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The development of a 16S rRNA gene based PCR for the identification of Streptococcus pneumoniaeand comparison with four other species specific PCR assays

  • Nabil Abdullah El Aila1,
  • Stefan Emler2,
  • Tarja Kaijalainen3,
  • Thierry De Baere1, 4,
  • Bart Saerens1,
  • Elife Alkan1,
  • Pieter Deschaght1,
  • Rita Verhelst1 and
  • Mario Vaneechoutte1Email author
BMC Infectious Diseases201010:104

DOI: 10.1186/1471-2334-10-104

Received: 24 November 2009

Accepted: 29 April 2010

Published: 29 April 2010

Abstract

Background

Streptococcus pneumoniae is one of the most frequently encountered pathogens in humans but its differentiation from closely related but less pathogenic streptococci remains a challenge.

Methods

This report describes a newly-developed PCR assay (Spne-PCR), amplifying a 217 bp product of the 16S rRNA gene of S. pneumoniae, and its performance compared to other genotypic and phenotypic tests.

Results

The new PCR assay designed in this study, proved to be specific at 57°C for S. pneumoniae, not amplifying S. pseudopneumoniae or any other streptococcal strain or any strains from other upper airway pathogenic species. PCR assays (psaA, LytA, ply, spn9802-PCR) were previously described for the specific amplification of S. pneumoniae, but psaA-PCR was the only one found not to cross-react with S. pseudopneumoniae.

Conclusion

Spne-PCR, developed for this study, and psaA-PCR were the only two assays which did not mis-identify S. pseudopneumoniae as S. pneumoniae. Four other PCR assays and the AccuProbe assay were unable to distinguish between these species.

Background

Streptococcus pneumoniae is one of the most pathogenic bacteria involved in human disease [1], causing bronchitis, pneumonia, as well as life-threatening meningitis and bloodstream infections [2]. Culture-based methods are usually applied to detect S. pneumoniae from patient samples and to differentiate it from other less pathogenic viridans streptococci, frequently encountered in respiratory samples. Differentiation is also important with regard to resistance testing, since different antibiotic susceptibility breakpoints are applied for S. pneumoniae with regard to other viridans species [3]. Culture-based identification methods usually rely on optochin susceptibility, agglutination and bile-solubility, sometimes confirmed by specific probes (Accuprobe™, Genprobe) [4].

However, straightforward phenotypic identification of pneumococci is hampered by the occurrence of optochin resistant S. pneumoniae variants [58] and. In addition, closely related S. pseudopneumoniae is difficult to distinguish from S. pneumoniae and is e.g. positive with AccuProbe as well [4].

It is of clinical relevance to rapidly and specifically detect S. pneumoniae. Therefore several PCR assays have been developed over the past decades [914].

This study compared the specificity of four published S. pneumoniae PCR assays to that of a new approach, based on the 16S rRNA gene. One novelty of this approach regards the in-silico design of specific primers using published Streptococcus sequences, filtered for quality and annotation-reliability by profile-based methods (SmartGene, Zug, Switzerland). The approach used by this program relies on a systematic analysis of all published 16S rRNA gene sequences for all streptococci (and closely related organisms), using sequence profiles to eliminate obviously incomplete or erroneous submissions, which could induce wrong alignments.

Sequences with a likely incorrect annotation (shown by low match scores to other sequences of the same species), with unexpected deletions/insertions, or with non useful annotations (e.g. "uncultured") were excluded, since they could induce misleading alignments. Thus, the most representative 16S rRNA sequences were determined for each species. Such a database of representative sequences was used to align closely related streptococcal species to identify specific positions in the 16S rRNA gene for the purpose of species-specific identification. Once these positions were identified, general searches on relevant published sequences of S. pneumoniae and closely related relatives confirmed the consistency of the sequence pattern found. This method helped to detect discriminative species-specific sequence patterns for S. pneumoniae and S. pseudopneumoniae, thus saving time and effort through reduction of non-specific results in wet-lab testing.

