Epidemiology of Chlamydia trachomatis and Repeat Positivity Following Detection in New York State.

BACKGROUND: In New York State, excluding New York City, chlamydia remains a persistent health concern. Our aim was to characterize chlamydia epidemiology and identify groups at higher risk of repeat positivity to inform targeted public health interventions. METHODS: We analyzed demographic and clinical data of laboratory-confirmed chlamydia cases in New York State from 2015 to 2019. Repeat positivity was defined as a second positive chlamydia test within 31 to 365 days of the initial positive test. We compared characteristics of individuals with single and repeat positivity and evaluated associations with repeat positivity using multivariable logistic regression models. RESULTS: During the study period, 176 273 individuals were diagnosed with chlamydia, with 17 253 experiencing repeat positivity. Repeat positivity was more common among individuals assigned female at birth. Key predictors of repeat positivity among females included non-Hispanic Black (adjusted odds ratio [aOR]: 1.33; 95% confidence interval [CI], 1.27-1.40) race/ethnicity, ages 13 to 19 (aOR: 1.62; 95% CI, 1.55-1.69), prior sexually transmitted infection (STI) diagnosis (aOR: 1.24; 95% CI, 1.18-1.31), symptomatic examination (aOR: 1.07; 95% CI, 1.02-1.13), and county/community (aOR: 1.10; 95% CI, 1.05-1.15) or private/public (aOR: 1.18; 95% CI, 1.11-1.25) provider. Among males, predictors included non-Hispanic Black (aOR: 1.57; 95% CI, 1.45-1.70) race/ethnicity, ages 13 to 19 (aOR: 1.27; 95% CI, 1.17-1.38), HIV coinfection (aOR: 1.30; 95% CI, 1.10-1.54), prior STI diagnosis (aOR: 1.31; 95% CI, 1.20-1.43), extragenital infection site (aOR: 2.59; 95% CI, 2.27-2.95), symptomatic examination (aOR: 1.21; 95% CI, 1.12-1.31), and county/community health (aOR: 1.09; 95% CI, 1.02-1.17) provider. CONCLUSIONS: Our findings provide valuable insights for sexual health interventions to prevent chlamydia transmission and recurrence. Prioritizing resources for prevention interventions and tailored sexual health promotion among non-Hispanic Black individuals is crucial. Additionally, targeted STI prevention efforts are needed for males who have sex with men and those initially diagnosed with extragenital infection. Research is warranted on STI prevention among people living with HIV or at high risk of HIV infection. Strengthening prevention strategies through Expedited Partner Therapy and sexual health education for individuals at risk of repeat positivity could enhance prevention efforts.

Assuring Adequate Treatment for Persons Diagnosed With Gonorrhea in New York State.

BACKGROUND: From November 2014 to May 2016, 57 local health departments in New York State (NYS) excluding New York City were offered a performance incentive (PI) to promote adherence to federally recommended treatment guidelines for gonorrhea. The rationale of the PI was to delay antibiotic resistance and disrupt transmission through attaining a high percentage of treatment adherence. METHODS: Surveillance data from the NYS Communicable Disease Electronic Surveillance System were used for analysis. We evaluated adherence per Centers for Disease Control and Prevention sexually transmitted diseases treatment guidelines for persons 12 years and older reported with uncomplicated gonorrhea during 4 time frames: Pre-PI, PI One, PI Two, and Post-PI. We measured adherence per the Centers for Disease Control and Prevention sexually transmitted disease treatment guidelines during each respective time frame and conducted χ tests to test for the association between treatment adequacy and time frame. RESULTS: During the Pre-PI, treatment was adequate in 82.0% of persons diagnosed with gonorrhea. After program implementation, treatment adequacy increased significantly (92.1% of diagnosed persons during PI One, 90.4% during PI Two, and 90.5% during the Post-PI; P ≤ 0.0001). The most common reason for inadequate or missing treatment was patient lost to follow-up. CONCLUSIONS: Public health intervention by the NYS Department of Health improved local health department adherence to federally recommended gonorrhea treatment guidelines, and improvements were maintained after the completion of the PI.

