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Yang AF, Sherman A, Nazarian E, Haas W, Mehr J, Pedrani M, Kirn T, Brant S, Boruchoff SE, Kaye KS, Mills JP. Evidence of transmission of New Delhi metallo-β-lactamase-producing Klebsiella pneumoniae through a gastrointestinal endoscope without an elevator channel. Infect Control Hosp Epidemiol 2024:1-6. [PMID: 38563218 DOI: 10.1017/ice.2024.55] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
OBJECTIVE To investigate the source and transmission dynamics of an endoscope-associated New Delhi metallo-β-lactamase-producing Klebsiella pneumonia (NDM-KP) outbreak. DESIGN Epidemiological and genomic investigation. SETTING Academic acute care hospital in New Jersey. PATIENTS Five patients with active NDM-KP infection identified on clinical isolates, and four NDM-KP colonized patients identified via rectal swab screening. RESULTS Over a twelve-month period, nine patients were identified with NDM-KP infection or colonization. Whole-genome sequencing (WGS) revealed that all of the identified cases were related by 25 mutational events or less. Seven of the cases were linked to gastrointestinal endoscopic procedures (four clinical cases and three positive screens among patients exposed to endoscopes suspected of transmission). Two cases demonstrated delayed transmission that occurred five months after the initial outbreak, likely through shared usage of a non-therapeutic gastroscope without an elevator channel. CONCLUSIONS Although all endoscope cultures in our investigation were negative, the epidemiological link to gastrointestinal endoscopes, the high degree of relatedness via WGS, and the identification of asymptomatic NDM-KP colonization among patients exposed to shared endoscopes make the endoscopic mode of transmission most likely. This investigation highlights the probable transmission of NDM-KP via a gastroscope without an elevator channel, observed several months after an initial outbreak. We hypothesize that persistent mechanical defects may have contributed to the delayed device-related transmission of NDM-KP.
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Affiliation(s)
- Ann Fan Yang
- Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Adrienne Sherman
- Communicable Disease Service, New Jersey Department of Health, Trenton, NJ, USA
| | | | - Wolfgang Haas
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Jason Mehr
- Communicable Disease Service, New Jersey Department of Health, Trenton, NJ, USA
| | - Michele Pedrani
- Department of Pathology & Laboratory Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Thomas Kirn
- Department of Pathology & Laboratory Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Steven Brant
- Department of Medicine, Division of Gastroenterology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Susan E Boruchoff
- Department of Medicine, Division of Allergy, Immunology, and Infectious Diseases, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Keith S Kaye
- Department of Medicine, Division of Allergy, Immunology, and Infectious Diseases, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - John P Mills
- Department of Medicine, Division of Allergy, Immunology, and Infectious Diseases, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
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Sabour S, Bantle K, Bhatnagar A, Huang JY, Biggs A, Bodnar J, Dale JL, Gleason R, Klein L, Lasure M, Lee R, Nazarian E, Schneider E, Smith L, Snippes Vagnone P, Therrien M, Tran M, Valley A, Wang C, Young EL, Lutgring JD, Brown AC. Descriptive analysis of targeted carbapenemase genes and antibiotic susceptibility profiles among carbapenem-resistant Acinetobacter baumannii tested in the Antimicrobial Resistance Laboratory Network-United States, 2017-2020. Microbiol Spectr 2024; 12:e0282823. [PMID: 38174931 PMCID: PMC10845962 DOI: 10.1128/spectrum.02828-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 11/16/2023] [Indexed: 01/05/2024] Open
Abstract
Acinetobacter baumannii is a Gram-negative bacillus that can cause severe and difficult-to-treat healthcare-associated infections. A. baumannii can harbor mobile genetic elements carrying genes that produce carbapenemase enzymes, further limiting therapeutic options for infections. In the United States, the Antimicrobial Resistance Laboratory Network (AR Lab Network) conducts sentinel surveillance of carbapenem-resistant Acinetobacter baumannii (CRAB). Participating clinical laboratories sent CRAB isolates to the AR Lab Network for characterization, including antimicrobial susceptibility testing and molecular detection of class A (Klebsiella pneumoniae carbapenemase), class B (Active-on-Imipenem, New Delhi metallo-β-lactamase, and Verona integron-encoded metallo-β-lactamase), and class D (Oxacillinase, blaOXA-23-like, blaOXA-24/40-like, blaOXA-48-like, and blaOXA-58-like) carbapenemase genes. During 2017‒2020, 6,026 CRAB isolates from 45 states were tested for targeted carbapenemase genes; 1% (64 of 5,481) of CRAB tested for targeted class A and class B genes were positive, but 83% (3,351 of 4,041) of CRAB tested for targeted class D genes were positive. The number of CRAB isolates carrying a class A or B gene increased from 2 of 312 (<1%) tested in 2017 to 26 of 1,708 (2%) tested in 2020. Eighty-three percent (2,355 of 2,846) of CRAB with at least one of the targeted carbapenemase genes and 54% (271 of 500) of CRAB without were categorized as extensively drug resistant; 95% (42 of 44) of isolates carrying more than one targeted gene had difficult-to-treat susceptibility profiles. CRAB isolates carrying targeted carbapenemase genes present an emerging public health threat in the United States, and their rapid detection is crucial to improving patient safety.IMPORTANCEThe Centers for Disease Control and Prevention has classified CRAB as an urgent public health threat. In this paper, we used a collection of >6,000 contemporary clinical isolates to evaluate the phenotypic and genotypic properties of CRAB detected in the United States. We describe the frequency of specific carbapenemase genes detected, antimicrobial susceptibility profiles, and the distribution of CRAB isolates categorized as multidrug resistant, extensively drug-resistant, or difficult to treat. We further discuss the proportion of isolates showing susceptibility to Food and Drug Administration-approved agents. Of note, 84% of CRAB tested harbored at least one class A, B, or D carbapenemase genes targeted for detection and 83% of these carbapenemase gene-positive CRAB were categorized as extensively drug resistant. Fifty-four percent of CRAB isolates without any of these carbapenemase genes detected were still extensively drug-resistant, indicating that infections caused by CRAB are highly resistant and pose a significant risk to patient safety regardless of the presence of one of these carbapenemase genes.