Methods

Bacterial strains

A total of 73 streptococcal strains were analyzed in this study, as listed in Table 1, i.e. 8 reference strains of Streptococcus mitis [11] and seven reference strains of S. oralis [11], including three reference strains and the type strain; 19 strains of S. pneumoniae, including two reference strains and the type strain and including 10 optochin resistant strains, for which it was concluded in a previous study [11] that these were genuine S. pneumoniae. In addition, a total of 30 optochin resistant pneumococcus-like streptococci already well-characterized in an earlier study [11], were also included. Finally, the type strain, two reference strains and one clinical strain of S. pseudopneumoniae [4] were included. A total of 12 isolates belonging to the species Haemophilus influenzae (NCTC 8143T), Moraxella catarrhalis (ATCC 25238T and clinical isolate VG S86 0025), Staphylococcus aureus (ATCC 29213 and NCTC 08530), S. epidermidis (CCM2 124T and CNRS N860069), Streptococcus agalactiae (LMG 14694T), S. anginosus (LMG 14502T), S. gallolyticus (LMG 16802T), S. mutans (LMG 14558T) and S. pyogenes (LMG 14237), i.e. species also present in the upper airway tract and/or other Streptococcus species, were used to test the specificity of primer set Spne1-Spne2Rb. In addition, S. parasanguinis (LMG 14537T and LMG 14538) and S. sanguinis (LMG 14656, LMG 14657 and LMG 14702T) isolates were used to test the specificity of primer set Spne1-Spne2Rb.
Table 1

Species and strains studied, phenotypic characteristics, and results for PCR assays

Speciesa

Strain Number

Original Numberb

Spne-PCR

psaA-PCR

lytA-PCR

ply-PCR

spn9802-PCR

Streptococcus mitis

STR025

LMG 14557T

-

-

-

-

-

Streptococcus mitis

STR056

LMG 14552

-

-

-

-

-

Streptococcus mitis

STR226

94 03 0728

-

-

-

-

-

Streptococcus mitis

STR227

94 04 0401

-

-

-

-

-

Streptococcus mitis

STR228

97 03 2943

-

-

-

-

-

Streptococcus mitis

STR229

98 05 5898

-

-

-

-

-

Streptococcus mitis

STR230

98 07 1207

-

-

-

-

-

Streptococcus mitis

STR231

98 09 0066

-

-

-

-

-

Streptococcus oralis

STR024

LMG 14553

-

-

-

-

-

Streptococcus oralis

STR028

LMG 14532T

-

-

-

-

-

Streptococcus oralis

STR029

LMG 14533

-

-

-

-

-

Streptococcus oralis

STR030

LMG 14534

-

-

-

-

-

Streptococcus oralis

STR232

94 08 5574

-

-

-

-

-

Streptococcus oralis

STR233

98 05 5050

-

-

-

-

-

Streptococcus oralis

STR234

98 10 1512

-

-

-

-

 

Streptococcus parasanguinis

STR031

LMG 14537T

-

NT

NT

NT

NT

Streptococcus parasanguinis

STR032

LMG 14538

-

NT

NT

NT

NT

Streptococcus sanguinis

STR038

LMG 14656

-

NT

NT

NT

-

Streptococcus sanguinis

STR039

LMG 14657

-

NT

NT

NT

-

Streptococcus sanguinis

STR059

LMG 14702T

-

NT

NT

NT

NT

Streptococcus pneumoniae

STR061

LMG 14545Tit>

+

+

+

+

+

Streptococcus pneumoniae

STR062

LMG 15155

+

+

+

+

+

Streptococcus pneumoniae

STR063

LMG 16738

+

+

+

+

+

Streptococcus pneumoniae

STR235

93 08 1310

+

+

+

+

+

Streptococcus pneumoniae

STR236

93 09 03230

+

+

+

+

+

Streptococcus pneumoniae

STR237

93 09 1111

+

+

+

+

+

Streptococcus pneumoniae

STR238

98 10 1630

+

+

+

+

+

Streptococcus pneumoniae

STR239

98 10 3326

+

+

+

+

+

Streptococcus pneumoniae

STR240

98 10 3367

+

+

+

+

+

Streptococcus pneumoniae. Group I: oR C+ A+

STR119

KTL004

+

+

+

+

+

Streptococcus pneumoniae. Group I: oR C+ A+

STR120

KTL005

+

+

+

+

+

Streptococcus pneumoniae. Group I: oR C+ A+

STR125

KTL013

+

+

+

+

+

Streptococcus pneumoniae. Group I: oR C+ A+

STR127

KTL017

+

+

+

+

+

Streptococcus pneumoniae. Group I: oR C+ A+

STR141

KTL043

+

+

+

+

+

Streptococcus pneumoniae. Group I: oR C+ A+

STR144

KTL051

+

+

+

+

+

Streptococcus pneumoniae. Group I: oR C+ A+

STR147

KTL056

+

+

+

+

+

Streptococcus pneumoniae. Group I: oR C+ A+

STR149

KTL063

+

+

+

+

+

Streptococcus pneumoniae. Group I: oR C+ A+

STR155a

KTL076

+

+

+

+

+

Streptococcus pneumoniae. Group I: oR C+ A+

STR164

KTL093

+

+

+

+

+

Streptococcus pseudopneumoniae. (Group I: oR C+ A+)

