Performance of the MagNA pure LC robot for extraction of Chlamydia trachomatis and Neisseria gonorrhoeae DNA from urine and swab specimens

The effect of multiple rounds of mass drug administration on the association between ocular Chlamydia trachomatis infection and follicular trachoma in preschool-aged children

Purpose

To examine the relationship between ocular Chlamydia trachomatis infection and follicular trachoma (TF) in children prior to and following multiple rounds of annual mass drug administration (MDA) with azithromycin.

Methodology/principal findings

Thirty-two communities with endemic trachoma in Kongwa District, Tanzania, were offered annual MDA as part of a district-wide trachoma control program. Presence of ocular C. trachomatis infection and TF were assessed in 3,200 randomly sampled children aged five years and younger, who were examined prior to each MDA. Infection was detected using the Amplicor CT/NG assay and TF was identified by clinical examination using the World Health Organization (WHO) simplified grading system. The association between chlamydial infection and TF in children was evaluated at baseline prior to any treatment, and 12 months after each of three annual rounds of mass treatment. Factors associated with infection were examined using generalized estimating equation models.

At baseline, the overall prevalence of chlamydial infection and TF was 22% and 31%, respectively. Among children with clinical signs of TF, the proportion of those with infection was 49% prior to treatment and declined to 30% after three MDAs. The odds of infection positivity among children with clinical signs of TF decreased by 26% (OR 0.74, 95% CI 0.65 to 0.84, p = <0.01) with each MDA, after adjusting for age. For children aged under one year, who did not receive treatment, the relationship was unchanged.

Conclusions/significance

The association between ocular C. trachomatis infection and TF weakened in children with each MDA, as both infection and clinical disease prevalence declined. However, there was still a significant proportion of TF cases with infection after three rounds of MDA. New strategies are needed to assess this residual infection for optimal treatment distribution.

Trachoma, which is caused by infection by the bacterium Chlamydia trachomatis, is the leading preventable cause of blindness worldwide. Annual mass drug administration with azithromycin is recommended for trachoma control; however, monitoring the impact of azithromycin, which targets C. trachomatis, relies on the clinical assessment of follicular trachoma. If the relationship between chlamydial infection and the presence or absence of follicular trachoma were to remain unchanged with each round of treatment, we would be able to predict the level of residual infection, and the need for additional treatment, from the prevalence of follicular trachoma. In this study, we examined the association between infection and presence or absence of follicular trachoma in children prior to and following multiple rounds of treatment. Findings suggest that with increasing rounds of treatment, the prevalence of infection declines in children both with and without signs of follicular trachoma. Newer strategies, including tests that can rapidly detect infection under field conditions, may be needed to assess residual infection in treated communities.

Pooling ocular swab specimens from Tanzania for testing by Roche Amplicor and Aptima Combo 2 assays for the detection of Chlamydia trachomatis: accuracy and cost-savings

Ocular swabs collected in Tanzania were evaluated by Amplicor CT PCR and Aptima Combo2 assays for the detection of Chlamydia trachomatis to determine if pooling could be used to reduce the cost of detection. Pooling would be an accurate method and has thus far resulted in a cost-savings of 62.2%.

Comparative evaluation of commercially available manual and automated nucleic acid extraction methods for rotavirus RNA detection in stools

Rotaviruses are a major cause of viral gastroenteritis in children. For accurate and sensitive detection of rotavirus RNA from stool samples by reverse transcription-polymerase chain reaction (RT-PCR), the extraction process must be robust. However, some extraction methods may not remove the strong RT-PCR inhibitors known to be present in stool samples. The objective of this study was to evaluate and compare the performance of six extraction methods used commonly for extraction of rotavirus RNA from stool, which have never been formally evaluated: the MagNA Pure Compact, KingFisher Flex and NucliSENS easyMAG instruments, the NucliSENS miniMAG semi-automated system, and two manual purification kits, the QIAamp Viral RNA kit and a modified RNaid kit. Using each method, total nucleic acid or RNA was extracted from eight rotavirus-positive stool samples with enzyme immunoassay optical density (EIA OD) values ranging from 0.176 to 3.098. Extracts prepared using the MagNA Pure Compact instrument yielded the most consistent results by qRT-PCR and conventional RT-PCR. When extracts prepared from a dilution series were extracted by the 6 methods and tested, rotavirus RNA was detected in all samples by qRT-PCR but by conventional RT-PCR testing, only the MagNA Pure Compact and KingFisher Flex extracts were positive in all cases. RT-PCR inhibitors were detected in extracts produced with the QIAamp Viral RNA Mini kit. The findings of this study should prove useful for selection of extraction methods to be incorporated into future rotavirus detection and genotyping protocols.

