Nabeeh A. Hasan

Nabeeh A. Hasan
National Jewish Health · Department of Medicine

PhD

About

72
Publications
7,313
Reads
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658
Citations
Introduction
I'm very interested in learning about Mycobacterium persistence and susceptibility.
Additional affiliations
November 2015 - November 2019
National Jewish Health
Position
  • Bioinformatics Analyst II
November 2015 - November 2019
National Jewish Health
Position
  • Analyst
October 2012 - present
University of Denver Anschutz Medical Campus/National Jewish Health Center
Position
  • PostDoc Position
Description
  • Next-generaton sequencing methods and Bioinformatics/Computational Biology in clinical Mycobacterium species
Education
August 2006 - December 2012
New Mexico State University
Field of study
  • Biology

Publications

Publications (72)
Article
Full-text available
Two mycobacteriophages were administered intravenously to a male with treatment-refractory Mycobacterium abscessus pulmonary infection and severe cystic fibrosis lung disease. The phages were engineered to enhance their capacity to lyse M. abscessus and were selected specifically as the most effective against the subject’s bacterial isolate. In the...
Article
Nontuberculous mycobacteria (NTM) are opportunistic pathogens that cause chronic pulmonary disease (PD). NTM infections are thought to be acquired from the environment; however, the basal environmental factors that drive and sustain NTM prevalence are not well understood. The highest prevalence of NTM PD cases in the United States is reported from...
Article
Rationale: Healthcare-associated transmission of nontuberculous mycobacteria (NTM) among people with cystic fibrosis (pwCF) has been investigated at CF Centers worldwide, with conflicting conclusions. We investigated transmission at the Colorado Adult CF Program. Objectives: To systematically investigate healthcare-associated transmission and/or...
Article
Full-text available
Background Healthcare-associated transmission of nontuberculous mycobacteria (NTM) among people with cystic fibrosis (pwCF) has been reported and is of increasing concern. No standardized epidemiologic investigation tool has been published for healthcare-associated NTM outbreak investigations. This report describes the design of an ongoing observat...
Article
Full-text available
Aims: Mycobacterium abscessus subsp. abscessus (MABS) is an emerging, opportunistic pathogen found globally in freshwater biofilms and soil. Typically, isolates are treated as a uniform group of organisms and very little is known about their comparative survival in healthy host cells. We posit that environmentally- and clinically derived isolates,...
Article
https://pdf.sciencedirectassets.com/272296/1-s2.0-S1569199321X00069/1-s2.0-S1569199321018993/main.pdf?X-Amz-Security-Token=IQoJb3JpZ2luX2VjEAwaCXVzLWVhc3QtMSJIMEYCIQDMH%2BUvHZjH%2B%2BFDGV%2BoxUTByvKedSK2yrDjMRNBASLVAAIhAPvYkcyVC9Qjz%2FAucUvG5iMSLtS%2B74r86ummUCxR4Z8OKoMECMX%2F%2F%2F%2F%2F%2F%2F%2F%2F%2FwEQBBoMMDU5MDAzNTQ2ODY1IgxELvl6bl30cUwvC7kq1wN...
Article
Whole genome sequencing (WGS) has recently been used to investigate acquisition of Mycobacterium abscessus (MABC). Investigators have reached conflicting conclusions about the meaning of genetic distances for interpretation of person-to-person transmission. Existing genomic studies were limited by a lack of WGS from environmental MABC isolates. In...
Article
Mycobacterium avium complex (MAC) species constitute most mycobacteria infections in persons with cystic fibrosis (CF) in the United States, but little is known about their genomic diversity or transmission. During 2016–2020, we performed whole-genome sequencing on 364 MAC isolates from 186 persons with CF from 42 cystic fibrosis care centers (CFCC...
Article
Full-text available
Mycobacterium abscessus, a multidrug-resistant nontuberculous mycobacterium, has emerged as a major pathogen affecting people with cystic fibrosis (CF). Although originally thought to be acquired independently from the environment, most individuals are infected with one of several dominant circulating clones (DCCs), indicating the presence of globa...
Article
Full-text available
Recent studies have characterized a dominant clone (Clone 1) of Mycobacterium abscessus subspecies massiliense ( M. massiliense ) associated with high prevalence in cystic fibrosis (CF) patients, pulmonary outbreaks in the United States (US) and United Kingdom (UK), and a Brazilian epidemic of skin infections. The prevalence of Clone 1 in non-CF pa...
Article
RationaleMycobacterium abscessus is a significant threat to individuals with cystic fibrosis (CF) due to innate drug resistance and potential transmission between patients. Recent studies described global dominant circulating clones of M. abscessus, but detailed genomic surveys have not yet been described for the United States (US). Objectives We e...
