Wastewater Surveillance for Poliovirus in Selected Jurisdictions, United States, 2022-2023.

Wastewater testing can inform public health action as a component of polio outbreak response. During 2022-2023, a total of 7 US jurisdictions (5 states and 2 cities) participated in prospective or retrospective testing of wastewater for poliovirus after a paralytic polio case was identified in New York state. Two distinct vaccine-derived poliovirus type 2 viruses were detected in wastewater from New York state and New York City during 2022, representing 2 separate importation events. Of those viruses, 1 resulted in persistent community transmission in multiple New York counties and 1 paralytic case. No poliovirus was detected in the other participating jurisdictions (Connecticut, New Jersey, Michigan, and Illinois and Chicago, IL). The value of routine wastewater surveillance for poliovirus apart from an outbreak is unclear. However, these results highlight the ongoing risk for poliovirus importations into the United States and the need to identify undervaccinated communities and increase vaccination coverage to prevent paralytic polio.

Using wastewater surveillance for mpox as a complement to traditional case-based reporting - Chicago, March-June 2023.

The Chicago Department of Public Health tested wastewater samples for the presence of Monkeypox Virus (MPXV) from March 13 through June 26, 2023. There were persistent detections prior to reported cases. This indicated the baseline levels of MPXV prevalence might warrant routine monitoring. Detections in areas without corresponding reported clinical cases might highlight areas where cases are being under-reported by traditional surveillance.

Extended-Spectrum Beta-Lactamase Shigella sonnei Cluster Among Men Who Have Sex with Men in Chicago, Illinois-July-October 2022.

Drug-resistant shigellosis is increasing, particularly among men who have sex with men (MSM). During July-October 2022, an extended-spectrum beta-lactamase producing Shigella sonnei cluster of 9 patients was identified in Chicago, of whom 8 were MSM and 6 were festival attendees. The cluster also included 4 domestic travelers to Chicago. Sexual health care for MSM should include shigellosis diagnosis and prevention.

Measles Outbreak Associated with a Migrant Shelter - Chicago, Illinois, February-May 2024.

Measles, a highly contagious respiratory virus with the potential to cause severe complications, hospitalization, and death, was declared eliminated from the United States in 2000; however, with ongoing global transmission, infections in the United States still occur. On March 7, 2024, the Chicago Department of Public Health (CDPH) confirmed a case of measles in a male aged 1 year residing in a temporary shelter for migrants in Chicago. Given the congregate nature of the setting, high transmissibility of measles, and low measles vaccination coverage among shelter residents, measles virus had the potential to spread rapidly among approximately 2,100 presumed exposed shelter residents. CDPH immediately instituted outbreak investigation and response activities in collaboration with state and local health departments, health care facilities, city agencies, and shelters. On March 8, CDPH implemented active case-finding and coordinated a mass vaccination campaign at the affected shelter (shelter A), including vaccinating 882 residents and verifying previous vaccination for 784 residents over 3 days. These activities resulted in 93% measles vaccination coverage (defined as receipt of ≥1 recorded measles vaccine dose) by March 11. By May 13, a total of 57 confirmed measles cases associated with residing in or having contact with persons from shelter A had been reported. Most cases (41; 72%) were among persons who did not have documentation of measles vaccination and were considered unvaccinated. In addition, 16 cases of measles occurred among persons who had received ≥1 measles vaccine dose ≥21 days before first known exposure. This outbreak underscores the need to ensure high vaccination coverage among communities residing in congregate settings.

Investigation of an Mpox Outbreak Affecting Many Vaccinated Persons in Chicago, Illinois-March 2023-June 2023.