Field evaluation of the Cepheid GeneXpert Chlamydia trachomatis assay for detection of infection in a trachoma endemic community in Tanzania

Purpose

To determine the sensitivity, specificity, and field utility of the Cepheid GeneXpert Chlamydia trachomatis (CT) Assay (GeneXpert) for ocular chlamydia infection compared to Roche Amplicor CT assay (Amplicor).

Methods

In a trachoma-endemic community in Kongwa Tanzania, 144 children ages 0 to 9 were surveyed to assess clinical trachoma and had two ocular swabs taken. One swab was processed at Johns Hopkins University, Baltimore MD, using Amplicor, (Roche Molecular Diagnostics) and the other swab was processed at a field station in Kongwa using the GeneXpert Chlamydia trachomatis/Neisseria gonorrhoeae assay (Cepheid). The sensitivity and specificity of GeneXpert was compared to the Amplicor assay.

Results

Of the 144 swabs taken the prevalence of follicular trachoma by clinical exam was 43.7%, and by evidence of infection according to Amplicor was 28.5%. A total of 17 specimens (11.8%) could not be processed by GeneXpert in the field due to lack of sample volume, other specimen issues or electricity failure. The sensitivity of GeneXpert when compared to Amplicor was 100% and the specificity was 95%. The GeneXpert test identified more positives in individuals with clinical trachoma than Amplicor, 55% versus 52%.

Conclusion

The GeneXpert test for C. trachomatis performed with high sensitivity and specificity and demonstrated excellent promise as a field test for trachoma control.

Trachoma, an eye infection caused by C. trachomatis, is the leading cause of infectious blindness worldwide, affecting the developing world. The current standard for trachoma treatment involves mass drug administration (MDA) of an antibiotic that is given to a community to reduce transmission. A field test for the presence of infection would be a useful adjunct in measuring MDA impact. However, the current standard for measuring infection involves expensive, delicate instrumentation that is often only in laboratories in developed countries or capital cities, and eye swab specimens are mostly shipped to the developed world for analysis.

This study compared a standard method for infection analysis, Roche Amplicor, in the United States, with a new test, the Cepheid GeneXpert, in the field in Tanzania. We collected 144 duplicate eye swabs in children ages 0–9 years. 12% of specimens could not be analyzed by GeneXpert due to correctable technical difficulties. Of those analyzed, 100% of samples negative by Amplicor were also negative by GeneXpert, and 95% of samples positive by GeneXpert were also positive by Amplicor. The GeneXpert was easy to use with minimal opportunities for contamination, and is a promising new test for field-testing infection in trachoma control efforts.

Design and baseline data of a randomized trial to evaluate coverage and frequency of mass treatment with azithromycin: the Partnership for Rapid Elimination of Trachoma (PRET) in Tanzania and The Gambia

OBJECTIVES

Trachoma is the principal cause of infectious blindness. As part of its strategy to eliminate trachoma, the World Health Organization recommends annual mass antibiotic treatment for at least 3 years with an 80% population coverage target. However, to date, ideal population coverage and mass treatment duration have not been determined and further evaluation of treatment recommendations in areas of varying endemicity is warranted. The studies presented here evaluate the impact of coverage level and frequency of mass treatment with single dose azithromycin on trachoma and ocular C. trachomatis infection.

