In 2020, during the COVID-19 pandemic, CDC established the National Wastewater Surveillance System and later expanded it to include mpox and influenza A data dashboards.(†) Wastewater utility partners have cited community health benefits as a motivating factor for participating in wastewater surveillance; a lack of public support for wastewater surveillance activities might lead utility partners to cease participation (1,2). However, little is known about public support for wastewater monitoring and its influence on protective health behaviors. As innovative surveillance strategies such as wastewater surveillance evolve, ethical considerations, including understanding public perceptions regarding support for these activities and potential risks to communities, are essential (3).

A survey of US infectious disease physicians indicated that few regularly reviewed wastewater surveillance (WWS) data but many reported examples of how WWS has affected or could affect their clinical practice. WWS data can be useful for physicians, but increased communication between public health professionals and physicians regarding WWS could improve its utility.

Zika virus (ZIKV) infection in pregnancy is associated with severe abnormalities of the brain and eye and other adverse outcomes. Zika en Embarazadas y Niños was a prospective cohort study conducted in multiple Colombian cities that enrolled pregnant women in their first trimester. Specimens collected from pregnant women (n = 1,519) during February 2017-September 2018 and their infants (n = 1,080) during June 2017-March 2019 were tested for prenatal ZIKV infection by nucleic acid amplification tests or IgM antibody testing. Zika virus infection in pregnancy was present in 3.2% of pregnant women (incidence rate [IR] per 1,000 person-months = 5.9, 95% CI: 4.3-7.8). Presumptive ZIKV infection was present in 0.8% of infants (IR = 1.6, 95% CI: 0.7-2.9). Five percent of infants with prenatal ZIKV exposure or infection presented with Zika-associated abnormalities; 4.7% were small for gestational age. Understanding the risk of ZIKV infection during pregnancy and associated adverse outcomes can help inform counseling efforts.

During the 2022 multinational mpox outbreak, U.S. mpox cases primarily occurred among adult gay, bisexual, and other men who have sex with men (1). Among all cases, 94% of patients reported exposure through sexual or other intimate contact (1). Currently, little is known about less common nonsexual mpox transmission. A systematic review of mpox transmission in countries with endemic mpox in Central Africa found that the secondary attack rate among unvaccinated household contacts ranged from 0% to 11%, with a pooled estimate of 8% (2). A better understanding of the risk for nonsexual transmission during the current outbreak in countries where mpox is not endemic is important for developing and implementing future prevention and control strategies.

Wastewater surveillance (WWS), the systematic detection of infectious agents in wastewater, provided a valuable tool for monitoring SARS-CoV-2 circulation during the COVID-19 pandemic; surveillance has expanded from 20 to 53 jurisdictions across the United States, with increasing capacity to test for more respiratory pathogens (1,2). This report highlights the use of wastewater data by the four National Wastewater Surveillance System’s (NWSS) Centers of Excellence (California; Colorado; Houston, Texas; and Wisconsin) to guide public health action during the 2022–23 respiratory disease season. This activity was reviewed by CDC, deemed not research, and was conducted consistent with applicable federal law and CDC policy.*

CONTEXT: Health departments (HDs) work on the front lines to ensure the health of their communities, providing a unique perspective to public health response activities. Say Yes! COVID Test (SYCT) is a US federally funded program providing free COVID-19 self-tests to communities with high COVID-19 transmission, low vaccination rates, and high social vulnerability. The collaboration with 9 HDs was key for the program distribution of 5.8 million COVID-19 self-tests between March 31 and November 30, 2021. OBJECTIVE: The objective of this study was to gather qualitative in-depth information on the experiences of HDs with the SYCT program to better understand the successes and barriers to implementing community-focused self-testing programs. DESIGN: Key informant (KI) interviews. SETTING: Online interviews conducted between November and December 2021. PARTICIPANTS: Sixteen program leads representing 9 HDs were purposefully sampled as KIs. KIs completed 60-minute structured interviews conducted by one trained facilitator and recorded. MAIN OUTCOME MEASURES: Key themes and lessons learned were identified using grounded theory. RESULTS: Based on perceptions of KIs, HDs that maximized community partnerships for test distribution were more certain that populations at a higher risk for COVID-19 were reached. Where the HD relied predominantly on direct-to-consumer distribution, KIs were less certain that communities at higher risk were served. Privacy and anonymity in testing were themes linked to higher perceived community acceptance. KIs reported that self-test demand and distribution levels increased during higher COVID-19 transmission levels. CONCLUSION: HDs that build bridges and engage with community partners and trusted leaders are better prepared to identify and link high-risk populations with health services and resources. When collaborating with trusted community organizations, KIs perceived that the SYCT program overcame barriers such as mistrust of government intervention and desire for privacy and motivated community members to utilize this resource to protect themselves against COVID-19.

