Delayed Recognition of Coronavirus Disease 2019 (COVID-19) in New York City: A Descriptive Analysis of COVID-19 Illness Prior to 29 February 2020.

BACKGROUND: On 30 January 2020, COVID-19 was declared a Public Health Emergency of International Concern (PHEIC) by the World Health Organization. Almost a month later, on 29 February 2020, the first case in New York City (NYC) was diagnosed. METHODS: Three hundred sixty persons with COVID-19-like illness were reported to the NYC Department of Health and Mental Hygiene (DOHMH) before 29 February, but 37 of these tested negative and 237 were never tested for severe acute respiratory syndrome coronavirus 2. Records of 86 persons with confirmed COVID-19 and reported symptom onset prior to 29 February 2020 were reviewed by 4 physician-epidemiologists. Case-patients were classified as possible delayed recognition (PDR) of COVID-19 when upon medical review the reported onset date was believed to reflect the initial symptoms of COVID-19, or insufficient evidence to classify, when the onset could not be determined with confidence. Clinical and epidemiological factors collected by DOHMH and supplemented with emergency department records were analyzed. RESULTS: Thirty-nine PDR COVID-19 cases were identified. The majority had severe disease with 69% presenting to an emergency department within 2 weeks of symptom onset. The first PDR COVID-19 case had symptom onset on 28 January 2020. Only 7 of the 39 cases (18%) had traveled internationally within 14 days of onset (none to China). CONCLUSIONS: COVID-19 was in NYC before being classified as a PHEIC, and eluded surveillance for another month. The delay in recognition limited mitigation efforts; by the time city- and statewide mandates were enacted, 16 and 22 days later, there was already widespread community transmission.

Climate Change and the Epidemiology of Infectious Diseases in the United States.

The earth is rapidly warming, driven by increasing atmospheric carbon dioxide and other gases that result primarily from fossil fuel combustion. In addition to causing arctic ice melting and extreme weather events, climatologic factors are linked strongly to the transmission of many infectious diseases. Changes in the prevalence of infectious diseases not only reflect the impacts of temperature, humidity, and other weather-related phenomena on pathogens, vectors, and animal hosts but are also part of a complex of social and environmental factors that will be affected by climate change, including land use, migration, and vector control. Vector- and waterborne diseases and coccidioidomycosis are all likely to be affected by a warming planet; there is also potential for climate-driven impacts on emerging infectious diseases and antimicrobial resistance. Additional resources for surveillance and public health activities are urgently needed, as well as systematic education of clinicians on the health impacts of climate change.

Coronavirus Disease 2019 (COVID-19) Outbreaks at 2 Construction Sites-New York City, October-November 2020.

During 23 October-16 November 2020, the New York City Department of Health and Mental Hygiene investigated coronavirus disease 2019 (COVID-19) outbreaks at 2 construction sites. Challenges in adhering to the New York State Department of Health "Interim COVID-19 Guidance for Construction" were reported. To minimize outbreaks, jurisdictions should increase tailored outreach to the construction industry, emphasizing infection prevention.

Brucella Exposure Risk Events in 10 Clinical Laboratories, New York City, USA, 2015 to 2017.

From 2015 to 2017, 11 confirmed brucellosis cases were reported in New York City, leading to 10 Brucella exposure risk events (Brucella events) in 7 clinical laboratories (CLs). Most patients had traveled to countries where brucellosis is endemic and presented with histories and findings consistent with brucellosis. CLs were not notified that specimens might yield a hazardous organism, as the clinicians did not consider brucellosis until they were notified that bacteremia with Brucella was suspected. In 3 Brucella events, the CLs did not suspect that slow-growing, small Gram-negative bacteria might be harmful. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), which has a limited capacity to identify biological threat agents (BTAs), was used during 4 Brucella events, which accounted for 84% of exposures. In 3 of these incidents, initial staining of liquid media showed Gram-positive rods or cocci, including some cocci in chains, suggesting streptococci. Over 200 occupational exposures occurred when the unknown isolates were manipulated and/or tested on open benches, including by procedures that could generate infectious aerosols. During 3 Brucella events, the CLs examined and/or manipulated isolates in a biological safety cabinet (BSC); in each CL, the CL had previously isolated Brucella Centers for Disease Control and Prevention recommendations to prevent laboratory-acquired brucellosis (LAB) were followed; no seroconversions or LAB cases occurred. Laboratory assessments were conducted after the Brucella events to identify facility-specific risks and mitigations. With increasing MALDI-TOF MS use, CLs are well-advised to adhere strictly to safe work practices, such as handling and manipulating all slow-growing organisms in BSCs and not using MALDI-TOF MS for identification until BTAs have been ruled out.

