Publications by authors named "Natalia A Kozak-Muiznieks"

13 Publications

  • Page 1 of 1

Genomic heterogeneity differentiates clinical and environmental subgroups of Legionella pneumophila sequence type 1.

PLoS One 2018 18;13(10):e0206110. Epub 2018 Oct 18.

Pneumonia Response and Surveillance Laboratory, Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States of America.

Legionella spp. are the cause of a severe bacterial pneumonia known as Legionnaires' disease (LD). In some cases, current genetic subtyping methods cannot resolve LD outbreaks caused by common, potentially endemic L. pneumophila (Lp) sequence types (ST), which complicates laboratory investigations and environmental source attribution. In the United States (US), ST1 is the most prevalent clinical and environmental Lp sequence type. In order to characterize the ST1 population, we sequenced 289 outbreak and non-outbreak associated clinical and environmental ST1 and ST1-variant Lp strains from the US and, together with international isolate sequences, explored their genetic and geographic diversity. The ST1 population was highly conserved at the nucleotide level; 98% of core nucleotide positions were invariant and environmental isolates unassociated with human disease (n = 99) contained ~65% more nucleotide diversity compared to clinical-sporadic (n = 139) or outbreak-associated (n = 28) ST1 subgroups. The accessory pangenome of environmental isolates was also ~30-60% larger than other subgroups and was enriched for transposition and conjugative transfer-associated elements. Up to ~10% of US ST1 genetic variation could be explained by geographic origin, but considerable genetic conservation existed among strains isolated from geographically distant states and from different decades. These findings provide new insight into the ST1 population structure and establish a foundation for interpreting genetic relationships among ST1 strains; these data may also inform future analyses for improved outbreak investigations.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0206110PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6193728PMC
March 2019

Comparative genome analysis reveals a complex population structure of Legionella pneumophila subspecies.

Infect Genet Evol 2018 04 7;59:172-185. Epub 2018 Feb 7.

Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States. Electronic address:

The majority of Legionnaires' disease (LD) cases are caused by Legionella pneumophila, a genetically heterogeneous species composed of at least 17 serogroups. Previously, it was demonstrated that L. pneumophila consists of three subspecies: pneumophila, fraseri and pascullei. During an LD outbreak investigation in 2012, we detected that representatives of both subspecies fraseri and pascullei colonized the same water system and that the outbreak-causing strain was a new member of the least represented subspecies pascullei. We used partial sequence based typing consensus patterns to mine an international database for additional representatives of fraseri and pascullei subspecies. As a result, we identified 46 sequence types (STs) belonging to subspecies fraseri and two STs belonging to subspecies pascullei. Moreover, a recent retrospective whole genome sequencing analysis of isolates from New York State LD clusters revealed the presence of a fourth L. pneumophila subspecies that we have termed raphaeli. This subspecies consists of 15 STs. Comparative analysis was conducted using the genomes of multiple members of all four L. pneumophila subspecies. Whereas each subspecies forms a distinct phylogenetic clade within the L. pneumophila species, they share more average nucleotide identity with each other than with other Legionella species. Unique genes for each subspecies were identified and could be used for rapid subspecies detection. Improved taxonomic classification of L. pneumophila strains may help identify environmental niches and virulence attributes associated with these genetically distinct subspecies.
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http://dx.doi.org/10.1016/j.meegid.2018.02.008DOI Listing
April 2018

Complete Genome Sequences of Legionella pneumophila subsp. fraseri Strains Detroit-1 and Dallas 1E.

Genome Announc 2017 Feb 2;5(5). Epub 2017 Feb 2.

Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA

We report here the complete genome sequences of two of the earliest known strains of Legionella pneumophila subsp. fraseri Detroit-1 is serogroup 1 and was isolated from a lung biopsy specimen in 1977. Dallas 1E is serogroup 5 and was isolated in 1978 from a cooling tower.
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http://dx.doi.org/10.1128/genomeA.01525-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5289675PMC
February 2017

Lessons From an Outbreak of Legionnaires' Disease on a Hematology-Oncology Unit.

Infect Control Hosp Epidemiol 2017 03 6;38(3):306-313. Epub 2016 Dec 6.

2Centers for Disease Control and Prevention,Atlanta,Georgia.