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Affiliation(s)
- Sarah Sabour
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Katie Bantle
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Amelia Bhatnagar
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jennifer Y. Huang
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Angela Biggs
- Maryland Department of Health, Baltimore, Maryland, USA
| | | | | | - Rachel Gleason
- Tennessee Department of Health, Nashville, Tennessee, USA
| | - Liore Klein
- Maryland Department of Health, Baltimore, Maryland, USA
| | - Megan Lasure
- Wisconsin State Laboratory of Hygiene, Madison, Wisconsin, USA
| | - Rachel Lee
- Texas Department of State Health Services, Austin, Texas, USA
| | | | - Emily Schneider
- Washington State Department of Health Public Health Laboratories, Shoreline, Washington, USA
| | - Lori Smith
- Utah Public Health Laboratory, Taylorsville, Utah, USA
| | | | | | - Michael Tran
- Washington State Department of Health Public Health Laboratories, Shoreline, Washington, USA
| | - Ann Valley
- Wisconsin State Laboratory of Hygiene, Madison, Wisconsin, USA
| | - Chun Wang
- Texas Department of State Health Services, Austin, Texas, USA
| | - Erin L. Young
- Utah Public Health Laboratory, Taylorsville, Utah, USA
| | - Joseph D. Lutgring
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Allison C. Brown
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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3
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Grossman MK, Rankin DA, Maloney M, Stanton RA, Gable P, Stevens VA, Ewing T, Saunders K, Kogut S, Nazarian E, Bhaurla S, Mephors J, Mongillo J, Stonehocker S, Prignano J, Valencia N, Charles A, McNamara K, Fritsch WA, Ruelle S, Plucinski CA, Sosa L, Ostrowsky B, Ham DC, Walters MS. Extensively Drug-Resistant Pseudomonas aeruginosa Outbreak associated with Artificial Tears. Clin Infect Dis 2024:ciae052. [PMID: 38315890 DOI: 10.1093/cid/ciae052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/09/2024] [Accepted: 01/19/2024] [Indexed: 02/07/2024] Open
Abstract
BACKGROUND Carbapenemase-producing, carbapenem-resistant Pseudomonas aeruginosa (CP-CRPA) are extensively drug resistant bacteria. We investigated the source of a multistate CP-CRPA outbreak. METHODS Cases were defined as a U.S. patient's first isolation of P. aeruginosa sequence type 1203 with the carbapenemase gene blaVIM-80 and cephalosporinase gene blaGES-9 from any specimen source collected and reported to CDC between January 1, 2022-May 15, 2023. We conducted a 1:1 matched case-control study at the post-acute care facility with the most cases, assessed exposures associated with case status for all case-patients, and tested products for bacterial contamination. RESULTS We identified 81 case-patients from 18 states, 27 of whom were identified through surveillance cultures. Four (7%) of 54 case-patients with clinical cultures died within 30 days of culture collection, and four (22%) of 18 with eye infections underwent enucleation. In the case-control study, case-patients had increased odds of receiving artificial tears compared to controls (crude matched OR: 5.0, 95% CI: 1.1, 22.8). Overall, artificial tears use was reported by 61 (87%) of 70 case-patients with information; 43 (77%) of 56 case-patients with brand information reported use of Brand A, an imported, preservative-free, over-the-counter (OTC) product. Bacteria isolated from opened and unopened bottles of Brand A were genetically related to patient isolates. FDA inspection of the manufacturing plant identified likely sources of contamination. CONCLUSIONS A manufactured medical product serving as the vehicle for carbapenemase-producing organisms is unprecedented in the U.S. The clinical impacts from this outbreak underscore the need for improved requirements for U.S. OTC product importers.