INTRODUCTION: We developed a standardized method, "Possible poor treatment response" (PPTR), to help ascertain efficacy endpoints in Study S31/A5349 (NCT02410772), an open-label trial comparing two 4-month rifapentine-based regimens with a standard 6-month regimen for the treatment of pulmonary TB. We describe the use of the PPTR process and evaluate whether the goals of minimizing bias in efficacy endpoint assessment and attainment of relevant data to determine outcome for all participants were achieved. METHODS/DESIGN: A PPTR event was defined as the occurrence of one or more pre-specified triggers. Each PPTR required initiation of a standardized evaluation process that included obtaining multiple sputum samples for microbiology. RESULTS: Among 2,343 participants with culture-confirmed drug-susceptible TB, 454 individuals (19.4%) had a total of 534 individual PPTR events, of which 76.6% were microbiological (positive smear or culture at or after 17 weeks). At least one PPTR event was experienced by 92.4% (133 of 144) of participants with TB-related unfavorable outcome, and between 13.8 and 14.7% of participants with favorable and not assessable outcomes. 75% of participants with TB-related unfavorable outcomes had microbiological confirmation of failure to achieve disease-free cure. DISCUSSION: Standardized methodologies, such as our PPTR approach, could facilitate unbiased efficacy outcome determinations, improve discrimination between outcomes that are related and unrelated to regimen efficacy, and enhance the ability to conduct pooled analyses of contemporary trials. Clinical trial registration available at www. CLINICALTRIALS: gov, ID: NCT02410772.

High prevalences of HIV and other sexually transmitted infections (STIs) have been reported in the current global monkeypox outbreak, which has affected primarily gay, bisexual, and other men who have sex with men (MSM) (1-5). In previous monkeypox outbreaks in Nigeria, concurrent HIV infection was associated with poor monkeypox clinical outcomes (6,7). Monkeypox, HIV, and STI surveillance data from eight U.S. jurisdictions* were matched and analyzed to examine HIV and STI diagnoses among persons with monkeypox and assess differences in monkeypox clinical features according to HIV infection status. Among 1,969 persons with monkeypox during May 17-July 22, 2022, HIV prevalence was 38%, and 41% had received a diagnosis of one or more other reportable STIs in the preceding year. Among persons with monkeypox and diagnosed HIV infection, 94% had received HIV care in the preceding year, and 82% had an HIV viral load of <200 copies/mL, indicating HIV viral suppression. Compared with persons without HIV infection, a higher proportion of persons with HIV infection were hospitalized (8% versus 3%). Persons with HIV infection or STIs are disproportionately represented among persons with monkeypox. It is important that public health officials leverage systems for delivering HIV and STI care and prevention to reduce monkeypox incidence in this population. Consideration should be given to prioritizing persons with HIV infection and STIs for vaccination against monkeypox. HIV and STI screening and other recommended preventive care should be routinely offered to persons evaluated for monkeypox, with linkage to HIV care or HIV preexposure prophylaxis (PrEP) as appropriate.

PURPOSE: Information on incentives for COVID-19 testing is needed to understand effective practices that encourage testing uptake. We describe characteristics of those who received an incentive after performing a rapid antigen test. DESIGN: Cross-sectional descriptive analysis of survey data. SETTING: During April 29-May 9, 2021, COVID-19 rapid antigen testing was offered in 2 Maryland cities. SAMPLE: Convenience sample of 553 adults (≥18 years) who tested and received an incentive; 93% consented to survey. MEASURES: Survey questions assessed reasons for testing, testing history, barriers, and demographics. ANALYSIS: Robust Poisson regressions were used to determine characteristic differences based on testing history and between participants who would re-test in the future without an incentive vs participants who would not. RESULTS: The most common reasons for testing were the desire to be tested (n = 280; 54%) and convenience of location (n = 146; 28%). Those motivated by an incentive to test (n = 110; 21%) were 5.83 times as likely to state they would not test again without an incentive, compared to those with other reasons for testing (95% CI: 2.67-12.72, P < .001). CRITICAL LIMITATIONS: No comparative study group. CONCLUSION: Results indicate internal motivation and convenience were prominent factors supporting testing uptake. Incentives may increase community testing participation, particularly among people who have never tested. Keywords COVID-19, pandemic, incentives, health behavior, community testing.