BACKGROUND: After months of few mpox cases, an increase in cases was reported in Chicago during May 2023, predominantly among fully vaccinated (FV) patients. We investigated the outbreak scope, differences between vaccinated and unvaccinated patients, and hypotheses for monkeypox virus (MPXV) infection after vaccination. METHODS: We interviewed patients and reviewed medical records to assess demographic, behavioral, and clinical characteristics; mpox vaccine status; and vaccine administration routes. We evaluated serum antibody levels after infection and compared patient viral genomes with MPXV sequences in available databases. We discussed potential vaccine compromise with partners who manufactured, handled, and administered the vaccine associated with breakthrough infections. RESULTS: During 18 March-27 June 2023, we identified 49 mpox cases; 57% of these mpox patients were FV. FV patients received both JYNNEOS doses subcutaneously (57%), intradermally (7%), or via heterologous administration (36%). FV patients had more median sex partners (3; interquartile range [IQR] = 1-4) versus not fully vaccinated patients (1; IQR = 1-2). Thirty-six of 37 sequenced specimens belonged to lineage B.1.20 of clade IIb MPXV, which did not demonstrate any amino acid changes relative to B.1, the predominant lineage from May 2022. Vaccinated patients demonstrated expected humoral antibody responses; none were hospitalized. No vaccine storage excursions were identified. Approximately 63% of people at risk for mpox in Chicago were FV during this period. CONCLUSIONS: Our investigation indicated that cases were likely due to frequent behaviors associated with mpox transmission, even with relatively high vaccine effectiveness and vaccine coverage. Cases after vaccination might occur in similar populations.

A response playbook for early detection and population surveillance of new SARS-CoV-2 variants in a regional public health laboratory.

BACKGROUND: Timely genomic surveillance is required to inform public health responses to new SARS-CoV-2 variants. However, the processes involved in local genomic surveillance introduce inherent time constraints. The Regional Innovative Public Health Laboratory in Chicago developed and employed a genomic surveillance response playbook for the early detection and surveillance of emerging SARS-CoV-2 variants. METHODS: The playbook outlines modifications to sampling strategies, laboratory workflows, and communication processes based on the emerging variant's predicted viral characteristics, observed public health impact in other jurisdictions and local community risk level. The playbook outlines procedures for implementing and reporting enhanced and accelerated genomic surveillance, including supplementing whole genome sequencing (WGS) with variant screening by quantitative PCR (qPCR). RESULTS: The ability of the playbook to improve the response to an emerging variant was tested for SARS-CoV-2 Omicron BA.1. Increased submission of clinical remnant samples from local hospital laboratories enabled detection of a new variant at an average of 1.4% prevalence with 95% confidence rather than 3.5% at baseline. Genotyping qPCR concurred with WGS lineage assignments in 99.9% of 1541 samples with results by both methods, and was more sensitive, providing lineage results in 90.4% of 1833 samples rather than 85.1% for WGS, while significantly reducing the time to lineage result. CONCLUSIONS: The genomic surveillance response playbook provides a structured, stepwise, and data-driven approach to responding to emerging SARS-CoV-2 variants. These pre-defined processes can serve as a template for other genomic surveillance programs to streamline workflows and expedite the detection and public health response to emerging variants. Based on the processes piloted during the Omicron BA.1 response, this method has been applied to subsequent Omicron subvariants and can be readily applied to future SARS-CoV-2 emerging variants and other public health surveillance activities.

Health Care Personnel Exposure Risk Assessment and Management During a Mpox Outbreak in Chicago, Illinois, 17 May to 8 July 2022.

This report summarizes risk assessment interviews and follow-up with health care personnel (HCP) after exposure to patients with mpox disease during 17 May to 8 July 2022. HCP-case interactions were assessed using a standard questionnaire to categorize the risk associated with patient encounters. We assessed 150 interactions among 142 HCP and 30 cases. Four (2.7%) interactions were defined as high risk, 5 (3.3%) intermediate, 107 (71.3%) low, and 31 (20.7%) no risk. High and intermediate exposures were offered postexposure prophylaxis; 4 accepted. No documented mpox transmission after exposure was identified. These findings suggest transmission risk in health care settings during routine patient care is low.

Correlation of wastewater surveillance data with traditional influenza surveillance measures in Cook County, Illinois, October 2022-April 2023.

Influenza is a respiratory illness that can result in serious outcomes, particularly among persons who are immunocompromised, aged <5 years or aged >65 years. Traditional influenza surveillance approaches rely upon syndromic surveillance of emergency departments and public health reporting from clinicians and laboratories. Wastewater surveillance infrastructure developed to monitor SARS-CoV-2 is being used for influenza surveillance in the Chicago area. The goal was to evaluate timeliness and correlations between influenza virus detected through wastewater surveillance and traditional influenza surveillance measures to assess utility of wastewater surveillance for influenza at the county level. Specifically, we measured correlations between influenza virus gene copies in wastewater samples and 1) the number of intensive care unit admissions associated with a diagnosis of influenza, 2) the percentage emergency department (ED) visits for influenza-like-illness, and 3) the percentage of ED visits with influenza diagnosis at discharge2 in Cook County. Influenza concentrations in wastewater were strongly correlated with traditional influenza surveillance measures, particularly for catchment areas serving >100,000 residents. Wastewater indicators lagged traditional influenza surveillance measures by approximately one week when analyzed in cross-correlations. Although wastewater data lagged traditional influenza surveillance measures in this analysis, it can serve as a useful surveillance tool as a complement to syndromic surveillance; it is a form of influenza surveillance that does not rely on healthcare-seeking behavior or reporting by healthcare providers.