STR157

KTL079

-

-

+

+

+

Streptococcus pseudopneumoniae

STR269

CCUG 48465

-

-

+

+

+

Streptococcus pseudopneumoniae

STR270

CCUG 49455T

-

-

+

+

+

Streptococcus pseudopneumoniae

STR271

CCUG 50866

-

-

+

+

+

Streptococcus sp. Group IIa: oR C- A+

STR150

KTL065

-

-

+

+

+

Streptococcus sp. Group IIa: oR C- A+

STR162

KTL089

-

-

-

+

-

Streptococcus sp. Group IIa: oR C- A+

STR165

KTL096

-

-

+

+

-

Streptococcus sp. Group IIb: oR C- A-

STR122

KTL007

-

-

-

+

-

Streptococcus sp. Group IIb: oR C- A-

STR133

KTL028

-

-

-

+

-

Streptococcus sp. Group IIb: oR C- A-

STR130

KTL021

-

-

-

+

-

Streptococcus sp. Group IIb: oR C- A-

STR137

KTL035

-

-

-

+

-

Streptococcus sp. Group IIb: oR C- A-

STR152

KTL069

-

-

+

+

-

Streptococcus sp. Group IIb: oR C- A-

STR153

KTL072

-

-

-

+

-

Streptococcus sp. Group IIb: oR C- A-

STR131

KTL022

-

-

+

-

-

Streptococcus sp. Group IIb: oR C- A-

STR151 A

KTL068

-

-

-

-

-

Streptococcus sp. Group IIc: oR C- A-

STR118

KTL003

-

-

-

-

-

Streptococcus sp. Group IIc: oR C- A-

STR121

KTL006

-

-

-

-

-

Streptococcus sp. Group IIc: oR C- A-

STR136

KTL034

-

-

-

-

-

Streptococcus sp. Group IIc: oR C- A-

STR138

KTL038

-

-

-

-

-

Streptococcus sp. Group IIc: oR C- A-

STR145

KTL054

-

-

-

-

-

Streptococcus sp. Group IIc: oR C- A-

STR154

KTL073

-

-

-

-

-

Streptococcus sp. Group IIc: oR C- A-

STR123

KTL008

-

-

-

-

-

Streptococcus sp. Group IIc: oR C- A-

STR128

KTL019

-

-

-

-

-

Streptococcus sp. Group IIc: oR C- A-

STR132

KTL023

-

-

-

-

-

Streptococcus sp. Group IIc: oR C- A-

STR134

KTL029

-

-

-

-

-

Streptococcus sp. Group IIc: oR C- A-

STR139

KTL039

-

-

-

-

-

Streptococcus sp. Group IIc: oR C- A-

STR158

KTL081

-

-

-

-

-

Streptococcus sp. Group IIc: oR C- A-

STR159

KTL083

-

-

-

-

-

Streptococcus sp. Group IIc: oR C- A-

STR156

KTL077

-

-

-

-

-

Streptococcus sp. Group IIc: oR C- A-

STR140

KTL041

-

-

-

-

-

Streptococcus sp. Group IIc: oR C- A-

STR160

KTL085

-

-

-

-

-

Streptococcus sp. Group IIc: oR C- A-

STR161

KTL087

-

-

-

-

-

Streptococcus sp. Group IIc: oR C- A-

STR135

KTL030

-

-

-

-

-

Streptococcus sp. Group IIc: oR C- A-

STR143

KTL050

-

-

-

-

-

a: oR: optochin resistant, C: capsule, A: AccuProbe.

b: CCUG: Culture Collection of the University of Göteborg, Sweden; KTL: National Public Health Institute, Helsinki, Finland; LMG: LMG, Laboratorium voor Microbiologie, Gent Culture Collection.