Article
Full-text available
Although uncommon, nontuberculous mycobacterial (NTM) pulmonary infection in the Hawaiian Islands has a relatively high incidence and mortality compared to the mainland U.S. As a result, this study examines the possible geological and hydrological pathways by which NTM patients may become infected, including the environmental conditions that may fa...
Article
Full-text available
Nontuberculous mycobacteria (NTM) are environmental organisms that can cause opportunistic pulmonary disease with species diversity showing significant regional variation. In the United States, Hawai’i shows the highest rate of NTM pulmonary disease. The need for improved understanding of NTM reservoirs led us to identify NTM from patient respirato...
Article
Full-text available
Free-living amoebae are ubiquitous in aquatic environments and act as environmental reservoirs for nontuberculous mycobacteria. Mycobacterium avium subsp. hominissuis recovered from Acanthamoeba has been demonstrated to be more virulent in both human and murine models. Here, we investigate the persistence of M. avium subsp. hominissuis after short-...
Article
Full-text available
Globally and in the United States, the prevalence of NTM pulmonary disease—a potentially life-threatening but underdiagnosed chronic illness—is prominently rising. While NTM are ubiquitous in the environment, including in soil, the specific soil components that promote or inhibit NTM growth have not been elucidated. We hypothesized that NTM culture...
Article
Full-text available
Background: Nontuberculous mycobacterial (NTM) infections are increasing in prevalence, with current estimates suggesting that over 100,000 people in the United States are affected each year. It is unclear how certain species of mycobacteria transition from environmental bacteria to clinical pathogens, or what genetic elements influence the differ...
Preprint
Full-text available
Background: The increasing incidence of drug resistance in tuberculosis and other infectious diseases poses an escalating cause for concern, emphasizing the urgent need to devise robust computational and molecular methods identify drug resistant strains. Although machine learning-based approaches using whole-genome sequence data can facilitate the...
Preprint
Full-text available
Background Nontuberculous mycobacterial (NTM) infections are increasing in prevalence, with current estimates suggesting that over 100,000 people in the United States are affected each year. It is unclear how certain species of mycobacteria transition from environmental bacteria to clinical pathogens, or what genetic elements influence the differen...
Preprint
Full-text available
Background Nontuberculous mycobacterial (NTM) infections are increasing in prevalence, with current estimates suggesting that over 100,000 people in the United States are affected each year. It is unclear how certain species of mycobacteria transition from environmental bacteria to clinical pathogens, or what genetic elements influence the differen...
Article
Full-text available
Comparisons in infectivity among the clinically important nontuberculous mycobacterial (NTM) species have not been explored in great depth. Rapid-growing mycobacteria including Mycobacterium abscessus and Mycobacterium porcinum can cause indolent, but progressive lung disease. Slow-growing members of the Mycobacterium avium complex (MAC) are the mo...
Preprint
Full-text available
Nontuberculous mycobacteria (NTM) pose a threat to individuals with cystic fibrosis (CF) due to an increased prevalence of pulmonary infections, innate drug resistance of the bacteria, and potential transmission between CF patients. To explore the genetic diversity of NTM isolated from CF patients within the United States (US) and to identify poten...
Article
Full-text available
Mycobacterium chelonae is a member of the Mycobacterium chelonae-abscessus complex and a cause of opportunistic disease in fish, reptiles, birds, and mammals including humans. Isolates in the complex are often difficult to identify and have differing antimicrobial susceptibili-ties. Thirty-one previously identified rapidly-growing, non-tuberculous...
Data
Phylogenetic comparison of Mycobacterium chelonae-abscessus isolates by 16S rRNA analysis. Phylogenetic comparison of Mycobacterium chelonae-abscessus complex isolates relative to eight GenBank sequences using the 16S rRNA 1,522 bp locus and two M. syngnathidarum outliers as an outgroup. Phylogeny was produced using the best scoring Maximum Likelih...
Data
Phylogenetic comparison of Mycobacterium chelonae-abscessus isolates by 16S rRNA analysis. Phylogenetic comparison of Mycobacterium chelonae-abscessus complex isolates relative to eight GenBank sequences and sequences from Noguiera et al. (2007) using the 16S rRNA 1,522 bp locus and two M. syngnathidarum outliers as an outgroup. Phylogeny was produ...