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Affiliation(s)
- Marissa K Grossman
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, GA
- Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, GA
| | - Danielle A Rankin
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, GA
| | | | - Richard A Stanton
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, GA
| | - Paige Gable
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, GA
| | - Valerie A Stevens
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, GA
| | - Thomas Ewing
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, GA
| | - Katharine Saunders
- Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, GA
- Florida Department of Health, Tallahassee, FL
| | - Sarah Kogut
- New York State Department of Health, Albany, NY
| | | | - Sandeep Bhaurla
- Los Angeles County Department of Public Health, Los Angeles, CA
| | - Jehan Mephors
- Los Angeles County Department of Public Health, Los Angeles, CA
| | - Joshua Mongillo
- Utah Department of Health and Human Services, Salt Lake City, UT
| | | | | | | | | | - Kiara McNamara
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, GA
- Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, GA
- U.S. Public Health Service, Rockville, MD
| | | | | | | | - Lynn Sosa
- Connecticut Department of Public Health, Hartford, CT
| | - Belinda Ostrowsky
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, GA
| | - D Cal Ham
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, GA
| | - Maroya S Walters
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, GA
- U.S. Public Health Service, Rockville, MD
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4
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Lee J, Sunny S, Nazarian E, Fornek M, Abdallah M, Episcopia B, Rowlinson MC, Quale J. Carbapenem-Resistant Klebsiella pneumoniae in Large Public Acute-Care Healthcare System, New York, New York, USA, 2016-2022. Emerg Infect Dis 2023; 29:1973-1978. [PMID: 37735742 PMCID: PMC10521592 DOI: 10.3201/eid2910.230153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023] Open
Abstract
Controlling the spread of carbapenem-resistant Enterobacterales is a global priority. Using National Healthcare Safety Network data, we characterized the changing epidemiology of carbapenem-resistant Klebsiella pneumoniae (CRKP) in a large public health system in New York, New York, USA. During 2016-2020, CRKP cases declined; however, during 2021-June 2022, a notable increase occurred. Of 509 cases, 262 (51%) were considered community-onset, including 149 in patients who were living at home. Of 182 isolates with proven or presumptive (ceftazidime/avibactam susceptible) enzymes, 143 were serine carbapenemases; most confirmed cases were K. pneumoniae carbapenemase. The remaining 39 cases were proven or presumptive metallo-β-lactamases; all confirmed cases were New Delhi metallo-β-lactamases. After 2020, a marked increase occurred in the percentage of isolates possessing metallo-β-lactamases. Most patients with metallo-β-lactamases originated from long-term care facilities. An aggressive and universal program involving surveillance and isolation will be needed to control the spread of CRKP in the city of New York.
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Haas W, Singh N, Lainhart W, Mingle L, Nazarian E, Mitchell K, Nattanmai G, Kohlerschmidt D, Dickinson MC, Kacica M, Dumas N, Musser KA. Genomic Analysis of Vancomycin-Resistant Staphylococcus aureus Isolates from the 3rd Case Identified in the United States Reveals Chromosomal Integration of the vanA Locus. Microbiol Spectr 2023; 11:e0431722. [PMID: 36975781 PMCID: PMC10100801 DOI: 10.1128/spectrum.04317-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 03/06/2023] [Indexed: 03/29/2023] Open
Abstract
Vancomycin-resistant Staphylococcus aureus (VRSA) is a human pathogen of significant public health concern. Although the genome sequences of individual VRSA isolates have been published over the years, very little is known about the genetic changes of VRSA within a patient over time. A total of 11 VRSA, 3 vancomycin-resistant enterococci (VRE), and 4 methicillin-resistant S. aureus (MRSA) isolates, collected over a period of 4.5 months in 2004 from a patient in a long-term-care facility in New York State, were sequenced. A combination of long- and short-read sequencing technologies was used to obtain closed assemblies for chromosomes and plasmids. Our results indicate that a VRSA isolate emerged as the result of the transfer of a multidrug resistance plasmid from a coinfecting VRE to an MRSA isolate. The plasmid then integrated into the chromosome via homologous recombination mediated between two regions derived from remnants of transposon Tn5405. Once integrated, the plasmid underwent further reorganization in one isolate, while two others lost the staphylococcal cassette chromosome mec element (SCCmec) determinant that confers methicillin-resistance. The results presented here explain how a few recombination events can lead to multiple pulsed-field gel electrophoresis (PFGE) patterns that could be mistaken for vastly different strains. A vanA gene cluster that is located on a multidrug resistance plasmid that is integrated into the chromosome could result in the continuous propagation of resistance, even in the absence of selective pressure from antibiotics. The genome comparison presented here sheds light on the emergence and evolution of VRSA within a single patient that will enhance our understanding VRSA genetics. IMPORTANCE High-level vancomycin-resistant Staphylococcus aureus (VRSA) began to emerge in the United States in 2002 and has since then been reported worldwide. Our study reports the closed genome sequences of multiple VRSA isolates obtained in 2004 from a single patient in New York State. Our results show that the vanA resistance locus is located on a mosaic plasmid that confers resistance to multiple antibiotics. In some isolates, this plasmid integrated into the chromosome via homologous recombination between two ant(6)-sat4-aph(3') antibiotic resistance loci. This is, to our knowledge, the first report of a chromosomal vanA locus in VRSA; the effect of this integration event on MIC values and plasmid stability in the absence of antibiotic selection remains poorly understood. These findings highlight the need for a better understanding of the genetics of the vanA locus and plasmid maintenance in S. aureus to address the increase of vancomycin resistance in the health care setting.
