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McGovern OL, Kobayashi M, Shaw KA, Szablewski C, Gabel J, Holsinger C, Drenzek C, Brennan S, Milucky J, Farrar JL, Wolff BJ, Benitez AJ, Thurman KA, Diaz MH, Winchell JM, Schrag S. Use of Real-Time PCR for Chlamydia psittaci Detection in Human Specimens During an Outbreak of Psittacosis - Georgia and Virginia, 2018. MMWR Morb Mortal Wkly Rep 2021; 70:505-509. [PMID: 33830980 PMCID: PMC8030988 DOI: 10.15585/mmwr.mm7014a1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Psittacosis is typically a mild febrile respiratory illness caused by infection with the bacterium Chlamydia psittaci and usually transmitted to humans by infected birds (1). On average, 11 psittacosis cases per year were reported in the United States during 2000-2017. During August-October 2018, the largest U.S. psittacosis outbreak in 30 years (82 cases identified*) occurred in two poultry slaughter plants, one each in Virginia and Georgia, that shared source farms (2). CDC used C. psittaci real-time polymerase chain reaction (PCR) to test 54 human specimens from this outbreak. This was the largest number of human specimens from a single outbreak ever tested for C. psittaci using real-time PCR, which is faster and more sensitive than commercially available serologic tests. This represented a rare opportunity to assess the utility of multiple specimen types for real-time PCR detection of C. psittaci. C. psittaci was detected more frequently in lower respiratory specimens (59% [10 of 17]) and stool (four of five) than in upper respiratory specimens (7% [two of 28]). Among six patients with sputum and nasopharyngeal swabs tested, C. psittaci was detected only in sputum in five patients. Cycle threshold (Ct) values suggested bacterial load was higher in lower respiratory specimens than in nasopharyngeal swabs. These findings support prioritizing lower respiratory specimens for real-time PCR detection of C. psittaci. Stool specimens might also have utility for diagnosis of psittacosis.
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McGovern OL, Shaw K, Szablewski C, Gabel J, Holsinger C, Brennan S, Wolff B, Benitez AJ, Diaz M, Thurman KA, Winchell J, Kobayashi M. 2173. Detection of Chlamydia psittaci by rtPCR in Outbreak Specimens Tested at CDC—2018. Open Forum Infect Dis 2019. [PMCID: PMC6809482 DOI: 10.1093/ofid/ofz360.1853] [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: 11/23/2022] Open
Abstract
Background Psittacosis is a respiratory illness caused by Chlamydia psittaci. The most commonly available diagnostic tests are serologic tests, which have low sensitivity and can cross-react with other chlamydial species. Serologic tests also require paired sera collected weeks apart, which is impractical for patient management. Real-time polymerase chain reaction (rtPCR) testing for C. psittaci is rapid, sensitive, and specific. However, rtRCR testing is only available at the CDC Respiratory Diseases Branch laboratory, and appropriate clinical specimen types need to be validated since psittacosis case detection is infrequent. In 2018, the first large psittacosis outbreak in the United States in 30 years occurred, allowing assessment of rtPCR performance among multiple clinical specimen types. Methods rtPCR test positivity rate and turnaround time were determined among 89 specimens tested at CDC from 54 outbreak patients with suspected psittacosis. rtPCR testing was performed on nucleic acid extracted from clinical specimens using oligonucleotides targeting the C. psittaci locus tag CPSIT_RS01985. Clinical information was collected by patient interview and medical record review. Results Positivity rates among the most common specimen types were 4.4% (2/46) for nasopharyngeal (NP) swab, 36.4% (8/22) for sputum, and 80.0% (4/5) for stool. Of 21 (24%) specimens with available data, the average time from patient symptom onset to specimen collection was 6 days (range 1–11 days). C. psittaci was detected in specimens from 13 of 54 outbreak patients tested (Table 1); all 13 patients had radiographically-confirmed pneumonia, and 7 were rtPCR-positive from a lower respiratory specimen only. Paired sputum and NP swab specimens were tested for 6 patients; C. psittaci was detected in all sputum but only 1 NP swab. The positive NP swab was from a patient requiring intensive care unit admission and intubation. All results were reported within 1 business day of specimen receipt in the lab. Conclusion These data suggest that lower respiratory specimens are more sensitive than NP swabs for rtPCR detection of C. psittaci; stool might be a suitable alternative. Widespread implementation of rtPCR testing using appropriate specimen types could improve psittacosis detection and inform timely public health interventions. ![]()
Disclosures All authors: No reported disclosures.