METHODS

The Partnership for the Rapid Elimination of Trachoma supervises 2 randomized, community-based clinical trials in Tanzania and The Gambia. Although each trial is a stand-alone effort, protocols, data collection, and analytic approaches have been harmonized to permit generalizations. Communities in each site were randomized using a 2X2 factorial design to standard (80%-90.0%) versus high (over 90.0%) treatment coverage; communities were further randomized to annual treatment for 3 years versus a "graduation" rule where evidence indicates an absence of follicular trachoma or infection and annual treatment is halted.

RESULTS

Average prevalence of follicular trachoma in children age less than 5 years was 32.2% in Tanzania and 5.96% in The Gambia. Randomization appeared to be effective, as prevalence was not statistically different between the arms within each country.

CONCLUSIONS

There are challenges in harmonizing 2, large trials in Africa. Study outcomes will provide critical data to national trachoma control programs on treatment methodology and resource allocation toward elimination of the disease.

Trachoma prevalence and associated risk factors in the gambia and Tanzania: baseline results of a cluster randomised controlled trial

Background

Blinding trachoma, caused by ocular infection with Chlamydia trachomatis, is targeted for global elimination by 2020. Knowledge of risk factors can help target control interventions.

Methodology/Principal Findings

As part of a cluster randomised controlled trial, we assessed the baseline prevalence of, and risk factors for, active trachoma and ocular C. trachomatis infection in randomly selected children aged 0–5 years from 48 Gambian and 36 Tanzanian communities. Both children's eyes were examined according to the World Health Organization (WHO) simplified grading system, and an ocular swab was taken from each child's right eye and processed by Amplicor polymerase chain reaction to test for the presence of C. trachomatis DNA. Prevalence of active trachoma was 6.7% (335/5033) in The Gambia and 32.3% (1008/3122) in Tanzania. The countries' corresponding Amplicor positive prevalences were 0.8% and 21.9%. After adjustment, risk factors for follicular trachoma (TF) in both countries were ocular or nasal discharge, a low level of household head education, and being aged ≥1 year. Additional risk factors in Tanzania were flies on the child's face, being Amplicor positive, and crowding (the number of children per household). The risk factors for being Amplicor positive in Tanzania were similar to those for TF, with the exclusion of flies and crowding. In The Gambia, only ocular discharge was associated with being Amplicor positive.

Conclusions/Significance

These results indicate that although the prevalence of active trachoma and Amplicor positives were very different between the two countries, the risk factors for active trachoma were similar but those for being Amplicor positive were different. The lack of an association between being Amplicor positive and TF in The Gambia highlights the poor correlation between the presence of trachoma clinical signs and evidence of C. trachomatis infection in this setting. Only ocular discharge was associated with evidence of C. trachomatis DNA in The Gambia, suggesting that at this low endemicity, this may be the most important risk factor.

Trial Registration

ClinicalTrials.gov NCT00792922

Trachoma is caused by Chlamydia trachomatis and is the leading infectious cause of blindness. The World Health Organization's (WHO) control strategy includes antibiotic treatment of all community members, facial cleanliness, and environmental improvements. By determining how prevalent trachoma is, decisions can be made whether control activities need to be put in place. Knowing what factors make people more at risk of having trachoma can help target trachoma control efforts to those most at risk. We looked at the prevalence of active trachoma and C. trachomatis infection in the eyes of children aged 0–5 years in The Gambia and Tanzania. We also measured risk factors associated with having active trachoma or infection. The prevalence of both active trachoma and infection was lower in The Gambia (6.7% and 0.8%, respectively) than in Tanzania (32.3% and 21.9%, respectively). Risk factors for active trachoma were similar in the two countries. For infection, the risk factors in Tanzania were similar to those for TF, whereas in The Gambia, only ocular discharge was associated with infection. These results show that although the prevalence of active trachoma and infection is very different between the two countries, the risk factors for active trachoma are similar but those for infection are different.

