A program for real-time surveillance of SARS-CoV-2 genetics.

The COVID-19 pandemic brought forth an urgent need for widespread genomic surveillance for rapid detection and monitoring of emerging SARS-CoV-2 variants. It necessitated design, development, and deployment of a nationwide infrastructure designed for sequestration, consolidation, and characterization of patient samples that disseminates de-identified information to public authorities in tight turnaround times. Here, we describe our development of such an infrastructure, which sequenced 594,832 high coverage SARS-CoV-2 genomes from isolates we collected in the United States (U.

Comparison of species identification among differing rt-PCR assays in the United States.

Unlabelled: In the United States, the general laboratory method for diagnosing pertussis, caused by is real-time PCR (rt-PCR) targeting insertion sequence 481 (IS). Other species (, and ) can also cause a pertussis-like syndrome, and some commercial laboratory assays include the insertion sequence 1001 (pIS) that can detect /). Because IS exists in and , current commercial assays cannot differentiate these two species.

Chlamydia trachomatis Variants Escaping Detection in the Aptima Combo 2 Assay in the United States.

Background: The Aptima Combo 2 (AC2) assay manufactured by Hologic, Inc., detects Neisseria gonorrhoeae and/or Chlamydia trachomatis (CT) in urogenital and extragenital specimens by targeting either a 16S rRNA (N. gonorrhoeae) or 23S rRNA (CT) region.

Trichomonas vaginalis Detection in Urogenital Specimens from Symptomatic and Asymptomatic Men and Women by Use of the cobas TV/MG Test.

Trichomonas vaginalis is a prevalent sexually transmitted infection (STI). Diagnosis has historically relied on either microscopic analysis or culture, the latter being the previous gold standard. However, these tests are not readily available for male diagnosis, generally only perform well for symptomatic women, and are not as sensitive as nucleic acid amplification tests (NAATs).

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.

Mycoplasma genitalium Detection in Urogenital Specimens from Symptomatic and Asymptomatic Men and Women by Use of the cobas TV/MG Test.

(MG) infections are a growing concern within the field of sexually transmitted infections. However, diagnostic assays for have been limited in the United States. As most infections are asymptomatic, individuals can unknowingly pass the infection on, and the prevalence is likely to be underestimated.

Syphilis Testing among Men Who Have Had Rectal Gonorrhea and Chlamydia Tests, United States.

The Centers for Disease Control and Prevention (CDC) recommends syphilis screening at least annually for sexually active men who have sex with men (MSM). The objective of this study is to assess the frequency of MSM testing for syphilis and how syphilis test results compared with results of rectal gonorrhea and chlamydia tests. In collaboration with a large US commercial laboratory, we identified men aged 15-60 years who had rectal chlamydia or gonorrhea tests during 09/01/2013-09/30/2015 as presumed MSM.

Evaluation of the Performance of the Cobas CT/NG Test for Use on the Cobas 6800/8800 Systems for Detection of and in Male and Female Urogenital Samples.

The clinical performance of the Cobas CT/NG assay on the Cobas 6800/8800 systems (Cobas) for the detection of and was established in a multisite, prospective collection study using male and female urogenital specimens; supportive data from archived specimens were also included. The results obtained with the Cobas assay were compared with the patient infected status derived from a combination of U.S.

Detection of and with the cobas CT/NG v2.0 test: performance compared with the BD ProbeTec CT Q and GC Q amplified DNA and Aptima AC2 assays.

Objectives: Infections due to (CT) and (NG) are among the most common bacterial sexually transmitted infections worldwide, most of which are asymptomatic. Detection of infection using a variety of specimen types in symptomatic and asymptomatic subjects is important to effectively combat CT/NG infections. The performance of the cobas CT/NG v2.

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.

Age-specific chlamydial infection among pregnant women in the United States: evidence for updated recommendations.

Background: In the United States, chlamydia screening has been recommended for all pregnant women by the Centers for Disease Control and Prevention (CDC) but only for pregnant women who are at increased risk by the US Preventive Services Task Force (USPSTF). Very limited evidence, such as age-specific chlamydia positivity in pregnant women, has been used to develop these recommendations.

Methods: We analyzed data from a large commercial laboratory corporation in the United States in 2013.

