scholarly journals A Bioinformatic Pipeline for Improved Genome Analysis and Clustering of Isolates during Outbreaks of Legionnaires’ Disease

2020 ◽  
Author(s):  
Wolfgang Haas ◽  
Pascal Lapierre ◽  
Kimberlee A. Musser
Keyword(s):  
Public Health ◽  
New York ◽  
Legionella Pneumophila ◽  
New York State ◽  
Variant Calling ◽  
York State Department ◽  
Nucleotide Polymorphisms ◽  
Bioinformatic Pipeline ◽  
Public Health Departments ◽  
Legionnaires Disease

Legionnaires’ disease, a severe lung infection caused by the bacterium Legionella pneumophila, occurs as single cases or in outbreaks that are actively tracked by public health departments. To determine the point source of an outbreak, clinical isolates need to be compared to environmental samples to find matching isolates. One confounding factor is the genome plasticity of L. pneumophila, making an exact sequence comparison by whole-genome sequencing (WGS) challenging. Here, we present a WGS analysis pipeline, LegioCluster, designed to circumvent this problem by automatically selecting the best matching reference genome prior to mapping and variant calling. This approach reduces the number of false-positive variant calls, maximizes the fraction of all genomes that are being compared, and naturally clusters the isolates according to their reference strain. Isolates that are too distant from any genome in the database are added to the list of candidate references, thereby creating a new cluster. Short insertions and deletions are considered in addition to single nucleotide polymorphisms (SNP) for increased discriminatory power. This manuscript describes the use of this automated and "locked down" bioinformatic pipeline deployed at the New York State Department of Health's Wadsworth Center for investigating relatedness between clinical and environmental isolates. A similar pipeline has not been widely available for use to support this critically important public health investigation analysis.

scholarly journals Improvements to the Success of Outbreak Investigations of Legionnaires' Disease: 40 Years of Testing and Investigation in New York State

2021 ◽  
Author(s):  
Dianna Schoonmaker-Bopp ◽  
Elizabeth Nazarian ◽  
David Dziewulski ◽  
Ernest Clement ◽  
Deborah J. Baker ◽  
...  
Keyword(s):  
Public Health ◽  
New York ◽  
Environmental Samples ◽  
New York State ◽  
The United States ◽  
York State Department ◽  
Environmental Isolates ◽  
York State ◽  
Outbreak Investigations ◽  
Legionnaires Disease

Since 1978, the New York State Department of Health’s public health laboratory, Wadsworth Center (WC), in collaboration with epidemiology and environmental partners, has been committed to providing comprehensive public health testing for Legionella in New York. Statewide, clinical case counts have been increasing over time, with the highest numbers identified in 2017 and 2018 (1022 and 1426, respectively). Over the course of more than 40 years, the WC Legionella testing program has continuously implemented improved testing methods. The methods utilized have transitioning from solely culture-based methods for organism recovery to development of a suite of reference testing services including identification and characterization by PCR and pulsed-field gel electrophoresis (PFGE). In the last decade, whole-genome sequencing (WGS) has further refined the ability to link outbreak strains between clinical specimens and environmental samples. Here we review Legionnaires' disease outbreak investigations during this time period including comprehensive testing of both clinical and environmental samples. Between 1978 and 2017, 60 outbreaks involving clinical and environmental isolates with matching PFGE patterns were detected in 49 facilities from the 157 investigations at 146 facilities. However, 97 investigations were not solved due to the lack of clinical or environmental isolates or PFGE matches. We found 69% of patient specimens from New York State (NYS) were outbreak-associated, a much higher rate than other published reports. The consistent application of new cutting-edge technologies and environmental regulations have resulted in successful investigations resulting in remediation efforts. Importance Legionella , the causative agent of Legionnaires’ disease (LD) can cause severe respiratory illness. In 2018, there were nearly 10,000 cases of LD reported in the United States (1), with actual incidence believed to be much higher. About 10% of patients with LD will die and as high as 90% of patients diagnosed will be hospitalized. As Legionella are spread predominantly through engineered building water systems, identifying sources of outbreaks by assessing environmental sources is key to preventing further cases LD.

scholarly journals Allocation of Ventilators in a Public Health Disaster

2008 ◽  
Vol 2 (1) ◽  
pp. 20-26 ◽  
Author(s):  
Tia Powell ◽  
Kelly C. Christ ◽  
Guthrie S. Birkhead
Keyword(s):  
Public Health ◽  
New York ◽  
Clinical Guidelines ◽  
Task Force ◽  
New York State ◽  
Assessment System ◽  
Ethical Framework ◽  
Standards Of Care ◽  
York State Department ◽  
York State

ABSTRACTBackground: In a public health emergency, many more patients could require mechanical ventilators than can be accommodated.Methods: To plan for such a crisis, the New York State Department of Health and the New York State Task Force on Life and the Law convened a workgroup to develop ethical and clinical guidelines for ventilator triage.Results: The workgroup crafted an ethical framework including the following components: duty to care, duty to steward resources, duty to plan, distributive justice, and transparency. Incorporating the ethical framework, the clinical guidelines propose both withholding and withdrawing ventilators from patients with the highest probability of mortality to benefit patients with the highest likelihood of survival. Triage scores derive from the sepsis-related organ failure assessment system, which assigns points based on function in 6 basic medical domains. Triage may not be implemented by a facility without clear permission from public health authorities.Conclusions: New York State released the draft guidelines for public comment, allowing for revision to reflect both community values and medical innovation. This ventilator triage system represents a radical shift from ordinary standards of care, and may serve as a model for allocating other scarce resources in disasters. (Disaster Med Public Health Preparedness. 2008;2:20–26)

Window of Opportunity for New Disease Surveillance: Developing Keyword Lists for Monitoring Mental Health and Injury Through Syndromic Surveillance

