Prevalence of Mycoplasma genitalium infection in women with bacterial vaginosis.

BACKGROUND: Bacterial vaginosis (BV) is a common condition in reproductive-age women and is known to be positively associated with risk of acquisition of sexually transmitted infections (STI) such as chlamydia and gonorrhea. Mycoplasma genitalium is an emerging STI that has been linked to increased risk of pelvic inflammatory disease, adverse pregnancy outcomes and infertility. In the present study we sought to examine whether women diagnosed with symptomatic BV were at increased risk of having concurrent infection with Mycoplasma genitalium. METHODS: We used a novel PCR-based assay (ResistancePlus MG; SpeeDx Pty. Ltd., Sydney, Australia) to determine the prevalence of Mycoplasma genitalium infection and 23S rRNA macrolide-resistance mediating mutations (MRMM) in a cohort of 1532 women presenting with symptoms of vaginitis. RESULTS: M. genitalium was detected in 4.0% (62/1532) of samples with 37.1% (23/62) harboring MRMMs. The prevalence of M. genitalium infection in subjects with BV was significantly higher than in subjects with non-BV vaginitis (7.0% v 3.6%; OR = 1.97 (95% CI: 1.14-3.39). CONCLUSIONS: Prevalence of M. genitalium infection is associated with BV in women with symptomatic vaginitis. Improved management of BV is needed as a component of STI prevention strategies.

Health care utilization and costs following amplified versus non-amplified molecular probe testing for symptomatic patients with suspected vulvovaginitis: a US commercial payer population.

BACKGROUND: Vulvovaginitis (VV) is a common reason women seek medical attention in the USA. Both the non-specific clinical presentation and risk of preterm labor or delivery necessitate accurate identification of the causative agents to guide appropriate therapy. The diagnostic accuracy of amplified molecular probe testing (AMP) has been shown to exceed that of non-amplified molecular probe (NAMP) by 20%-25%. OBJECTIVE: To evaluate the impact of diagnosis with AMP testing on health care utilization, direct costs, and health outcomes, compared with NAMP, for symptomatic patients with suspected VV from a commercial payer perspective. METHODS: Symptomatic women (aged 18-64 years) who underwent VV testing with AMP or NAMP from January 1, 2012-December 31, 2016 were identified using the Truven Health Analytics MarketScan Database; those with continuous medical and pharmacy benefit enrollment 6 months pre/post AMP or NAMP testing were included. Patients were propensity score (PS) matched and 6-month all-cause health care resource utilization, all-cause direct costs (2017 USD), risk of all-cause hospitalization, and risk of preterm labor or delivery were compared between cohorts. RESULTS: After PS match (N=46,810 per group, mean age 34.2 years), AMP had significantly (all P<0.0001) fewer mean hospital outpatient visits (AMP 0.9 vs NAMP 1.0), primary care physician office visits (AMP 1.1 vs NAMP 1.2), and prescription medications (AMP 7.3 vs NAMP 8.0), and a 21% reduction in risk of hospitalization (risk ratio [RR]=0.79, 95% CI= 0.75-0.83, P<0.0001). Total medical expenditures per patient were lower for AMP than NAMP (mean AMP $3,287 vs NAMP $3,555, P<0.0001). Among pregnant women (N=2,175 per group), AMP had a 12% reduction in risk of preterm labor or delivery (RR =0.88, 95% CI=0.77-0.99, P=0.041). CONCLUSION: This real-world study offers evidence on the clinical utility for symptomatic patients with suspected VV diagnosed with AMP compared to NAMP - demonstrating an opportunity to improve the patient journey while delivering value-based care.

Multicenter study establishing the clinical validity of a nucleic-acid amplification-based assay for the diagnosis of bacterial vaginosis.

