Genetic identification of Staphylococcus aureus by polymerase chain reaction using single-base-pair mismatch in 16S ribosomal RNA gene

Current molecular approach for diagnosis of MRSA: a meta-narrative review

Introduction:

Detection and diagnosis of methicillin-resistant Staphylococcus aureus (MRSA) are important in ensuring a correct and effective treatment, further reducing its spread. A wide range of molecular approaches has been used for the diagnosis of antimicrobial resistance (AMR) in MRSA. This review aims to study and appraise widely used molecular diagnostic methods for detecting MRSA.

Methods:

This meta-narrative review was performed by searching PubMed using the following search terms: (molecular diagnosis) AND (antimicrobial resistance) AND (methicillin-resistant Staphylococcus aureus). Studies using molecular diagnostic techniques for the detection of MRSA were included, while non-English language, duplicates and non-article studies were excluded. After reviewing the libraries and a further manual search, 20 studies were included in this article. RAMESES publication standard for narrative reviews was used for this synthesis.

Results:

A total of 20 full papers were reviewed and appraised in this synthesis, consisting of PCR technique (n = 7), deoxyribonucleic acid (DNA) Microarray (n = 1), DNA sequencing (n = 2), Xpert MRSA/SA BC assay (n = 2), matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) (n = 2), MLST (n = 4), SCCmec typing (n = 1) and GENECUBE (n = 1).

Discussion:

Different diagnostic methods used to diagnose MRSA have been studied in this review. This study concludes that PCR has been extensively used due to its higher sensitivity and cost-effectiveness in the past five years

Biochemical and histopathological changes related to the topical application of Aloe vera ointment for canine pyoderma

Background and Aim:

Pyoderma is common in dogs, and its treatment requires a novel medication rather than antibiotic therapy. This study aimed to determine the biochemical and histopathological changes associated with the topical application of Aloe vera 20% and 40% ointments, compared with gentamicin 0.1% ointment, in dogs suffering from Staphylococcus aureus pyoderma.

Materials and Methods:

Serum and skin samples were collected from a negative control group before inducing pyoderma and from other subdivided groups on the 3^rd, 7^th, 10^th, and 14^th days post-inoculation for biochemical and histopathology examination.

Results:

Serum aspartate aminotransferase, alanine aminotransferase (ALT), urea, and creatinine concentrations were higher in the positive control dogs on the 3^rd day without treatment (DWT) compared with the negative control dogs (p<0.05). Compared with the healthy control dogs, serum zinc concentrations were lower in the positive control group on the 3^rd, 7^th, and 10^th DWT and in dogs treated with A. vera 20% and gentamicin 0.1% ointments on the 3^rd and 7^th days post-treatment (p<0.05). Grossly, skin had erythema, pruritus, and pus-filled pustules of the untreated group. Microscopically, skin showed epidermal necrosis and edema, dermal collagen necrosis, and severe neutrophilic infiltration.

Conclusion:

Compared with A. vera 20% and gentamicin 0.1% ointments, the topical application of A. vera 40% ointment-induced quicker skin healing and decreased the inflammatory changes caused by S. aureus inoculation, based on biochemical and histopathological changes reflective of its curative efficiency. A. vera 40% ointment may be a suitable alternative to antibiotics for the treatment of staphylococcal pyoderma in dogs.

Controllable fabrication of magnetic core–shell nanocomposites with high peroxide mimetic properties for bacterial detection and antibacterial applications

Pathogenic bacterial infection has become a growing threat to public health; therefore, exploration of a sensitive and specific method for the identification of bacteria is very important.

PCR-based Approaches for the Detection of Clinical Methicillin-resistant Staphylococcus aureus

Staphylococcus aureus is an important pathogen that can cause a variety of infections, including superficial and systematic infections, in humans and animals. The persistent emergence of multidrug resistant S. aureus, particularly methicillin-resistant S. aureus, has caused dramatically economic burden and concerns in the public health due to limited options of treatment of MRSA infections. In order to make a correct choice of treatment for physicians and understand the prevalence of MRSA, it is extremely critical to precisely and timely diagnose the pathogen that induces a specific infection of patients and to reveal the antibiotic resistant profile of the pathogen. In this review, we outlined different PCR-based approaches that have been successfully utilized for the rapid detection of S. aureus, including MRSA and MSSA, directly from various clinical specimens. The sensitivity and specificity of detections were pointed out. Both advantages and disadvantages of listed approaches were discussed. Importantly, an alternative approach is necessary to further confirm the detection results from the molecular diagnostic assays.

