Diagnostic PCR: making internal amplification control mandatory.
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International Cooperation↗
Biomedical subjects
A Abdulmawjood
Publications and source records attributed to A Abdulmawjood.
Diagnostic PCR: making internal amplification control mandatory.
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Molecular Diagnostic Techniques↗
Identification and molecular characterization of beta-hemolytic streptococci isolated from harbor seals (Phoca vitulina) and grey seals (Halichoerus grypus) of the German North and Baltic Seas.
Bacteriological investigations of seals of the German North and Baltic seas resulted in the isolation of bacteria of the genus Streptococcus belonging to Lancefield's serological groups C, F, and L. According to biochemical, serological, and 16S ribosomal DNA analysis, the group C and group F streptococci were identified as Streptococcus phocae. The group L streptococci could be classified as Streptococcus dysgalactiae subsp. dysgalactiae.
Animals↗
Practical considerations in design of internal amplification controls for diagnostic PCR assays.
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Base Sequence↗
Development of PCR assays for detection of Streptococcus canis.
Streptococcus canis isolates, also including S. canis of artificially contaminated milk, could be identified by polymerase chain reaction (PCR) amplification using oligonucleotide primers designed according to species-specific parts of the 16S rRNA gene and, after sequencing, according to S. canis-specific parts of the 16S-23S rDNA intergenic spacer region and with oligonucleotide primers detecting an internal fragment of the group G streptococcal CAMP factor gene cfg. The 16S rRNA gene- and CAMP factor gene cfg-specific oligonucleotide primers could be used together in a multiplex PCR. No cross-reactivities could be observed with other group G streptococcal isolates or with any of the other control strains of various streptococcal species and serogroups. The PCR methods presented in this study allowed a rapid and reliable identification of S. canis and might help to improve the diagnosis of this bacterial species in animal and human infections.
Animals↗
Toward an international standard for PCR-based detection of Escherichia coli O157. Part 1. Assay development and multi-center validation.
As part of a major European research project, a diagnostic PCR assay, including an internal amplification control, was developed and validated in a collaborative trial for the detection of Escherichia coli O157. The assay is based on amplification of sequences of the rfbE O157 gene. The collaborative trial, including 12 international laboratories, was carried out in two phases: phase (a) was performed with identical PCR reagents, including the internal control, provided by the sending laboratory; phase (b) was performed on the same samples and internal control but using in-house PCR reagents of own choice. Phase (a) showed an inclusivity (detection of target strains) of 96.8% and the exclusivity (negative response from nontarget strains) was 100%. The overall performance resulted of phase (a) in an accordance of 98.8, concordance of 98.6, and a concordance odds ratio of 1.11. Phase (b) results showed an accuracy of 100% with all partners and by using different polymerase types and thermocycler models. This indicates that the assay, under consideration as an international standard, was just as reproducible between laboratories, as repeatable within a laboratory. The assay is taken further for validation on carcass-rinse samples.
Animals↗
Inter- and intraspecies variations of the 16S-23S rDNA intergenic spacer region of various streptococcal species.
The 16S-23S rDNA intergenic spacer regions (ISR) of different streptococcal species and subspecies were amplified with primers derived from the highly conserved flanking regions of the 16S rRNA and 23S rRNA genes. The single sized amplicons showed a uniform pattern for S. agalactiae, S. dysgalactiae subsp. dysgalactiae (serogroup C), S. dysgalactiae subsp. equisimilis (serogroup G), S. dysgalactiae subsp. dysgalactiae (serogroup L), S. canis, S. phocae, S. uberis, S. parauberis, S. pyogenes and S. equi subsp. equi, respectively. The amplicons of S. equi subsp. zooepidemicus, S. porcinus and S. suis appeared with 3, 5 and 3 different sizes, respectively. ISR of selected strains of each species or subspecies investigated were sequenced and multiple aligned. This allowed a separation of ISR into regions, with 7 regions for S. agalactiae, S. dysgalactiae subsp. dysgalactiae (serogroup C), S. dysgalactiae subsp. equisimilis (serogroup G), S. dysgalactiae subsp. dysgalactiae (serogroup L), S. canis, S. phocae, S. pyogenes and S. suis, 8 regions for S. uberis and S. parauberis and mostly 9 regions for S. equi subsp. equi, S. equi subsp. zooepidemicus and S. porcinus. Region 4, encoding the transfer RNA for alanine (tRNA(Ala)), was present and identical for all isolates investigated. The size and sequence of ISR appears to be a unique marker for streptococci of various species and subspecies and could be used for bacterial identification. In addition the size and sequence variations of ISR of S. equi subsp. zooepidemicus, S. porcinus and S. suis allows a molecular typing of isolates of these species possibly useful in epidemiological aspects.
