scholarly journals Fine-scale differentiation between Bacillus anthracis and Bacillus cereus group signatures in metagenome shotgun data

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e5515 ◽  
Author(s):  
Robert A. Petit III ◽  
James M. Hogan ◽  
Matthew N. Ezewudo ◽  
Sandeep J. Joseph ◽  
Timothy D. Read
Keyword(s):  
New York ◽  
New York City ◽  
Bacillus Cereus ◽  
Bacillus Anthracis ◽  
Genome Sequence ◽  
York City ◽  
False Positive ◽  
Lethal Factor ◽  
Analysis Tool ◽  
Sequencing Errors

Background It is possible to detect bacterial species in shotgun metagenome datasets through the presence of only a few sequence reads. However, false positive results can arise, as was the case in the initial findings of a recent New York City subway metagenome project. False positives are especially likely when two closely related are present in the same sample. Bacillus anthracis, the etiologic agent of anthrax, is a high-consequence pathogen that shares >99% average nucleotide identity with Bacillus cereus group (BCerG) genomes. Our goal was to create an analysis tool that used k-mers to detect B. anthracis, incorporating information about the coverage of BCerG in the metagenome sample. Methods Using public complete genome sequence datasets, we identified a set of 31-mer signatures that differentiated B. anthracis from other members of the B. cereus group (BCerG), and another set which differentiated BCerG genomes (including B. anthracis) from other Bacillus strains. We also created a set of 31-mers for detecting the lethal factor gene, the key genetic diagnostic of the presence of anthrax-causing bacteria. We created synthetic sequence datasets based on existing genomes to test the accuracy of a k-mer based detection model. Results We found 239,503 B. anthracis-specific 31-mers (the Ba31 set), 10,183 BCerG 31-mers (the BCerG31 set), and 2,617 lethal factor k-mers (the lef31 set). We showed that false positive B. anthracis k-mers—which arise from random sequencing errors—are observable at high genome coverages of B. cereus. We also showed that there is a “gray zone” below 0.184× coverage of the B. anthracis genome sequence, in which we cannot expect with high probability to identify lethal factor k-mers. We created a linear regression model to differentiate the presence of B. anthracis-like chromosomes from sequencing errors given the BCerG background coverage. We showed that while shotgun datasets from the New York City subway metagenome project had no matches to lef31 k-mers and hence were negative for B. anthracis, some samples showed evidence of strains very closely related to the pathogen. Discussion This work shows how extensive libraries of complete genomes can be used to create organism-specific signatures to help interpret metagenomes. We contrast “specialist” approaches to metagenome analysis such as this work to “generalist” software that seeks to classify all organisms present in the sample and note the more general utility of a k-mer filter approach when taxonomic boundaries lack clarity or high levels of precision are required.

scholarly journals Rubella Surveillance and Diagnostic Testing among a Low-Prevalence Population, New York City, 2012–2013

2017 ◽  
Vol 24 (9) ◽  
Author(s):  
Beth M. Isaac ◽  
Jane R. Zucker ◽  
Francesca R. Giancotti ◽  
Emily Abernathy ◽  
Joseph Icenogle ◽  
...  
Keyword(s):  
New York ◽  
New York City ◽  
York City ◽  
False Positive ◽  
Diagnostic Tests ◽  
Indirect Elisa ◽  
Diagnostic Testing ◽  
Immunoglobulin M ◽  
Enzyme Linked Immunosorbent Assay ◽  
Department Of Health

ABSTRACT The New York City Department of Health and Mental Hygiene (DOHMH) receives clinical and laboratory reports for rubella. Because rubella immunoglobulin M (IgM) assays may produce false-positive results and rubella infections may be asymptomatic, interpretation of positive IgM results can be challenging. Rubella reports received by DOHMH in 2012 to 2013 were reviewed. The rubella IgM testing purpose was determined through case investigation. Results of IgM testing by indirect enzyme-linked immunosorbent assay (ELISA) and capture enzyme immunoassay (EIA) were compared to determine positive predictive value (PPV) and specificity. DOHMH received 199 rubella reports; 2 were true cases. Of all reports, 77.9% were tested for rubella IgM erroneously, 19.6% were tested for diagnostic purposes, 2.0% had unknown test purpose, and 0.5% were not tested. PPV of indirect ELISA was 6% overall, 14% for diagnostic tests, and 0% for tests ordered erroneously. PPV of capture EIA was 29% overall, 50% for diagnostic tests, and 0% for tests ordered erroneously. Overall, specificity was 52% for indirect ELISA and 85% for capture EIA. Limiting rubella IgM testing to patients for whom rubella diagnosis is suspected and using a more specific IgM assay have the potential to reduce false-positive rubella IgM results.

scholarly journals Genome Sequence of Mycobacteriophage Cabrinians

2016 ◽  
Vol 4 (1) ◽  
Author(s):  
Dylan Chudoff ◽  
Andrew Conboy ◽  
Danielle Conboy ◽  
Mireille Atoulelou ◽  
Sakina Hasan ◽  
...  
Keyword(s):  
New York ◽  
New York City ◽  
Soil Sample ◽  
Genome Sequence ◽  
York City ◽  
Mycobacterium Smegmatis ◽  
Genome Length ◽  
Mycobacterium Phlei ◽  
A Genome

Mycobacteriophage Cabrinians is a newly isolated phage capable of infecting both Mycobacterium phlei and Mycobacterium smegmatis and was recovered from a soil sample in New York City, NY. Cabrinians has a genome length of 56,669 bp, encodes 101 predicted proteins, and is a member of mycobacteriophages in cluster F.

scholarly journals Frequency and Characteristics of Biological False-Positive Test Results for Syphilis Reported in Florida and New York City, USA, 2013 to 2017