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Affiliation(s)
- Wolfgang Haas
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Navjot Singh
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - William Lainhart
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Lisa Mingle
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Elizabeth Nazarian
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Kara Mitchell
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Geetha Nattanmai
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Donna Kohlerschmidt
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | | | - Marilyn Kacica
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Nellie Dumas
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Kimberlee A. Musser
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
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Chan JL, Nazarian E, Musser KA, Snavely EA, Fung M, Doernberg SB, Pouch SM, Leekha S, Anesi JA, Kodiyanplakkal RP, Turbett SE, Walters MS, Epstein L. Prevalence of carbapenemase-producing organisms among hospitalized solid organ transplant recipients, five U.S. hospitals, 2019-2020. Transpl Infect Dis 2022; 24:e13785. [PMID: 34989092 DOI: 10.1111/tid.13785] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 11/29/2021] [Accepted: 12/03/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND Passive reporting to the Centers for Disease Control and Prevention has identified carbapenemase-producing organisms (CPOs) among solid organ transplant (SOT) recipients, potentially representing an emerging source of spread. We analyzed CPO prevalence in wards where SOT recipients receive inpatient care to inform public health action to prevent transmission. METHODS From September 2019 to June 2020, five U.S. hospitals conducted consecutive point prevalence surveys (PPS) of all consenting patients admitted to transplant units, regardless of transplant status. We used the Cepheid Xpert® Carba-R assay to identify carbapenemase genes (blaKPC , blaNDM , blaVIM , blaIMP , blaOXA-48 ) from rectal swabs. Laboratory-developed molecular tests were used to retrospectively test for a wider range of blaIMP and blaOXA variants. RESULTS In total, 154 patients were screened and 92 (60%) were SOT recipients. CPOs were detected among 7 (8%) SOT recipients, from two of five screened hospitals: 4 blaKPC , 1 blaNDM , 2 blaOXA-23 . CPOs were detected in 2 (3%) of 62 non-transplant patients. In three of five participating hospitals, CPOs were not identified among any patients admitted to transplant units. CONCLUSIONS Longitudinal surveillance in transplant units, as well as PPS in areas with diverse CPO epidemiology, may inform the utility of routine screening in SOT units to prevent the spread of CPOs. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- June L Chan
- Wadsworth Center, New York State Department of Health, Albany, NY
| | | | | | - Emily A Snavely
- Wadsworth Center, New York State Department of Health, Albany, NY
| | - Monica Fung
- University of California San Francisco, San Francisco, CA
| | | | | | - Surbhi Leekha
- University of Maryland Medical Center, Baltimore, MD
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Schoonmaker-Bopp D, Nazarian E, Dziewulski D, Clement E, Baker DJ, Dickinson MC, Saylors A, Codru N, Thompson L, Lapierre P, Dumas N, Limberger R, Musser KA. Improvements to the Success of Outbreak Investigations of Legionnaires' Disease: 40 Years of Testing and Investigation in New York State. Appl Environ Microbiol 2021; 87:e0058021. [PMID: 34085864 PMCID: PMC8315175 DOI: 10.1128/aem.00580-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 05/21/2021] [Indexed: 12/04/2022] Open
Abstract
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 (1,022 and 1,426, respectively). Over the course of more than 40 years, the WC Legionella testing program has continuously implemented improved testing methods. The methods utilized have transitioned 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 observed in other published reports. The consistent application of new cutting-edge technologies and environmental regulations has 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 (https://www.cdc.gov/legionella/fastfacts.html; https://wonder.cdc.gov/nndss/static/2018/annual/2018-table2h.html), 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 is spread predominantly through engineered building water systems, identifying sources of outbreaks by assessing environmental sources is key to preventing further cases LD.