NT: not tested

DNA-extraction was carried out by alkaline lysis as described previously [15]. always starting from one colony.

spn9802-PCR assay

The amplification reactions were performed as described previously [9], with minor modifications. Briefly, amplification was performed in a reaction mixture of 10 μl, containing 5 μl PCR GoTaqGreen Mix (Promega Benelux, Leiden, the Netherlands), 2 μM of each of the forward primer spn9802-143F and the reverse primer spn9802-304R and 1 μl of the DNA extract. The following thermal cycling profile was applied, using a Veriti™ Thermal Cycler (Applied Biosystems, Foster City, Ca.): initial denaturation at 94°C for 2 min, then 25 cycles consisting of 94°C for 10 sec, 58°C for 15 sec and 72°C for 1 min, followed by a final extension step at 72°C for 5 min. All PCR products were electrophoresed in 2% agarose gels and stained with ethidium bromide.

Newly developed PCR assay: 16S rRNA gene based Spne-PCR assay

Extensive data-mining using commercial software (Integrated Database Network System IDNS™, SmartGene, Zug, Switzerland), which allows rapid screening of validated published sequences of species of interest against other closely related species was used to design primers for the specific amplification of S. pneumoniae. Primers were designed to match exactly 2 positions within the 16S rRNA gene, which allow to distinguish S. pneumoniae from S. pseudopneumoniae (Figure 1).
https://static-content.springer.com/image/art%3A10.1186%2F1471-2334-10-104/MediaObjects/12879_2009_Article_1084_Fig1_HTML.jpg
Figure 1

Sequence and position of the primers, newly developed in this study, specific for amplification of S. pneumoniae , and the homologous sequences for the S. mitis group species.

Amplifications were performed on an Applied Biosystems Veriti thermal cycler in reaction mixtures of 10 μl containing 5 μl PCR GoTaqGreen Mix (Promega Benelux, Leiden, the Netherlands), 0.5 μM of each of the two primers and 1 μl of the DNA extract. The 16S rRNA gene primers Spne1-Spne2Rb was designed to amplify S. pneumoniae, and the stringent annealing temperature was determined by gradient PCR as 57°C (Figure 2)
https://static-content.springer.com/image/art%3A10.1186%2F1471-2334-10-104/MediaObjects/12879_2009_Article_1084_Fig2_HTML.jpg
Figure 2

Gradient Spne-PCR results for six S. pneumoniae and two S. pseudopneumoniae isolates. M: marker (100 basepair ladder); lanes 1-6: S. pneumoniae isolates STR235 (lane 1), STR236 (lane 2), STR237 (lane 3), STR239 (lane 4), STR144 (lane 5), STR147 (lane 6); lanes 7-8:S. pseudopneumoniae isolates STR269 (lane 7) and STR157 (lane 8).

The cycling parameters were 94°C for 2 min, followed by 30 cycles of 10 sec at 94°C, 15 sec at 57°C, 1 min at 72°C, and final extension at 72°C for 5 min. The indicated primers are amplifying a 217 bp product of the 16S rRNA gene of S. pneumoniae.

Other PCR assays, i.e. ply- [16], psaA- [17] and lytA-PCR [18] were described previously [11].

Sequence analysis

Published streptococcal and other 16S rRNA sequences were extracted from EMBL using proprietary extraction methods based on sequence profiles and annotation searches; representative sequences for each species were determined using a proprietary algorithm developed by SmartGene for bacterial 16S rRNA sequences (SmartGene IDNS™ Bacteria Module). Sequences were analyzed and compared using search and alignment functions of the IDNS™ Bacteria Module of SmartGene. Results were exported as CLUSTAL-A or FASTA files for further analysis.

Results & Discussion

Previously we reported on encapsulation, AccuProbe hybridization and psaA, lytA and ply-PCR results for a collection of 49 optochin resistant alpha-hemolytic streptococcal isolates, suspected of being atypical pneumococci [11]. We concluded that for some strains identification problems continue to exist, despite the application of combined genotypic and phenotypic tests and we found psaA-PCR to be the most specific genotypic technique for the identification of genuine pneumococci and optochin resistant pneumococci. In addition, in this study, 16S rRNA gene based primers Spne1 and Spne2Rb (Spne-PCR) were designed to amplify S. pneumoniae isolates and we tested these primers for specific amplification of S. pneumoniae using the same, previously well-studied selection of isolates [11], to which three S. pseudopneumoniae and two S. parasanguinis isolates were added. Also, we tested the specificity of a PCR assay, i.e. spn9802-PCR [9], that was described in the meantime for amplification of S. pneumoniae.