Rapid Environmental Contamination with Candida auris and Multidrug-Resistant Bacterial Pathogens Near Colonized Patients.

BACKGROUND: Environmental contamination is suspected to play an important role in Candida auris transmission. Understanding speed and risks of contamination after room disinfection could inform environmental cleaning recommendations. METHODS: We conducted a prospective multicenter study of environmental contamination associated with C. auris colonization at six ventilator-capable skilled nursing facilities and one acute-care hospital in Illinois and California. Known C. auris carriers were sampled at five body-sites followed by sampling of nearby room surfaces before disinfection and at 0, 4, 8, and 12-hours post-disinfection. Samples were cultured for C. auris and bacterial multidrug-resistant organisms (MDROs). Odds of surface contamination after disinfection were analyzed using multilevel generalized estimating equations. RESULTS: Among 41 known C. auris carriers, colonization was detected most frequently on palms/fingertips (76%) and nares (71%). C. auris contamination was detected on 32.2% (66/205) of room surfaces pre-disinfection and 20.5% (39/190) of room surfaces by 4-hours post-disinfection. A higher number of C. auris-colonized body sites was associated with higher odds of environmental contamination at every time point following disinfection, adjusting for facility of residence. In the rooms of 38 (93%) C. auris carriers co-colonized with a bacterial MDRO, 2%-24% of surfaces were additionally contaminated with the same MDRO by 4-hours post-disinfection. CONCLUSIONS: C. auris can contaminate the healthcare environment rapidly after disinfection, highlighting the challenges associated with environmental disinfection. Future research should investigate long-acting disinfectants, antimicrobial surfaces, and more effective patient skin antisepsis to reduce the environmental reservoir of C. auris and bacterial MDROs in healthcare settings.

SARS-CoV-2 Reinfection Risk in Persons with HIV, Chicago, Illinois, USA, 2020-2022.

Understanding if persons with HIV (PWH) have a higher risk for SARS-CoV-2 reinfection may help tailor future COVID-19 public health guidance. To determine whether HIV infection was associated with increased risk for SARS-CoV-2 reinfection, we followed adult residents of Chicago, Illinois, USA, with SARS-CoV-2 longitudinally from their first reported infection through May 31, 2022. We matched SARS-CoV-2 laboratory data and COVID-19 vaccine administration data to Chicago's Enhanced HIV/AIDS Reporting System. Among 453,587 Chicago residents with SARS-CoV-2, a total of 5% experienced a SARS-CoV-2 reinfection, including 192/2,886 (7%) PWH and 23,642/450,701 (5%) persons without HIV. We observed higher SARS-CoV-2 reinfection incidence rates among PWH (66 [95% CI 57-77] cases/1,000 person-years) than PWOH (50 [95% CI 49-51] cases/1,000 person-years). PWH had a higher adjusted rate of SARS-CoV-2 reinfection (1.46, 95% CI 1.27-1.68) than those without HIV. PWH should follow the recommended COVID-19 vaccine schedule, including booster doses.

Erratum: Multicenter evaluation of contamination of the healthcare environment near patients with Candida auris skin colonization - ERRATUM.

[This corrects the article DOI: 10.1017/ash.2022.205.].

HIV and Sexually Transmitted Infections Among Persons with Monkeypox - Eight U.S. Jurisdictions, May 17-July 22, 2022.

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.

Tracking changes in SARS-CoV-2 transmission with a novel outpatient sentinel surveillance system in Chicago, USA.