Clinical and Pathological Evaluation of Mycobacterium marinum Group Skin Infections Associated With Fish Markets in New York City.

BACKGROUND: From December 2013 through May 2014, physicians, dermatopathologists, and public health authorities collaborated to characterize an outbreak of Mycobacterium marinum and other nontuberculous mycobacterial skin and soft tissue infections (SSTIs) associated with handling fish in New York City's Chinatown. Clinicopathologic and laboratory investigations were performed on a series of patients. METHODS: Medical records were reviewed for 29 patients. Culture results were available for 27 patients and 24 biopsy specimens were evaluated by histopathology, immunohistochemistry (IHC) staining for acid-fast bacilli (AFB), and mycobacterial polymerase chain reaction (PCR) assays. RESULTS: All patients received antibiotics. The most commonly prescribed antibiotic regimen was clarithromycin and ethambutol. Of the 29 patients in this case series, 16 (55%) received surgical treatment involving incision and drainage, mass excision, and synovectomy. Of these, 7 (44%) had deep tissue involvement. All patients showed improvement. For those with culture results, 11 of 27 (41%) were positive for M. marinum; the remainder showed no growth. Poorly formed granulomas (96%), neutrophils (75%), and necrosis (79%) were found in 24 biopsies. Of 15 cases that were culture-negative and analyzed by other methods, 9 were PCR positive for M. marinum group species, 8 were IHC positive, and 3 were positive by AFB stains. CONCLUSIONS: A multidisciplinary approach was used to identify cases in an outbreak of M. marinum infections. The use of histopathology, culture, and IHC plus PCR from full thickness skin biopsy can lead to improved diagnosis of M. marinum SSTIs compared to relying solely on mycobacterial culture, the current gold standard.

Notes from the Field: Fungal Bloodstream Infections Associated with a Compounded Intravenous Medication at an Outpatient Oncology Clinic - New York City, 2016.

On May 24, 2016, the New York City Department of Health and Mental Hygiene notified CDC of two cases of Exophiala dermatitidis bloodstream infections among patients with malignancies who had received care from a single physician at an outpatient oncology facility (clinic A). Review of January 1-May 31, 2016 microbiology records identified E. dermatitidis bloodstream infections in two additional patients who also had received care at clinic A. All four patients had implanted vascular access ports and had received intravenous (IV) medications, including a compounded IV flush solution containing saline, heparin, vancomycin, and ceftazidime, compounded and administered at clinic A.

Ebola virus disease in a humanitarian aid worker - New York City, October 2014.

In late October 2014, Ebola virus disease (Ebola) was diagnosed in a humanitarian aid worker who recently returned from West Africa to New York City (NYC). The NYC Department of Health and Mental Hygiene (DOHMH) actively monitored three close contacts of the patient and 114 health care personnel. No secondary cases of Ebola were detected. In collaboration with local and state partners, DOHMH had developed protocols to respond to such an event beginning in July 2014. These protocols included safely transporting a person at the first report of symptoms to a local hospital prepared to treat a patient with Ebola, laboratory testing for Ebola, and monitoring of contacts. In response to this single case of Ebola, initial health care worker active monitoring protocols needed modification to improve clarity about what types of exposure should be monitored. The response costs were high in both human resources and money: DOHMH alone spent $4.3 million. However, preparedness activities that include planning and practice in effectively monitoring the health of workers involved in Ebola patient care can help prevent transmission of Ebola.

Surveillance and preparedness for Ebola virus disease -- New York City, 2014.

In July 2014, as the Ebola virus disease (Ebola) epidemic expanded in Guinea, Liberia, and Sierra Leone, an air traveler brought Ebola to Nigeria and two American health care workers in West Africa were diagnosed with Ebola and later medically evacuated to a U.S. hospital. New York City (NYC) is a frequent port of entry for travelers from West Africa, a home to communities of West African immigrants who travel back to their home countries, and a home to health care workers who travel to West Africa to treat Ebola patients. Ongoing transmission of Ebolavirus in West Africa could result in an infected person arriving in NYC. The announcement on September 30 of an Ebola case diagnosed in Texas in a person who had recently arrived from an Ebola-affected country further reinforced the need in NYC for local preparedness for Ebola.

Transmission of yellow fever vaccine virus through blood transfusion and organ transplantation in the USA in 2021: report of an investigation.