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Affiliation(s)
| | - Elizabeth Nazarian
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - David Dziewulski
- Bureau of Water Supply Protection, New York State Department of Health, Albany, New York, USA
| | - Ernest Clement
- Bureau of Communicable Disease Control, New York State Department of Health, Albany, New York, USA
| | - Deborah J. Baker
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | | | - Amy Saylors
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Neculai Codru
- Bureau of Water Supply Protection, New York State Department of Health, Albany, New York, USA
| | - Lisa Thompson
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Pascal Lapierre
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Nellie Dumas
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Ronald Limberger
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Kimberlee A. Musser
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
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8
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Chan JL, Nazarian E, Musser KA, Fung M, Doernberg SB, Pouch SM, Pouch SM, Leekha S, Anesi JA, Kodiyanplakkal RP, Turbett S, Walters MS, Epstein L, Epstein L. 918. Pilot Surveillance for Carbapenemase Gene-positive Organisms Among Hospitalized Solid Organ Transplant Recipients. Open Forum Infect Dis 2020. [PMCID: PMC7776677 DOI: 10.1093/ofid/ofaa439.1106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Background Carbapenemase gene-positive organisms (CPOs) are associated with infections with high mortality rates and have the potential to facilitate epidemic spread of carbapenem resistance. Passive reporting to CDC identified CPOs among organ transplant recipients, potentially representing an emerging reservoir for spread. We aimed to determine the prevalence of CPOs in hospital units where solid organ transplant (SOT) recipients receive care in order to inform public health action to prevent transmission. Methods All healthcare facilities identified one medical unit where SOT recipients received inpatient care and conducted point prevalence surveys (PPS) of all consenting patients on 1-2 designated calendar days. We used the Cepheid Xpert® Carba-R assay to identify carbapenemase genes (blaKPC, blaNDM, blaVIM, blaIMP, blaOXA-48) from rectal swabs; carbapenemase-positive swabs were cultured for organisms. All laboratory testing was conducted at the Wadsworth Center, part of CDC’s Antibiotic Resistance Laboratory Network. Results Five participating hospitals performed nine PPS from September 2019 through June 2020. In total, 154 patients were screened and 92 (60%) were SOT recipients (Table). The most common transplanted organs were kidney (44, 48%) and liver (39, 42%). Carbapenemase genes were detected among 5 (5%) SOT recipients, all from a single healthcare facility; 4 (80%) were blaKPC and 1 (20%) was blaNDM. Of the positive specimens cultured, blaKPC was carried by Enterobacter cloacae complex (ECC), Klebsiella pneumoniae, and Klebsiella oxytoca and blaNDM was carried by K. oxytoca; blaKPC was carried by both ECC and K. pneumoniae in a single individual. For SOT patients with CPOs, the median interval from transplantation to swab collection was 108 days (range: 12 to 323). CPOs were only detected in 1 (2%) of 62 non-transplant patients. TABLE Characteristics of Carbapenemase Gene-positive Organism (CPO) Pilot Surveillance Participants ![]()
Conclusion Among participating facilities, most did not identify CPOs among patients admitted to transplant units. These findings represent a small number of patients and facilities; additional PPS in areas with varied CPO epidemiology are needed to understand whether SOT recipients should be routinely screened for CPOs. Disclosures All Authors: No reported disclosures
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Affiliation(s)
| | | | | | - Monica Fung
- University of California San Francisco, San Francisco, California
| | | | | | | | | | | | | | | | | | - Lauren Epstein
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Lauren Epstein
- Centers for Disease Control and Prevention, Atlanta, Georgia
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9
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Prussing C, Snavely EA, Singh N, Lapierre P, Lasek-Nesselquist E, Mitchell K, Haas W, Owsiak R, Nazarian E, Musser KA. Nanopore MinION Sequencing Reveals Possible Transfer of bla KPC-2 Plasmid Across Bacterial Species in Two Healthcare Facilities. Front Microbiol 2020; 11:2007. [PMID: 32973725 PMCID: PMC7466660 DOI: 10.3389/fmicb.2020.02007] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 07/29/2020] [Indexed: 11/13/2022] Open
Abstract
Carbapenemase-producing Enterobacteriaceae are a major threat to global public health. Klebsiella pneumoniae carbapenemase (KPC) is the most commonly identified carbapenemase in the United States and is frequently found on mobile genetic elements including plasmids, which can be horizontally transmitted between bacteria of the same or different species. Here we describe the results of an epidemiological investigation of KPC-producing bacteria at two healthcare facilities. Using a combination of short-read and long-read whole-genome sequencing, we identified an identical 44 kilobase plasmid carrying the bla KPC-2 gene in four bacterial isolates belonging to three different species (Citrobacter freundii, Klebsiella pneumoniae, and Escherichia coli). The isolates in this investigation were collected from patients who were epidemiologically linked in a region in which KPC was uncommon, suggesting that the antibiotic resistance plasmid was transmitted between these bacterial species. This investigation highlights the importance of long-read sequencing in investigating the relatedness of bacterial plasmids, and in elucidating potential plasmid-mediated outbreaks caused by antibiotic resistant bacteria.