The present study sought to validate the clinical performance of a previously described PCR-based assay for the diagnosis of bacterial vaginosis (BV). A total of 1579 patients were enrolled in 5 locations; samples were classified as BV positive (n=538) or negative (n=1,041) based on an algorithm utilizing quantitative Gram-stain analysis of vaginal discharge and clinical evaluation (Amsel criteria); a next-generation sequencing (NGS) approach to determining diversity of vaginal microbiota was used to resolve discordant results between BV-PCR and Nugent/Amsel. BV-PCR demonstrated a sensitivity of 96.0% (483/503) and a specificity of 90.2% (885/981) when measured against the conventional test standard, with 95 samples (6.0%) being classified as indeterminate. After resolution of discordant results by NGS, including elimination of the PCR indeterminate category, the resolved sensitivity, specificity, and positive and negative predictive values of the BV-PCR assay were 98.7%, 95.9%, 92.9%, and 96.9%, respectively. The results of this study conclusively demonstrate that a relatively simple, 3-biomarker, molecular amplification construct can effectively diagnose BV in symptomatic women. Results generated using this assay were congruent with those obtained using conventional and molecular reference methods.

Characterization of HIV diversity, phylodynamics and drug resistance in Washington, DC.

BACKGROUND: Washington DC has a high burden of HIV with a 2.0% HIV prevalence. The city is a national and international hub potentially containing a broad diversity of HIV variants; yet few sequences from DC are available on GenBank to assess the evolutionary history of HIV in the US capital. Towards this general goal, here we analyze extensive sequence data and investigate HIV diversity, phylodynamics, and drug resistant mutations (DRM) in DC. METHODS: Molecular HIV-1 sequences were collected from participants infected through 2015 as part of the DC Cohort, a longitudinal observational study of HIV+ patients receiving care at 13 DC clinics. Sequences were paired with Cohort demographic, risk, and clinical data and analyzed using maximum likelihood, Bayesian and coalescent approaches of phylogenetic, network and population genetic inference. We analyzed 601 sequences from 223 participants for int (~864 bp) and 2,810 sequences from 1,659 participants for PR/RT (~1497 bp). RESULTS: Ninety-nine and 94% of the int and PR/RT sequences, respectively, were identified as subtype B, with 14 non-B subtypes also detected. Phylodynamic analyses of US born infected individuals showed that HIV population size varied little over time with no significant decline in diversity. Phylogenetic analyses grouped 13.5% of the int sequences into 14 clusters of 2 or 3 sequences, and 39.0% of the PR/RT sequences into 203 clusters of 2-32 sequences. Network analyses grouped 3.6% of the int sequences into 4 clusters of 2 sequences, and 10.6% of the PR/RT sequences into 76 clusters of 2-7 sequences. All network clusters were detected in our phylogenetic analyses. Higher proportions of clustered sequences were found in zip codes where HIV prevalence is highest (r = 0.607; P<0.00001). We detected a high prevalence of DRM for both int (17.1%) and PR/RT (39.1%), but only 8 int and 12 PR/RT amino acids were identified as under adaptive selection. We observed a significant (P<0.0001) association between main risk factors (men who have sex with men and heterosexuals) and genotypes in the five well-supported clusters with sufficient sample size for testing. DISCUSSION: Pairing molecular data with clinical and demographic data provided novel insights into HIV population dynamics in Washington, DC. Identification of populations and geographic locations where clustering occurs can inform and complement active surveillance efforts to interrupt HIV transmission.

Evaluation of Level of Agreement in Bordetella Species Identification in Three U.S. Laboratories during a Period of Increased Pertussis.

While PCR is the most common method used for detecting Bordetella pertussis in the United States, most laboratories use insertion sequence 481 (IS481), which is not specific for B. pertussis; therefore, the relative contribution of other Bordetella species is not understood. The objectives of this study were to evaluate the proportion of other Bordetella species misidentified as B. pertussis during a period of increased pertussis incidence, determine the level of agreement in Bordetella species detection between U.S. commercial laboratories and the CDC, and assess the relative diagnostic sensitivity of CDC's PCR assay when using a different PCR master mix. Specimens collected between May 2012 and May 2013 were tested at two U.S. commercial laboratories for B. pertussis and B. parapertussis detection. Every fifth specimen positive for IS481 and/or IS1001 with cycle threshold (CT) values of ≤35 was sent to CDC for PCR testing that identifies Bordetella species. Specimens with indeterminate or negative results in the CDC PCR were tested using an alternate PCR master mix. Of 755 specimens, there was agreement in species identification for 83.4% (n = 630). Of the specimens with different identifications (n = 125), 79.2% (n = 99) were identified as indeterminate B. pertussis at CDC. Overall, 0.66% (n = 5) of the specimens were identified as B. holmesii or B. bronchiseptica at CDC. Of 115 specimens with indeterminate or negative results, 46.1% (n = 53) were B. pertussis positive when tested by an alternate master mix, suggesting a possible increase in assay sensitivity. This study demonstrates good agreement between the two U.S. commercial laboratories and CDC and little misidentification of Bordetella species during the 2012 U.S. epidemic.