OBJECTIVE: During the COVID-19 pandemic, the unemployment rate in the United States peaked at 14.8% in April 2020. We examined patterns in unemployment following this peak in counties with rapid increases in COVID-19 incidence. METHOD: We used CDC aggregate county data to identify counties with rapid increases in COVID-19 incidence (rapid riser counties) during July 1-October 31, 2020. We used a linear regression model with fixed effect to calculate the change of unemployment rate difference in these counties, stratified by the county's social vulnerability (an indicator compiled by CDC) in the two months before the rapid riser index month compared to the index month plus one month after the index month. RESULTS: Among the 585 (19% of U.S. counties) rapid riser counties identified, the unemployment rate gap between the most and least socially vulnerable counties widened by 0.40 percentage point (p<0.01) after experiencing a rapid rise in COVID-19 incidence. Driving the gap were counties with lower socioeconomic status, with a higher percentage of people in racial and ethnic minority groups, and with limited English proficiency. CONCLUSION: The widened unemployment gap after COVID-19 incidence rapid rise between the most and least socially vulnerable counties suggests that it may take longer for socially and economically disadvantaged communities to recover. Loss of income and benefits due to unemployment could hinder behaviors that prevent spread of COVID-19 (e.g., seeking healthcare) and could impede response efforts including testing and vaccination. Addressing the social needs within these vulnerable communities could help support public health response measures.

Vaccination protects against infection with SARS-CoV-2 (the virus that causes COVID-19) and related hospitalizations (1,2), and surviving a previous infection protects against B.1.1.7 (Alpha) and B.1.617.2 (Delta) variant reinfections† (2). Since the SARS-CoV-2 B.1.1.529 (Omicron) variant became predominant in the United States in late December 2021, reported reinfections have increased§ (3). Early reinfections (those occurring within 90 days of previous infection) are not well understood (4). Because some persons have prolonged detection of viral RNA after infection,¶ repeat positive nucleic acid amplification test (NAAT) results within 90 days could reflect prolonged shedding from earlier infection, presenting technical challenges to documenting and characterizing early reinfections. This report describes 10 patients from four states, with whole genome sequencing (WGS)–confirmed Omicron variant infections within 90 days of a previous Delta infection. This activity was reviewed by CDC, approved by respective institutional review boards, and was conducted consistent with applicable federal law and CDC policy.**

During November 19-21, 2021, an indoor convention (event) in New York City (NYC), was attended by approximately 53,000 persons from 52 U.S. jurisdictions and 30 foreign countries. In-person registration for the event began on November 18, 2021. The venue was equipped with high efficiency particulate air (HEPA) filtration, and attendees were required to wear a mask indoors and have documented receipt of at least 1 dose of a COVID-19 vaccine.* On December 2, 2021, the Minnesota Department of Health reported the first case of community-acquired COVID-19 in the United States caused by the SARS-CoV-2 B.1.1.529 (Omicron) variant in a person who had attended the event (1). CDC collaborated with state and local health departments to assess event-associated COVID-19 cases and potential exposures among U.S.-based attendees using data from COVID-19 surveillance systems and an anonymous online attendee survey. Among 34,541 attendees with available contact information, surveillance data identified test results for 4,560, including 119 (2.6%) persons from 16 jurisdictions with positive SARS-CoV-2 test results. Most (4,041 [95.2%]), survey respondents reported always wearing a mask while indoors at the event. Compared with test-negative respondents, test-positive respondents were more likely to report attending bars, karaoke, or nightclubs, and eating or drinking indoors near others for at least 15 minutes. Among 4,560 attendees who received testing, evidence of widespread transmission during the event was not identified. Genomic sequencing of 20 specimens identified the SARS-CoV-2 B.1.617.2 (Delta) variant (AY.25 and AY.103 sublineages) in 15 (75%) cases, and the Omicron variant (BA.1 sublineage) in five (25%) cases. These findings reinforce the importance of implementing multiple, simultaneous prevention measures, such as ensuring up-to-date vaccination, mask use, physical distancing, and improved ventilation in limiting SARS-CoV-2 transmission, during large, indoor events.(†).

