Data on the detailed clinical progression of COVID-19 in conjunction with epidemiological and virological characteristics are limited. In this case series, we describe the first 12 US patients ...confirmed to have COVID-19 from 20 January to 5 February 2020, including 4 patients described previously
. Respiratory, stool, serum and urine specimens were submitted for SARS-CoV-2 real-time reverse-transcription polymerase chain reaction (rRT-PCR) testing, viral culture and whole genome sequencing. Median age was 53 years (range: 21-68); 8 patients were male. Common symptoms at illness onset were cough (n = 8) and fever (n = 7). Patients had mild to moderately severe illness; seven were hospitalized and demonstrated clinical or laboratory signs of worsening during the second week of illness. No patients required mechanical ventilation and all recovered. All had SARS-CoV-2 RNA detected in respiratory specimens, typically for 2-3 weeks after illness onset. Lowest real-time PCR with reverse transcription cycle threshold values in the upper respiratory tract were often detected in the first week and SARS-CoV-2 was cultured from early respiratory specimens. These data provide insight into the natural history of SARS-CoV-2. Although infectiousness is unclear, highest viral RNA levels were identified in the first week of illness. Clinicians should anticipate that some patients may worsen in the second week of illness.
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GEOZS, IJS, IMTLJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBMB, UL, UM, UPUK, ZAGLJ
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.
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GEOZS, IJS, IMTLJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBMB, UL, UM, UPUK, ZAGLJ
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.
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DOBA, IZUM, KILJ, NUK, ODKLJ, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Abstract
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.
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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.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
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.
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).
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.
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.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Background
Patients with coronavirus disease 2019 (Covid-19) may experience venous thrombosis while data regarding arterial thrombosis are sparse.
Methods
Prospective multicenter study in 5 hospitals ...including 373 patients with Covid-19-related pneumonia. Demographic data, laboratory findings including coagulation tests and comorbidities were reported. During the follow-up any arterial or venous thrombotic events and death were registered.
Results
Among 373 patients, 75 (20%) had a thrombotic event and 75 (20%) died. Thrombotic events included 41 venous thromboembolism and 34 arterial thrombosis. Age, cardiovascular disease, intensive care unit treatment, white blood cells, D-dimer, albumin and troponin blood levels were associated with thrombotic events. In a multivariable regression logistic model, intensive care unit treatment (Odds Ratio OR: 6.0; 95% Confidence Interval CI 2.8–12.6;
p
< 0.001); coronary artery disease (OR: 2.4; 95% CI 1.4–5.0;
p
= 0.022); and albumin levels (OR: 0.49; 95% CI 0.28–0.87;
p
= 0.014) were associated with ischemic events. Age, sex, chronic obstructive pulmonary disease, diabetes, heart failure, coronary heart disease, intensive care unit treatment, in-hospital thrombotic events, D-dimer, C-reactive protein, troponin, and albumin levels were associated with mortality. A multivariable Cox regression analysis showed that in-hospital thrombotic events (hazard ratio HR: 2.72; 95% CI 1.59–4.65;
p
< 0.001), age (HR: 1.035; 95% CI 1.014–1.057;
p
= 0.001), and albumin (HR: 0.447; 95% CI 0.277–0.723;
p
= 0.001) predicted morality.
Conclusions
Covid-19 patients experience an equipollent rate of venous and arterial thrombotic events, that are associated with poor survival. Early identification and appropriate treatment of Covid-19 patients at risk of thrombosis may improve prognosis.
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EMUNI, FIS, FZAB, GEOZS, GIS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
Background:
Carbapenem-resistant
Acinetobacter baumannii
(CRAB) is primarily associated with hospital-acquired infections and is an urgent public health threat due to its ability to contaminate the ...environment and cause severe disease. In 2019, Illinois began pilot surveillance for CRAB requiring select laboratories to submit specimens for molecular characterization. On July 17, 2020, the Chicago Department of Public Health (CDPH) was notified of an increase in CRAB infections in a 20-bed ICU at an acute-care hospital in Chicago (hospital A) during the initial COVID-19 surge. We summarize the outbreak investigation findings and infection control recommendations.
Methods:
Clinical cultures were collected from patients in hospital A, and CRAB-positive isolates were sent to the Wisconsin State Laboratory of Hygiene for mechanism of resistance and antibiotic susceptibility testing. On-site assessments and remote follow-ups were conducted by CDPH infection preventionists to evaluate infection control practices including environmental cleaning, hand hygiene compliance, and use of personal protective equipment (PPE). The Illinois Department of Public Health and CDPH summarized the testing results, facilitated a containment response, and provided recommendations for infection control.
Results:
From March 18, 2020, to September 30, 2021, 56 patients with CRAB infections were identified from hospital A, and 33 (59%) of these cases were pan-nonsusceptible. Most specimen sources were sputum (n = 30, 54%), followed by blood (n = 13, 23%), urine (n = 6, 11%) and other (n = 7, 13%). Among isolates with mechanism testing (n = 54), 45 (83%) were positive for OXA-24/40 and 9 (17%) were positive for OXA-23. Of the CRAB-positive patients, 28 (50%) were previously positive for SARS-CoV-2. To date, 25 of these patients (45%) have been discharged and 31 (55%) have died. Two onsite visits and 7 remote-assistance sessions were conducted as part of the investigation. In response to increased COVID-19 hospitalizations, hospital A moved to crisis-capacity PPE use and encountered staffing shortages, which led to compromised infection control measures. Cleaning agents (Quat disinfectant cleaner) were also found to be ineffective against CRAB and required long contact times.
Conclusions:
In response to the CRAB outbreak at hospital A, CDPH recommended that the hospital stop crisis-capacity protocols for PPE, conduct admission screening and point-prevalence testing for CRAB, implement a hand hygiene campaign, and use an EPA-registered List K product for environmental cleaning. These recommendations were implemented in May 2021, and no CRAB cases have been reported since July 2021. To reduce CRAB transmission during the pandemic, facility leadership must commit resources to educate staff on effective infection control practices including conventional use of PPE, appropriate cleaning agents, and improved hand hygiene.
Funding:
None
Disclosures:
None
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.
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BFBNIB, INZLJ, NMLJ, NUK, OILJ, PNG, SAZU, UKNU, UL, UM, UPUK, VSZLJ, ZRSKP
Recognizing that public health crises often hit hardest in underresourced communities, two academic medical centers have partnered with the Chicago Department of Public Health to provide rapid ...responses to outbreaks.
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