Comparison of nucleic acid amplification assays with BD affirm VPIII for diagnosis of vaginitis in symptomatic women.

A commercially available, nonamplified, nucleic acid probe-based test system (BD Affirm VPIII) was compared with nucleic acid amplification (NAA)-based assays for determining the etiology of vaginitis in a cohort of 323 symptomatic women. First, a semiquantitative, multiplexed PCR assay (BV-PCR) and the Affirm VPIII Gardnerellavaginalis test were compared with a unified bacterial-vaginosis (BV) reference standard incorporating both Nugent Gram stain scores and Amsel clinical criteria. In the evaluable population of 305 patients, BV-PCR was 96.9% (191/197) sensitive and 92.6% specific (100/108) for BV, while Affirm VPIII was 90.1% sensitive (179/197) and 67.6% specific (73/108). Second, a multiplexed PCR assay detecting Candida albicans and Candida glabrata (CAN-PCR) was compared with the Affirm VPIII Candida test using a reference standard for vulvovaginal candidiasis (VVC) of yeast culture plus exclusion of alternate vaginitis etiologies. In the population evaluated (n = 102), CAN-PCR was 97.7% sensitive (42/43) and 93.2% specific (55/59) and Affirm VP III was 58.1% sensitive (25/43) and 100% specific (59/59) for VVC. Finally, the results of a commercial NAA test (GenProbe Aptima Trichomonas vaginalis assay; ATV) for T. vaginalis were compared with the Affirm VPIII Trichomonas vaginalis test. In the absence of an independent reference standard for trichomonal vaginitis (TV), a positive result in either assay was deemed to represent true infection. In the evaluable cohort of 388 patients, the sensitivity of ATV was 98.1% (53/54) versus 46.3% (25/54) for Affirm VPIII. The diagnostic accuracy of the combined NAA-based test construct was approximately 20 to 25% higher than that of the Affirm VPIII when modeled in populations with various prevalences of infectious vaginitis.

Development and validation of a semiquantitative, multitarget PCR assay for diagnosis of bacterial vaginosis.

Quantitative PCR assays were developed for 4 organisms reported previously to be useful positive indicators for the diagnosis of bacterial vaginosis (BV)--Atopobium vaginae, Bacterial Vaginosis-Associated Bacterium 2 (BVAB-2), Gardnerella vaginalis, and Megasphaera-1--and a single organism (Lactobacillus crispatus) that has been implicated as a negative indicator for BV. Vaginal samples (n = 169), classified as positive (n = 108) or negative (n = 61) for BV based on a combination of the Nugent Gram stain score and Amsel clinical criteria, were analyzed for the presence and quantity of each of the marker organisms, and the results were used to construct a semiquantitative, multiplex PCR assay for BV based on detection of 3 positive indicator organisms (A. vaginae, BVAB-2, and Megasphaera-1) and classification of samples using a combinatorial scoring system. The prototype BV PCR assay was then used to analyze the 169-member developmental sample set and, in a prospective, blinded manner, an additional 227 BV-classified vaginal samples (110 BV-positive samples and 117 BV-negative samples). The BV PCR assay demonstrated a sensitivity of 96.7% (202/209), a specificity of 92.2% (153/166), a positive predictive value of 94.0%, and a negative predictive value of 95.6%, with 21 samples (5.3%) classified as indeterminate for BV. This assay provides a reproducible and objective means of evaluating critical components of the vaginal microflora in women with signs and symptoms of vaginitis and is comparable in diagnostic accuracy to the conventional gold standard for diagnosis of BV.

