Interlaboratory Comparison of PCR-Based Identifica
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微生物临床杂志 2005年第1期
Neisseria Unit and the French National Reference Center for Meningococci, Institut Pasteur, Paris, France
Irish Meningococcal and Meningitis Reference Laboratory, The Children's University Hospital, Dublin, Ireland
WHO Collaborating Center for Reference and Research on Meningococci, Division of Infectious Disease Control, Norwegian Institute of Public Health
Institute of Oral Biology, University of Oslo, Oslo, Norway
Scottish Meningococcus and Pneumococcus Reference Laboratory, Stobhill Hospital
Division of Infection and Immunity, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow
Meningococcal Reference Unit, Health Protection Agency, Manchester Royal Infirmary, Manchester, United Kingdom
Institute for Hygiene and Microbiology, National Reference Center for Meningococci, University of Würzburg, Germany
National Reference Centre for Meningococci, Austrian Agency for Health and Food Safety, Graz, Austria
National Reference Laboratory for Meningococcal Infections, National Institute of Public Health, Prague, Czech Republic
National Meningococcal Reference Laboratory, NIPH, Athens, Greece
National Reference Laboratory for Pathogenic Neisseria, Department of Clinical Microbiology, University Hospital, rebro, Sweden
Centre Muraz, Bobo Dioulasso, Burkina Faso
ABSTRACT
Twenty clinical samples (18 cerebrospinal fluid samples and 2 articular fluid samples) were sent to 11 meningococcus reference centers located in 11 different countries. Ten of these laboratories are participating in the EU-MenNet program (a European Union-funded program) and are members of the European Monitoring Group on Meningococci. The remaining laboratory was located in Burkina Faso. Neisseria meningitidis was sought by detecting several meningococcus-specific genes (crgA, ctrA, 16S rRNA, and porA). The PCR-based nonculture method for the detection of N. meningitidis gave similar results between participants with a mean sensitivity and specificity of 89.7 and 92.7%, respectively. Most of the laboratories also performed genogrouping assays (siaD and mynB/sacC). The performance of genogrouping was more variable between laboratories, with a mean sensitivity of 72.7%. Genogroup B gave the best correlation between participants, as all laboratories routinely perform this PCR. The results for genogroups A and W135 were less similar between the eight participating laboratories that performed these PCRs.
INTRODUCTION
In cases of suspected invasive infection due to Neisseria meningitidis, measures must be taken promptly to confirm the diagnosis, to administer appropriate antimicrobial chemotherapy, and to prevent secondary cases among close contacts (by vaccination and/or chemoprophylaxis). This requires the rapid identification and characterization of strains of N. meningitidis. Strains from serogroups A, B, C, Y, and W135 are responsible for over 99% of invasive meningococcal infections in Europe (26). It is essential to determine the serogroup involved (capsular immunoreactivity) before implementing vaccination strategies, as the currently available vaccines are based on capsular polysaccharides and vaccines are only available against strains of serogroups A, C, Y, and W135. Culture-based confirmation methods are hindered by the inability to isolate bacteria following early antibiotic treatment, which is recommended whenever meningococcal infection is suspected (7). Conventional non-culture-based methods, such as the latex agglutination method, can be used for diagnosis and serogrouping. Recent studies demonstrated that the sensitivity of the latex agglutination method can be improved by ultrasound treatment. However, a specific ultrasonic instrument is necessary, and some experience is required in interpreting results (15, 28, 31).
