Evaluation of 2-SP transport medium for detection of Chlamydia trachomatis and Neisseria gonorrhoeae by two automated amplification systems and culture for chlamydia

Whole-Genome Sequencing of Human Enteroviruses from Clinical Samples by Nanopore Direct RNA Sequencing

Enteroviruses are small RNA viruses that affect millions of people each year by causing an important burden of disease with a broad spectrum of symptoms. In routine diagnostic laboratories, enteroviruses are identified by PCR-based methods, often combined with partial sequencing for genotyping. In this proof-of-principle study, we assessed direct RNA sequencing (DRS) using nanopore sequencing technology for fast whole-genome sequencing of viruses directly from clinical samples. The approach was complemented by sequencing the corresponding viral cDNA via Illumina MiSeq sequencing. DRS of total RNA extracted from three different enterovirus-positive stool samples produced long RNA fragments, covering between 59% and 99.6% of the most similar reference genome sequences. The identification of the enterovirus sequences in the samples was confirmed by short-read cDNA sequencing. Sequence identity between DRS and Illumina MiSeq enterovirus consensus sequences ranged between 94% and 97%. Here, we show that nanopore DRS can be used to correctly identify enterovirus genotypes from patient stool samples with high viral load and that the approach also provides rich metatranscriptomic information on sample composition for all life domains.

Rapid and Cost-Efficient Enterovirus Genotyping from Clinical Samples Using Flongle Flow Cells

Enteroviruses affect millions of people worldwide and are of significant clinical importance. The standard method for enterovirus identification and genotyping still relies on Sanger sequencing of short diagnostic amplicons. In this study, we assessed the feasibility of nanopore sequencing using the new flow cell “Flongle” for fast, cost-effective, and accurate genotyping of human enteroviruses from clinical samples. PCR amplification of partial VP1 gene was performed from multiple patient samples, which were multiplexed together after barcoding PCR and sequenced multiple times on Flongle flow cells. The nanopore consensus sequences obtained from mapping reads to a reference database were compared to their Sanger sequence counterparts. Using clinical specimens sampled over different years, we were able to correctly identify enterovirus species and genotypes for all tested samples, even when doubling the number of barcoded samples on one flow cell. Average sequence identity across sequencing runs was >99.7%. Phylogenetic analysis showed that the consensus sequences achieved with Flongle delivered accurate genotyping. We conclude that the new Flongle-based assay with its fast turnover time, low cost investment, and low cost per sample represents an accurate, reproducible, and cost-effective platform for enterovirus identification and genotyping.

Prevalences of sexually transmitted infections in young adults and female sex workers in Peru: a national population-based survey

Background

We assessed prevalences of seven sexually transmitted infections (STIs) in Peru, stratified by risk behaviours, to help to define care and prevention priorities.

Methods

In a 2002 household-based survey of the general population, we enrolled randomly selected 18–29-year-old residents of 24 cities with populations greater than 50 000 people. We then surveyed female sex workers (FSWs) in these cities. We gathered data for sexual behaviour; vaginal specimens or urine for nucleic acid amplification tests for Neisseria gonorrhoeae, Chlamydia trachomatis, and Trichomonas vaginalis; and blood for serological tests for syphilis, HIV, and (in subsamples) herpes simplex virus 2 (HSV2) and human T-lymphotropic virus. This study is a registered component of the PREVEN trial, number ISRCTN43722548.