On December 2, 2021, the Minnesota Department of Health (MDH) notified CDC of a COVID-19 case caused by sequence-confirmed SARS-CoV-2 B.1.1.529 (Omicron) variant in a Minnesota resident (patient A), the first such case identified in the state and one of the earliest identified in the United States. Patient A had attended a large indoor convention in New York, New York with approximately 53,000 attendees from 52 U.S jurisdictions and 30 foreign countries during November 19-21, 2021, and had close contact(†) during 5 days with 29 fellow attendees. The convention required attendees to have received ≥1 COVID-19 vaccine dose and enforced mask-use while indoors. On November 22, these close contact attendees were directly and immediately notified by patient A of their exposure to SARS-CoV-2, and they sought testing over the next few days while quarantined or isolated. As part of the larger investigation into SARS-CoV-2 transmission at the convention, a subinvestigation was conducted during December by CDC, MDH, and respective state and local health departments to characterize the epidemiology of Omicron variant infection among this group of close contacts and determine the extent of secondary household transmission. Among 30 convention attendees that included patient A (the index patient) and the 29 other close contacts, 23 were interviewed, among whom all were fully vaccinated, including 11 (48%) who had received a booster dose; all 23 sought testing, and 16 (70%) received a positive SARS-CoV-2 test result. Fewer attendees who had received a booster dose before the convention received a positive test result (six of 11) compared with those who had not received a booster dose (10 of 12). The 16 attendees with positive test results had a total of 20 household contacts, 18 of whom sought testing after exposure; six received a positive test result for SARS-CoV-2. None of the persons with positive test results was hospitalized or died. There was limited convention-associated transmission identified outside of this cluster; the larger investigation included cases of both SARS-CoV-2 B.1.617.2 (Delta) and Omicron, and all Omicron cases were associated with this group (1). Data from this investigation reinforces the importance of COVID-19 booster doses in combination with early notification and other multicomponent prevention measures to limit transmission and prevent severe illness from Omicron and other SARS-CoV-2 variants.

The United States of America has a diverse population of over 331 million people.1 Groups historically identified as racial and ethnic minorities (which make up more than one third of the US population)1 have been economically and socially marginalized, leading to lower access to education, health care and financial capital, therefore putting some of these groups at increased risk for poor health outcomes.2 The coronavirus disease 2019 (COVID-19) pandemic has amplified existing health inequities; disparities in COVID-19 cases, hospitalizations and deaths, and now vaccination rates, have been identified.3,4 Here, we provide a high-level summary of strategies implemented by the United States Centers for Disease Control and Prevention (CDC) to address COVID-19 inequities impacting racial and ethnic minority groups.

During July 2021, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) B.1.617.2 variant infections, including vaccine breakthrough infections, occurred after large public gatherings in Provincetown, Massachusetts, USA, prompting a multistate investigation. Public health departments identified primary and secondary cases by using coronavirus disease surveillance data, case investigations, and contact tracing. A primary case was defined as SARS-CoV-2 detected <14 days after travel to or residence in Provincetown during July 3-17. A secondary case was defined as SARS-CoV-2 detected <14 days after close contact with a person who had a primary case but without travel to or residence in Provincetown during July 3-August 10. We identified 1,098 primary cases and 30 secondary cases associated with 26 primary cases among fully and non-fully vaccinated persons. Large gatherings can have widespread effects on SARS-CoV-2 transmission, and fully vaccinated persons should take precautions, such as masking, to prevent SARS-CoV-2 transmission, particularly during substantial or high transmission.

Pregnant and recently pregnant women are at increased risk for severe illness and death from COVID-19 compared with women who are not pregnant or were not recently pregnant (1,2). CDC recommends COVID-19 vaccination for women who are pregnant, recently pregnant, trying to become pregnant, or might become pregnant in the future.*(,)(†) This report describes 15 COVID-19-associated deaths after infection with SARS-CoV-2 (the virus that causes COVID-19) during pregnancy in Mississippi during March 1, 2020-October 6, 2021.