DNA, Bacterial↗
Identification and epidemiological characterization of Streptococcus uberis isolated from bovine mastitis using conventional and molecular methods.
In the present study 130 S. uberis strains and one S. parauberis strain isolated from bovine milk samples of 58 different farms of various locations in Hesse, Germany, as well as two reference strains of each species were comparatively investigated for cultural, biochemical, serological and molecular properties. All S. uberis strains produced the enzyme beta-D-glucuronidase, while the S. parauberis strains were negative. The S. uberis and S. parauberis 16S rRNA genes were amplified by polymerase chain reaction and subsequently digested with the restriction enzymes RsaI and AvaII yielding species-specific restriction patterns. Both species were additionally identified by amplifying species-specific parts of the genes encoding the 16S rRNA, the 23S rRNA and the 16S-23S rDNA intergenic spacer region, respectively. The CAMP factor gene cfu, a potential virulence factor of S. uberis, was amplified, corresponding to a phenotypically positive CAMP-reaction, using cfu-specific oligonucleotide primers. In addition the streptokinase/plasminogen activator encoding genes skc/pauA, a second potential virulence factor, could be amplified for 126 of the 130 S. uberis but not for S. parauberis. A DNA fingerprinting of S. uberis strains, performed by macrorestriction analysis of their chromosomal DNA by pulsed-field gel electrophoresis, revealed that most of the isolates were not related to each other. However, identical DNA patterns were noted for some of the isolates within different quarters of an individual cow and also for different cows within the same farm. The generally unrelated DNA patterns indicated that S. uberis is a pathogen with multiple environmental habitats and that infections are caused by a great variety of strains.
Animals↗
Two methods for construction of internal amplification controls for the detection of Escherichia coli O157 by polymerase chain reaction.
For the detection of food born bacteria by polymerase chain reaction (PCR) in food products, an internal amplification control (IAC) is required in order to prevent false negative results that might be caused by PCR inhibitors. In the present study, two IACs were constructed using two different methods. These IACs were designed in a way that the same primer pair can be used to amplify the target DNA and coamplify the IAC. The first IAC with a size of approximately 200 bp was constructed by deleting a part of the amplicon of the original target DNA (500 bp) between the two primer sites to produce an IAC smaller than the target DNA. The second IAC with a size of approximately 600 bp was synthesized in a one step PCR reaction. The primers used in this reaction possessed 5' over-hanging ends, which were identical to the primers used in the diagnostic reaction, whereas their 3' ends were complementary to the (pUC19) predetermined DNA sequence of defined length and sequence. The concentration of IACs appeared to be critical. Too much IAC DNA template would out-compete the target DNA template, thus giving a false negative result. However the use of an optimal IAC concentration increased the reliability of the PCR assays and appeared to be useful for food diagnostics.
DNA Primers↗
Evaluation of PCR methods for rapid identification and differentiation of Streptococcus uberis and Streptococcus parauberis.
Streptococcus uberis and Streptococcus parauberis reference strains and isolates obtained from routine diagnostics were investigated by PCR with oligonucleotide primers designed according to species-specific parts of the 16S rRNA gene, the 23S rRNA gene, and the 16S-23S rRNA intergenic spacer region of both species. All three primer pairs allowed an identification of 67 isolates as S. uberis and 4 isolates as S. parauberis.
Animals↗
Determination of intraspecies variations of the V2 region of the 16S rRNA gene of Streptococcus equi subsp. zooepidemicus.