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Affiliation(s)
| | - Kelly Shaw
- Virginia Department of Health, Richmond, Virginia
| | | | - Julie Gabel
- Georgia Department of Public Health, Atlanta, Georgia
| | | | | | - Bernard Wolff
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | - Maureen Diaz
- Centers for Disease Control and Prevention, Atlanta, Georgia
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Wolff BJ, Bramley AM, Thurman KA, Whitney CG, Whitaker B, Self WH, Arnold SR, Trabue C, Wunderink RG, McCullers J, Edwards KM, Jain S, Winchell JM. Improved Detection of Respiratory Pathogens by Use of High-Quality Sputum with TaqMan Array Card Technology. J Clin Microbiol 2017; 55:110-121. [PMID: 27795345 PMCID: PMC5228222 DOI: 10.1128/jcm.01805-16] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [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: 08/26/2016] [Accepted: 10/12/2016] [Indexed: 11/20/2022] Open
Abstract
New diagnostic platforms often use nasopharyngeal or oropharyngeal (NP/OP) swabs for pathogen detection for patients hospitalized with community-acquired pneumonia (CAP). We applied multipathogen testing to high-quality sputum specimens to determine if more pathogens can be identified relative to NP/OP swabs. Children (<18 years old) and adults hospitalized with CAP were enrolled over 2.5 years through the Etiology of Pneumonia in the Community (EPIC) study. NP/OP specimens with matching high-quality sputum (defined as ≤10 epithelial cells/low-power field [lpf] and ≥25 white blood cells/lpf or a quality score [q-score] definition of 2+) were tested by TaqMan array card (TAC), a multipathogen real-time PCR detection platform. Among 236 patients with matched specimens, a higher proportion of sputum specimens had ≥1 pathogen detected compared with NP/OP specimens in children (93% versus 68%; P < 0.0001) and adults (88% versus 61%; P < 0.0001); for each pathogen targeted, crossing threshold (CT) values were earlier in sputum. Both bacterial (361 versus 294) and viral detections (245 versus 140) were more common in sputum versus NP/OP specimens, respectively, in both children and adults. When available, high-quality sputum may be useful for testing in hospitalized CAP patients.
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Affiliation(s)
- Bernard J Wolff
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Anna M Bramley
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Kathleen A Thurman
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Cynthia G Whitney
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Brett Whitaker
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Wesley H Self
- Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Sandra R Arnold
- University of Tennessee Health Science Center/Saint Thomas Health, Nashville, Tennessee, USA
- Le Bonheur Children's Hospital, Memphis, Tennessee, USA
| | - Christopher Trabue
- University of Tennessee Health Science Center/Saint Thomas Health, Nashville, Tennessee, USA
| | | | - Jon McCullers
- University of Tennessee Health Science Center/Saint Thomas Health, Nashville, Tennessee, USA
- Le Bonheur Children's Hospital, Memphis, Tennessee, USA
- St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | | | - Seema Jain
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jonas M Winchell
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Henderson KC, Sheppard ES, Rivera-Betancourt OE, Choi JY, Dluhy RA, Thurman KA, Winchell JM, Krause DC. The multivariate detection limit for Mycoplasma pneumoniae as determined by nanorod array-surface enhanced Raman spectroscopy and comparison with limit of detection by qPCR. Analyst 2015; 139:6426-34. [PMID: 25335653 DOI: 10.1039/c4an01141d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Mycoplasma pneumoniae is a cell wall-less bacterial pathogen of the human respiratory tract that accounts for up to 20% of community-acquired pneumonia. At present, the standard for detection and genotyping is quantitative polymerase chain reaction (qPCR), which can exhibit excellent sensitivity but lacks standardization and has limited practicality for widespread, point-of-care use. We previously described a Ag nanorod array-surface enhanced Raman spectroscopy (NA-SERS) biosensing platform capable of detecting M. pneumoniae in simulated and true clinical throat swab samples with statistically significant specificity and sensitivity. We report here that differences in sample preparation influence the integrity of mycoplasma cells for NA-SERS analysis, which in turn impacts the resulting spectra. We have established a multivariate detection limit (MDL) using NA-SERS for M. pneumoniae intact-cell sample preparations. Using an adaptation of International Union of Pure and Applied Chemistry (IUPAC)-recommended methods for analyzing multivariate data sets, we found that qPCR had roughly 10× better detection limits than NA-SERS when expressed in CFU ml(-1) and DNA concentration (fg). However, the NA-SERS MDL for intact M. pneumoniae was 5.3 ± 1.0 genome equivalents (cells per μl). By comparison, qPCR of a parallel set of samples yielded a limit of detection of 2.5 ± 0.25 cells per μl. Therefore, for certain standard metrics NA-SERS provides a multivariate detection limit for M. pneumoniae that is essentially identical to that determined via qPCR.