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Affiliation(s)
- Catharine Prussing
- Wadsworth Center, New York State Department of Health, Albany, NY, United States
| | - Emily A. Snavely
- Wadsworth Center, New York State Department of Health, Albany, NY, United States
| | - Navjot Singh
- Wadsworth Center, New York State Department of Health, Albany, NY, United States
| | - Pascal Lapierre
- Wadsworth Center, New York State Department of Health, Albany, NY, United States
| | | | - Kara Mitchell
- Wadsworth Center, New York State Department of Health, Albany, NY, United States
| | - Wolfgang Haas
- Wadsworth Center, New York State Department of Health, Albany, NY, United States
| | - Rita Owsiak
- Maine Center for Disease Control and Prevention, Department of Health and Human Services, Augusta, ME, United States
| | - Elizabeth Nazarian
- Wadsworth Center, New York State Department of Health, Albany, NY, United States
| | - Kimberlee A. Musser
- Wadsworth Center, New York State Department of Health, Albany, NY, United States
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10
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Bardossy AC, Snavely EA, Nazarian E, Annambhotla P, Basavaraju SV, Pepe D, Maloney M, Musser KA, Haas W, Barros N, Pierce VM, Walters M, Epstein L. Donor-derived transmission through lung transplantation of carbapenem-resistant Acinetobacter baumannii producing the OXA-23 carbapenemase during an ongoing healthcare facility outbreak. Transpl Infect Dis 2020; 22:e13256. [PMID: 32034865 PMCID: PMC10833477 DOI: 10.1111/tid.13256] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 01/13/2020] [Accepted: 01/26/2020] [Indexed: 11/30/2022]
Abstract
We describe a rare instance of donor-derived OXA-23-producing carbapenem-resistant Acinetobacter baumannii transmission during lung transplantation and the subsequent public health response. This investigation highlights how transplantation can introduce rare multidrug-resistant organisms into different healthcare facilities and regions.
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Affiliation(s)
- Ana C. Bardossy
- Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Emily A. Snavely
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | | | - Pallavi Annambhotla
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Sridhar V. Basavaraju
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Dana Pepe
- Yale School of Medicine, New Haven, CT, USA
- Connecticut Department of Public Health, Healthcare-Associated Infections Antimicrobial Resistance Program, Hartford, CT, USA
| | - Meghan Maloney
- Connecticut Department of Public Health, Healthcare-Associated Infections Antimicrobial Resistance Program, Hartford, CT, USA
| | | | - Wolfgang Haas
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Nicolas Barros
- Transplant Infectious Diseases and Compromised Host Program, Massachusetts General Hospital, Boston, MA, USA
| | - Virginia M. Pierce
- Microbiology Laboratory, Pathology Service, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Harvard Medical School, Boston, MA, USA
| | - Maroya Walters
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Lauren Epstein
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
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11
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Bhattacharyya RP, Bandyopadhyay N, Ma P, Son SS, Liu J, He LL, Wu L, Khafizov R, Boykin R, Cerqueira GC, Pironti A, Rudy RF, Patel MM, Yang R, Skerry J, Nazarian E, Musser KA, Taylor J, Pierce VM, Earl AM, Cosimi LA, Shoresh N, Beechem J, Livny J, Hung DT. Simultaneous detection of genotype and phenotype enables rapid and accurate antibiotic susceptibility determination. Nat Med 2019; 25:1858-1864. [PMID: 31768064 PMCID: PMC6930013 DOI: 10.1038/s41591-019-0650-9] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 10/11/2019] [Indexed: 12/13/2022]
Abstract
Multidrug resistant organisms (MDROs) are a serious threat to human health1,2. Fast, accurate antibiotic susceptibility testing (AST) is a critical need in addressing escalating antibiotic resistance, since delays in identifying MDROs increase mortality3,4 and use of broad-spectrum antibiotics, further selecting for resistant organisms. Yet current growth-based AST assays, such as broth microdilution5, require several days before informing key clinical decisions. Rapid AST would transform the care of infected patients while ensuring that our antibiotic arsenal is deployed as efficiently as possible. Growth-based assays are fundamentally constrained in speed by doubling time of the pathogen, and genotypic assays are limited by the ever-growing diversity and complexity of bacterial antibiotic resistance mechanisms. Here, we describe a rapid assay for combined Genotypic and Phenotypic AST through RNA detection, GoPhAST-R, that classifies strains with 94–99% accuracy by coupling machine learning analysis of early antibiotic-induced transcriptional changes with simultaneous detection of key genetic resistance determinants to increase accuracy of resistance detection, facilitate molecular epidemiology, and enable early detection of emerging resistance mechanisms. This two-pronged approach provides phenotypic AST 24–36 hours faster than standard workflows, with <4 hour assay time on a pilot instrument for hybridization-based multiplexed RNA detection implemented directly from positive blood cultures.