Molecular diagnostics of clinically important staphylococci

Bacterial species of the genus Staphylococcus known as important human and animal pathogens are the cause of a number of severe infectious diseases. Apart from the major pathogen Staphylococcus aureus, other species until recently considered to be nonpathogenic may also be involved in serious infections. Rapid and accurate identification of the disease-causing agent is therefore prerequisite for disease control and epidemiological surveillance. Modern methods for identification and typing of bacterial species are based on genome analysis and have many advantages compared to phenotypic methods. The genotypic methods currently used in molecular diagnostics of staphylococcal species, particularly of S. aureus, are reviewed. Attention is also paid to new molecular methods with the highest discriminatory power. Efforts made to achieve interlaboratory reproducibility of diagnostic methods are presented.

eap Gene as novel target for specific identification of Staphylococcus aureus

The cell surface-associated extracellular adherence protein (Eap) mediates adherence of Staphylococcus aureus to host extracellular matrix components and inhibits inflammation, wound healing, and angiogenesis. A well-characterized collection of S. aureus and non-S. aureus staphylococcal isolates (n = 813) was tested for the presence of the Eap-encoding gene (eap) by PCR to investigate the use of the eap gene as a specific diagnostic tool for identification of S. aureus. Whereas all 597 S. aureus isolates were eap positive, this gene was not detectable in 216 non-S. aureus staphylococcal isolates comprising 47 different species and subspecies of coagulase-negative staphylococci and non-S. aureus coagulase-positive or coagulase-variable staphylococci. Furthermore, non-S. aureus isolates did not express Eap homologs, as verified on the transcriptional and protein levels. Based on these data, the sensitivity and specificity of the newly developed PCR targeting the eap gene were both 100%. Thus, the unique occurrence of Eap in S. aureus offers a promising tool particularly suitable for molecular diagnostics of this pathogen.

Identification of emetic toxin producing Bacillus cereus strains by a novel molecular assay

Bacillus cereus causes two types of gastrointestinal diseases: emesis and diarrhea. The emetic type of the disease is attributed to the heat-stable depsipeptide cereulide and symptoms resemble Staphylococcus aureus intoxication, but there is no rapid method available to detect B. cereus strains causing this type of disease. In this study, a polymerase chain reaction (PCR) fragment of unknown function was identified, which was shown to be specific for emetic toxin producing strains of B. cereus. The sequence of this amplicon was determined and a PCR assay was developed on this basis. One hundred B. cereus isolates obtained from different food poisoning outbreaks and diverse food sources from various geographical locations and 29 strains from other species belonging to the B. cereus group were tested by this assay. In addition, 49 non-B. cereus group strains, with special emphasis on food pathogens, were used to show that the assay is specific for emetic toxin producing B. cereus strains. The presented PCR assay is the first molecular tool for the rapid detection of emetic toxin producing B. cereus strains.

A single base extension technique for the analysis of known mutations utilizing capillary gel electrophoreisis with electrochemical detection

A novel single nucleotide polymorphism (SNP) detection system is described in which the accuracy of DNA polymerase and advantages of electrochemical detection are demonstrated. A model SNP system is presented to illustrate the potential advantages in coupling the single base extension (SBE) technique to capillary gel electrophoresis (CGE) with electrochemical detection. An electrochemically labeled primer, with a ferrocene acetate covalently attached to its 5' end, is used in the extension reaction. When the Watson-Crick complementary ddNTP is added to the SBE reaction, the primer is extended by a single nucleotide. The reaction mixture is subsequently separated by CGE, and the ferrocene-tagged fragments are detected at the separation anode with sinusoidal voltammetry. This work demonstrates the first single base resolution separation of DNA coupled with electrochemical detection. The unextended primer (20-mer) and the 21-mer extension product are separated with a resolution of 0.8.