Project Vigilancia de Embarazadas con Zika (VEZ), an intensified surveillance of pregnant women with symptoms of the Zika virus disease (ZVD) in Colombia, aimed to evaluate the relationship between symptoms of ZVD during pregnancy and adverse pregnancy, birth, and infant outcomes and early childhood neurodevelopmental outcomes. During May-November 2016, pregnant women in three Colombian cities who were reported with symptoms of ZVD to the national surveillance system, or with symptoms of ZVD visiting participating clinics, were enrolled in Project VEZ. Data from maternal and pediatric (up to two years of age) medical records were abstracted. Available maternal specimens were tested for the presence of the Zika virus ribonucleic acid and/or anti-Zika virus immunoglobulin antibodies. Of 1213 enrolled pregnant women with symptoms of ZVD, 1180 had a known pregnancy outcome. Results of the Zika virus laboratory testing were available for 569 (48.2%) pregnancies with a known pregnancy outcome though testing timing varied and was often distal to the timing of symptoms; 254 (21.5% of the whole cohort; 44.6% of those with testing results) were confirmed or presumptive positive for the Zika virus infection. Of pregnancies with a known outcome, 50 (4.2%) fetuses/infants had Zika-associated brain or eye defects, which included microcephaly at birth. Early childhood adverse neurodevelopmental outcomes were more common among those with Zika-associated birth defects than among those without and more common among those with laboratory evidence of a Zika virus infection compared with the full cohort. The proportion of fetuses/infants with any Zika-associated brain or eye defect was consistent with the proportion seen in other studies. Enhancements to Colombia's existing national surveillance enabled the assessment of adverse outcomes associated with ZVD in pregnancy.

In January 2020, Santa Clara County, California, USA, began identifying laboratory-confirmed coronavirus disease among residents. County staff conducted case and contact investigations focused on households and collected detailed case demographic, occupation, exposure, and outcome information. We describe the first 200 test-positive cases during January 31-March 20, 2020, to inform future case and contact investigations. Probable infection sources included community transmission (104 cases), known close contact with a confirmed case-patient (66 cases), and travel (30 cases). Disease patterns across race and ethnicity, occupational, and household factors suggested multiple infection risk factors. Disproportionately high percentages of case-patients from racial and ethnic subgroups worked outside the home (Hispanic [86%] and Filipino [100%]); household transmission was more common among persons from Vietnam (53%). Even with the few initial cases, detailed case and contact investigations of household contacts capturing occupational and disaggregated race and ethnicity data helped identify at-risk groups and focused solutions for disease control.

During February 2021, an opening event was held indoors at a rural Illinois bar that accommodates approximately 100 persons. The Illinois Department of Public Health (IDPH) and local health department staff members investigated a COVID-19 outbreak associated with this opening event. Overall, 46 COVID-19 cases were linked to the event, including cases in 26 patrons and three staff members who attended the opening event and 17 secondary cases. Four persons with cases had COVID-19-like symptoms on the same day they attended the event. Secondary cases included 12 cases in eight households with children, two on a school sports team, and three in a long-term care facility (LTCF). Transmission associated with the opening event resulted in one school closure affecting 650 children (9,100 lost person-days of school) and hospitalization of one LTCF resident with COVID-19. These findings demonstrate that opening up settings such as bars, where mask wearing and physical distancing are challenging, can increase the risk for community transmission of SARS-CoV-2, the virus that causes COVID-19. As community businesses begin to reopen, a multicomponent approach should be emphasized in settings such as bars to prevent transmission* (1). This includes enforcing consistent and correct mask use, maintaining ≥6 ft of physical distance between persons, reducing indoor bar occupancy, prioritizing outdoor seating, improving building ventilation, and promoting behaviors such as staying at home when ill, as well as implementing contact tracing in combination with isolation and quarantine when COVID-19 cases are diagnosed.

INTRODUCTION: With the growing use of online study management systems and rapid availability of data, timely data review and quality assessments are necessary to ensure proper clinical trial implementation. In this report we describe central monitoring used to ensure protocol compliance and accurate data reporting, implemented during a large phase 3 clinical trial. MATERIAL AND METHODS: The Tuberculosis Trials Consortium (TBTC) Study 31/AIDS Clinical Trials Group (ACTG) study A5349 (S31) is an international, multi-site, randomized, open-label, controlled, non-inferiority phase 3 clinical trial comparing two 4-month regimens to a standard 6 month regimen for treatment of drug-susceptible tuberculosis (TB) among adolescents and adults with a sample size of 2500 participants. RESULTS: Central monitoring utilized primary study data in a five-tiered approach, including (1) real-time data checks & topic-specific intervention reports, (2) missing forms reports, (3) quality assurance metrics, (4) critical data reports and (5) protocol deviation identification, aimed to detect and resolve quality challenges. Over the course of the study, 240 data checks and reports were programed across the five tiers used. DISCUSSION: This use of primary study data to identify issues rapidly allowed the study sponsor to focus quality assurance and data cleaning activities on prioritized data, related to protocol compliance and accurate reporting of study results. Our approach enabled us to become more efficient and effective as we informed sites about deviations, resolved missing or inconsistent data, provided targeted guidance, and gained a deeper understanding of challenges experienced at clinical trial sites. TRIAL REGISTRATION: This trial was registered with ClinicalTrials.gov (Identifier: NCT02410772) on April 8, 2015.