OBJECTIVES To define the scope of an outbreak of Legionnaires' disease (LD), to identify the source, and to stop transmission. DESIGN AND SETTING Epidemiologic investigation of an LD outbreak among patients and a visitor exposed to a newly constructed hematology-oncology unit. METHODS An LD case was defined as radiographically confirmed pneumonia in a person with positive urinary antigen testing and/or respiratory culture for Legionella and exposure to the hematology-oncology unit after February 20, 2014. Cases were classified as definitely or probably healthcare-associated based on whether they were exposed to the unit for all or part of the incubation period (2-10 days). We conducted an environmental assessment and collected water samples for culture. Clinical and environmental isolates were compared by monoclonal antibody (MAb) and sequence-based typing. RESULTS Over a 12-week period, 10 cases were identified, including 6 definite and 4 probable cases. Environmental sampling revealed Legionella pneumophila serogroup 1 (Lp1) in the potable water at 9 of 10 unit sites (90%), including all patient rooms tested. The 3 clinical isolates were identical to environmental isolates from the unit (MAb2-positive, sequence type ST36). No cases occurred with exposure after the implementation of water restrictions followed by point-of-use filters. CONCLUSIONS Contamination of the unit's potable water system with Lp1 strain ST36 was the likely source of this outbreak. Healthcare providers should routinely test patients who develop pneumonia at least 2 days after hospital admission for LD. A single case of LD that is definitely healthcare associated should prompt a full investigation. Infect Control Hosp Epidemiol 2017;38:306-313.
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http://dx.doi.org/10.1017/ice.2016.281DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5887123PMC
March 2017

Legionella clemsonensis sp. nov.: a green fluorescing Legionella strain from a patient with pneumonia.

Microbiol Immunol 2016 Oct;60(10):694-701

Department of Biological Sciences, Life Sciences Building.

A novel Legionella species was identified based on sequencing, cellular fatty acid analysis, biochemical reactions, and biofilm characterization. Strain D5610 was originally isolated from the bronchial wash of a patient in Ohio, USA. The bacteria were gram-negative, rod-shaped, and exhibited green fluorescence under long wave UV light. Phylogenetic analysis and fatty acid composition revealed a distinct separation within the genus. The strain grows between 26-45°C and forms biofilms equivalent to L. pneumophila Philadelphia 1. These characteristics suggest that this isolate is a novel Legionella species, for which the name Legionella clemsonensis sp nov. is proposed.
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http://dx.doi.org/10.1111/1348-0421.12439DOI Listing
October 2016

Legionnaires' Disease Outbreak at a Resort in Cozumel, Mexico.

Open Forum Infect Dis 2016 Sep 10;3(3):ofw170. Epub 2016 Aug 10.

Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública , Cuernavaca, Morelos , Mexico.

 A Legionnaires' disease (LD) outbreak at a resort on Cozumel Island in Mexico was investigated by a joint Mexico-United States team in 2010. This is the first reported LD outbreak in Mexico, where LD is not a reportable disease.  Reports of LD among travelers were solicited from US health departments and the European Working Group for Infections. Records from the resort and Cozumel Island health facilities were searched for possible LD cases. In April 2010, the resort was searched for possible exposure sources. The temperature and total chlorine of the water at 38 sites in the resort were measured, and samples from those sites were tested for .  Nine travelers became ill with laboratory-confirmed LD within 2 weeks of staying at the resort between May 2008 and April 2010. The resort and its potable water system were the only common exposures. No possible LD cases were identified among resort workers. were found to have extensively colonized the resort's potable water system. matching a case isolate were found in the resort's potable water system.  Medical providers should test for LD when treating community-acquired pneumonia that is severe or affecting patients who traveled in the 2 weeks before the onset of symptoms. When an LD outbreak is detected, the source should be identified and then aggressively remediated. Because LD can occur in tropical and temperate areas, all countries should consider making LD a reportable disease if they have not already done so.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5047414PMC
http://dx.doi.org/10.1093/ofid/ofw170DOI Listing
September 2016

Dynamics of genome change among Legionella species.

Sci Rep 2016 09 16;6:33442. Epub 2016 Sep 16.

Department of Medicine and University of California, San Francisco, San Francisco, California, USA.

Legionella species inhabit freshwater and soil ecosystems where they parasitize protozoa. L. pneumonphila (LP) serogroup-1 (Lp1) is the major cause of Legionnaires' Disease (LD), a life-threatening pulmonary infection that can spread systemically. The increased global frequency of LD caused by Lp and non-Lp species underscores the need to expand our knowledge of evolutionary forces underlying disease pathogenesis. Whole genome analyses of 43 strains, including all known Lp serogroups 1-17 and 17 emergent LD-causing Legionella species (of which 33 were sequenced in this study) in addition to 10 publicly available genomes, resolved the strains into four phylogenetic clades along host virulence demarcations. Clade-specific genes were distinct for genetic exchange and signal-transduction, indicating adaptation to specific cellular and/or environmental niches. CRISPR spacer comparisons hinted at larger pools of accessory DNA sequences in Lp than predicted by the pan-genome analyses. While recombination within Lp was frequent and has been reported previously, population structure analysis identified surprisingly few DNA admixture events between species. In summary, diverse Legionella LD-causing species share a conserved core-genome, are genetically isolated from each other, and selectively acquire genes with potential for enhanced virulence.
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http://dx.doi.org/10.1038/srep33442DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5025774PMC
September 2016

Three Genome Sequences of Legionella pneumophila subsp. pascullei Associated with Colonization of a Health Care Facility.