PCR-based methods for the diagnosis of meningococcal infections have recently been developed. The PCR approach has proven to be useful for meningitis surveillance even in remote areas of the African meningitis belt, such as Niger and Sudan, where culture-based identification methods cannot usually be implemented (18, 29). The most frequently tested specimens are blood and cerebrospinal fluid (CSF). However, other samples can also be tested depending on the clinical presentation, such as purpuric lesion biopsies and synovial and pericardial fluids. Several different strategies are currently used and usually involve a two-step process: (i) detection of meningococcal DNA and (ii) genogrouping to identify serogroups. The detection of N. meningitidis DNA may involve the amplification of specific or universal sequences within conserved genes such as the 16S rRNA gene and sequencing of the PCR product to identify the bacterial species (2, 10, 20, 25). PCR strategies that target N. meningitidis-specific genes are also used to detect meningococcal DNA. Several chromosomal loci have been targeted, including the multicopy insertion sequence IS1106 (17), the gene encoding dihydropteroate synthase (dhps) (21), the major porin genes porA and porB (8, 25, 35), the ctrA gene, which encodes an outer membrane protein involved in capsule transport (9, 17, 19, 30), and the crgA gene, which encodes a transcriptional regulator belonging to the LysR family (33). When meningococcal DNA is detected, the serogroup can be determined by genogrouping. Several PCR-based genogrouping assays have been developed for strains belonging to serogroups A, B, C, Y, W135, X, Z, and 29E (3-5, 12, 25, 33). The siaD gene encodes the polysialyltransferase responsible for the polymerization of homopolymers or heteropolymers of sialic acid-containing polysaccharides in strains belonging to serogroups B, C, Y, and W135 (14). Serogroup-specific alleles of the siaD gene can be detected by PCR with oligonucleotides specific for each serogroup. Serogroup A strains can be identified by amplifying the mynB/sacC gene (25, 27, 33), which is probably responsible for the polymerization of N-acetyl-D-mannosamine phosphate (32). No nonculture standard methods are yet available for the detection and typing of N. meningitidis. To implement such universal tools, we first analyzed the performance of the currently available PCR-based assays. For this purpose, we compared the approaches used in 10 laboratories participating in the EU-MenNet program (a European Union-funded program) and belonging to the European Monitoring Group on Meningococci and in the laboratory of the Centre Muraz at Bobo Dioulasso in Burkina Faso.
MATERIALS AND METHODS
Samples and conventional bacteriology. Twenty biological samples (18 CSF and 2 synovial fluid samples) were obtained from 20 different patients who were admitted to several hospitals with clinically diagnosed meningitis or arthritis. Samples were named MenNet01 to MenNet20 (Table 1). All patients had two or more of the following clinical symptoms or signs: fever, meningismus, purpura, and arthralgia. The French Reference Laboratory for Meningococci analyzed all samples by conventional bacteriology techniques (smear examination, culture, and antigen detection). The Pastorex (Bio-Rad, Marnes-La-Coquette, France) latex agglutination kit was used to detect capsular antigens and to determine the serogroup of each strain. This kit contains specific antibody-coated latex beads for the detection of N. meningitidis serogroups A, B, C, both Y/W135, Haemophilus influenzae, and Streptococcus pneumoniae. Samples were cultured, and bacteria were isolated by using standard methods (16).
Sample preparation for molecular diagnosis. Samples were subjected to one freeze-thaw cycle, heated at 100°C for 3 min, and then centrifuged for 5 min at 10,000 x g. Two hundred microliters of each supernatant was shipped at room temperature to the participating laboratories in 11 different countries: Austria, Burkina Faso, Czech Republic, England, France, Germany, Greece, Ireland, Norway, Scotland, and Sweden. Each laboratory performed its in-house PCR assays that targeted a range of meningococcal genes: (16S rRNA, crgA, ctrA, porA, and IS1106) (4-6, 10, 12, 25, 33, 34) (Table 2). Laboratories were named L1 through L11 (Table 1). Genogrouping was performed with oligonucleotides specific for the siaD and mynB/sacC genes (Table 3). In two laboratories, the serogroup of genogrouping-negative samples was inferred on the basis of the sequence of the VR1 and VR2 regions of the porA gene. Particular sequence combinations within these two regions are associated with certain serogroups, e.g., VR1-VR20 and VR2-VR9 are associated with serogroup A strains (24).
Data analysis. The results were analyzed by using Microsoft Excel. The modal PCR result (consensus) was determined for each sample. The performance of the PCR-based methods was calculated by comparing the modal PCR results to the results obtained with conventional bacteriology techniques. The performance of the different gene targets was calculated by using the modal results as the reference. The results from the participating laboratories were compared by using the modal results as the reference. The sensitivity and specificity of N. meningitidis identification were calculated by using a two-way table as the percentage of samples that gave positive and negative consensus results in each laboratory, respectively.