The 16S rRNA gene of 39 S. equi subsp. zooepidemicus strains and two S. equi subsp. equi strains was amplified by polymerase chain reaction and subsequently digested with the restriction enzyme Hinc II. A restriction profile with two fragments with sizes of 1250 bp and 200 bp could be observed for both S. equi subsp. equi strains and for 30 of the 39 S. equi subsp. zooepidemicus strains indicating a sequence variation within the V2 region of the 16S rRNA gene of the remaining nine S. equi subsp. zooepidemicus isolates. A segment of the 16S rRNA gene including the hypervariable V2 region of 11 S. equi subsp. zooepidemicus and two S. equi subsp. equi could be amplified by PCR and sequenced. The sequence of the V2 region of eight S. equi subsp. zooepidemicus strains appeared to be identical or almost identical to the sequence of the two S. equi subsp. equi strains. The sequence of the remaining three S equi subsp. zooepidemicus strains differed significantly from the sequence of S. equi subsp. equi. These differences allowed a division of S. equi subsp. zooepidemicus strains into two 16S rRNA types and might possibly have consequences for the taxonomic position of these phenotypically indistinguishable strains of one subspecies. A molecular typing could additionally be performed by amplification of the gene encoding the 16S-23S rRNA spacer region. A single amplicon of the spacer gene of 1100 bp could be observed for one S. equi subsp. zooepidemicus, an amplicon of 950 bp for two S. equi subsp. equi strains and 10 S. equi subsp. zooepidemicus strains, a amplicon of 780 bp for 27 S. equi subsp. zooepidemicus strains and a single amplicon of 600 bp for one S. equi subsp. zooepidemicus strain. The variations of the V2 region of the 16S rRNA gene and the size variations of the 16S-23S rRNA spacer gene were not related to each other. Both variations could be used for molecular typing of this species, possibly useful in epidemiological aspects.
Animals↗
Identification of streptococci isolated from various sources by determination of cfb gene and other CAMP-factor genes.
In the present study, the CAMP-factor (cfb) gene of streptococci of serological group B (Streptococcus agalactiae) and the CAMP-factor (cfu) gene of S. uberis could be amplified by polymerase chain reaction. A cfb specific amplicon could be observed for all 128 phenotypically CAMP-positive S. agalactiae, for the phenotypically CAMP-negative S. agalactiae strain 74-360, and for 2 S. difficile reference strains. A cfu specific amplicon could be observed for all 7 phenotypically CAMP-positive S. uberis. Four S. agalactiae strains isolated from 4 cows with mastitis appeared to be phenotypically CAMP-negative and negative in the cfb gene PCR. The CAMP-positive and CAMP-negative isolates, including both S. difficile, could be identified as S. agalactiae by amplification of a S. agalactiae specific part of the V2 region of the 16S rRNA and a species-specific part of the 16S-23S rRNA intergenic spacer region. Amplification of an internal fragment of the cfb gene with a reduced annealing temperature yielded positive reactions not only for CAMP-positive S. agalactiae, but also for phenotypically CAMP-positive S. pyogenes (n = 4), S. canis (n = 28), and S. uberis (n = 7), indicating a close relation of the CAMP genes of these 4 species. The relation could be further demonstrated by sequencing the internal fragment of the CAMP-factor (cfg) gene of S. canis and comparing the sequence with those of S. agalactiae, S. pyogenes, and S. uberis.
Animals↗
Isolation and further characterization of phase variants of Streptococcus equi subsp. zooepidemicus.
In the present study the soft agar technique was used to isolate phase variants of S. equi subsp. zooepidemicus-cultures isolated from infections of horses. The phase variants were characterized by a compact or diffuse colony morphology in this media. The variants could be cultivated separately and further characterized genotypically by RAPD analysis and by macrorestriction analysis of their chromosomal DNA by pulsed-field gel electrophoresis, indicating the identity of both strains of each pair. The diffuse colony variants grew uniformly turbid after cultivation in fluid media, did not haemagglutinate rabbit erythrocytes, and displayed a reduced surface hydrophobicity in hexadecane and phenyl-sepharose adherence tests. The compact colony variants generally grew as sediment with clear supernatant in fluid media, haemagglutinated rabbit erythrocytes and showed an enhanced surface hydrophobicity in both hydrophobicity tests. The presented soft agar technique allowed a demonstration of phase variation of S. equi subsp. zooepidemicus and a subsequent isolation of the variants. This might be an important prerequisite to understanding the pathogenic importance of phase variation among isolates of this bacterial species.