Data
Nucleotide location substitution for whole 16S sequence of M. chelonae isolates. Delineation of sequevars identified within clinical isolates at 16S rRNA. (XLSX)
Data
dDNA-DNA hybridization of M. chelonae-abscessus isolates and two M. syngnathidarum outliers. dDDH relatedness of clinical isolates compared to M. chelonae ATCC 35752T and “M. chelonae chemovar niacinogenes” ATCC 19237. Confidence intervals are denoted within brackets. (XLSX)
Data
Drug susceptibility data of Mycobacterium chelonae-abscessus clinical isolates reported as MICs.a a Green shading represents susceptible (S); Green to yellow shading represents intermediate susceptible (I); Red to yellow shading represents intermediate resistant (I); Red shading represents resistant (R). Susceptibility patterns interpreted using CL...
Data
Phylogenetic comparison of Mycobacterium chelonae-abscessus isolates by ITS analysis. Phylogenetic comparison of Mycobacterium sp. clinical isolates relative to eight reference sequences at the ITS locus using two M. syngnathidarum outliers as an outgroup. Phylogeny was produced using the best scoring Maximum Likelihood model with 1000 bootstrap re...
Data
Phylogenetic comparison of Mycobacterium chelonae-abscessus isolates by 16S rRNA, rpoB and hsp65 analysis. Phylogenetic comparison of Mycobacterium chelonae-abscessus clinical isolates from the USA, Belgium, and Germany relative to four GenBank sequences and two M. syngnathidarum outliers using the concatenated whole hsp65 1,626 bp, partial rpoB 75...
Data
Phylogenetic comparison of Mycobacterium chelonae-abscessus isolates by partial hsp65 PRA analysis. Summary of in-silico PCR-restriction length polymorphism analysis results performed on the partial hsp65 (441 bp) fragment (hsp65 PRA). Results are arranged according to the Taylor et al. (63) algorithm with slight modification to account for fragmen...
Data
Phylogenetic comparison of Mycobacterium chelonae-abscessus isolates by partial rpoB analysis. Phylogenetic comparison of Mycobacterium chelonae-abscessus isolates relative to six reference strains and two M. syngnathidarum outliers at the partial rpoB 752 bp locus. Phylogeny was produced using the best scoring Maximum Likelihood model with 1000 bo...
Data
Phylogenetic comparison of Mycobacterium chelonae-abscessus isolates by rpoB and hsp65 analysis. Phylogenetic comparison of Mycobacterium chelonae-abscessus clinical isolates relative to seven reference sequences and two M. syngnathidarum outliers using the concatenated whole hsp65 1,626 bp and partial rpoB 752 bp sequences. Phylogeny was produced...
Article
Full-text available
A surgical heater–cooler unit has been implicated as the source for Mycobacterium chimaera infections among cardiac surgery patients in several countries. We isolated M. chimaera from heater–cooler units and patient infections in the United States. Whole-genome sequencing corroborated a risk for these units acting as a reservoir for this pathogen.
Article
Full-text available
Accurate and timely mycobacterial species identification is imperative for successful diagnosis, treatment, and management of disease caused by nontuberculous mycobacteria (NTM). The current most widely utilized method for NTM species identification is Sanger sequencing of one or more genomic loci, followed by BLAST sequence analysis. MALDI-TOF MS...
Article
Full-text available
Mycobacterium chimaera, a nontuberculous mycobacterium (NTM) belonging to the Mycobacterium avium complex (MAC), is an opportunistic pathogen that can cause respiratory and disseminated disease. We report the complete genome sequence of a strain, SJ42, isolated from an immunocompromised male presenting with MAC pneumonia, assembled from Illumina an...
Article
Full-text available
A novel slowly growing, non-chromogenic species of the class Actinobacteria was isolated from a human respiratory sample in Nebraska, USA, in 2012. Analysis of the internal transcribed spacer sequence supported placement into the genus Mycobacterium with high sequence similarity to a previously undescribed strain isolated from a patient respiratory...
Article
Full-text available
Mycobacterium chimaera is a nontuberculous mycobacterium species commonly found in the environment. Here, we report the first complete genome sequence of a strain from the investigation of invasive infections following open-heart surgeries that used contaminated LivaNova Sorin Stockert 3T heater-cooler devices.
Article
Full-text available
Mycobacterium avium subsp. hominissuis is an environmentally acquired bacterium known to cause pulmonary and soft tissue infections, lymphadenitis, and disseminated disease in humans. We report here the complete genome sequence of strain H87, isolated from an indoor water sample, as a single circular chromosome of 5,626,623 bp with a G+C content of...
Article
Full-text available
Mycobacterium chimaera is a nontuberculous mycobacterial species that causes cardiovascular, pulmonary, and postsurgical infections. Here, we report the first complete genome sequence of M. chimaera . This genome is 6.33 Mbp, with a G+C content of 67.56%, and encodes 4,926 protein-coding genes, as well as 74 tRNAs, one ncRNA, and three rRNA genes.