RESULTS
Conventional bacteriological analysis. Samples were collected from patients with clinically diagnosed meningitis (n = 18) or arthritis (n = 2). They were divided into four categories according to the results of conventional bacteriological analysis. Samples in category I (MenNet05, 06, 07, 09, 10, and 19) were culture positive for N. meningitidis (culture-proven meningococcal infections). In category II (MenNet08 and 13), culture was negative but direct smear and/or antigen detection for N. meningitidis was positive (possible meningococcal disease). The third category contained samples that were culture negative but showed positive direct smear and/or antigen detection for another bacterium (samples MenNet04 and 12) (Table 1). The fourth category included samples (MenNet01, 02, 03, 11, 14, 15, 16, 17, 18, and 20) that were negative by culture, antigen detection, and direct smear. Conventional bacteriology confirmed the diagnosis in 10 cases (50%), 8 (40%) of which were due to N. meningitidis (Table 1).
Molecular diagnosis of N. meningitidis. All participating laboratories first carried out a meningococcal screening PCR; four laboratories (L1, L2, L5, and L10) targeted the ctrA gene and four laboratories targeted the crgA gene (L3, L7, L9, and L11). Two of the latter laboratories (L7 and L9) used additional secondary target genes for the identification of N. meningitidis (crgA plus 16S rRNA or crgA plus IS1106). Two laboratories (L4 and L6) used a 16S rRNA gene PCR. L8 amplified porA and 16S rRNA genes as a secondary target (Table 2). Genogrouping was subsequently performed with oligonucleotides designed to amplify the siaD and mynB/sacC genes. We first analyzed the congruence of the data among participants (i.e., the consensus results). These consensus results (Table 1) confirmed the diagnosis of N. meningitidis in 15 cases (75%). For samples that were positive by culture, latex, or direct smear detection, a good correlation was observed between conventional bacteriology techniques and molecular diagnosis, with the exception of sample MenNet19. The culture method showed that this sample contained an N. meningitidis serogroup C strain. Nine of the laboratories failed to detect meningococcal DNA in this sample. One laboratory (L3) identified N. meningitidis genogroup C, and another (L2) only detected meningococcal DNA but did not determine the genogroup (Table 1). In eight cases (40%), meningococcal infection was confirmed by PCR alone. Two samples that were positive by conventional bacteriology for other bacterial agents (samples MenNet04 and 12 that were positive for S. pneumoniae by latex agglutination and smear positive for gram-positive diplococci, respectively) were negative in the meningococcal PCR assays. The sequences of the VR1 and VR2 regions of porA determined by laboratories 6 and 8 suggested that MenNet13 and MenNet14 contained a serogroup A strain, in agreement with the consensus results (Table 1). However, L8 failed to detect serogroup W135 in MenNet06 by using this sequencing approach, which suggested the presence of serogroup B (Table 1).
Performance of nonculture diagnostic methods. The scores of each individual laboratory in relation to the consensus results for each sample were between 55 and 100% (mean, 89.1%) (Table 1). We calculated the sensitivity and specificity of each participating laboratory for the identification of N. meningitidis by using the identification consensus results as a reference (Table 1 and Fig. 1). Almost all laboratories obtained good scores when only the detection of N. meningitidis was considered (Fig. 1A). The mean sensitivity and specificity were 89.7 and 92.7%, respectively. The performance of each of the four genes used (ctrA, crgA, 16S rRNA, and porA) for the identification of N. meningitidis was analyzed by comparing the results from laboratories using the same gene target. The mean sensitivity and specificity were similar for all of these targets (Fig. 2). However, the small number of laboratories using each type of target, in particular those that used porA (one laboratory) and the 16S rRNA genes (two laboratories), may hinder a reliable comparison.
Each laboratory correctly determined the genogroups of between 30 and 95% (mean, 73%) of strains relative to the consensus (Tables 1 and 3). In several instances, genogrouping by PCR failed and the final diagnosis remained N. meningitidis. This was in part because some of the laboratories (L1, L2, and L10) only performed B and C genogrouping, as these are the most frequent serogroups in Europe (Table 1). The results were less consistent for genogrouping than for identification of N. meningitidis (Table 1 and Fig. 1). The mean sensitivity was 72.7%, indicating that genogrouping was less sensitive than PCR-based identification of N. meningitidis.
