locus, at the base 3319, a 1300-bp insertion with a DNA sequence corresponding to IS256. Among the 120 clinical isolates, 51 (43%) turned out completely ica-positive, 69 completely ica-negative (57%). The genes of the ica locus appear, in all cases of the present collection, strictly linked each other, so they are either all present or all absent. In this collection, IS256 was present in eight out of the 69 ica-negative strains and in 34 out of the 51 ica-positive strains. IS256, also when present in bacterial genomic DNA, was never found inside the ica locus, thus suggesting that insertion/excision of this element is not a natural occurring mechanism for off/on switching of biofilm production.

Development of a multiplex PCR technique for detection and epidemiological typing of salmonella in human clinical samples

We have developed a multiplex PCR assay for Salmonella detection and epidemiological typing. Six sets of primers were designed to detect the major Salmonella serotypes and phage types in Spain. An internal amplification control was designed in order to detect PCR inhibition. The different amplification profiles obtained allowed us to detect Salmonella bacteria and to distinguish the clinically prevalent Salmonella enterica serotypes Enteritidis, Typhimurium and subspecies I serotype 4,5,12:i:-. Using this method, we could detect a specific band for DT104 and U302 phage types in Salmonella serotype Typhimurium. Salmonella enterica serotype Hadar and other C2 serogroup strains showed two specific band profiles. In the validation stage, the assay was reproducible for all serotypes studied, apart from some C2 serogroup strains. When the technique was applied to clinical stool specimens, the prevalent serotypes Enteritidis and Typhimurium were detected with a sensitivity of 93%, specificity of 100%, and efficiency of 98%. Also, a low PCR inhibition rate (8%) was obtained. The overall agreement of the multiplex PCR with conventional culture-based techniques was 95% for Salmonella typing using Cohen's kappa index.

Staphylococcus epidermidis-fibronectin binding and its inhibition by heparin

Staphylococcus epidermidis is able to adhere onto biomaterials and to cause implant infections. Recently, host matrix proteins, which in vivo cover the implants, have been indicated as substrates for adhesion by specific bacterial adhesins. Here, the binding of S. epidermidis to fibronectin, a main protein of the extracellular matrix, and the effect of heparin on this interaction were studied by dynamic force spectroscopy (DFS). Novelties are that S. epidermidis strains analysed by DFS were clinical isolates from prosthesis-associated infections, genotyped and phenotyped for their adhesion properties to fibronectin and examined as living cells. Thus, fibronectin-binding staphylococci adhered to the fibronectin-coated substratum and formed a continuous layer assuring their contact with the fibronectin-coated cantilever tip during the approach-retraction cycles of the DFS measurements. Results show that only a single molecular binding site of fibronectin is involved in the interaction with S. epidermidis, that it takes place at the domain near the C-terminus and that it is specifically inhibited by heparin.

Detection of pathogenic bacteria in shellfish using multiplex PCR followed by CovaLink NH microwell plate sandwich hybridization

Outbreak of diseases associated with consumption of raw shellfish especially oysters is a major concern to the seafood industry and public health agencies. A multiplex PCR amplification of targeted gene segments followed by DNA-DNA sandwich hybridization was optimized to detect the etiologic agents. First, a multiplex PCR amplification of hns, spvB, vvh, ctx and tl was developed enabling simultaneous detection of total Salmonella enterica serotype Typhimurium, Vibrio vulnificus, Vibrio cholerae and Vibrio parahaemolyticus from both pure cultures and seeded oysters. Amplicons were then subjected to a colorimetric CovaLink NH microwell plate sandwich hybridization using phosphorylated and biotinlylated oligonucleotide probes, the nucleotide sequences of which were located internal to the amplified DNA. The results from the hybridization with the multiplexed PCR amplified DNA exhibited a high signal/noise ratio ranging between 14.1 and 43.2 measured at 405 nm wavelength. The sensitivity of detection for each pathogen was 10(2) cells/g of oyster tissue homogenate. The results from this study showed that the combination of the multiplex PCR with a colorimetric microwell plate sandwich hybridization assay permits a specific, sensitive, and reproducible system for the detection of the microbial pathogens in shellfish, thereby improving the microbiological safety of shellfish to consumers.