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Hastings DL, Harrington KJ, Kutty PK, Rayman RJ, Spindola D, Diaz MH, Thurman KA, Winchell JM, Safranek TJ. Mycoplasma pneumoniae outbreak in a long-term care facility--Nebraska, 2014. MMWR Morb Mortal Wkly Rep 2015; 64:296-9. [PMID: 25811678 PMCID: PMC4584882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
On June 20, 2014, a Nebraska long-term care facility notified the East Central District Health Department (ECDHD) and Nebraska Department of Health and Human Services (NDHHS) of an outbreak of respiratory illness characterized by cough and fever in 22 residents and resulting in four deaths during the preceding 2 weeks. To determine the etiologic agent, identify additional cases, and implement control measures, Nebraska and CDC investigators evaluated the facility's infection prevention measures and collected nasopharyngeal (NP) and oropharyngeal (OP) swabs or autopsy specimens from patients for real-time polymerase chain reaction (PCR) testing at CDC. The facility was closed to new admissions until 1 month after the last case, droplet precautions were implemented, ill residents were isolated, and group activities were canceled. During the outbreak, a total of 55 persons experienced illnesses that met the case definition; 12 were hospitalized, and seven died. PCR detected Mycoplasma pneumoniae DNA in 40% of specimens. M. pneumoniae should be considered a possible cause of respiratory illness outbreaks in long-term care facilities. Morbidity and mortality from respiratory disease outbreaks at long-term care facilities might be minimized if facilities monitor for respiratory disease clusters, report outbreaks promptly, prioritize diagnostic testing in outbreak situations, and implement timely and strict infection control measures to halt transmission.
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Affiliation(s)
- Deborah L. Hastings
- Epidemic Intelligence Service, CDC
- Nebraska Department of Health and Human Services
| | | | - Preeta K. Kutty
- National Center for Immunization and Respiratory Diseases, CDC
| | | | | | - Maureen H. Diaz
- National Center for Immunization and Respiratory Diseases, CDC
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Thurman KA, Warner AK, Cowart KC, Benitez AJ, Winchell JM. Detection of Mycoplasma pneumoniae, Chlamydia pneumoniae, and Legionella spp. in clinical specimens using a single-tube multiplex real-time PCR assay. Diagn Microbiol Infect Dis 2011; 70:1-9. [PMID: 21397428 PMCID: PMC7126442 DOI: 10.1016/j.diagmicrobio.2010.11.014] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2010] [Revised: 11/19/2010] [Accepted: 11/25/2010] [Indexed: 11/19/2022]
Abstract
A multiplex real-time PCR assay for the detection of Mycoplasma pneumoniae (MP181), Chlamydia (Chlamydophila) pneumoniae (CP-Arg), Legionella spp. (Pan-Leg), and the human RNase P (RNase P) gene was developed for rapid testing of atypical bacterial respiratory pathogens in clinical specimens. This method uses 4 distinct hydrolysis probes to detect 3 leading causes of community-acquired pneumonia. The assay was evaluated for specificity and sensitivity by testing against 35 related organisms, a dilution series of each specific target and 197 clinical specimens. Specificity testing demonstrated no cross-reactivity. A comparison to previously validated singleplex real-time PCR assays for each agent was also performed. The analytical sensitivity for specific pathogen targets in both the singleplex and multiplex was identical (50 fg), while efficiencies ranged from 82% to 97% for the singleplex assays and from 90% to 100% for the multiplex assay. The clinical sensitivity of the multiplex assay was improved for the Pan-Leg and CP-Arg targets when compared to the singleplex. The MP181 assay displayed equivalent performance. This multiplex assay provides an overall improvement in the diagnostic capability for these agents by demonstrating a sensitive, high-throughput and rapid method. This procedure may allow for a practical and efficient means to test respiratory clinical specimens for atypical pneumonia agents in health care settings and facilitate an appropriate public health response to outbreaks.