The genogroup B PCR, which was performed by all of the laboratories, gave the best score (the mean score of correct identification among all laboratories was 85.4%), and two samples (MenNet02 and 03) were correctly identified by all laboratories (Table 1). Lower scores were obtained for the other genogroups, particularly for genogroups A and W135 (mean correct scores were 45 and 50%, respectively). However, only eight laboratories performed A, Y, and W135 genogrouping, and the number of samples belonging to these genogroups was small (Table 1). The participating laboratories obtained good scores for the meningococcus-negative samples (mean score was 87.4%).
DISCUSSION
PCR-based methods are increasingly used to diagnose meningococcal infections and are considered to be rapid and reliable methods for laboratory confirmation and epidemiological surveillance, especially when culture-based methods fail. The standardization of the different PCR-based diagnostic approaches may help to suggest common schemes and algorithms for the management of these life-threatening infections. The European Monitoring Group on Meningococci (a consortium of microbiologists and epidemiologists working in reference laboratories in Europe that ensures the exchange of information on meningococcal infections) and the EU-MenNet provided the ideal opportunity to compare the PCR-based methods used in different laboratories to confirm meningococcal infection. We found that 75% (15 of 20 samples) of our samples were PCR positive for N. meningitidis, whereas only 40% (8 of 20 samples) were positive according to conventional bacteriology techniques.
The samples tested in this study were collected, boiled, and centrifuged before being sent to the participating laboratories. It may be better to send frozen samples, although the bacterial DNA in boiled samples seemed to withstand transport at room temperature quite well. It is not essential to purify DNA from CSF unless a PCR-inhibitory effect is observed. Only one sample that was culture positive for N. meningitidis (MenNet19) gave a negative consensus PCR result. This may be because the genomic DNA was altered during transport or because a very low concentration of target DNA was present in the sample. However, the percent agreement with each consensus result varied between the tested samples and between the participating laboratories (Table 1). Differences in sample handling and preparation may be, at least in part, responsible for the variable results obtained for some samples. Improvements of the DNA extraction procedure and their impact on the performance of the PCR-based diagnostic methods were not analyzed in this study. A new study for this purpose is currently being designed.
The two-step approach (identification of N. meningitidis followed by genogrouping) seems to provide rapid confirmation and serogroup information for the immediate management of meningococcal infections: treatment of the case and prophylactic measures (vaccination and/or chemoprophylaxis) among contacts to prevent secondary cases.
The genes used for nonculture identification of N. meningitidis (ctrA, crgA, porA, and 16S rRNA) gave equivalent results, and genogrouping for serogroup B gave the best correlation among the participants.
The performance of genogrouping for the other serogroups varied among the participants, particularly for serogroups A and W135. We recommend the use of the oligonucleotides used by L3, L7, and L4, which correctly predicted serogroup A (Table 1 and Table 3). It should be noted that in many European countries, invasive disease due to serogroup A is rare. Therefore, due to the cost-benefit ratio, many reference laboratories do not stock the reagents required for nonculture detection of serogroup A meningococci.
We found that porA sequencing successfully detected serogroup A strains. However, this assay may be less reliable for other serogroups, particularly in an endemic disease situation. Strains of serogroup A tend to express less variable polymorphic serotypes (PorB) and serosubtypes (PorA) than strains of serogroups B, C, Y, and W135 (1, 24). Due to a high rate of recombination, genes are randomly associated on the N. meningitidis chromosome, resulting in a low level of linkage disequilibrium between meningococcal genes. Hence, the correlation between serogroup and serosubtype is not perfect (13, 23).
The development of specific and sensitive PCR methods is highly important for the management of meningococcal infections, particularly for urgent diagnosis, large-scale epidemiological surveillance during outbreaks, and when culture methods fail. Moreover, multilocus sequence typing can also be used as a nonculture approach directly on clinical samples (11, 22). However, nonculture assays for the diagnosis of meningococcal disease should not be considered a replacement for culture, as viable bacteria provide crucial information about meningococcal phenotypes, including antibiotic susceptibility patterns, and the pathophysiological behavior of the N. meningitidis strain.