Findings

15 261 individuals from the general population and 4485 FSWs agreed to participate in our survey. Overall prevalence of infection with HSV2, weighted for city size, was 13·5% in men, 13·6% in women, and 60·6% in FSWs (all values in FSWs standardised to age composition of women in the general population). The prevalence of C trachomatis infection was 4·2% in men, 6·5% in women, and 16·4% in FSWs; of T vaginalis infection was 0·3% in men, 4·9% in women, and 7·9% in FSWs; and of syphilis was 0·5% in men, 0·4% in women, and 0·8% in FSWs. N gonorrhoeae infection had a prevalence of 0·1% in men and women, and of 1·6% in FSWs. Prevalence of HIV infection was 0·5% in men and FSWs, and 0·1% in women. Four (0·3%) of 1535 specimens were positive for human T-lymphotropic virus 1. In men, 65·0% of infections with HIV, 71·5% of N gonorrhoeae, and 41·4% of HSV2 and 60·9% of cases of syphilis were in the 13·3% who had sex with men or unprotected sex with FSWs in the past year. In women from the general population, 66·7% of infections with HIV and 16·7% of cases of syphilis were accounted for by the 4·4% who had been paid for sex by any of their past three partners.

Interpretation

Defining of high-risk groups could guide targeting of interventions for communicable diseases—including STIs—in the general Peruvian population.

Funding

Wellcome Trust-Burroughs Wellcome Fund Infectious Disease Initiative and US National Institutes of Health.

Comparison of the Becton Dickinson strand displacement amplification and Cobas Amplicor Roche PCR for the detection of Chlamydia trachomatis: pooling versus individual tests

The objective of the study was to examine the influence of pooling Chlamydia trachomatis specimens. We compared Becton Dickinson ProbeTec strand displacement amplification (SDA) with Cobas Amplicor Roche (PCR). With PCR as the standard, SDA performed equally well in single-sample testing. For pooled PCR samples (compared to individual PCR), we found a sensitivity of 100% and a specificity of 98.9%. For pooled SDA tests (compared to individual SDA), we found a sensitivity of 86.5% and a specificity of 98.9%. Our conclusion is that 2-sucrose phosphate buffer (2-SP) can be used for individual SDA testing. A reduced sensitivity was found for pooled SDA samples, and we cannot recommend that SDA be used for pooling with 2-SP. Further pooling studies with other transport media are warranted.

Neisseria gonorrhoeae and Chlamydia trachomatis infections in patients attending STD and family planning clinics in Bissau, Guinea-Bissau

Accurate clinical and laboratory data about sexually transmitted diseases (STD) prevalence in Guinea-Bissau are not available. These data are important, since HIV2 is prevalent in this country, rates of HIV1 are increasing and STDs facilitate HIV transmission. Since DNA amplification methods have demonstrated to accurately diagnose chlamydial infections and gonorrhoea, the Amplicor CT/NG PCR Assay with Internal Control of Amplification (Roche Diagnostic System, Branchburg, NJ, USA) was used to estimate the prevalence of Neisseria gonorrhoeae and Chlamydia trachomatis genital infections in STDs and Family Planning Clinic attenders in Bissau, from March to July 1997. Two hundred and two cervical swabs and 31 urethral swabs were examined. Two women were excluded from this study because their cervical swabs contained inhibitory substances. N. gonorrhoeae was identified in 34/200 (17%) women and in 12/31 (38.7%) men. C. trachomatis was detected in 8/200 (4%) women there were no positive C. trachomatis results among the 31 men with urethritis. One woman presented a mixed infection with both organisms. The prevalence difference between men and women was not statistically significant (P=0.6) for C. trachomatis infection, but it was significant for N. gonorrhoeae infection (P=0.01). The prevalence rates of these infections found in this study, support the need for an urgent strategy to control STD in the region.

Evaluation of the Roche Neisseria gonorrhoeae 16S rRNA PCR for confirmation of AMPLICOR PCR-positive samples and comparison of its diagnostic performance according to storage conditions and preparation of endocervical specimens

The AMPLICOR PCR was used to detect Neisseria gonorrhoeae in endocervical specimens. A 16S rRNA PCR performed on N. gonorrhoeae-positive samples showed sensitivities of 73.2, 64.3, and 94.4% for samples treated directly with AMPLICOR lysis buffer, samples suspended in 2-sucrose phosphate, and samples suspended in diluted phosphate-buffered saline, respectively.

