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Competing Interests: All authors have completed and submitted the International Committee of Medical Journal Editors form for disclosure of potential conflicts of interest. No potential conflicts of interest were disclosed.

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.

We report the presentation and management of 17 cases of Exophiala dermatitidis and Rhodotorula mucilaginosa bloodstream infections caused by a compounded parenteral medication at an oncology clinic. Twelve patients were asymptomatic. All central venous catheters were removed and antifungal therapy, primarily voriconazole, was administered to patients. Three patients died.

Mycobacterium marinum, a bacterium found in freshwater and saltwater, can infect persons with direct exposure to fish or aquariums. During December 2013, the New York City Department of Health and Mental Hygiene learned of four suspected or confirmed M. marinum skin or soft tissue infections (SSTIs) among persons who purchased whole fish from Chinese markets. Ninety-eight case-patients with non-tuberculous mycobacteria (NTM) SSTIs were identified with onset June 2013-March 2014. Of these, 77 (79%) were female. The median age was 62 years (range 30-91). Whole genome sequencing of clinical isolates revealed two main clusters and marked genetic diversity. Environmental samples from distributors yielded NTM though not M. marinum. We compared 56 case-patients with 185 control subjects who shopped in Chinese markets, frequency-matched by age group and sex. Risk factors for infection included skin injury to the finger or hand (odds ratio [OR]: 15·5; 95% confidence interval [CI]: 6·9-37·3), hand injury while preparing fish or seafood (OR 8·3; 95% CI 3·8-19·1), and purchasing tilapia (OR 3·6; 95% CI 1·1-13·9) or whiting (OR 2·7; 95% CI 1·1-6·6). A definitive environmental outbreak source was not identified.

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., (Published by Oxford University Press for the Infectious Diseases Society of America 2015. This work is written by (a) US Government employee(s) and is in the public domain in the US.)

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.

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.

The largest reported outbreak of waterborne Escherichia coli O157:H7 in the United States occurred in upstate New York following a county fair in August 1999. Culture methods were used to isolate E. coli O157:H7 from specimens from 128 of 775 patients with suspected infections. Campylobacter jejuni was also isolated from stools of 44 persons who developed diarrheal illness after attending this fair. There was one case of a confirmed coinfection with E. coli O157:H7 and C. jejuni. Molecular detection of stx(1) and stx(2) Shiga toxin genes, immunomagnetic separation (IMS), and selective culture enrichment were utilized to detect and isolate E. coli O157:H7 from an unchlorinated well and its distribution points, a dry well, and a nearby septic tank. PCR for stx(1) and stx(2) was shown to provide a useful screen for toxin-producing E. coli O157:H7, and IMS subculture improved recovery. Pulsed-field gel electrophoresis (PFGE) was used to compare patient and environmental E. coli O157:H7 isolates. Among patient isolates, 117 of 128 (91.5%) were type 1 or 1a (three or fewer bands different). Among the water distribution system isolates, 13 of 19 (68%) were type 1 or 1a. Additionally, PFGE of C. jejuni isolates revealed that 29 of 35 (83%) had indistinguishable PFGE patterns. The PFGE results implicated the water distribution system as the main source of the E. coli O157:H7 outbreak. This investigation demonstrates the potential for outbreaks involving more than one pathogen and the importance of analyzing isolates from multiple patients and environmental samples to develop a better understanding of bacterial transmission during an outbreak.

Two outbreaks of respiratory tract illness associated with prolonged cough occurring in 1998 and 1999 in New York State were investigated. A PCR test for Bordetella pertussis was primarily used by a private laboratory to confirm 680 pertussis cases. Several clinical specimens had positive culture results for B. pertussis during both outbreaks, which confirmed that B. pertussis was circulating during the outbreaks. However, testing by the New York State Department of Health reference laboratory suggested that some of the PCR results may have been falsely positive. In addition, features of the outbreak that suggested that B. pertussis may not have been the primary agent of infection included a low attack rate among incompletely vaccinated children and a significant amount of illness among patients testing PCR negative for B. pertussis. These investigations highlight the importance of appropriate clinical laboratory quality assurance programs, of the limitations of the PCR test, and of interpreting laboratory results in context of clinical disease.