Short communication: Transmitted drug resistance and molecular epidemiology in antiretroviral naive HIV type 1-infected patients in Rhode Island.

Transmission of HIV-1 drug resistance has important clinical and epidemiological consequences including earlier treatment failure and forward transmission of resistance strains in high-risk groups. To evaluate the prevalence and molecular epidemiology of transmitted drug resistance in Rhode Island, we collected genotypic, demographic, clinical, and laboratory data from treatment-naive individuals presenting to the largest outpatient HIV clinic in the state from January 2007 to November 2007. Sequences from 35 treatment-naive individuals were available, 83% of whom were men who had sex with men (MSM). All sequences were HIV-1 subtype B. Drug resistance mutations were identified in 7/35 [20%; 95% confidence interval (CI), 0.08-0.37] patients, six of whom had K103N. Two phylogenetic transmission clusters were found, involving 17% (6/35) of individuals, three in each cluster. We did not find an association between belonging to a cluster and age, gender, AIDS-defining illness, CD4 cell count, or viral load. Drug resistance mutations were more commonly observed in transmission clusters (p = 0.08). Individuals in one cluster all had K103N and were MSM who had attended local bathhouses. Individuals forming clusters were significantly more likely to have visited a bathhouse compared to nonclusters (p = 0.02). The prevalence of transmitted drug resistance in Rhode Island is high, further justifying genotypic testing on presentation to care and prior to treatment initiation. Molecular epidemiological analysis and association of resistance with phylogenetic networks using data obtained for clinical purposes may serve as useful tools for the prevention of drug resistance transmission and for contact tracing.

Nucleic-acid amplification testing of urine vs. patient complaint-driven evaluation.

The present pilot study compared the ability of a conventional patient complaint-driven approach to that of nucleic-acid amplification testing (NAAT) of urine to identify those individuals among an adult, urban, Emergency Department (ED) population infected with Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG), and Trichomonas vaginalis (TV). Urine for NAAT was collected for testing after individuals had completed a questionnaire and before being seen by a physician. A total of 614 subjects were enrolled, and complete physical examinations were performed on 348 (56.6%) individuals, with women being significantly more likely to receive such an evaluation (odds ratio [OR] 3.09; 95% confidence interval [CI] 1.96-4.86); p < 0.001). A total of 153 (24.9%) of the study cohort tested positive for a least one sexually transmitted disease (STD), and only a reported history of STD (OR 1.74; 95% CI (1.18-2.57); p = 0.005) and a history of a new sexual partner in the last 3 months (OR 1.79; 95% CI 1.13-2.82); p = 0.012) were predictive of a positive STD test. NAAT of urine samples on patients who did not receive a complete physical examination resulted in a 33% (51/153) increase in diagnostic yield in this cohort of ED attendees.

Diagnostic performance of rapid diagnostic tests versus blood smears for malaria in US clinical practice.

BACKGROUND: Approximately 4 million US travelers to developing countries are ill enough to seek health care, with 1500 malaria cases reported in the United States annually. The diagnosis of malaria is frequently delayed because of the time required to prepare malaria blood films and lack of technical expertise. An easy, reliable rapid diagnostic test (RDT) with high sensitivity and negative predictive value (NPV), particularly for Plasmodium falciparum, would be clinically useful. The objective of this study was to determine the diagnostic performance of a RDT approved by the US Food and Drug Administration compared with traditional thick and thin blood smears for malaria diagnosis. METHODS: This prospective study tested 852 consecutive blood samples that underwent thick and thin smears and blinded malaria RDTs at 3 hospital laboratories during 2003-2006. Polymerase chain reaction verified positive test results and discordant results. RESULTS: Malaria was noted in 95 (11%) of the 852 samples. The RDT had superior performance than the standard Giemsa thick blood smear (p = .003). The RDT's sensitivity for all malaria was 97% (92 of 95 samples), compared with 85% (81 of 95) for the blood smear, and the RDT had a superior NPV of 99.6%, compared with 98.2% for the blood smear (p = .001). The P. falciparum performance was excellent, with 100% rapid test sensitivity, compared with only 88% (65 of 74) by blood smear (p = .003). CONCLUSIONS: This operational study demonstrates that the US Food and Drug Administration-approved RDT for malaria is superior to a single set of blood smears performed under routine US clinical laboratory conditions. The most valuable clinical role of the RDT is in the rapid diagnosis or the exclusion of P. falciparum malaria, which is particularly useful in outpatient settings when evaluating febrile travelers.