Public health indicators typically used for COVID-19 surveillance can be biased or lag changing community transmission patterns. In this study, we investigate whether sentinel surveillance of recently symptomatic individuals receiving outpatient diagnostic testing for SARS-CoV-2 could accurately assess the instantaneous reproductive number R(t) and provide early warning of changes in transmission. We use data from community-based diagnostic testing sites in the United States city of Chicago. Patients tested at community-based diagnostic testing sites between September 2020 and June 2021, and reporting symptom onset within four days preceding their test, formed the sentinel population. R(t) calculated from sentinel cases agreed well with R(t) from other indicators. Retrospectively, trends in sentinel cases did not precede trends in COVID-19 hospital admissions by any identifiable lead time. In deployment, sentinel surveillance held an operational recency advantage of nine days over hospital admissions. The promising performance of opportunistic sentinel surveillance suggests that deliberately designed outpatient sentinel surveillance would provide robust early warning of increasing transmission.

Multiple Variants of SARS-CoV-2 in a University Outbreak After Spring Break - Chicago, Illinois, March-May 2021.

To prevent transmission of SARS-CoV-2, the virus that causes COVID-19, colleges and universities have implemented multiple strategies including testing, isolation, quarantine, contact tracing, masking, and vaccination. In April 2021, the Chicago Department of Public Health (CDPH) was notified of a large cluster of students with COVID-19 at an urban university after spring break. A total of 158 cases of COVID-19 were diagnosed among undergraduate students during March 15-May 3, 2021; the majority (114; 72.2%) lived in on-campus dormitories. CDPH evaluated the role of travel and social connections, as well as the potential impact of SARS-CoV-2 variants, on transmission. Among 140 infected students who were interviewed, 89 (63.6%) reported recent travel outside Chicago during spring break, and 57 (40.7%) reported indoor social exposures. At the time of the outbreak, undergraduate-aged persons were largely ineligible for vaccination in Chicago; only three of the students with COVID-19 (1.9%) were fully vaccinated. Whole genome sequencing (WGS) of 104 specimens revealed multiple distinct SARS-CoV-2 lineages, suggesting several nearly simultaneous introductions. Most specimens (66; 63.5%) were B.1.1.222, a lineage not widely detected in Chicago before or after this outbreak. These results demonstrate the potential for COVID-19 outbreaks on university campuses after widespread student travel during breaks, at the beginning of new school terms, and when students participate in indoor social gatherings. To prevent SARS-CoV-2 transmission, colleges and universities should encourage COVID-19 vaccination; discourage unvaccinated students from travel, including during university breaks; implement serial COVID-19 screening among unvaccinated persons after university breaks; encourage masking; and implement universal serial testing for students based on community transmission levels.

Integrated genomic, epidemiologic investigation of Candida auris skin colonization in a skilled nursing facility.

Candida auris is a fungal pathogen of high concern due to its ability to cause healthcare-associated infections and outbreaks, its resistance to antimicrobials and disinfectants and its persistence on human skin and in the inanimate environment. To inform surveillance and future mitigation strategies, we defined the extent of skin colonization and explored the microbiome associated with C. auris colonization. We collected swab specimens and clinical data at three times points between January and April 2019 from 57 residents (up to ten body sites each) of a ventilator-capable skilled nursing facility with endemic C. auris and routine chlorhexidine gluconate (CHG) bathing. Integrating microbial-genomic and epidemiologic data revealed occult C. auris colonization of multiple body sites not targeted commonly for screening. High concentrations of CHG were associated with suppression of C. auris growth but not with deleterious perturbation of commensal microbes. Modeling human mycobiome dynamics provided insight into underlying alterations to the skin fungal community as a possible modifiable risk factor for acquisition and persistence of C. auris. Failure to detect the extensive, disparate niches of C. auris colonization may reduce the effectiveness of infection-prevention measures that target colonized residents, highlighting the importance of universal strategies to reduce C. auris transmission.

Positive Correlation Between Candida auris Skin-Colonization Burden and Environmental Contamination at a Ventilator-Capable Skilled Nursing Facility in Chicago.