All five PCR assays were negative for seven commonly found respiratory tract species, for 8 S. mitis group isolates, for 7 S. oralis isolates and for the 19 optochin R streptococcal isolates for which we had already concluded in the previous study [11] that they were non S. pneumoniae. In addition, Spne-PCR was negative for the three S. sanguinis and the two S. parasanguinis isolates.

All five PCR assays were positive for the nine optochin susceptible S. pneumoniae isolates included and for the ten optochin resistant streptococci, which had been considered as S. pneumoniae already, based on the PCR results from our previous study [11](Table 1).

Thus far, all five PCR assays were found to be equally specific. However, for a total of 11 optochin R streptococcal isolates, designated during the previous study as group IIa and group IIb, four were positive with lytA-PCR, nine with ply-PCR and Spn9802-PCR (9), whereas none of these isolates yielded a positive result when tested with psaA-PCR and Spne-PCR.

The S. pseudopneumoniae type strain CCUG 49455T, the two S. pseudopneumoniae reference isolates CCUG 48465 and CCUG 50866, and one optochin-resistant pneumococcus-like isolate (KTL079) were positive with lytA-PCR, ply-PCR and spn9802-PCR, but negative with Spne-PCR and psaA-PCR. Sequence determination of the 16S rRNA gene (accession number: FJ827123) identified this clinical isolate unambiguously as S. pseudopneumoniae. This isolate was also positive with AccuProbe (Table 1).

Several primer sets have been described for the species specific amplification of S. pneumoniae. However, in our hands, the primer sets lytA [18, 19], ply [16] and spn9208 [20], were found to amplify strains of S. pseudopneumoniae as well. Also the commercial AccuProbe hybridization assay yielded a false positive result for the single S. pseudopneumoniae isolate that was tested by others [4] and for one strain (KTL079) that was tested by us in our previous study [11].

The PCR-assay Spne-PCR, described here, is specific for S. pneumoniae, without cross-reactivity to the four S. pseudopneumoniae strains tested. The differentiation of S. pneumoniae from S. pseudopneumoniae is important since the pathogenic potential of S. pneumoniae is far higher than that of S. pseudopneumoniae. The clinical relevance of S. pseudopneumoniae has not yet been established, although it may be associated with chronic obstructive pulmonary disease [21].

In addition, the advantage of a specific PCR test on the basis of the 16S rRNA gene is that there are several copies of this gene, i.e. 5 to 6 in other Streptococcus species [22] and 4 copies in the fully sequenced genome of S. pneumoniae R6 (AE007317), thus possibly enhancing sensitivity when this PCR is applied for the direct detection and identification of S. pneumoniae in clinical samples.

In addition, 16S rRNA gene sequencing is a standard method in microbial taxonomy and can be applied directly on the amplified products of this PCR assay to to help resolve potentially ambiguous results.

Conclusions

Spne-PCR, described here, and psaA-PCR [17] were the only two out of 5 PCR assays tested, which did not misidentify S. pseudopneumoniae as S. pneumoniae. The approach using representative sequences rather than unfiltered data from Genbank enabled us to select the correct sites for reliable species differentiation out of less relevant and consistent variations and allowed us to design highly specific primers. Future studies should enable us to develop an assay specifically for S. pseudopneumoniae and a real-time, multiplex assay for rapid discrimination of the most important viridans streptococci in bacterial cultures or patient samples.

Declarations

Acknowledgements

Nabil Abdullah El Aila is indebted for a PhD Research funded by BOF-DOS of the University of Ghent-Belgium. Pieter Deschaght is indebted for a PhD Research funded by the IWT (Belgium). BOF-DOS or IWT were not involved in the development of the study design, the collection, analysis, and interpretation of the data, in the writing of the report nor in the decision to submit the paper for publication.

Authors’ Affiliations

(1)
Laboratory Bacteriology Research, Department of Chemistry, Microbiology and Immunology, University of Ghent
(2)
SmartGene
(3)
National Reference Laboratory for Pneumococcus, National Institute for Health and Welfare (THL)
(4)
Scientific Institute of Public Health

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  23. Pre-publication history

    1. The pre-publication history for this paper can be accessed here:http://www.biomedcentral.com/1471-2334/10/104/prepub

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© El Aila et al; licensee BioMed Central Ltd. 2010

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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