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Thurman KA, Cowart KC, Winchell JM. Comparison of nucleic acid extraction methods for the detection of Mycoplasma pneumoniae. Diagn Microbiol Infect Dis 2009; 65:435-8. [DOI: 10.1016/j.diagmicrobio.2009.08.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2009] [Revised: 08/07/2009] [Accepted: 08/08/2009] [Indexed: 11/29/2022]
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Mitchell SL, Budhiraja S, Thurman KA, Lanier Thacker W, Winchell JM. Evaluation of two real-time PCR chemistries for the detection of Chlamydophila pneumoniae in clinical specimens. Mol Cell Probes 2009; 23:309-11. [PMID: 19647071 DOI: 10.1016/j.mcp.2009.07.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2009] [Revised: 07/10/2009] [Accepted: 07/20/2009] [Indexed: 10/20/2022]
Abstract
Chlamydophila pneumoniae is an atypical bacterial respiratory pathogen that is responsible for approximately 3-10% of community-acquired pneumonia cases. We report the evaluation of two distinct real-time PCR assays for rapid and specific detection of C. pneumoniae. We tested 401 clinical specimens, finding 5.7% positive, and confirmed a localized outbreak.
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Affiliation(s)
- Stephanie L Mitchell
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
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Thurman KA, Walter ND, Schwartz SB, Mitchell SL, Dillon MT, Baughman AL, Deutscher M, Fulton JP, Tongren JE, Hicks LA, Winchell JM. Comparison of laboratory diagnostic procedures for detection of Mycoplasma pneumoniae in community outbreaks. Clin Infect Dis 2009; 48:1244-9. [PMID: 19331586 DOI: 10.1086/597775] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND Mycoplasma pneumoniae continues to be a significant cause of community-acquired pneumonia (CAP). A more definitive methodology for reliable detection of M. pneumoniae is needed to identify outbreaks and to prevent potentially fatal extrapulmonary complications. METHODS We analyzed 2 outbreaks of CAP due to M. pneumoniae. Nasopharyngeal and/or oropharyngeal swab specimens and serum samples were obtained from persons with clinically defined cases, household contacts, and asymptomatic individuals. Real-time polymerase chain reaction (PCR) for M. pneumoniae was performed on all swab specimens, and the diagnostic utility was compared with that of 2 commercially available serologic test kits. RESULTS For cases, 21% yielded positive results with real-time PCR, whereas 81% and 54% yielded positive results with the immunoglobulin M and immunoglobulin G/immunoglobulin M serologic tests, respectively. For noncases, 1.8% yielded positive results with real-time PCR, whereas 63% and 79% yielded serologically positive results with the immunoglobulin M and immunoglobulin G/immunoglobulin M kits, respectively. The sensitivity of real-time PCR decreased as the duration between symptom onset and sample collection increased, with a peak sensitivity of 48% at 0-21 days. A specificity of 43% for the immunoglobulin M antibody detection assay was observed for persons aged 10-18 years, but the sensitivity increased to 82% for persons aged 19 years. DISCUSSION Thorough data analysis indicated that no single available test was reliable for the identification of an outbreak of CAP due to M. pneumoniae. A combination of testing methodologies proved to be the most reliable approach for identification of outbreaks of CAP due to M. pneumoniae, especially in the absence of other suspected respiratory pathogens.
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Affiliation(s)
- Kathleen A Thurman
- Respiratory Diseases Branch, Office of Workforce and Career Development, Atlanta, Georgia, USA
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