Genome Announc 2016 May 5;4(3). Epub 2016 May 5.

Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA

Here, we report the complete genome sequences of three Legionella pneumophila subsp. pascullei strains (including both serogroup 1 and 5 strains) that were found in the same health care facility in 1982 and 2012.
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http://dx.doi.org/10.1128/genomeA.00335-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4859183PMC
May 2016

Genomic Resolution of Outbreak-Associated Legionella pneumophila Serogroup 1 Isolates from New York State.

Appl Environ Microbiol 2016 06 31;82(12):3582-3590. Epub 2016 May 31.

Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA

Unlabelled: A total of 30 Legionella pneumophila serogroup 1 isolates representing 10 separate legionellosis laboratory investigations ("outbreaks") that occurred in New York State between 2004 and 2012 were selected for evaluation of whole-genome sequencing (WGS) approaches for molecular subtyping of this organism. Clinical and environmental isolates were available for each outbreak and were initially examined by pulsed-field gel electrophoresis (PFGE). Sequence-based typing alleles were extracted from WGS data yielding complete sequence types (ST) for isolates representing 8 out of the 10 outbreaks evaluated in this study. Isolates from separate outbreaks sharing the same ST also contained the fewest differences in core genome single nucleotide polymorphisms (SNPs) and the greatest proportion of identical allele sequences in a whole-genome multilocus sequence typing (wgMLST) scheme. Both core SNP and wgMLST analyses distinguished isolates from separate outbreaks, including those from two outbreaks sharing indistinguishable PFGE profiles. Isolates from a hospital-associated outbreak spanning multiple years shared indistinguishable PFGE profiles but displayed differences in their genome sequences, suggesting the presence of multiple environmental sources. Finally, the rtx gene demonstrated differences in the repeat region sequence among ST1 isolates from different outbreaks, suggesting that variation in this gene may be useful for targeted molecular subtyping approaches for L. pneumophila This study demonstrates the utility of various genome sequence analysis approaches for L. pneumophila for environmental source attribution studies while furthering the understanding of Legionella ecology.

Importance: We demonstrate that whole-genome sequencing helps to improve resolution of Legionella pneumophila isolated during laboratory investigations of legionellosis compared to traditional subtyping methods. These data can be important in confirming the environmental sources of legionellosis outbreaks. Moreover, we evaluated various methods to analyze genome sequence data to help resolve outbreak-related isolates.
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http://dx.doi.org/10.1128/AEM.00362-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4959152PMC
June 2016

Legionellosis Outbreak Associated With a Hotel Fountain.

Open Forum Infect Dis 2015 Dec 28;2(4):ofv164. Epub 2015 Dec 28.

Chicago Department of Public Health, Illinois.

Background.  In August 2012, the Chicago Department of Public Health (CDPH) was notified of acute respiratory illness, including 1 fatality, among a group of meeting attendees who stayed at a Chicago hotel during July 30-August 3, 2012. Suspecting Legionnaires' disease (LD), CDPH advised the hotel to close their swimming pool, spa, and decorative lobby fountain and began an investigation. Methods.  Case finding included notification of individuals potentially exposed during July 16-August 15, 2012. Individuals were interviewed using a standardized questionnaire. An environmental assessment was performed. Results.  One hundred fourteen cases were identified: 11 confirmed LD, 29 suspect LD, and 74 Pontiac fever cases. Illness onsets occurred July 21-August 22, 2012. Median age was 48 years (range, 22-82 years), 64% were male, 59% sought medical care (15 hospitalizations), and 3 died. Relative risks for hotel exposures revealed that persons who spent time near the decorative fountain or bar, both located in the lobby were respectively 2.13 (95%, 1.64-2.77) and 1.25 (95% CI, 1.09-1.44) times more likely to become ill than those who did not. Legionella pneumophila serogroup 1 was isolated from samples collected from the fountain, spa, and women's locker room fixtures. Legionella pneumophila serogroup 1 environmental isolates and a clinical isolate had matching sequence-based types. Hotel maintenance records lacked a record of regular cleaning and disinfection of the fountain. Conclusions.  Environmental testing identified Legionella in the hotel's potable water system. Epidemiologic and laboratory data indicated the decorative fountain as the source. Poor fountain maintenance likely created favorable conditions for Legionella overgrowth.
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http://dx.doi.org/10.1093/ofid/ofv164DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4692259PMC
December 2015

The importance of clinical surveillance in detecting legionnaires' disease outbreaks: a large outbreak in a hospital with a Legionella disinfection system-Pennsylvania, 2011-2012.