Evaluation of COBAS AMPLICOR (Roche): accuracy in detection of Chlamydia trachomatis and Neisseria gonorrhoeae by coamplification of endocervical specimens

We evaluated further the accuracy of the COBAS AMPLICOR (Roche) (CA) PCR-based system in detection of Chlamydia trachomatis and Neisseria gonorrhoeae in endocervical specimens. Endocervical specimens collected for any indication for testing for C. trachomatis and N. gonorrhoeae among a university hospital health system population were included. Testing for C. trachomatis was done by two PCR methods, CA and manual microwell AMPLICOR (Roche) (MWA), and by culture; testing for N. gonorrhoeae was done by CA and culture. Discrepancy resolution was performed. Reproducibility testing and hands-on labor time measurements for CA were done. Among 654 C. trachomatis samples, the prevalence of true positivity was 9.2%, and among the 618 N. gonorrhoeae samples, the prevalence of true positivity was 4.4%. For detection of C. trachomatis, the sensitivity, specificity, and negative and positive predictive values were, respectively, as follows for each test: CA, 93.3, 99.7, 99.3, and 96.4%; MWA, 91.7, 99.7, 99.2, and 96.5%; and culture, 65.0, 100, 96.6, and 100%. For detection of N. gonorrhoeae those values were as follows: CA, 96.3, 100, 99.8, and 100%; and culture, 92.6, 100, 99.7, and 100%. Hands-on labor time for each clinical result was estimated to be at 7.5 min. The prevalence of inhibitory specimens was 3.5%, including two positive C. trachomatis samples which would have been missed otherwise. The direct cost of each clinical result with CA was estimated to be $9.09. Our methods include a diverse range of indications for testing among women, using endocervical swabbing samples, 2 M sucrose phosphate transport medium, and discrepancy resolution for comparison. Under our test conditions, the CA system is an accurate, rapid, and cost- and labor-efficient method for detection of C. trachomatis and N. gonorrhoeae.

Detection of Chlamydia trachomatis in symptomatic and asymptomatic populations with urogenital specimens by AMP CT (Gen-probe incorporated) compared to others commercially available amplification assays

The present study was designed to evaluate the sensitivity and specificity of AMP CT (Gen-Probe Incorporated, San Diego, CA, USA) on urogenital specimens taken from symptomatic patients and on first void urine (FVU) specimens from asymptomatic patients. In symptomatic patients, 618 specimens from 140 men (140 urethral swabs and 140 FVU) and 202 women (202 endocervical swabs and 136 FVU) were tested by using cell culture, AMP CT and Amplicor Chlamydia trachomatis MWP (microwell plate) (Roche Diagnostics, Somerville, NJ, USA) on genital samples, and AMP CT and Amplicor on FVU. A clinical specimen was considered to be truly positive if either the cell culture was positive and/or both AMP CT and Amplicor were positive. In the asymptomatic population, a total of 300 FVU (136 women and 164 men) were tested by four amplification methods, AMP CT, LCx (Abbott, Abbott Park, IL, USA), Amplicor MWP, and Cobas Amplicor. A subject was considered to be infected when two or more amplification methods were positive. In the symptomatic population (prevalence 13%), concordant results were observed in 320/342 cases (93.5%). After analysis of discordant results, the sensitivity of AMP CT, Amplicor, and culture was 100%, 95.5%, 68.8%, respectively, and the specificity was 98.3%, 99.3%, 100% respectively. The number of false negative results by AMP CT in urine, probably due to labile inhibitors, was 3/276 (1%). In the asymptomatic population, the results were concordant in 298/300 (99.3%), seven positive and 291 negative. Two results were considered false positives, one by Cobas Amplicor, one by AMP CT. Compared to other amplification methods, AMP CT is at least as sensitive for the identification of chlamydial infection in symptomatic and asymptomatic men and women on genital or urine specimens.