Detection of Trichomonas vaginalis DNA by use of self-obtained vaginal swabs with the BD ProbeTec Qx assay on the BD Viper system.

Trichomonas vaginalis is the most prevalent nonviral sexually transmitted infection worldwide, and improved diagnostic methods are critical for controlling this pathogen. Diagnostic assays that can be used in conjunction with routine chlamydia/gonorrhea nucleic acid-based screening are likely to have the most impact on disease control. Here we describe the performance of the new BD T.

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.

Suboptimal adherence to repeat testing recommendations for men and women with positive Chlamydia tests in the United States, 2008-2010.

Background: Chlamydia is prevalent among young persons in the United States. Infected persons have a high prevalence of infection several months later, most likely from reinfection. Retesting of all men and women with a positive test is recommended 3 months after treatment.

Evaluation of the Roche cobas® CT/NG test for detection of Chlamydia trachomatis and Neisseria gonorrhoeae in male urine.

Background: The Roche cobas® CT/NG test (c4800), performed on the cobas 4800 system, is a new diagnostic assay using an automated workstation to isolate nucleic acids from clinical specimens and a real-time instrument for the detection of Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG). This study compared the performance characteristics of the c4800 with the Becton Dickinson ProbeTec™ CT/GC Q(x) assay (Q(x)) and Gen-Probe® Aptima Combo 2 (AC2) assay for the detection of CT and NG in male urine using patient-infected-status (PIS).

Methods: Urine and urethral swabs were obtained from men attending STD, family planning, or OB/GYN clinics from 11 geographically distinct locations.

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.

H-NS binding and repression of the ctx promoter in Vibrio cholerae.

Expression of the ctx and tcp genes, which encode cholera toxin and the toxin coregulated pilus, the Vibrio cholerae O1 virulence determinants having the largest contribution to cholera disease, is repressed by the nucleoid-associated protein H-NS and activated by the AraC-like transcriptional regulator ToxT. To elucidate the molecular mechanism by which H-NS controls transcription of the ctxAB operon, H-NS repression and binding were characterized by using a promoter truncation series, gel mobility shift assays, and DNase I footprinting. Promoter regions found to be important for H-NS repression correlated with in vitro binding.

Comparison of APTIMA Trichomonas vaginalis transcription-mediated amplification to wet mount microscopy, culture, and polymerase chain reaction for diagnosis of trichomoniasis in men and women.

Objective: We evaluated the performance characteristics of APTIMA Trichomonas vaginalis (ATV) transcription-mediated amplification (TMA) for diagnosis of T vaginalis (TV) infection from female vaginal swab, endocervical swab, and urine specimens and from male urethral swab and urine specimens. Performance of ATV TMA was compared with wet mount microscopy, culture, and polymerase chain reaction (PCR).

Study Design: In all, 296 female and 298 male subjects who attended the Jefferson County Health Department sexually transmitted diseases clinic were enrolled in the study and provided specimens for each test.

Successful treatment of Pasteurella multocida meningitis with aztreonam.

This is the first reported case of the successful treatment of Pasteurella multocida meningitis with aztreonam in a patient with multiple antibiotic allergies.

Successful treatment of Pasteurella multocida meningitis with aztreonam.

This is the first reported case of the successful treatment of Pasteurella multocida meningitis with aztreonam in a patient with multiple antibiotic allergies.

Sequence diversity in the glycoprotein B gene complicates real-time PCR assays for detection and quantification of cytomegalovirus.

Real-time quantitative PCR systems (Q-PCR) for the rapid detection and quantification of microorganisms in clinical specimens employ oligodeoxyribonucleotide primers and probes for specificity, which makes them vulnerable to false negatives caused by sequence diversity in the template. Schaade et al. (J.

Vibrio cholerae H-NS domain structure and function with respect to transcriptional repression of ToxR regulon genes reveals differences among H-NS family members.

H-NS is an abundant bacterial protein involved in transcriptional silencing of a variety of environmentally responsive genes during growth under non-permissive conditions. We have previously demonstrated a direct role for H-NS in the negative modulation of expression of several genes within the ToxR virulence regulon of Vibrio cholerae. Here we have undertaken extensive mutagenesis of the structural and functional domains of the H-NS protein to determine the contribution of each to the regulation of gene expression.