ACKNOWLEDGMENTS
This work was supported by European Union Contract no. QLK2-CT-2001-01436.
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Irish Meningococcal and Meningitis Reference Laboratory, The Children's University Hospital, Dublin, Ireland
WHO Collaborating Center for Reference and Research on Meningococci, Division of Infectious Disease Control, Norwegian Institute of Public Health
Institute of Oral Biology, University of Oslo, Oslo, Norway
Scottish Meningococcus and Pneumococcus Reference Laboratory, Stobhill Hospital
Division of Infection and Immunity, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow
Meningococcal Reference Unit, Health Protection Agency, Manchester Royal Infirmary, Manchester, United Kingdom
Institute for Hygiene and Microbiology, National Reference Center for Meningococci, University of Würzburg, Germany
National Reference Centre for Meningococci, Austrian Agency for Health and Food Safety, Graz, Austria
National Reference Laboratory for Meningococcal Infections, National Institute of Public Health, Prague, Czech Republic
National Meningococcal Reference Laboratory, NIPH, Athens, Greece
National Reference Laboratory for Pathogenic Neisseria, Department of Clinical Microbiology, University Hospital, rebro, Sweden
Centre Muraz, Bobo Dioulasso, Burkina Faso
ABSTRACT
Twenty clinical samples (18 cerebrospinal fluid samples and 2 articular fluid samples) were sent to 11 meningococcus reference centers located in 11 different countries. Ten of these laboratories are participating in the EU-MenNet program (a European Union-funded program) and are members of the European Monitoring Group on Meningococci. The remaining laboratory was located in Burkina Faso. Neisseria meningitidis was sought by detecting several meningococcus-specific genes (crgA, ctrA, 16S rRNA, and porA). The PCR-based nonculture method for the detection of N. meningitidis gave similar results between participants with a mean sensitivity and specificity of 89.7 and 92.7%, respectively. Most of the laboratories also performed genogrouping assays (siaD and mynB/sacC). The performance of genogrouping was more variable between laboratories, with a mean sensitivity of 72.7%. Genogroup B gave the best correlation between participants, as all laboratories routinely perform this PCR. The results for genogroups A and W135 were less similar between the eight participating laboratories that performed these PCRs.
INTRODUCTION
In cases of suspected invasive infection due to Neisseria meningitidis, measures must be taken promptly to confirm the diagnosis, to administer appropriate antimicrobial chemotherapy, and to prevent secondary cases among close contacts (by vaccination and/or chemoprophylaxis). This requires the rapid identification and characterization of strains of N. meningitidis. Strains from serogroups A, B, C, Y, and W135 are responsible for over 99% of invasive meningococcal infections in Europe (26). It is essential to determine the serogroup involved (capsular immunoreactivity) before implementing vaccination strategies, as the currently available vaccines are based on capsular polysaccharides and vaccines are only available against strains of serogroups A, C, Y, and W135. Culture-based confirmation methods are hindered by the inability to isolate bacteria following early antibiotic treatment, which is recommended whenever meningococcal infection is suspected (7). Conventional non-culture-based methods, such as the latex agglutination method, can be used for diagnosis and serogrouping. Recent studies demonstrated that the sensitivity of the latex agglutination method can be improved by ultrasound treatment. However, a specific ultrasonic instrument is necessary, and some experience is required in interpreting results (15, 28, 31).