Clin Infect Dis 2015 Jun 25;60(11):1596-602. Epub 2015 Feb 25.

Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia.

Background: Healthcare-associated Legionnaires' disease (LD) is a preventable pneumonia with a 30% case fatality rate. The Centers for Disease Control and Prevention guidelines recommend a high index of suspicion for the diagnosis of healthcare-associated LD. We characterized an outbreak and evaluated contributing factors in a hospital using copper-silver ionization for prevention of Legionella growth in water.

Methods: Through medical records review at a large, urban tertiary care hospital in November 2012, we identified patients diagnosed with LD during 2011-2012. Laboratory-confirmed cases were categorized as definite, probable, and not healthcare associated based on time spent in the hospital during the incubation period. We performed an environmental assessment of the hospital, including collection of samples for Legionella culture. Clinical and environmental isolates were compared by genotyping. Copper and silver ion concentrations were measured in 11 water samples.

Results: We identified 5 definite and 17 probable healthcare-associated LD cases; 6 case patients died. Of 25 locations (mostly potable water) where environmental samples were obtained for Legionella-specific culture, all but 2 showed Legionella growth; 11 isolates were identical to 3 clinical isolates by sequence-based typing. Mean copper and silver concentrations were at or above the manufacturer's recommended target for Legionella control. Despite this, all samples where copper and silver concentrations were tested showed Legionella growth.

Conclusions: This outbreak was linked to the hospital's potable water system and highlights the importance of maintaining a high index of suspicion for healthcare-associated LD, even in the setting of a long-term disinfection program.
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http://dx.doi.org/10.1093/cid/civ153DOI Listing
June 2015

Draft Genome Sequence of Legionella pneumophila D-5864, a Serogroup 6 Strain.

Genome Announc 2015 Jan 8;3(1). Epub 2015 Jan 8.

Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA

Legionella pneumophila is the leading etiology of legionellosis infections in North America and Europe. Here we report the draft genome sequence of L. pneumophila D-5864, a serogroup 6 strain, which was isolated from a bronchial alveolar lavage specimen of a male patient from Arizona in 2009. Genes within the lipopolysaccharide (LPS)-biosynthesis region could potentially be determinants of serogroup specificity.
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http://dx.doi.org/10.1128/genomeA.01379-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4290988PMC
January 2015

Prevalence of sequence types among clinical and environmental isolates of Legionella pneumophila serogroup 1 in the United States from 1982 to 2012.

J Clin Microbiol 2014 Jan 6;52(1):201-11. Epub 2013 Nov 6.

Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.

Since the establishment of sequence-based typing as the gold standard for DNA-based typing of Legionella pneumophila, the Legionella laboratory at the Centers for Disease Control and Prevention (CDC) has conducted routine sequence-based typing (SBT) analysis of all incoming L. pneumophila serogroup 1 (Lp1) isolates to identify potential links between cases and to better understand genetic diversity and clonal expansion among L. pneumophila bacteria. Retrospective genotyping of Lp1 isolates from sporadic cases and Legionnaires' disease (LD) outbreaks deposited into the CDC reference collection since 1982 has been completed. For this study, we compared the distribution of sequence types (STs) among Lp1 isolates implicated in 26 outbreaks in the United States, 571 clinical isolates from sporadic cases of LD in the United States, and 149 environmental isolates with no known association with LD. The Lp1 isolates under study had been deposited into our collection between 1982 and 2012. We identified 17 outbreak-associated STs, 153 sporadic STs, and 49 environmental STs. We observed that Lp1 STs from outbreaks and sporadic cases are more similar to each other than either group is to environmental STs. The most frequent ST for both sporadic and environmental isolates was ST1, accounting for 25% and 49% of the total number of isolates, respectively. The STs shared by both outbreak-associated and sporadic Lp1 included ST1, ST35, ST36, ST37, and ST222. The STs most commonly found in sporadic and outbreak-associated Lp1 populations may have an increased ability to cause disease and thus may require special attention when detected.
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http://dx.doi.org/10.1128/JCM.01973-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3911437PMC
January 2014