Evaluation of an automated extraction method for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae by Cobas Amplicor PCR from different sample materials

A commercially available automated device (MagNA Pure LC) was adapted for nucleic acid extraction of urogenital specimen for subsequent PCR detection of Chlamydia trachomatis and Neisseria gonorrhoeae in a clinical laboratory. Results were compared to the standard manual extraction procedure and showed excellent correlation, with even slightly increased sensitivity.

Performance of three nucleic acid amplification tests for detection of Chlamydia trachomatis and Neisseria gonorrhoeae by use of self-collected vaginal swabs obtained via an Internet-based screening program

Use of self-obtained vaginal specimens processed by nucleic acid amplification tests (NAATs) has significantly increased the utilization of nontraditional locations for Chlamydia trachomatis and Neisseria gonorrhoeae screening programs. One important emerging source of such venues includes home-based self-sampling kits available via the Internet. The objective of our study was to evaluate the performance of three commercially available NAATs (Becton-Dickinson ProbeTec SDA, Gen-Probe Aptima Combo2 TMA, and Roche Amplicor PCR) for detection of C. trachomatis and N. gonorrhoeae in vaginal samples obtained via an Internet-based screening program. From July 2004 to August 2005, 500 self-collected vaginal swabs were tested for C. trachomatis and N. gonorrhoeae by using all three NAATs. Another 500 samples were collected between August 2005 and November 2007 and tested by ProbeTec and Combo2; PCR testing was discontinued due to low specificity for N. gonorrhoeae. All tests were conducted according to the manufacturers' procedures; the "gold standard" for an infected C. trachomatis or N. gonorrhoeae patient was defined as > or = 2 positive NAAT results. Of the first 500 swabs submitted, 46 were C. trachomatis infected (9.2%) and 5 were N. gonorrhoeae infected (1.0%), and 3 of these were coinfected (0.6%). All C. trachomatis and N. gonorrhoeae Combo2-positive/ProbeTec-negative samples were confirmed as true positives by an alternative NAAT. For C. trachomatis, ProbeTec, Combo2, and PCR had sensitivities of 82.6%, 100%, and 100%, with specificities of 100%, 100%, and 99.3%, respectively. For N. gonorrhoeae, ProbeTec, Combo2, and PCR had sensitivities of 80%, 100%, and 100%, with specificities of 100%, 100%, and 98.8%, respectively. Of the total 1,000 swabs submitted, 92 were C. trachomatis infected (9.2%) and 15 were N. gonorrhoeae infected (1.5%), and 7 of these were coinfected (0.7%). There were no ProbeTec-positive/Combo2-negative samples. For C. trachomatis, ProbeTec and Combo2 had sensitivities of 81.5% and 100%, with specificities of 100% and 100%, respectively. For N. gonorrhoeae, ProbeTec and Combo2 had sensitivities of 80% and 100%, with specificities of 100% and 100%, respectively. Overall, ProbeTec had 17 C. trachomatis false-negative results (1.7%) and 3 N. gonorrhoeae false-negative results (0.3%), while Combo2 had none. Our results were consistent with the sensitivities and specificities stated by the manufacturers. NAATs perform well for detection of chlamydia and gonorrhea with self-obtained vaginal swabs shipped in a dry state to a laboratory. For 1,000 self-collected vaginal swabs tested by NAATs, the sensitivities for C. trachomatis and N. gonorrhoeae for Combo2 were 100% and 100%, while they were 81.5% and 80%, respectively, for ProbeTec. For 500 PCR samples, the C. trachomatis sensitivity was 100% and the N. gonorrhoeae sensitivity was 100%, with specificities of 99.3% and 98.8%, respectively.

[Mycoplasma pneumoniae infections: retrospective study in Basse-Normandie, 1997-2005. Epidemiology--diagnostic utility of serology and PCR for a rapid diagnostic]

But de l'étude

L'objectif de cette étude est de décrire l'épidémiologie des infections à Mycoplasma pneumoniae (Mpn) en Basse-Normandie par une analyse rétrospective des résultats sérologiques et PCR, et de valider ces deux outils pour un diagnostic précoce de ces infections.