PCR-based methods for the diagnosis of meningococcal infections have recently been developed. The PCR approach has proven to be useful for meningitis surveillance even in remote areas of the African meningitis belt, such as Niger and Sudan, where culture-based identification methods cannot usually be implemented (18, 29). The most frequently tested specimens are blood and cerebrospinal fluid (CSF). However, other samples can also be tested depending on the clinical presentation, such as purpuric lesion biopsies and synovial and pericardial fluids. Several different strategies are currently used and usually involve a two-step process: (i) detection of meningococcal DNA and (ii) genogrouping to identify serogroups. The detection of N. meningitidis DNA may involve the amplification of specific or universal sequences within conserved genes such as the 16S rRNA gene and sequencing of the PCR product to identify the bacterial species (2, 10, 20, 25). PCR strategies that target N. meningitidis-specific genes are also used to detect meningococcal DNA. Several chromosomal loci have been targeted, including the multicopy insertion sequence IS1106 (17), the gene encoding dihydropteroate synthase (dhps) (21), the major porin genes porA and porB (8, 25, 35), the ctrA gene, which encodes an outer membrane protein involved in capsule transport (9, 17, 19, 30), and the crgA gene, which encodes a transcriptional regulator belonging to the LysR family (33). When meningococcal DNA is detected, the serogroup can be determined by genogrouping. Several PCR-based genogrouping assays have been developed for strains belonging to serogroups A, B, C, Y, W135, X, Z, and 29E (3-5, 12, 25, 33). The siaD gene encodes the polysialyltransferase responsible for the polymerization of homopolymers or heteropolymers of sialic acid-containing polysaccharides in strains belonging to serogroups B, C, Y, and W135 (14). Serogroup-specific alleles of the siaD gene can be detected by PCR with oligonucleotides specific for each serogroup. Serogroup A strains can be identified by amplifying the mynB/sacC gene (25, 27, 33), which is probably responsible for the polymerization of N-acetyl-D-mannosamine phosphate (32). No nonculture standard methods are yet available for the detection and typing of N. meningitidis. To implement such universal tools, we first analyzed the performance of the currently available PCR-based assays. For this purpose, we compared the approaches used in 10 laboratories participating in the EU-MenNet program (a European Union-funded program) and belonging to the European Monitoring Group on Meningococci and in the laboratory of the Centre Muraz at Bobo Dioulasso in Burkina Faso.
MATERIALS AND METHODS
Samples and conventional bacteriology. Twenty biological samples (18 CSF and 2 synovial fluid samples) were obtained from 20 different patients who were admitted to several hospitals with clinically diagnosed meningitis or arthritis. Samples were named MenNet01 to MenNet20 (Table 1). All patients had two or more of the following clinical symptoms or signs: fever, meningismus, purpura, and arthralgia. The French Reference Laboratory for Meningococci analyzed all samples by conventional bacteriology techniques (smear examination, culture, and antigen detection). The Pastorex (Bio-Rad, Marnes-La-Coquette, France) latex agglutination kit was used to detect capsular antigens and to determine the serogroup of each strain. This kit contains specific antibody-coated latex beads for the detection of N. meningitidis serogroups A, B, C, both Y/W135, Haemophilus influenzae, and Streptococcus pneumoniae. Samples were cultured, and bacteria were isolated by using standard methods (16).
Sample preparation for molecular diagnosis. Samples were subjected to one freeze-thaw cycle, heated at 100°C for 3 min, and then centrifuged for 5 min at 10,000 x g. Two hundred microliters of each supernatant was shipped at room temperature to the participating laboratories in 11 different countries: Austria, Burkina Faso, Czech Republic, England, France, Germany, Greece, Ireland, Norway, Scotland, and Sweden. Each laboratory performed its in-house PCR assays that targeted a range of meningococcal genes: (16S rRNA, crgA, ctrA, porA, and IS1106) (4-6, 10, 12, 25, 33, 34) (Table 2). Laboratories were named L1 through L11 (Table 1). Genogrouping was performed with oligonucleotides specific for the siaD and mynB/sacC genes (Table 3). In two laboratories, the serogroup of genogrouping-negative samples was inferred on the basis of the sequence of the VR1 and VR2 regions of the porA gene. Particular sequence combinations within these two regions are associated with certain serogroups, e.g., VR1-VR20 and VR2-VR9 are associated with serogroup A strains (24).
Data analysis. The results were analyzed by using Microsoft Excel. The modal PCR result (consensus) was determined for each sample. The performance of the PCR-based methods was calculated by comparing the modal PCR results to the results obtained with conventional bacteriology techniques. The performance of the different gene targets was calculated by using the modal results as the reference. The results from the participating laboratories were compared by using the modal results as the reference. The sensitivity and specificity of N. meningitidis identification were calculated by using a two-way table as the percentage of samples that gave positive and negative consensus results in each laboratory, respectively.