Primary diagnosis of whipple disease manifesting as lymphadenopathy: use of polymerase chain reaction for detection of Tropheryma whippelii

Whipple disease is a rare, chronic multisystem disease associated with the recently characterized organism Tropheryma whippelii. Extraintestinal manifestation involving the central nervous system, heart, and joints occasionally occurs. Involvement of the abdominal lymph nodes, especially the mesenteric and periaortic nodes, is not uncommon. However, peripheral lymphadenopathy as the sole clinical manifestation of Whipple disease is rare. We describe 2 patients with Whipple disease whose initial manifestation was lymphadenopathy. Lymph nodes from both patients showed infiltration of the sinuses by macrophages containing periodic acid-Schiff-positive, diastase-resistant, sickle-like structures. Electron microscopic evaluation confirmed the presence of rod-like organisms. DNA from each sample was amplified by the polymerase chain reaction using a specific set of oligonucleotide primers developed against the 16S ribosomal RNA coding sequence of T. whippelii. The histopathologic features and differential diagnosis of lipogranulomatous lymphadenopathy secondary to Whipple disease, as well as use of molecular-based assays, are discussed.

Identification of Staphylococcus aureus based on PCR amplification of species specific genomic 826 bp sequence derived from a common 44-kb Sma I restriction fragment

Primers were designed for polymerase chain reaction (PCR)-amplification of a genomic sequence specific to Staphylococcus aureus strains. The sequence corresponds to a part of the 44-kb Sma I fragment (fragment L on the S. aureus NCTC 8325 restriction map) which was found to be common to strains of the S. aureus species (Pantůcek et al 1996, International Journal of Systematic Bacteriology, 46: 216-222). The labelled 44-kb Sma I restriction fragment derived from S. aureus NCTC 8325-4 was hybridized to the Eco RI restriction patterns of genomic DNA from 13 strains representing different macrorestriction types of S. aureus subsp. aureus. This made it possible to reveal the 2052 bp Eco RI restriction subfragment and to demonstrate its presence in all the tested strains. From the sequence of this subfragment, primers were designed by means of which the 826 bp amplicons were obtained in all 216 tested strains of S. aureus. No hybridization and PCR-products were observed in 40 collection strains of other staphylococcal species and subspecies as well as in 45 clinical strains of coagulase-negative staphylococci. These results lead us to the conclusion that the use of the above primers makes it possible to identify rapidly and reliably S. aureus strains of various provenance and different genotypes.

Development of a PCR assay for identification of staphylococci at genus and species levels

We have developed a PCR-based assay which allows the detection of staphylococci at the genus level by targeting the tuf gene, which encodes the elongation factor Tu. Degenerate PCR primers derived from consensus regions of several tuf genes were used to amplify a target region of 884 bp from 11 representative staphylococcal species. Subsequently, the entire nucleotide sequence of these amplicons was determined. The analysis of a multiple alignment of these sequences revealed regions conserved among staphylococci but distinct from those of other gram-positive bacteria genetically related to staphylococci. PCR primers complementary to these regions could amplify specifically and efficiently a DNA fragment of 370 bp for all of 27 different staphylococcal species tested. There was no amplification with genomic DNA prepared from 53 nonstaphylococcal species tested to verify the specificity of the assay (20 gram positive and 33 gram negative). Furthermore, this assay amplified efficiently all 27 American Type Culture Collection (ATCC) staphylococcal reference strains as well as 307 clinical isolates of staphylococci from the Québec City region. Analysis of the multiple sequence alignment for the 884-bp fragment for the 11 staphylococcal species as well as comparison of the sequences for the 370-bp amplicon from five unrelated ATCC and clinical strains for each of the species S. aureus, S. epidermidis, S. haemolyticus, S. hominis, and S. saprophyticus demonstrated sufficient interspecies polymorphism to generate genus- and species-specific capture probes. This sequence information allowed the development of Staphylococcus-specific and species-specific (targeting S. aureus, S. epidermidis, S. haemolyticus, S. hominis, or S. saprophyticus) capture probes hybridizing to the 370-bp amplicon. In conclusion, this PCR assay is suitable for detection of staphylococci at both genus and species levels.

Use of PCR analysis for detecting low levels of bacteria and mold contamination in pharmaceutical samples

PCR assays were developed and compared to standard methods for quality evaluation of pharmaceutical raw materials and finished products with low levels of microbial contamination. Samples were artificially contaminated with less than 10 CFU of Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, and Aspergillus niger. Bacterial DNA was extracted from each enrichment broth by mild lysis in Tris-EDTA-Tween 20 buffer containing proteinase K while mold DNA was extracted by boiling samples in Tris-EDTA-SDS buffer for 1 h. A 10-microl aliquot of extracted DNA was added to Ready-To-Go PCR beads and specific primers for E. coli, S. aureus, and P. aeruginosa. However, 50-microl aliquots of extracted mold DNA were used for amplification of specific A. niger DNA sequences. Standard methods required 6-8 days while PCR detection of all microorganisms was completed within 27 h. Low levels of microbial contamination were detected in all raw materials and products using PCR assays. Rapid quality evaluation of pharmaceutical samples resulted in optimization of product manufacturing, quality control, and release of finished products.