BACKGROUND: In 2021, four patients who had received solid organ transplants in the USA developed encephalitis beginning 2-6 weeks after transplantation from a common organ donor. We describe an investigation into the cause of encephalitis in these patients. METHODS: From Nov 7, 2021, to Feb 24, 2022, we conducted a public health investigation involving 15 agencies and medical centres in the USA. We tested various specimens (blood, cerebrospinal fluid, intraocular fluid, serum, and tissues) from the organ donor and recipients by serology, RT-PCR, immunohistochemistry, metagenomic next-generation sequencing, and host gene expression, and conducted a traceback of blood transfusions received by the organ donor. FINDINGS: We identified one read from yellow fever virus in cerebrospinal fluid from the recipient of a kidney using metagenomic next-generation sequencing. Recent infection with yellow fever virus was confirmed in all four organ recipients by identification of yellow fever virus RNA consistent with the 17D vaccine strain in brain tissue from one recipient and seroconversion after transplantation in three recipients. Two patients recovered and two patients had no neurological recovery and died. 3 days before organ procurement, the organ donor received a blood transfusion from a donor who had received a yellow fever vaccine 6 days before blood donation. INTERPRETATION: This investigation substantiates the use of metagenomic next-generation sequencing for the broad-based detection of rare or unexpected pathogens. Health-care workers providing vaccinations should inform patients of the need to defer blood donation for at least 2 weeks after receiving a yellow fever vaccine. Despite mitigation strategies and safety interventions, a low risk of transfusion-transmitted infections remains. FUNDING: US Centers for Disease Control and Prevention (CDC), the Biomedical Advanced Research and Development Authority, and the CDC Epidemiology and Laboratory Capacity Cooperative Agreement for Infectious Diseases.

Candida auris Colonization After Discharge to a Community Setting: New York City, 2017-2019.

BACKGROUND: Patients colonized with multidrug-resistant Candida auris and discharged to a community setting can subsequently seek care in a different healthcare facility and might be a source of nosocomial transmission of C auris. METHODS: We designed a case management pilot program for a cohort of New York City residents who had a history of positive C auris culture identified during clinical or screening activities in healthcare settings and discharged to a community setting during 2017-2019. Approximately every 3 months, case managers coordinated C auris colonization assessments, which included swabs of groin, axilla, and body sites yielding C auris previously. Patients eligible to become serially negative were those with ≥2 C auris colonization assessments after initial C auris identification. Clinical characteristics of serially negative and positive patients were compared. RESULTS: The cohort included 75 patients. Overall, 45 patients were eligible to become serially negative and had 552 person-months of follow-up. Of these 45 patients, 28 patients were serially negative (62%; rate 5.1/100 person-months), 8 were serially positive, and 9 could not be classified as either. There were no clinical characteristics that were significantly different between serially negative and positive patients. The median time from initial C auris identification to being serially negative at assessments was 8.6 months (interquartile range, 5.7-10.8 months). CONCLUSIONS: A majority of patients, assessed at least twice after C auris identification, no longer had C auris detectable on serial colonization assessments.

Public health and environmental response to the first case of naturally acquired inhalational anthrax in the United States in 30 years: infection of a new york city resident who worked with dried animal hides.

In Pennsylvania on February 16, 2006, a New York City resident collapsed with rigors and was hospitalized. On February 21, the Centers for Disease Control and Prevention and the New York City Department of Health and Mental Hygiene were notified that Bacillus anthracis had been identified in the patient's blood. Although the patient's history of working with dried animal hides to make African drums indicated the likelihood of a natural exposure to aerosolized anthrax spores, bioterrorism had to be ruled out first. Ultimately, this case proved to be the first case of naturally occurring inhalational anthrax in 30 years. This article describes the epidemiologic and environmental investigation to identify other cases and persons at risk and to determine the source of exposure and scope of contamination. Because stricter regulation of the importation of animal hides from areas where anthrax is enzootic is difficult, public healthcare officials should consider the possibility of future naturally occurring anthrax cases caused by contaminated hides. Federal protocols are needed to assist in the local response, which should be tempered by our growing understanding of the epidemiology of naturally acquired anthrax. These protocols should include recommended methods for reliable and efficient environmental sample collection and laboratory testing, and environmental risk assessments and remediation.

Public Health Management of Persons Under Investigation for Ebola Virus Disease in New York City, 2014-2016.

During 2014-2016, the largest outbreak of Ebola virus disease (EVD) in history occurred in West Africa. The New York City Department of Health and Mental Hygiene (DOHMH) worked with health care providers to prepare for persons under investigation (PUIs) for EVD in New York City. From July 1, 2014, through December 29, 2015, we classified as a PUI a person with EVD-compatible signs or symptoms and an epidemiologic risk factor within 21 days before illness onset. Of 112 persons who met PUI criteria, 74 (66%) sought medical care and 49 (44%) were hospitalized. The remaining 38 (34%) were isolated at home with daily contact by DOHMH staff members. Thirty-two (29%) PUIs received a diagnosis of malaria. Of 10 PUIs tested, 1 received a diagnosis of EVD. Home isolation minimized unnecessary hospitalization. This case study highlights the importance of developing competency among clinical and public health staff managing persons suspected to be infected with a high-consequence pathogen.