Patients et méthodes

De 1997 à août 2005, 6156 sérums et 6123 prélèvements respiratoires ont été réalisés chez des patients hospitalisés et analysés pour une recherche d'infection à Mpn, soit par PCR, soit par sérologie Elisa, soit par les deux. Pendant la période épidémique (2004–2005), les résultats de 1489 patients ont été analysés.

Résultats

Sur les neuf années, la séroprévalence moyenne se chiffre à 40,4 % et 525 cas d'infection ont été diagnostiqués par PCR et/ou sérologie, se profilant nettement sous l'aspect de deux pics épidémiques espacés de sept ans. Pendant la période épidémique, la séroprévalence augmente (50,2 %) et l'incidence est de 8,3 %. L'analyse des caractéristiques épidémiologiques des 124 cas diagnostiqués montre : une prédominance chez l'enfant et l'adulte jeune, une fréquence saisonnière estivohivernale, l'existence de co-infection virale. L'analyse des résultats chez 36 patients ayant bénéficié des deux tests diagnostiques, PCR et sérologie, montre une concordance dans seulement 41,7 % des cas.

Conclusion

Les infections à Mpn surviennent sur un mode endémo-épidémique, avec une incidence élevée lors des pics épidémiques, particulièrement chez l'enfant. Nous disposons actuellement d'outils bactériologiques performants permettant de réaliser un diagnostic précoce et fiable. Chez l'enfant, il convient d'associer une sérologie (IgM) et une PCR sur un prélèvement nasopharyngé ; chez l'adulte il faudra privilégier la PCR.

Detection of Chlamydia trachomatis DNA using MagNA Pure DNA extraction and Cobas Amplicor CT/NG amplification

The automated MagNA Pure DNA extraction method for Chlamydia trachomatis was compared with the manual Cobas Amplicor protocol using 100 microL of input sample volume from 964 specimens. Agreement between protocols was 96.1%. The automated extraction method had a sensitivity of 99% and a specificity of 100%. Amplification inhibition observed after manual preparation of samples (3.8%) was not apparent following automated extraction. Using 200 microL of sample in the automated extraction process lowered the detection limit without raising the inhibition rate. Furthermore, the automated extraction method halved the hands-on time required for the procedure.

Pathogen Detection in the Genomic Era

In the 21st century, one of the greatest challenges to public health and clinical microbiologists is the rapid detection and identification of emerging and reemerging pathogens. Complex factors such as genetic variation in the host and pathogen, environmental changes, population pressures, and global travel can all influence the emergence of infectious diseases. The SARS epidemic of 2003 highlighted the potential of an emerging pathogen to spread globally in a very short time frame (Peruski and Peruski, 2003). The diagnostics of such infectious diseases has been greatly affected in the past 20 years. No longer is cultivation and microscopy the only means of detecting infectious agents. With the introduction of molecular diagnostics, the ability to detect minute amounts of microbial nucleic acids in clinical specimens has revolutionized clinical microbiology. In particular, the utility of PCR allows the detection and quantitation of specific agents in a matter of hours. PCR sequencing of specific segments of nucleic acid allows for the determination of specific drug resistance that now aids in guiding viral therapies.

Current and developing technologies for monitoring agents of bioterrorism and biowarfare

Recent events have made public health officials acutely aware of the importance of rapidly and accurately detecting acts of bioterrorism. Because bioterrorism is difficult to predict or prevent, reliable platforms to rapidly detect and identify biothreat agents are important to minimize the spread of these agents and to protect the public health. These platforms must not only be sensitive and specific, but must also be able to accurately detect a variety of pathogens, including modified or previously uncharacterized agents, directly from complex sample matrices. Various commercial tests utilizing biochemical, immunological, nucleic acid, and bioluminescence procedures are currently available to identify biological threat agents. Newer tests have also been developed to identify such agents using aptamers, biochips, evanescent wave biosensors, cantilevers, living cells, and other innovative technologies. This review describes these current and developing technologies and considers challenges to rapid, accurate detection of biothreat agents. Although there is no ideal platform, many of these technologies have proved invaluable for the detection and identification of biothreat agents.