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Affiliation(s)
- Roby P Bhattacharyya
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Infectious Diseases Division, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Nirmalya Bandyopadhyay
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Peijun Ma
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Sophie S Son
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jamin Liu
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Lorrie L He
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Lidan Wu
- NanoString Technologies, Inc., Seattle, WA, USA
| | | | - Rich Boykin
- NanoString Technologies, Inc., Seattle, WA, USA
| | - Gustavo C Cerqueira
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Personal Genome Diagnostics, Ellicott City, MD, USA
| | - Alejandro Pironti
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Robert F Rudy
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Milesh M Patel
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Rui Yang
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Jennifer Skerry
- Microbiology Laboratory, Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | | | - Kimberly A Musser
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Jill Taylor
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Virginia M Pierce
- Microbiology Laboratory, Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Ashlee M Earl
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Lisa A Cosimi
- Infectious Diseases Division, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Noam Shoresh
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Jonathan Livny
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Deborah T Hung
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA. .,Department of Genetics, Harvard Medical School, Boston, MA, USA. .,Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA.
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12
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Ostrowsky B, Snavely E, Kogut S, Giardina R, Adams E, Nazarian E, Musser KA, Jean-Denis R, Greenko J, Lutterloh E. 491. Working Together: A Tale of Carbapenemase-Producing Organism Investigations in Three New York City Nursing Homes. Open Forum Infect Dis 2019. [PMCID: PMC6809173 DOI: 10.1093/ofid/ofz360.2510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Background Methods Results Conclusion Disclosures
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Affiliation(s)
- Belinda Ostrowsky
- Centers for Disease Control and Prevention, Franklin Square, New York
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13
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Wells M, Lasek-Nesselquist E, Schoonmaker-Bopp D, Baker D, Thompson L, Wroblewski D, Nazarian E, Lapierre P, Musser KA. Insights into the long-term persistence of Legionella in facilities from whole-genome sequencing. Infect Genet Evol 2018; 65:200-209. [PMID: 30075256 DOI: 10.1016/j.meegid.2018.07.040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 07/27/2018] [Accepted: 07/30/2018] [Indexed: 10/28/2022]
Abstract
We investigated the value of whole-genome sequencing (WGS) and single nucleotide polymorphism (SNP) analyses in determining the relationships among and evolutionary rates of Legionella species with long-term persistence in three healthcare facilities. We examined retrospective clinical and environmental isolates of Legionella micdadei and Legionella pneumophila serogroup 1 isolates with identical PFGE DNA fingerprints sampled over the course of up to 18 years. WGS analyses demonstrated that heterogeneous populations of Legionella were present within each facility despite displaying the same PFGE profiles. Additionally, clustering of some clinical isolates with those from a separate but related institution exposed a source of infection not previously detected, underscoring the importance of considering phylogenetic relationships when assessing epidemiological links. The data supported an average substitution rate of 0.80 SNPs per genome per year for L. micdadei but a reliable estimate for L. pneumophila serogroup 1 could not be obtained due to complicating factors such as non-chronological links among isolates and inadequate sampling depths. While the substitution rate for L. micdadei is consistent with previous estimates for L. pneumophila, the lack of a temporal signal in our sequence data for L. pneuomphila serogroup 1 isolates suggests either insufficient change to provide an estimate or variable evolutionary rates, which could reflect the presence of both actively dividing and viable but non-culturable Legionella spp. in the built environment. This study highlights the increased discriminatory power of WGS SNP analysis as compared to PFGE, emphasizes the need for extended sampling, and provides insight into the evolution of Legionella from longitudinal investigations.
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Affiliation(s)
- Megan Wells
- Union College, 807 Union St., Schenectady, NY 12308, USA
| | - Erica Lasek-Nesselquist
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave., Albany, NY 12208, USA.