RESULTS
Conventional bacteriological analysis. Samples were collected from patients with clinically diagnosed meningitis (n = 18) or arthritis (n = 2). They were divided into four categories according to the results of conventional bacteriological analysis. Samples in category I (MenNet05, 06, 07, 09, 10, and 19) were culture positive for N. meningitidis (culture-proven meningococcal infections). In category II (MenNet08 and 13), culture was negative but direct smear and/or antigen detection for N. meningitidis was positive (possible meningococcal disease). The third category contained samples that were culture negative but showed positive direct smear and/or antigen detection for another bacterium (samples MenNet04 and 12) (Table 1). The fourth category included samples (MenNet01, 02, 03, 11, 14, 15, 16, 17, 18, and 20) that were negative by culture, antigen detection, and direct smear. Conventional bacteriology confirmed the diagnosis in 10 cases (50%), 8 (40%) of which were due to N. meningitidis (Table 1).
Molecular diagnosis of N. meningitidis. All participating laboratories first carried out a meningococcal screening PCR; four laboratories (L1, L2, L5, and L10) targeted the ctrA gene and four laboratories targeted the crgA gene (L3, L7, L9, and L11). Two of the latter laboratories (L7 and L9) used additional secondary target genes for the identification of N. meningitidis (crgA plus 16S rRNA or crgA plus IS1106). Two laboratories (L4 and L6) used a 16S rRNA gene PCR. L8 amplified porA and 16S rRNA genes as a secondary target (Table 2). Genogrouping was subsequently performed with oligonucleotides designed to amplify the siaD and mynB/sacC genes. We first analyzed the congruence of the data among participants (i.e., the consensus results). These consensus results (Table 1) confirmed the diagnosis of N. meningitidis in 15 cases (75%). For samples that were positive by culture, latex, or direct smear detection, a good correlation was observed between conventional bacteriology techniques and molecular diagnosis, with the exception of sample MenNet19. The culture method showed that this sample contained an N. meningitidis serogroup C strain. Nine of the laboratories failed to detect meningococcal DNA in this sample. One laboratory (L3) identified N. meningitidis genogroup C, and another (L2) only detected meningococcal DNA but did not determine the genogroup (Table 1). In eight cases (40%), meningococcal infection was confirmed by PCR alone. Two samples that were positive by conventional bacteriology for other bacterial agents (samples MenNet04 and 12 that were positive for S. pneumoniae by latex agglutination and smear positive for gram-positive diplococci, respectively) were negative in the meningococcal PCR assays. The sequences of the VR1 and VR2 regions of porA determined by laboratories 6 and 8 suggested that MenNet13 and MenNet14 contained a serogroup A strain, in agreement with the consensus results (Table 1). However, L8 failed to detect serogroup W135 in MenNet06 by using this sequencing approach, which suggested the presence of serogroup B (Table 1).
Performance of nonculture diagnostic methods. The scores of each individual laboratory in relation to the consensus results for each sample were between 55 and 100% (mean, 89.1%) (Table 1). We calculated the sensitivity and specificity of each participating laboratory for the identification of N. meningitidis by using the identification consensus results as a reference (Table 1 and Fig. 1). Almost all laboratories obtained good scores when only the detection of N. meningitidis was considered (Fig. 1A). The mean sensitivity and specificity were 89.7 and 92.7%, respectively. The performance of each of the four genes used (ctrA, crgA, 16S rRNA, and porA) for the identification of N. meningitidis was analyzed by comparing the results from laboratories using the same gene target. The mean sensitivity and specificity were similar for all of these targets (Fig. 2). However, the small number of laboratories using each type of target, in particular those that used porA (one laboratory) and the 16S rRNA genes (two laboratories), may hinder a reliable comparison.
Each laboratory correctly determined the genogroups of between 30 and 95% (mean, 73%) of strains relative to the consensus (Tables 1 and 3). In several instances, genogrouping by PCR failed and the final diagnosis remained N. meningitidis. This was in part because some of the laboratories (L1, L2, and L10) only performed B and C genogrouping, as these are the most frequent serogroups in Europe (Table 1). The results were less consistent for genogrouping than for identification of N. meningitidis (Table 1 and Fig. 1). The mean sensitivity was 72.7%, indicating that genogrouping was less sensitive than PCR-based identification of N. meningitidis.