Viral pathogens in acute exacerbations of chronic obstructive pulmonary disease.

The objective of this study is to determine the prevalence of respiratory syncytial virus (RSV) and other viral respiratory pathogens in emergency department (ED) patients with acute exacerbations of chronic obstructive pulmonary disease (AECOPD). COPD patients presenting to the ED with <10 days of AECOPD symptoms were eligible. We used PCR to test nasal swabs for common viral respiratory pathogens. We completed viral studies on 76 patients from two EDs. Patients had a mean age of 72 years, and were 68% male, 99% white, and 29% current smokers. Influenza vaccination was reported by 87%. Viruses were detected in 19 of 76 patients (25%). These included RSV A (2) and B (4); parainfluenza 1 (1), 2 (0), and 3 (2); influenza A (3) and B (0); rhinovirus (4); and human metapneumovirus (3). A putative viral etiology was identified in 25% of AECOPD presenting for emergency care, of which approximately one-third were RSV-related.

Evaluation of malaria screening in newly arrived refugees to the United States by microscopy and rapid antigen capture enzyme assay.

Before an empiric malaria treatment program, >60% of Liberian refugees had malaria on arrival to Minnesota. We compared microscopy with rapid antigen testing for detecting asymptomatic parasitemia. Nine of 103 (8.7%) had malaria by polymerase chain reaction (blood smear and rapid testing had a sensitivity of 22%). The empiric treatment program has decreased the rate of imported asymptomatic malaria. Blood film and rapid antigen testing are poor screening tests.

The changing epidemiology of HIV/AIDS at a Minnesota hospital: impact of demographic change and viral diversity.

The past decade has seen a dramatic influx of African-born immigrants and refugees into Minnesota. The impact of this on Hennepin County Medical Center (HCMC), a public teaching hospital located in Minneapolis, has been considerable, especially in the management of HIV-infected persons given that approximately 30% of newly diagnosed individuals seen at HCMC in the past 3 years acquired the virus in Africa. An ongoing and permanent alteration in the demographics of HIV/AIDS in this part of the American midwest is clearly occurring, therefore, accompanied by considerable diversification of the viral makeup of the epidemic. The following article describes currently available data on the viral characteristics of the African-born HIV-infected population of Minnesota and highlights the potential impact of this expanding viral diversity on the ability of the clinical laboratory at HCMC to provide the virologic information necessary to manage effectively patients infected with the HIV virus.

Use of sequence data generated in the Bayer Tru Gene genotyping assay to recognize and characterize non-subtype-b human immunodeficiency virus type 1 strains.

Human immunodeficiency virus type 1 (HIV-1) protease (PR) and reverse transcriptase (RT) gene sequences obtained during antiretroviral resistance testing with a commercial genotyping assay (Tru Gene; Bayer Corp.) were analyzed to assess the utility of these data for detecting and characterizing non-subtype-B HIV-1 strains. A total of 125 viral sequences obtained from patients believed to have acquired their HIV-1 infection in Africa were analyzed, of which 121 were determined to belong to non-B subtypes. Utilizing Tru Gene sequence data alone, 92 (76%) of these viruses could be subtyped by conventional phylogenetic analysis. The addition of supplemental RT sequence data enabled a further 28 (23.1%) viruses to be classified, while one (0.9%) sample could not be classified conclusively. Two internet-accessible databases that generate HIV-1 subtypes from PR and RT sequences (HIV-SEQ and Geno 2 Pheno) were also evaluated, and both achieved 88% concordance (106/120) with phylogenetic analysis. Non-subtype-B and B-subtype HIV-1 sequences could be readily discriminated by tallying silent polymorphisms listed on the Tru Gene research report. The mean number of silent polymorphisms in the non-B HIV-1 sequences identified in this study was 58.3 (95% confidence interval [CI], 41.1 to 75.5), compared with 20.7 (95% CI, 9.9 to 31.5) for the four subtype B viruses in the study cohort and 118 case-matched B-subtype controls. Sequence data generated in the Tru Gene HIV-1 genotyping assay could, therefore, provide a ready means of tracking the prevalence and identity of non-B subtypes in HIV-1-infected populations undergoing routine antiretroviral resistance testing.