Genome-scale analyses of Escherichia coli and Salmonella enterica AraC reveal noncanonical targets and an expanded core regulon.

Escherichia coli AraC is a well-described transcription activator of genes involved in arabinose metabolism. Using complementary genomic approaches, chromatin immunoprecipitation (ChIP)-chip, and transcription profiling, we identify direct regulatory targets of AraC, including five novel target genes: ytfQ, ydeN, ydeM, ygeA, and polB. Strikingly, only ytfQ has an established connection to arabinose metabolism, suggesting that AraC has a broader function than previously described. We demonstrate arabinose-dependent repression of ydeNM by AraC, in contrast to the well-described arabinose-dependent activation of other target genes. We also demonstrate unexpected read-through of transcription at the Rho-independent terminators downstream of araD and araE, leading to significant increases in the expression of polB and ygeA, respectively. AraC is highly conserved in the related species Salmonella enterica. We use ChIP sequencing (ChIP-seq) and RNA sequencing (RNA-seq) to map the AraC regulon in S. enterica. A comparison of the E. coli and S. enterica AraC regulons, coupled with a bioinformatic analysis of other related species, reveals a conserved regulatory network across the family Enterobacteriaceae comprised of 10 genes associated with arabinose transport and metabolism.

Pertactin-negative variants of Bordetella pertussis in New York State: a retrospective analysis, 2004-2013.

The first report of pertactin-negative variants of Bordetella pertussis in the United States has raised questions about the role of acellular pertussis vaccines in the recent increase of pertussis cases. Our laboratory utilized a sequence-based method to identify mutations in the pertactin gene responsible for these variants and assessed vaccination status from the associated cases.

Syphilis Treatment Among People Who Are Pregnant in Six U.S. States, 2018-2021.

OBJECTIVE: To describe syphilis treatment status and prenatal care among people with syphilis during pregnancy to identify missed opportunities for preventing congenital syphilis. METHODS: Six jurisdictions that participated in SET-NET (Surveillance for Emerging Threats to Pregnant People and Infants Network) conducted enhanced surveillance among people with syphilis during pregnancy based on case investigations, medical records, and linkage of laboratory data with vital records. Unadjusted risk ratios (RRs) were used to compare demographic and clinical characteristics by syphilis stage (primary, secondary, or early latent vs late latent or unknown) and treatment status during pregnancy (adequate per the Centers for Disease Control and Prevention's "Sexually Transmitted Infections Treatment Guidelines, 2021" vs inadequate or not treated) and by prenatal care (timely: at least 30 days before pregnancy outcome; nontimely: less than 30 days before pregnancy outcome; and no prenatal care). RESULTS: As of September 15, 2023, of 1,476 people with syphilis during pregnancy, 855 (57.9%) were adequately treated and 621 (42.1%) were inadequately treated or not treated. Eighty-two percent of the cohort received timely prenatal care. Although those with nontimely or no prenatal care were more likely to receive inadequate or no treatment (RR 2.50, 95% CI, 2.17-2.88 and RR 2.73, 95% CI, 2.47-3.02, respectively), 32.1% of those with timely prenatal care were inadequately or not treated. Those with reported substance use or a history of homelessness were nearly twice as likely to receive inadequate or no treatment (RR 2.04, 95% CI, 1.82-2.28 and RR 1.83, 95% CI, 1.58-2.13, respectively). CONCLUSION: In this surveillance cohort, people without timely prenatal care had the highest risk for syphilis treatment inadequacy; however, almost a third of people who received timely prenatal care were not adequately treated. These findings underscore gaps in syphilis screening and treatment for pregnant people, especially those experiencing substance use and homelessness, and the need for systems-based interventions, such as treatment outside of traditional prenatal care settings.