The genogroup B PCR, which was performed by all of the laboratories, gave the best score (the mean score of correct identification among all laboratories was 85.4%), and two samples (MenNet02 and 03) were correctly identified by all laboratories (Table 1). Lower scores were obtained for the other genogroups, particularly for genogroups A and W135 (mean correct scores were 45 and 50%, respectively). However, only eight laboratories performed A, Y, and W135 genogrouping, and the number of samples belonging to these genogroups was small (Table 1). The participating laboratories obtained good scores for the meningococcus-negative samples (mean score was 87.4%).
DISCUSSION
PCR-based methods are increasingly used to diagnose meningococcal infections and are considered to be rapid and reliable methods for laboratory confirmation and epidemiological surveillance, especially when culture-based methods fail. The standardization of the different PCR-based diagnostic approaches may help to suggest common schemes and algorithms for the management of these life-threatening infections. The European Monitoring Group on Meningococci (a consortium of microbiologists and epidemiologists working in reference laboratories in Europe that ensures the exchange of information on meningococcal infections) and the EU-MenNet provided the ideal opportunity to compare the PCR-based methods used in different laboratories to confirm meningococcal infection. We found that 75% (15 of 20 samples) of our samples were PCR positive for N. meningitidis, whereas only 40% (8 of 20 samples) were positive according to conventional bacteriology techniques.
The samples tested in this study were collected, boiled, and centrifuged before being sent to the participating laboratories. It may be better to send frozen samples, although the bacterial DNA in boiled samples seemed to withstand transport at room temperature quite well. It is not essential to purify DNA from CSF unless a PCR-inhibitory effect is observed. Only one sample that was culture positive for N. meningitidis (MenNet19) gave a negative consensus PCR result. This may be because the genomic DNA was altered during transport or because a very low concentration of target DNA was present in the sample. However, the percent agreement with each consensus result varied between the tested samples and between the participating laboratories (Table 1). Differences in sample handling and preparation may be, at least in part, responsible for the variable results obtained for some samples. Improvements of the DNA extraction procedure and their impact on the performance of the PCR-based diagnostic methods were not analyzed in this study. A new study for this purpose is currently being designed.
The two-step approach (identification of N. meningitidis followed by genogrouping) seems to provide rapid confirmation and serogroup information for the immediate management of meningococcal infections: treatment of the case and prophylactic measures (vaccination and/or chemoprophylaxis) among contacts to prevent secondary cases.
The genes used for nonculture identification of N. meningitidis (ctrA, crgA, porA, and 16S rRNA) gave equivalent results, and genogrouping for serogroup B gave the best correlation among the participants.
The performance of genogrouping for the other serogroups varied among the participants, particularly for serogroups A and W135. We recommend the use of the oligonucleotides used by L3, L7, and L4, which correctly predicted serogroup A (Table 1 and Table 3). It should be noted that in many European countries, invasive disease due to serogroup A is rare. Therefore, due to the cost-benefit ratio, many reference laboratories do not stock the reagents required for nonculture detection of serogroup A meningococci.
We found that porA sequencing successfully detected serogroup A strains. However, this assay may be less reliable for other serogroups, particularly in an endemic disease situation. Strains of serogroup A tend to express less variable polymorphic serotypes (PorB) and serosubtypes (PorA) than strains of serogroups B, C, Y, and W135 (1, 24). Due to a high rate of recombination, genes are randomly associated on the N. meningitidis chromosome, resulting in a low level of linkage disequilibrium between meningococcal genes. Hence, the correlation between serogroup and serosubtype is not perfect (13, 23).
The development of specific and sensitive PCR methods is highly important for the management of meningococcal infections, particularly for urgent diagnosis, large-scale epidemiological surveillance during outbreaks, and when culture methods fail. Moreover, multilocus sequence typing can also be used as a nonculture approach directly on clinical samples (11, 22). However, nonculture assays for the diagnosis of meningococcal disease should not be considered a replacement for culture, as viable bacteria provide crucial information about meningococcal phenotypes, including antibiotic susceptibility patterns, and the pathophysiological behavior of the N. meningitidis strain.
ACKNOWLEDGMENTS
This work was supported by European Union Contract no. QLK2-CT-2001-01436.
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