Staphylococcus lugdunensis carrying the mecA gene causes catheter-associated bloodstream infection in premature neonate

A premature neonate had a catheter-associated bloodstream infection due to Staphylococcus lugdunensis. The MIC of oxacillin for the strain was >256 microg/ml, and the mecA gene of S. lugdunensis was detected by PCR. The infection was resolved after removal of the line and treatment with vancomycin for 2 weeks.

Rapid detection of methicillin-resistant Staphylococcus aureus directly from sterile or nonsterile clinical samples by a new molecular assay

A rapid procedure was developed for detection and identification of methicillin-resistant Staphylococcus aureus (MRSA) directly from sterile sites or mixed flora samples (e.g., nose or inguinal swabs). After a rapid conditioning of samples, the method consists of two main steps: (i) immunomagnetic enrichment in S. aureus and (ii) amplification-detection profile on DNA extracts using multiplex quantitative PCR (5'-exonuclease qPCR, TaqMan). The triplex qPCR assay measures simultaneously the following targets: (i) mecA gene, conferring methicillin resistance, common to both S. aureus and Staphylococcus epidermidis; (ii) femA gene from S. aureus; and (iii) femA gene from S. epidermidis. This quantitative approach allows discrimination of the origin of the measured mecA signal. qPCR data were calibrated using two reference strains (MRSA and methicillin-resistant S. epidermidis) processed in parallel to clinical samples. This 96-well format assay allowed analysis of 30 swab samples per run and detection of the presence of MRSA with exquisite sensitivity compared to optimal culture-based techniques. The complete protocol may provide results in less than 6 h (while standard procedure needs 2 to 3 days), thus allowing prompt and cost-effective implementation of contact precautions.

Rapid detection of methicillin-resistant staphylococci from blood culture bottles by using a multiplex PCR assay

Rapid detection and accurate identification of methicillin-resistant staphylococci are critical for the effective management of infections caused by these organisms. We describe a multiplex PCR-based assay for the direct detection of methicillin-resistant staphylococci from blood culture bottles (BacT/Alert; Organon-Teknika, Durham, N.C.). A simple lysis method followed by a multiplex PCR assay designed to detect the nuc, mecA, and bacterial 16S rRNA genes was performed. A total of 306 blood culture specimens were collected over a period of 10 months from June 1998 to April 1999, consisting of 236 blood cultures growing staphylococci (including 124 methicillin-resistant Staphylococcus spp.), 50 positive blood cultures which grew organisms other than staphylococci, and 20 blood cultures that were negative for bacterial and fungal pathogens after 5 days of incubation and terminal subculture. DNA extraction, PCR, and detection could be completed in 2.5 h. Of the positive blood cultures with staphylococci, the multiplex PCR assay had a sensitivity and specificity of 99.2% and 100%, respectively. Our results show that rapid, direct detection of methicillin-resistant staphylococci is possible, allowing clinicians to make prompt and effective decisions for the management of patients with staphylococcal bacteremia.

Multiplex PCR strategy for rapid identification of structural types and variants of the mec element in methicillin-resistant Staphylococcus aureus

Full characterization of methicillin-resistant Staphylococcus aureus (MRSA) requires definition of not only the bacterial genetic background but also the structure of the complex and heterologous mec element these bacteria carry, which is associated with drug resistance determinant mecA. We report the development, validation, and application of a multiplex PCR strategy that allows quick presumptive characterization of the mec element types based on the structural features that were shown to be typical of mec elements carried by several MRSA clones. The strategy was validated by using a representative collection of pandemic MRSA clones in which the full structure of the associated mec elements was previously determined by hybridization and PCR screenings and also by DNA sequencing. The method was tested together with multilocus sequence typing and other typing methods for the characterization of 18 isolates representative of the MRSA clones recovered during a hospital outbreak in Barcelona, Spain. The multiplex PCR was shown to be rapid, robust, and capable in a single assay of identifying five structural types of the mec element among these strains, three major and two minor variants, each one of which has been already been seen among MRSA characterized earlier. This technique should be a useful addition to the armamentarium of molecular typing tools for the characterization of MRSA clonal types and for the rapid tentative identification of structural variants of the mec element.