Understanding and determining the etiology of autism.

Worldwide, the rate of autism has been steadily rising. There are several environmental factors in concert with genetic susceptibilities that are contributing to this rise. Impaired methylation and mutations of mecp2 have been associated with autistic spectrum disorders, and related Rett syndrome. Genetic polymorphisms of cytochrome P450 enzymes have also been linked to autism, specifically CYP27B1 that is essential for proper vitamin D metabolism. Vitamin D is important for neuronal growth and neurodevelopment, and defects in metabolism or deficiency have been implicated in autistic individuals. Other factors that have been considered include: maternally derived antibodies, maternal infection, heavy metal exposure, folic acid supplementation, epigenetics, measles, mumps, rubella vaccination, and even electromagnetic radiation. In each case, the consequences, whether direct or indirect, negatively affect the nervous system, neurodevelopment, and environmental responsive genes. The etiology of autism is a topic of controversial debate, while researchers strive to achieve a common objective. The goal is to identify the cause(s) of autism to understand the complex interplay between environment and gene regulation. There is optimism that specific causes and risk factors will be identified. The results of future investigations will facilitate enhanced screening, prevention, and therapy for "at risk" and autistic patients.

Syphilis among adult males with a history of male-to-male sexual contact living with diagnosed HIV in New York State (excluding New York City): The challenge of intersecting epidemics.

Since 2009, syphilis has been increasing in New York State (NYS) excluding New York City (NYC) among men with a history of male-to-male sexual contact (MSM). Because MSM make up a disproportionate number of new HIV infections, this study aims to: 1) establish yearly rates of early syphilis diagnosis, 2) assess factors associated with early syphilis diagnosis, and 3) describe missed opportunities for earlier diagnosis of syphilis among MSM living with diagnosed HIV(MSMLWDH) in NYS, excluding NYC. A cohort of adult MSMLWDH alive in 2013 were followed through 2016 to identify individuals with at least one early syphilis diagnosis between July 2014 and December 2016. Early syphilis diagnosis rates were calculated for 2015 and 2016. Crude relative risks and 95% confidence intervals were calculated to determine associations between available covariates and both syphilis diagnosis and missed opportunities. Missed opportunities were defined as reports of an HIV-related laboratory test within a given window corresponding to syphilis staging where syphilis testing was not performed at the same time. Of 7,512 MSMLWDH, 50.0% were non-Hispanic white, 85.4% aged ≥35, and 320(4.3%) had an early syphilis diagnosis. Yearly rates were: 1,838/100,000, and 1,681/100,000 in 2015 and 2016, respectively. Persons who were non-Hispanic black, living with diagnosed HIV for less than three years, aged <45, and were always virally suppressed or always in HIV care were significantly more likely to have a syphilis diagnosis. Over half of individuals had evidence of a missed opportunity for earlier syphilis diagnosis. Syphilis stage at diagnosis, older age, and syphilis diagnosis not concurrent with an HIV-related laboratory test were associated with a higher likelihood of having a missed opportunity. This study supports high interrelatedness of the syphilis and HIV epidemics among MSM. Since syphilis can impact HIV viral load suppression status, efforts to end the HIV epidemic need to be coupled with syphilis elimination efforts.

RIP: an mRNA localization technique.

A detailed understanding of post-transcriptional gene expression is necessary to correlate the different elements involved in the many levels of RNA-protein interactions that are needed to coordinate the cellular biomolecular machinery. The profile of mRNA, a major component of this machinery, can be examined after isolation from specific RNA-binding proteins (RBPs). RIP-Chip or ribonomic profiling is a versatilein vivo technique that has been widely used to study post-transcriptional gene regulation and the localization of mRNA. Here we elaborately detail the methodology for mRNA isolation using RBP immunoprecipitation (RIP) as a primary approach. Specific antibodies are used to target RBPs, which are then used to capture the associated mRNA.