BACKGROUND: Candida auris is an emerging multidrug-resistant yeast that contaminates healthcare environments causing healthcare-associated outbreaks. The mechanisms facilitating contamination are not established. METHODS: C. auris was quantified in residents' bilateral axillary/inguinal composite skin swabs and environmental samples during a point-prevalence survey at a ventilator-capable skilled-nursing facility (vSNF A) with documented high colonization prevalence. Environmental samples were collected from all doorknobs, windowsills and handrails of each bed in 12 rooms. C. auris concentrations were measured using culture and C. auris-specific quantitative polymerase chain reaction (qPCR) The relationship between C. auris concentrations in residents' swabs and associated environmental samples were evaluated using Kendall's tau-b (τ b) correlation coefficient. RESULTS: C. auris was detected in 70/100 tested environmental samples and 31/57 tested resident skin swabs. The mean C. auris concentration in skin swabs was 1.22 × 105 cells/mL by culture and 1.08 × 106 cells/mL by qPCR. C. auris was detected on all handrails of beds occupied by colonized residents, as well as 10/24 doorknobs and 9/12 windowsills. A positive correlation was identified between the concentrations of C. auris in skin swabs and associated handrail samples based on culture (τ b = 0.54, P = .0004) and qPCR (τ b = 0.66, P = 3.83e-6). Two uncolonized residents resided in beds contaminated with C. auris. CONCLUSIONS: Colonized residents can have high C. auris burdens on their skin, which was positively related with contamination of their surrounding healthcare environment. These findings underscore the importance of hand hygiene, transmission-based precautions, and particularly environmental disinfection in preventing spread in healthcare facilities.

Community-Based Testing for SARS-CoV-2 - Chicago, Illinois, May-November 2020.

On May 13, 2020, Chicago established a free community-based testing (CBT) initiative for SARS-CoV-2, the virus that causes COVID-19, using reverse transcription-polymerase chain reaction (RT-PCR). The initiative focused on demographic groups and geographic areas that were underrepresented in testing by clinical providers and had experienced high COVID-19 incidence, including Hispanic persons and those who have been economically marginalized. To assess the CBT initiative, the Chicago Department of Public Health (CDPH) compared demographic characteristics, economic marginalization, and test positivity between persons tested at CBT sites and persons tested in all other testing settings in Chicago. During May 13-November 14, a total of 253,904 SARS-CoV-2 RT-PCR tests were conducted at CBT sites. Compared with those tested in all other testing settings in Chicago, persons tested at CBT sites were more likely to live in areas that are economically marginalized (38.6% versus 32.0%; p<0.001) and to be Hispanic (50.9% versus 20.7%; p<0.001). The cumulative percentage of positive test results at the CBT sites was higher than that at all other testing settings (11.1% versus 7.1%; p<0.001). These results demonstrate the ability of public health departments to establish community-based testing initiatives that reach communities with less access to testing in other settings and that experience disproportionately higher incidences of COVID-19.

Lack of Serologic Evidence of Infection Among Health Care Personnel and Other Contacts of First 2 Confirmed Patients With COVID-19 in Illinois, 2020.

OBJECTIVES: Widespread global transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus causing coronavirus disease 2019 (COVID-19), continues. Many questions remain about asymptomatic or atypical infections and transmission dynamics. We used comprehensive contact tracing of the first 2 confirmed patients in Illinois with COVID-19 and serologic SARS-CoV-2 antibody testing to determine whether contacts had evidence of undetected COVID-19. METHODS: Contacts were eligible for serologic follow-up if previously tested for COVID-19 during an initial investigation or had greater-risk exposures. Contacts completed a standardized questionnaire during the initial investigation. We classified exposure risk as high, medium, or low based on interactions with 2 index patients and use of personal protective equipment (PPE). Serologic testing used a SARS-CoV-2 spike enzyme-linked immunosorbent assay on serum specimens collected from participants approximately 6 weeks after initial exposure to either index patient. The 2 index patients provided serum specimens throughout their illness. We collected data on demographic, exposure, and epidemiologic characteristics. RESULTS: Of 347 contacts, 110 were eligible for serologic follow-up; 59 (17% of all contacts) enrolled. Of these, 53 (90%) were health care personnel and 6 (10%) were community contacts. Seventeen (29%) reported high-risk exposures, 15 (25%) medium-risk, and 27 (46%) low-risk. No participant had evidence of SARS-CoV-2 antibodies. The 2 index patients had antibodies detected at dilutions >1:6400 within 4 weeks after symptom onset. CONCLUSIONS: In serologic follow-up of the first 2 known patients in Illinois with COVID-19, we found no secondary transmission among tested contacts. Lack of seroconversion among these contacts adds to our understanding of conditions (ie, use of PPE) under which SARS-CoV-2 infections might not result in transmission and demonstrates that SARS-CoV-2 antibody testing is a useful tool to verify epidemiologic findings.