We assessed maternal and infant cytomegalovirus (CMV) infection in Colombia. Maternal serum was tested for CMV immunoglobulin G antibodies at a median of 10 (interquartile range: 8-12) weeks gestation (n=1,501). CMV DNA polymerase chain reaction was performed on infant urine to diagnose congenital (≤21 days of life) and postnatal (>21 days) infection. Maternal CMV seroprevalence was 98.1% (95% confidence interval [CI]: 97.5-98.8%). Congenital CMV prevalence was 8.4 (95% CI: 3.9-18.3; 6/711) per 1,000 live births. Among 472 infants without confirmed congenital CMV infection subsequently tested at age 6 months, 258 (54.7%, 95% CI: 50.2%-59.1%) had postnatal infection. This article is protected by copyright. All rights reserved.

During January 1, 2020-August 10, 2020, an estimated 5 million cases of coronavirus disease 2019 (COVID-19) were reported in the United States.* Published state and national data indicate that persons of color might be more likely to become infected with SARS-CoV-2, the virus that causes COVID-19, experience more severe COVID-19-associated illness, including that requiring hospitalization, and have higher risk for death from COVID-19 (1-5). CDC examined county-level disparities in COVID-19 cases among underrepresented racial/ethnic groups in counties identified as hotspots, which are defined using algorithmic thresholds related to the number of new cases and the changes in incidence.(†) Disparities were defined as difference of ≥5% between the proportion of cases and the proportion of the population or a ratio ≥1.5 for the proportion of cases to the proportion of the population for underrepresented racial/ethnic groups in each county. During June 5-18, 205 counties in 33 states were identified as hotspots; among these counties, race was reported for ≥50% of cumulative cases in 79 (38.5%) counties in 22 states; 96.2% of these counties had disparities in COVID-19 cases in one or more underrepresented racial/ethnic groups. Hispanic/Latino (Hispanic) persons were the largest group by population size (3.5 million persons) living in hotspot counties where a disproportionate number of cases among that group was identified, followed by black/African American (black) persons (2 million), American Indian/Alaska Native (AI/AN) persons (61,000), Asian persons (36,000), and Native Hawaiian/other Pacific Islander (NHPI) persons (31,000). Examining county-level data disaggregated by race/ethnicity can help identify health disparities in COVID-19 cases and inform strategies for preventing and slowing SARS-CoV-2 transmission. More complete race/ethnicity data are needed to fully inform public health decision-making. Addressing the pandemic's disproportionate incidence of COVID-19 in communities of color can reduce the community-wide impact of COVID-19 and improve health outcomes.