Effect of timing of amantadine chemoprophylaxis on severity of outbreaks of influenza a in adult long-term care facilities.

BACKGROUND: Long-term care facilities (LTCFs) are vulnerable to outbreaks of influenza. There are limited data on the impact of antiviral chemoprophylaxis on the duration of outbreaks of influenza. We investigated the association of timely initiation of amantadine chemoprophylaxis on the duration and severity of outbreaks of influenza A in LTCFs in New York, New York. METHODS: Outbreaks of influenza A occurring from October through May each year during the period 2001-2004 in LTCFs in New York were defined as a single laboratory-confirmed case or a cluster of > or = 2 cases of influenza-like illness on a unit of an LTCF. For those facilities that provided amantadine chemoprophylaxis, we examined the association between the time to initiation of chemoprophylaxis after outbreak onset and duration of outbreak, incidence rate, and case-fatality proportion using simple t tests, multivariate analyses of covariance, and linear regression modeling. RESULTS: Adjusting for influenza season year, facility bed capacity, and the proportion of residents who were vaccinated against influenza, LTCFs that initiated chemoprophylaxis 15 days after outbreak onset (25 facilities) had significantly longer duration of outbreaks (18.3 vs. 6.7 days; P < .001), higher incidence rates (10.5 cases per 100 residents vs. 6.2 cases per 100 residents; P < .023), and higher case-fatality rates (3.3 deaths per 100 residents with influenza A vs. 0.45 deaths per 100 residents with influenza A; P < .005) than did LTCFs that initiated chemoprophylaxis 5 days after outbreak onset (27 facilities). CONCLUSIONS: LTCFs that initiated chemoprophylaxis >5 days after initiation of outbreaks of influenza A had significantly longer outbreaks, significantly higher incidence rates, and significantly higher case-fatality rates. These data support prompt initiation of amantadine chemoprophylaxis after identification of influenza A in LTCFs.

Healthcare-Associated Transmission of Plasmodium falciparum in New York City.

A patient with no risk factors for malaria was hospitalized in New York City with Plasmodium falciparum infection. After investigating all potential sources of infection, we concluded the patient had been exposed to malaria while hospitalized less than 3 weeks earlier. Molecular genotyping implicated patient-to-patient transmission in a hospital setting. Infect. Control Hosp. Epidemiol. 2015;37(1):113-115.

Lack of Evidence for Plague or Anthrax on the New York City Subway.

Ackelsberg et al. point out a lack of evidence in the dataset of Afshinekoo et al. for the presence of plague and anthrax on the New York City subway.

A cluster of methicillin-susceptible Staphylococcus aureus infections at a rheumatology practice, New York City, 2011.

A cluster of 5 methicillin-susceptible Staphylococcus aureus infections occurred after administration of methylprednisolone acetate injections in a rheumatology practice. A site visit was conducted to inspect examination rooms, observe techniques, and review charts. The investigation revealed a pervasive lack of aseptic technique that led to multiple opportunities for medication contamination.

The NYC native air sampling pilot project: using HVAC filter data for urban biological incident characterization.

Native air sampling (NAS) is distinguished from dedicated air sampling (DAS) devices (eg, BioWatch) that are deployed to detect aerosol disseminations of biological threat agents. NAS uses filter samples from heating, ventilation, and air conditioning (HVAC) systems in commercial properties for environmental sampling after DAS detection of biological threat agent incidents. It represents an untapped, scientifically sound, efficient, widely distributed, and comparably inexpensive resource for postevent environmental sampling. Calculations predict that postevent NAS would be more efficient than environmental surface sampling by orders of magnitude. HVAC filter samples could be collected from pre-identified surrounding NAS facilities to corroborate the DAS alarm and delineate the path taken by the bioaerosol plume. The New York City (NYC) Native Air Sampling Pilot Project explored whether native air sampling would be acceptable to private sector stakeholders and could be implemented successfully in NYC. Building trade associations facilitated outreach to and discussions with property owners and managers, who expedited contact with building managers of candidate NAS properties that they managed or owned. Nominal NAS building requirements were determined; procedures to identify and evaluate candidate NAS facilities were developed; data collection tools and other resources were designed and used to expedite candidate NAS building selection and evaluation in Manhattan; and exemplar environmental sampling playbooks for emergency responders were completed. In this sample, modern buildings with single or few corporate tenants were the best NAS candidate facilities. The Pilot Project successfully demonstrated that in one urban setting a native air sampling strategy could be implemented with effective public-private collaboration.