Animals↗
The role of hyaluronic acid capsular material of Streptococcus equi subsp. zooepidemicus in mediating adherence to HeLa cells and in resisting phagocytosis.
Hyaluronic acid is thought to be one of the critical virulence factors of Streptococcus equi subsp. zooepidemicus. The present study was designed to study the role of hyaluronic acid capsular material in mediating adherence and to resist the phagocytosis of the host's immune defence. The studies were performed with two encapsulated S. equi subsp. zooepidemicus and two unencapsulated phase variants. The bacteria had been previously isolated from diseased pigs and monkeys in Indonesia. The presence of capsular material was determined using the hyaluronic acid decapsulation test and by electron microscopic studies. Both encapsulated bacteria showed mucoid colonies after cultivation on blood agar, grew with diffuse colonies in soft agar media and reacted negatively in the salt aggregation test. The unencapsulated bacteria grew with small colonies on blood agar, formed compact colonies in soft agar media and reacted positively in the salt aggregation test. Adherence and phagocytosis studies revealed that the encapsulated bacteria adhered significantly more to HeLa cells and were less phagocytosed by murine macrophages compared to unencapsulated bacteria. Pretreatment of the HeLa cells using hyaluronic acid or pretreatment of the bacteria by hyaluronidase decreased the adherence value of encapsulated bacteria. Pretreatment of bacteria with pronase had no effect. The presented results strongly indicate that the hyaluronic acid capsular material contributes to adherence properties of S. equi subsp. zooepidemicus and might help the bacteria to resist phagocytosis by macrophages.
Animals↗
Amplification of 16S ribosomal RNA gene sequences for the identification of streptococci of Lancefield group B.
The 16S r RNA gene of 49 streptococci of serological group B isolated from various origins was amplified by polymerase chain reaction (PCR) and subsequently digested with the restriction enzymes Rsa I and Msp I. The restriction profiles of all group B streptococci appeared to be identical indicating no intraspecies sequence variations of this gene. A fragment of the gene of two group B-streptococcal reference strains, including the hypervariable V2 region, could be amplified by PCR and sequenced. The sequence appeared to be identical and allowed the design of species-specific oligonucleotide primers. The primer pair used produced an amplicon with a size of 1250 bp and correctly identified all 49 group B-streptococci investigated but none of the control strains of various species and serogroups. This primer could be used in a multiplex PCR and allowed a rapid identification of bacteria of this species.
Base Sequence↗
Properties of serological group B streptococci of dog, cat and monkey origin.
This study was designed to identify and characterize further Streptococcus agalactiae isolated during routine diagnostics from three diseased dogs and a cat, as well as from the inner organs of a monkey which died on a sepsis with beta-haemolytic streptococci. The cultures could be identified as streptococci of serological group B by cultural, biochemical and serological properties and by restriction fragment length polymorphism analysis of polymerase chain reaction (PCR)-amplified 16S ribosomal DNA. A further characterization of the isolates by serotyping and by determination of antibiotic resistances revealed a close relationship of these isolates to the human biotype of this species.
Animals↗
Species identification of Streptococcus porcinus by restriction fragment length polymorphism analysis of 16S ribosomal DNA.
Streptococcus porcinus reference strains and routine isolates belonging to Lancefield's serogroup E, P, U and V and to various serotypes of serogroup E were examined for their 16S ribosomal DNA fingerprint pattern. Oligonucleotide primers complementary to 16S rRNA genes were used to amplify gene fragments by polymerase chain reaction from genomic DNA. The amplified 1450 bp fragment was subsequently digested with the restriction enzyme BpiI resulting in two fragments with a size of approximately 1250 bp and 200 bp. All 45 S porcinus investigated in the present study could be identified on the basis of this characteristic 16S rDNA fingerprint pattern and clearly differentiated from 16 control strains of various species and serogroups of genus Streptococcus. The present results demonstrate the potential application of 16S rDNA analysis for identification of S porcinus, a species which might express various group- and type-specific antigens.
Animals↗