Article
Full-text available
[This corrects the article DOI: 10.1371/journal.pntd.0005068.].
Article
Full-text available
Background. There is an ongoing multinational outbreak of invasive M. chimaera (Mc) infections linked to heater-cooler devices (HCDs) used during cardiopulmonary bypass (CPB). We report the experience of 4 US centers. Methods. Cases were persons with a positive culture for Mc (or M. avium complex if species ID not done) from normally sterile sites...
Article
Full-text available
Lung disease caused by nontuberculous mycobacteria (NTM) is an emerging infectious disease of global significance. Epidemiologic studies have shown the Hawaiian Islands have the highest prevalence of NTM lung infections in the United States. However, potential environmental reservoirs and species diversity have not been characterized. In this cross...
Data
Accession Numbers For Study Isolates. Mycobacteria isolates derived from Hawaiian Island and Continental U.S.A. clinical and household specimens. Species identification and NCBI GenBank accession numbers are provided for each isolate. (PDF)
Article
Full-text available
In the spring of 2015, investigators in Switzerland reported a cluster of six patients with invasive infection with Mycobacterium chimaera, a species of nontuberculous mycobacterium ubiquitous in soil and water. The infected patients had undergone open-heart surgery that used contaminated heater-cooler devices during extracorporeal circulation (1)....
Conference Paper
Rationale: Hawai'i currently has the highest rate of NTM lung disease in the United States. Our previous work indicated that Mycobacterium chimaera predominates in clinical samples and household environments in Hawai’i. It is plausible that environmental NTM may vary in virulence compared to clinical isolates. We previously showed a unique virulenc...
Article
Full-text available
We report the draft genome of Elizabethkingia strain ATCC 33958, which has been classified as Elizabethkingia miricola. Similar to other Elizabethkingia species, the ATCC 33958 draft genome contains numerous β-lactamase genes. ATCC 33958 also harbors a urease gene cluster which supports classification as E. miricola. Copyright © 2015 Matyi et al.
Article
Full-text available
Mycobacterium chelonae is a rapidly growing opportunistic nontuberculous mycobacterial (NTM) species that causes infections in humans and other hosts. Here, we report the draft genome sequence of Mycobacterium chelonae type strain ATCC 35752, consisting of 4.89 Mbp, 63.96% G+C content, 4,489 protein-coding genes, 48 tRNAs, and 3 rRNA genes. FOOTNOT...
Conference Paper
Rationale: The prevalence of environmental nontuberculous mycobacteria (NTM) has not been described for Hawai’i, which currently has the highest rate of NTM lung disease in the United States (US) among persons aged 65 and older. Previous studies on the continental US demonstrate recovery of complex (MAC) including M. avium and M. intracellulare fro...
Article
Full-text available
Nontuberculous mycobacterial infections caused by Mycobacterium abscessus are responsible for a range of disease manifestations from pulmonary to skin infections and are notoriously difficult to treat, due to innate resistance to many antibiotics. Previous population studies of clinical M. abscessus isolates utilized multilocus sequence typing or p...
Article
Full-text available
Three recently sequenced strains isolated from patients during an outbreak of Mycobacterium abscessus subsp. massiliense infections at a cystic fibrosis center in the United States were compared with 6 strains from an outbreak at a cystic fibrosis center in the United Kingdom and worldwide strains. Strains from the 2 cystic fibrosis outbreaks showe...
Data
Single nucleotide polymorphisms shared and unique for subsets of Mycobacterium abscessus isolates from cystic fibrosis and soft tissue outbreak localities.
Article
Full-text available
Several epidemiology studies suggest that host genetic factors play important roles in susceptibility, protection and progression of tuberculosis infection. Here we have reviewed the implications of some genetic polymorphisms in pathways related to tuberculosis susceptibility, severity and development. Large case-control studies examining single-nu...
Article
Full-text available
Rapidly growing, non-tuberculous mycobacteria (NTM) in the Mycobacterium abscessus (MAB) species are emerging pathogens that cause various diseases including skin and respiratory infections. The species has undergone recent taxonomic nomenclature refinement, and is currently recognized as two subspecies, M. abscessus subsp. abscessus (MAB-A) and M....
Conference Paper
Full-text available
Background / Purpose: Tuberculosis is a leading cause of death due to infectious disease in the world, with an estimated 1.4 million deaths per year. There has been an upsurge in the emergence of multiple (MDR) and extremely (XDR) drug-resistant strains of M. tuberculosis in recent years, threatening to make the disease more difficult to treat or...