BACKGROUND: Zika virus (ZIKV) infection during pregnancy can cause serious birth defects, including brain and eye abnormalities. The clinical importance of detection of ZIKV ribonucleic acid (RNA) in amniotic fluid is unknown. OBJECTIVES: To describe patterns of ZIKV RNA testing of amniotic fluid relative to other clinical specimens and to examine the association between ZIKV detection in amniotic fluid and Zika-associated birth defects. Our null hypothesis was that ZIKV detection in amniotic fluid was not associated with Zika-associated birth defects. STUDY DESIGN: We conducted a retrospective cohort analysis of women with amniotic fluid specimens submitted to Colombia's National Institute of Health as part of national ZIKV surveillance from January 2016 to January 2017. Specimens (maternal serum, amniotic fluid, cord blood, umbilical cord tissue, and placental tissue) were tested for the presence of ZIKV RNA using a singleplex or multiplex real-time reverse transcriptase-polymerase chain reaction (rRT-PCR) assay. Birth defect information was abstracted from maternal prenatal and infant birth records and reviewed by expert clinicians. Chi-square and Fisher's exact tests were used to compare the frequency of Zika-associated birth defects (defined as brain abnormalities [with or without microcephaly, but excluding neural tube defects and their associated findings] or eye abnormalities) by frequency of detection of ZIKV RNA in amniotic fluid. RESULTS: Our analysis included 128 women with amniotic fluid specimens. Seventy-five women (58%) had prenatally-collected amniotic fluid, 42 (33%) at delivery, and 11 (9%) had missing collection dates. Ninety-one women had both amniotic fluid and other clinical specimens submitted for testing, allowing for comparison across specimen types. Of those 91 women, 68 had evidence of ZIKV infection based on detection of ZIKV RNA (ZIKV+) in >1 specimen. Testing of amniotic fluid collected prenatally or at delivery identified 39 (57%) of these ZIKV infections (15 [22%] identified only in amniotic fluid), and 29 (43%) infections were identified in other specimen types and not amniotic fluid. Among women included in the analysis, 89 had pregnancy outcome information available, allowing for assessment of the presence of Zika-associated birth defects. Zika-associated birth defects were significantly (p<0.05) more common among pregnancies with ZIKV+ amniotic fluid specimens collected prenatally (19/32, 59%) than for those with no laboratory evidence of ZIKV infection in any specimen (6/23, 26%), but the proportion was similar in pregnancies with only ZIKV+ specimens other than amniotic fluid (10/23, 43%). Though Zika-associated birth defects were more common among women with any ZIKV+ amniotic fluid specimen (i.e., collected prenatally or at delivery; 21/43, 49%) than those with no laboratory evidence of ZIKV infection (6/23, 26%), this comparison did not reach statistical significance (p=0.07). CONCLUSIONS: Testing of amniotic fluid provided additional evidence for maternal diagnosis of ZIKV infection. Zika-associated birth defects were more common among women with ZIKV RNA detected in prenatal amniotic fluid specimens than women with no laboratory evidence of ZIKV infection, but similar to women with ZIKV RNA detected in other, non-amniotic fluid specimen types.

Two near-identical clinical Streptococcus pyogenes isolates of emm subtype emm43.4 with a pbp2x missense mutation (T553K) were detected. Minimum inhibitory concentrations (MICs) for ampicillin and amoxicillin were 8-fold higher, and the MIC for cefotaxime was 3-fold higher than for near-isogenic control isolates, consistent with a first-step in developing beta-lactam resistance.

Invasive pneumococcal disease (IPD) has greatly decreased since implementation in the U.S. of the 7 valent conjugate vaccine (PCV7) in 2000 and 13 valent conjugate vaccine (PCV13) in 2010. We used whole genome sequencing (WGS) to predict phenotypic traits (serotypes, antimicrobial phenotypes, and pilus determinants) and determine multilocus genotypes from 5334 isolates (~90% of cases) recovered during 2015-2016 through Active Bacterial Core surveillance. We identified 44 serotypes; 26 accounted for 98% of the isolates. PCV13 serotypes (inclusive of serotype 6C) accounted for 1503 (28.2%) isolates, with serotype 3 most common (657/5334, 12.3%), while serotypes 1 and 5 were undetected. Of 305 isolates from children <5 yrs, 60 (19.7%) were of PCV13 serotypes 19A, 19F, 3, 6B, and 23F (58/60 were 19A, 19F, or 3). We quantitated MLST-based lineages first detected during the post-PCV era (since 2002) that potentially arose through serotype-switching. The 7 predominant emergent post-PCV strain complexes included 23B/CC338, 15BC/CC3280, 19A/CC244, 4/CC439, 15A/CC156, 35B/CC156, and 15BC/CC156. These strains accounted for 332 isolates (6.2% of total) and were more frequently observed in children <5 yrs (17.7%; 54/305). Fifty-seven categories of recently emerged (in the post PCV7 period) putative serotype-switch variants were identified, accounting for 402 isolates. Many of these putative switch variants represented newly emerged resistant strains. Penicillin-nonsusceptibility (MICs > 0.12 mug/ml) was found among 22.4% (1193/5334) isolates, with higher penicillin MICs (2-8 mug/ml) found in 8.0% (425/5334) of isolates that were primarily (372/425, 87.5%) serotypes 35B and 19A. Most (792/1193, 66.4%) penicillin-nonsusceptible isolates were macrolide-resistant, 410 (34.4%) of which were erm gene positive and clindamycin-resistant. The proportion of macrolide-resistant isolates increased with increasing penicillin MICs; even isolates with reduced penicillin susceptibility (MIC = 0.06 mug/ml) were much more likely to be macrolide-resistant than basally penicillin-susceptible isolates (MIC < 0.03 mug/ml). The contribution of recombination to strain diversification was assessed through quantitating 35B/CC558-specific bioinformatic pipeline features among non-CC558 CCs and determining the sizes of gene replacements. Although IPD has decreased greatly and stabilized in the post-PCV13 era, the species continually generates recombinants that adapt to selective pressures exerted by vaccines and antimicrobials. These data serve as a baseline for monitoring future changes within each invasive serotype.