2016 ◽  
Vol 11 (2) ◽  
pp. 173-178 ◽  
Author(s):  
Ursula Lauper ◽  
Jian-Hua Chen ◽  
Shao Lin
Keyword(s):  
Public Health ◽  
Mental Health ◽  
New York ◽  
Syndromic Surveillance ◽  
New York State ◽  
Hurricane Sandy ◽  
York State Department ◽  
Free Text ◽  
York State ◽  
The Impact

AbstractStudies have documented the impact that hurricanes have on mental health and injury rates before, during, and after the event. Since timely tracking of these disease patterns is crucial to disaster planning, response, and recovery, syndromic surveillance keyword filters were developed by the New York State Department of Health to study the short- and long-term impacts of Hurricane Sandy. Emergency department syndromic surveillance is recognized as a valuable tool for informing public health activities during and immediately following a disaster. Data typically consist of daily visit reports from hospital emergency departments (EDs) of basic patient data and free-text chief complaints. To develop keyword lists, comparisons were made with existing CDC categories and then integrated with lists from the New York City and New Jersey health departments in a collaborative effort. Two comprehensive lists were developed, each containing multiple subcategories and over 100 keywords for both mental health and injury. The data classifiers using these keywords were used to assess impacts of Sandy on mental health and injuries in New York State. The lists will be validated by comparing the ED chief complaint keyword with the final ICD diagnosis code. (Disaster Med Public Health Preparedness. 2017;11:173–178)

PUBLIC HEALTH, NURSING AND MEDICAL SOCIAL WORK

PEDIATRICS ◽  
1953 ◽  
Vol 11 (5) ◽  
pp. 544-548
Keyword(s):  
Public Health ◽  
New York ◽  
Health Workers ◽  
New York State ◽  
World Health ◽  
Health Improvement ◽  
York State Department ◽  
Economic Values ◽  
Health Nursing ◽  
Health Organization

WORLD HEALTH DAY, April 7, 1953, has been marked by the publication of a World Health Organization pamphlet, Health is Wealth. This is an abridgement of an unusually informative monograph by Prof. C.-E.A. Winslow of Yale, The Cost of Sickness and the Price of Health. At the Fifth World Health Assembly, furthermore, a series of technical discussions were held on the theme "The Economic Values of Preventive Medicine." In these discussions, Dr. Winslow presented a paper highlighting some of the significant facts in this field. Many of the statements in this paper are apt and timely. "Economic values do not provide the only—or even the primary—inspiration for the world-wide campaign for public health. . . . It is men and women who are fundamentally of importance, not dollars. . . ." Yet, in day-to-day activities of public health workers in a "tough and practical world," it is essential to convince peoples and governments that specific goals of health improvement can be obtained and their attainment is feasible within world economics. Thirty years ago, Hermann M. Biggs coined a slogan which is still carried as a motto by the New York State Department of Health: "Public Health is Purchasable, Within Natural Limitations a Community Can Determine Its Own Death-Rate." The following is an excerpt from Dr. Winslow's paper:

New York State Public Health System Response to Hurricane Sandy: An Analysis of Survey Feedback

2016 ◽  
Vol 10 (3) ◽  
pp. 454-462 ◽  
Author(s):  
Asante Shipp Hilts ◽  
Stephanie Mack ◽  
Yunshu Li ◽  
Millicent Eidson ◽  
Trang Nguyen ◽  
...  
Keyword(s):  
Public Health ◽  
New York ◽  
New York State ◽  
Hurricane Sandy ◽  
System Response ◽  
York State Department ◽  
Health Staff ◽  
Local Health ◽  
York State ◽  
Public Health Staff

AbstractObjectiveThe objective was to provide a broad spectrum of New York State and local public health staff the opportunity to contribute anonymous feedback on their own and their agencies’ preparedness and response to Hurricane Sandy, perceived challenges, and recommendations for preparedness improvement.MethodsIn 2015, 2 years after Hurricane Sandy, public health staff who worked on Hurricane Sandy response were identified and were provided a link to the anonymous survey. Quantitative analyses were used for survey ratings and qualitative content analyses were used for open-ended questions.ResultsSurveys were completed by 129 local health department (LHD) staff in 3 counties heavily impacted by Sandy (Nassau, Suffolk, and Westchester) and 69 staff in the New York State Department of Health who supported the LHDs. Staff agreed that their Hurricane Sandy responsibilities were clearly defined and that they had access to adequate information to perform their jobs. Challenges were reported in the operational, communication, service interruptions, and staff categories, with LHD staff also reporting challenges with shelters.ConclusionsNew York local and state public health staff indicated that they were prepared for Hurricane Sandy. However, their feedback identified specific challenges and recommendations that can be addressed to implement improved preparedness and response strategies. (Disaster Med Public Health Preparedness. 2016;10:454–462)

SHOE-FITTING FLUOROSCOPES

PEDIATRICS ◽  
1953 ◽  
Vol 11 (2) ◽  
pp. 189-190
Author(s):  
GEORGE M. WHEATLEY
Keyword(s):  
New York ◽  
New York City ◽  
New York State ◽  
York State Department ◽  
Health Departments ◽  
York State ◽  
X Ray ◽  
Public Health Departments ◽  
Department Of Health ◽  
Extreme Care

THE dangers of radiation have been recognized for many years. Even experienced physicians use x-ray equipment with extreme care and only when benefits from diagnosis and treatment can be expected to outweigh possible harm. It is not surprising, therefore, that roentgenologists and public health departments have become increasingly disturbed over the use of x-ray shoe-fitting machines in retail shoe stores. The New York State Department of Health and the New York City Department of Health have recently altered the Sanitary Code in order to regulate the use of fluoroscopes in shoe stores.

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