A study of results generated using the Abbott LCx-GC assay fails to reveal a performance-based rationale for the 2002 level 1 recall.

To establish the effect of a quality control failure on the performance of the LCx-GC nucleic-acid amplification assay for Neisseria gonorrhoeae (Abbott Laboratories, Abbott Park, IL) in the field, we conducted a retrospective analysis comparing the clinical and analytic performance of the recalled lots with those not implicated in the recall. Our analysis revealed no statistically significant differences between recalled lots (n = 8,686 tests) and nonrecalled lots (n = 8,699 tests) with respect to multiple parameters of assay performance, including frequency distribution of patient results (P = .575), prevalence of indeterminate results (P = .245), mean positive control signals (P = .26), and within-run calibrator precision (P = .68). The LCx-GC system's lack of an electronic data storage and retrieval capability prevented assessment of the impact of the quality control failure on the clinical performance of recalled lots, such as the one described herein, from being conducted in real time.

Comparison of selective and nonselective enrichment broth media for the detection of vaginal and anorectal colonization with group B streptococcus.

The use of a selective enrichment broth medium has been widely recommended to optimize the recovery of group B streptococci (GBS) from genital and anorectal samples. Because selective antibiotic-containing versions of broth media are significantly more expensive than their nonselective parent formulations, we sought to examine whether the use of the nonselective Todd-Hewitt broth (THB) could accomplish comparable recovery of GBS to the recommended, selective version of this medium (Lim broth). During the study, vaginal and anorectal swab samples submitted to our laboratory for GBS culture were all inoculated onto Columbia colistin-nalidixic acid agar (CNA) and into either THB or Lim broth (alternated on a weekly basis). During the 45-week study period, 1200 samples (600 in each study arm) were evaluated. GBS were recovered from 164 samples (27.3%) in the Lim arm of the study, of which 60 (36.7%) were positive only on subculture of broths. In the THB study arm, 161 samples (26.8%) yielded GBS, of which 58 (36.0%) were positive only in broths. This study conclusively demonstrates that a nonselective enrichment broth media provides comparable sensitivity to the recommended selective broth for detection of GBS colonization during pregnancy.

Loa loa presenting in a ThinPrep Pap test: case report and review of parasites in cervicovaginal cytology specimens.

Parasites other than Trichomonas vaginalis may occasionally present in Pap tests obtained during gynecologic examination. We present a case of Loa loa found on a Pap test from an apparently healthy 19-yr-old woman who had immigrated to the US at the age of 15 from Cameroon. We discuss the cytologic features from this case and then briefly review Loa loa and the presence of parasites in Pap tests and other cervicovaginal specimens.

Detection of fluconazole-resistant isolates of Candida glabrata by using an agar screen assay.

The ability of a fluconazole-containing agar screen assay to accurately detect isolates of Candida glabrata resistant to the azole antifungal agent fluconazole was evaluated on a collection of 100 clinical isolates of this organism. Results were correlated with the MIC of fluconazole for these isolates and compared with the results of a previously published disk diffusion-based fluconazole resistance screening test. Agar screen assay results were in categorical agreement with MIC-based determinations for 97% (97/100) of the isolates tested. This correlation was higher than that obtained with the disk diffusion technique, which categorized only 87% (87/100) of isolates correctly, and suggests that the agar screening approach can effectively expedite fluconazole susceptibility testing of C. glabrata isolates.

Early detection of central nervous system tuberculosis with the gen-probe nucleic Acid amplification assay: utility in an inner city hospital.

Central nervous system tuberculosis is a serious clinical problem, the treatment of which is sometimes hampered by delayed diagnosis. We investigated the utility of the Gen-Probe nucleic acid amplification assay for the rapid diagnosis of tuberculous meningitis and as a noninvasive method of identifying intracranial tuberculoma.