Species-specific and ubiquitous-DNA-based assays for rapid identification of Staphylococcus aureus

Staphylococcus aureus is the cause of serious infections in humans, including endocarditis, deep-seated abscesses, and bacteremia, which lead to toxic and septic shock syndromes. Rapid and direct identification of this bacterium specifically and ubiquitously directly from clinical specimens would be useful in improving the diagnosis of S. aureus infections in the clinical microbiology laboratory. A wide variety of kits based on biochemical characteristics efficiently identify S. aureus, but the rapidity and the accuracy of each of these methods combined with testing of clinically relevant antibiotic resistance genes need to be improved. On the basis of hybridization assays with randomly selected clones from an S. aureus genomic library, we have identified a chromosomal DNA fragment which is specific for S. aureus and which detected all 82 S. aureus isolates tested. This 442-bp fragment was sequenced and was used to design a set of PCR amplification primers. The PCR assay was also specific and ubiquitous for the identification from bacterial cultures of 195 clinical strains of S. aureus isolated from a variety of anatomical sites and obtained from hospitals throughout the world. The PCR assay that we have developed is simple and can be performed in about 1 h. This DNA-based test provides a novel diagnostic tool for the diagnosis of S. aureus infections.

Identification of staphylococcal and streptococcal causes of bovine mastitis using 16S-23S rRNA spacer regions

Bovine mastitis is caused mainly by certain Staphylococcus and Streptococcus species. The sequences of the 16S-23S rRNA spacer regions were determined for the nine species which cause mastitis: Staphylococcus aureus, Staphylococcus chromogenes, Staphylococcus epidermidis, Staphylococcus hyicus, Staphylococcus simulans, Staphylococcus xylosus, Streptococcus agalactiae, Streptococcus dysgalactiae and Streptococcus uberis. Significant variation was found between the spacer sequences of different species with the lengths of the spacers varying from 240 to 461 bp. Between genera the spacers shared only short conserved regions (8-9 bp) and within genera the sequence identities varied from 53 to 85%. This variation made it possible to construct specific primer pairs for these species and genera. The specificities of these primers were tested with 25 bacterial species and 51 isolates from cattle with clinical mastitis. The DNA-based identification of the mastitis species was mostly successful.

Simultaneous detection of Streptococcus pneumoniae and Haemophilus influenzae by nested PCR amplification from cerebrospinal fluid samples

Haemophilus influenzae and Streptococcus pneumoniae are often the cause of serious diseases such as meningitis. We designed a nested PCR assay to identify these pathogens from cerebrospinal fluid samples. The first-step PCR was able to detect eubacterial rRNA genes with a unified set of universal primers. In the second-step PCR, the identification primers, HI I and II and SP I and II, could detect H. influenzae and S. pneumoniae respectively through amplification of the rRNA spacer between the 16S and 23S rRNA genes. We suggest that the two-step PCR assay can be used as a novel method for the immediate and retrospective diagnosis of bacterial meningitis caused by H. influenzae and S. pneumoniae.

Rapid identification and typing of Staphylococcus aureus by nested PCR amplified ribosomal DNA spacer region

We designed a polymerase chain reaction (PCR) assay for rapid detection of prokaryotic 16S-23S spacer regions. This PCR assay consisted of nested DNA amplifications. The first-step PCR was able to detect the general presence of eubacteriales with a unified set of universal primers. The universal primers were selected from highly conserved regions in 16S and 23S ribosomal RNA (rRNA) genes and amplified DNAs from all 62 different species of bacteria tested. In the second-step PCR, the identification primers could detect four important bacterial species through amplification of the rRNA spacer regions between the 16S-23S rRNA genes. For Staphylococcus aureus, intraspecies variation in spacer amplification products was observed with S. aureus specific primers. We suggest that the nested PCR assay could be used as a novel method for the identification and typing in epidemiological studies of S. aureus.