2019 ◽  
Vol 57 (11) ◽  
Author(s):  
James Matthias ◽  
Ellen J. Klingler ◽  
Julia A. Schillinger ◽  
Gayle Keller ◽  
Craig Wilson ◽  
...  
Keyword(s):  
New York ◽  
New York City ◽  
York City ◽  
False Positive ◽  
High Titer ◽  
Transmitted Disease ◽  
Fold Increase ◽  
Positive Test ◽  
Test Results ◽  
False Positive Test

ABSTRACT Discordant syphilis test results, with a reactive nontreponemal test and nonreactive treponemal test are usually considered biological false-positive test results (BFPs), which can be attributed to other conditions. Syphilis surveillance laws mandate laboratory reporting of reactive syphilis tests, which include many BFPs. We describe the frequency of BFPs, titer distributions, and titer increases from reported test results in Florida and New York City (NYC). Reactive nontreponemal tests for individuals with at least one nonreactive treponemal test and no reactive treponemal test were extracted from sexually transmitted disease (STD) surveillance systems in Florida and NYC from 2013 to 2017. Characteristics of individuals with BFPs were analyzed after selecting the observation with the highest titer from each individual. We next considered all results from individuals to characterize persons who had a 4-fold titer increase between successive nontreponemal tests. Among 526,540 reactive nontreponemal tests, there were 57,580 BFPs (11%) from 39,920 individuals. Over 90% (n = 52,330) of BFPs were low titer (≤1:4), but 654 (1%) were high-titer BFPs (≥1:32). Very high-titer (≥1:128) BFPs were more common among individuals over 60 years of age (odds ratio [OR], 2.68; 95% confidence interval [CI], 1.22 to 5.91). A 4-fold increase in titer was observed among 1,863 (14%) individuals with more than one reported BFP. Most BFPs detected by surveillance were low titer, but some were high titer and some had a 4-fold increase in titer. Review of patient histories might identify underlying conditions contributing to these high and rising titers.

scholarly journals P725 Frequency and characteristics of biologic false positive tests for syphilis, reported in florida and new york city, 2013–2017

2019 ◽  
Author(s):  
James Matthias ◽  
Ellen Klingler ◽  
Julia Schillinger ◽  
Thomas Peterman ◽  
Craig Wilson
Keyword(s):  
New York ◽  
New York City ◽  
York City ◽  
False Positive

An Important Armenian MS. with Greek Miniatures

1942 ◽  
Vol 74 (3-4) ◽  
pp. 155-162
Author(s):  
H. Kurdian
Keyword(s):  
New York ◽  
New York City ◽  
York City ◽  
Christian Iconography

In 1941 while in New York City I was fortunate enough to purchase an Armenian MS. which I believe will be of interest to students of Eastern Christian iconography.

Hospitals: N.Y. Appellate Court Denies Move to Privatize Public Hospital

1999 ◽  
Vol 27 (2) ◽  
pp. 202-203
Author(s):  
Robert Chatham
Keyword(s):  
New York ◽  
New York City ◽  
York City ◽  
Public Health System ◽  
Municipal Hospital ◽  
The Public ◽  
Public Benefit ◽  
For Profit ◽  
Benefit Corporation ◽  
The City

The Court of Appeals of New York held, in Council of the City of New York u. Giuliani, slip op. 02634, 1999 WL 179257 (N.Y. Mar. 30, 1999), that New York City may not privatize a public city hospital without state statutory authorization. The court found invalid a sublease of a municipal hospital operated by a public benefit corporation to a private, for-profit entity. The court reasoned that the controlling statute prescribed the operation of a municipal hospital as a government function that must be fulfilled by the public benefit corporation as long as it exists, and nothing short of legislative action could put an end to the corporation's existence.In 1969, the New York State legislature enacted the Health and Hospitals Corporation Act (HHCA), establishing the New York City Health and Hospitals Corporation (HHC) as an attempt to improve the New York City public health system. Thirty years later, on a renewed perception that the public health system was once again lacking, the city administration approved a sublease of Coney Island Hospital from HHC to PHS New York, Inc. (PHS), a private, for-profit entity.

Cultural Competence Needed to Distinguish Disorder from Difference: Beyond Kumbaya

2015 ◽  
Vol 22 (2) ◽  
pp. 64-76 ◽  
Author(s):  
Catherine J. Crowley ◽  
Kristin Guest ◽  
Kenay Sudler
Keyword(s):  
New York ◽  
New York City ◽  
Public Schools ◽  
Cultural Competence ◽  
York City ◽  
Cultural Sensitivity ◽  
Graduate Program ◽  
Language Disorder ◽  
New York State ◽  
Deep Understanding

What does it mean to have true cultural competence as an speech-language pathologist (SLP)? In some areas of practice it may be enough to develop a perspective that values the expectations and identity of our clients and see them as partners in the therapeutic process. But when clinicians are asked to distinguish a language difference from a language disorder, cultural sensitivity is not enough. Rather, in these cases, cultural competence requires knowledge and skills in gathering data about a student's cultural and linguistic background and analyzing the student's language samples from that perspective. This article describes one American Speech-Language-Hearing Association (ASHA)-accredited graduate program in speech-language pathology and its approach to putting students on the path to becoming culturally competent SLPs, including challenges faced along the way. At Teachers College, Columbia University (TC) the program infuses knowledge of bilingualism and multiculturalism throughout the curriculum and offers bilingual students the opportunity to receive New York State certification as bilingual clinicians. Graduate students must demonstrate a deep understanding of the grammar of Standard American English and other varieties of English particularly those spoken in and around New York City. Two recent graduates of this graduate program contribute their perspectives on continuing to develop cultural competence while working with diverse students in New York City public schools.

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