OBJECTIVES: Our objective was to evaluate and exploit a whole genome sequence (WGS) bioinformatics pipeline for predicting antimicrobial resistance and capsular serotypes from invasive group B streptococci (iGBS). METHODS: For 1975 iGBS recovered during 2015 from CDC's Active Bacterial Core surveillance, we compared pipeline predictions to broth dilution testing. Fifty-six isolates from earlier surveillance were included for testing beta-lactams.. Conventional serotyping was compared to WGS-based assignments for 302 isolates. RESULTS: All 28 isolates with reduced susceptibility to beta-lactam antibiotics harbored one of 19 rare PBP2x types. Resistances to erythromycin/clindamycin (808/1975 isolates, 41.0%), erythromycin (235/1975, 11.9%), and lincosamide/streptogramin A/pleuromutilins (56/1975, 2.8%) were predicted by presence of erm-methylase, mef, and lsa determinants, respectively (41 of 56 lsa gene positive isolates also contained lnu, erm, and/or mef genes). Presence of both erm and lsa determinants (25 isolates) predicted nonsusceptibility to quinupristin/dalfopristin. Most isolates (1680/1975, 85.1%) were tet gene-positive, although 41/1565 (2.6%) tetM-positive isolates were tetracycline-susceptible. All 53 fluoroquinolone-resistant isolates contained ParC and/or GyrA substitutions. Resistances to rifampin (8 isolates), trimethoprim, chloramphenicol and vancomycin (2 isolates each) were predicted by the pipeline. Resistance to macrolides/lincosamides without pipeline prediction was rare and correlated to divergent resistance genes or rRNA A2062G substitution. A selection of 267 isolates assigned WGS-based serotypes were also conventionally serotyped. Of these, 246 (92.1%) were in agreement, with the remaining 21 (7.8%) conventionally non-serotypeable. For thirty-two of 1975 isolates (1.6%), WGS-based serotypes could not be assigned. CONCLUSION: WGS-based assignment of iGBS resistance features and serotypes is an accurate substitute for phenotypic testing.

Leptospirosis, caused by spirochetes of the genus Leptospira, is a globally widespread, neglected and emerging zoonotic disease. While whole genome analysis of individual pathogenic, intermediately pathogenic and saprophytic Leptospira species has been reported, comprehensive cross-species genomic comparison of all known species of infectious and non-infectious Leptospira, with the goal of identifying genes related to pathogenesis and mammalian host adaptation, remains a key gap in the field. Infectious Leptospira, comprised of pathogenic and intermediately pathogenic Leptospira, evolutionarily diverged from non-infectious, saprophytic Leptospira, as demonstrated by the following computational biology analyses: 1) the definitive taxonomy and evolutionary relatedness among all known Leptospira species; 2) genomically-predicted metabolic reconstructions that indicate novel adaptation of infectious Leptospira to mammals, including sialic acid biosynthesis, pathogen-specific porphyrin metabolism and the first-time demonstration of cobalamin (B12) autotrophy as a bacterial virulence factor; 3) CRISPR/Cas systems demonstrated only to be present in pathogenic Leptospira, suggesting a potential mechanism for this clade's refractoriness to gene targeting; 4) finding Leptospira pathogen-specific specialized protein secretion systems; 5) novel virulence-related genes/gene families such as the Virulence Modifying (VM) (PF07598 paralogs) proteins and pathogen-specific adhesins; 6) discovery of novel, pathogen-specific protein modification and secretion mechanisms including unique lipoprotein signal peptide motifs, Sec-independent twin arginine protein secretion motifs, and the absence of certain canonical signal recognition particle proteins from all Leptospira; and 7) and demonstration of infectious Leptospira-specific signal-responsive gene expression, motility and chemotaxis systems. By identifying large scale changes in infectious (pathogenic and intermediately pathogenic) vs. non-infectious Leptospira, this work provides new insights into the evolution of a genus of bacterial pathogens. This work will be a comprehensive roadmap for understanding leptospirosis pathogenesis. More generally, it provides new insights into mechanisms by which bacterial pathogens adapt to mammalian hosts.