| | - Dianna Schoonmaker-Bopp
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave., Albany, NY 12208, USA
| | - Deborah Baker
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave., Albany, NY 12208, USA
| | - Lisa Thompson
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave., Albany, NY 12208, USA
| | - Danielle Wroblewski
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave., Albany, NY 12208, USA
| | - Elizabeth Nazarian
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave., Albany, NY 12208, USA
| | - Pascal Lapierre
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave., Albany, NY 12208, USA
| | - Kimberlee A Musser
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave., Albany, NY 12208, USA
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14
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Lapierre P, Nazarian E, Zhu Y, Wroblewski D, Saylors A, Passaretti T, Hughes S, Tran A, Lin Y, Kornblum J, Morrison SS, Mercante JW, Fitzhenry R, Weiss D, Raphael BH, Varma JK, Zucker HA, Rakeman JL, Musser KA. Legionnaires' Disease Outbreak Caused by Endemic Strain of Legionella pneumophila, New York, New York, USA, 2015. Emerg Infect Dis 2018; 23:1784-1791. [PMID: 29047425 PMCID: PMC5652421 DOI: 10.3201/eid2311.170308] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
During the summer of 2015, New York, New York, USA, had one of the largest and deadliest outbreaks of Legionnaires’ disease in the history of the United States. A total of 138 cases and 16 deaths were linked to a single cooling tower in the South Bronx. Analysis of environmental samples and clinical isolates showed that sporadic cases of legionellosis before, during, and after the outbreak could be traced to a slowly evolving, single-ancestor strain. Detection of an ostensibly virulent Legionella strain endemic to the Bronx community suggests potential risk for future cases of legionellosis in the area. The genetic homogeneity of the Legionella population in this area might complicate investigations and interpretations of future outbreaks of Legionnaires’ disease.
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15
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Benowitz I, Fitzhenry R, Boyd C, Dickinson M, Levy M, Lin Y, Nazarian E, Ostrowsky B, Passaretti T, Rakeman J, Saylors A, Shamoonian E, Smith TA, Balter S. Rapid Identification of a Cooling Tower-Associated Legionnaires' Disease Outbreak Supported by Polymerase Chain Reaction Testing of Environmental Samples, New York City, 2014-2015. J Environ Health 2018; 80:8-12. [PMID: 29780175 PMCID: PMC5956537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We investigated an outbreak of eight Legionnaires' disease cases among persons living in an urban residential community of 60,000 people. Possible environmental sources included two active cooling towers (air-conditioning units for large buildings) <1 km from patient residences, a market misting system, a community-wide water system used for heating and cooling, and potable water. To support a timely public health response, we used real-time polymerase chain reaction (PCR) to identify Legionella DNA in environmental samples within hours of specimen collection. We detected L. pneumophila serogroup 1 DNA only at a power plant cooling tower, supporting the decision to order remediation before culture results were available. An isolate from a power plant cooling tower sample was indistinguishable from a patient isolate by pulsed-field gel electrophoresis, suggesting the cooling tower was the outbreak source. PCR results were available <1 day after sample collection, and culture results were available as early as 5 days after plating. PCR is a valuable tool for identifying Legionella DNA in environmental samples in outbreak settings.
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Affiliation(s)
- Isaac Benowitz
- Epidemic Intelligence Service, Centers for Disease Control and Prevention
| | | | | | | | | | - Ying Lin
- New York City Department of Health and Mental Hygiene
| | | | | | | | | | | | | | | | - Sharon Balter
- New York City Department of Health and Mental Hygiene
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16
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Raphael BH, Baker DJ, Nazarian E, Lapierre P, Bopp D, Kozak-Muiznieks NA, Morrison SS, Lucas CE, Mercante JW, Musser KA, Winchell JM. Genomic Resolution of Outbreak-Associated Legionella pneumophila Serogroup 1 Isolates from New York State. Appl Environ Microbiol 2016; 82:3582-3590. [PMID: 27060122 PMCID: PMC4959152 DOI: 10.1128/aem.00362-16] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 04/04/2016] [Indexed: 01/05/2023] Open
Abstract
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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Affiliation(s)
- Brian H Raphael
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Deborah J Baker
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Elizabeth Nazarian
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Pascal Lapierre
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Dianna Bopp
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | | | - Shatavia S Morrison
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Claressa E Lucas
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jeffrey W Mercante
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Kimberlee A Musser
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Jonas M Winchell
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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17
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Benowitz I, Fitzhenry R, Boyd C, Dickinson M, Levi M, Lin Y, Nazarian E, Ostrowsky B, Passaretti T, Rakeman J, Shamoonian E, Saylors A, Balter S, Smith TA. Rapid Detection of a Winter Outbreak of Legionellosis—New York City, 2014–2015. Open Forum Infect Dis 2015. [DOI: 10.1093/ofid/ofv133.133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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18
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Ramautar AE, Halse TA, Arakaki L, Antwi M, Del Rosso P, Dorsinville M, Nazarian E, Steiner-Sichel L, Lee L, Dickinson M, Wroblewski D, Dumas N, Musser K, Isaac B, Rakeman J, Weiss D. Direct molecular testing to assess the incidence of meningococcal and other bacterial causes of meningitis among persons reported with unspecified bacterial meningitis. Diagn Microbiol Infect Dis 2015; 83:305-11. [DOI: 10.1016/j.diagmicrobio.2015.06.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 06/05/2015] [Accepted: 06/10/2015] [Indexed: 11/29/2022]
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