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Wolff BJ, Waller JL, Benitez AJ, Gaines A, Conley AB, Rishishwar L, Chande AT, Morrison SS, Jordan IK, Diaz MH, Winchell JM. Genomic analysis of Chlamydia psittaci from a multistate zoonotic outbreak in two chicken processing plants. J Genomics 2023; 11:40-44. [PMID: 37670735 PMCID: PMC10475345 DOI: 10.7150/jgen.86558] [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: 05/27/2023] [Accepted: 07/27/2023] [Indexed: 09/07/2023] Open
Abstract
Four Chlamydia psittaci isolates were recovered from clinical specimens from ill workers during a multistate outbreak at two chicken processing plants. Whole genome sequencing analyses revealed high similarity to C. psittaci genotype D. The isolates differed from each other by only two single nucleotide polymorphisms, indicating a common source.
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Affiliation(s)
- Bernard J. Wolff
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jessica L. Waller
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Alvaro J. Benitez
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Anna Gaines
- Applied Bioinformatics Laboratory, Atlanta, GA, USA
| | | | - Lavanya Rishishwar
- Applied Bioinformatics Laboratory, Atlanta, GA, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Aroon T. Chande
- Applied Bioinformatics Laboratory, Atlanta, GA, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Shatavia S. Morrison
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - I. King Jordan
- Applied Bioinformatics Laboratory, Atlanta, GA, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Maureen H. Diaz
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jonas M. Winchell
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
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2
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Wolff BJ, Gaines A, Conley AB, Norris E, Rishishwar L, Chande AT, Yang E, Diaz MH, Winchell JM. Multiplex Real-time PCR Assay for the Detection of all Chlamydia Species and Simultaneous Differentiation of C. psittaci and C. pneumoniae in Human Clinical Specimens. Ann Lab Med 2023; 43:375-380. [PMID: 36843406 PMCID: PMC9989537 DOI: 10.3343/alm.2023.43.4.375] [Citation(s) in RCA: 1] [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: 08/24/2022] [Revised: 11/04/2022] [Accepted: 01/10/2023] [Indexed: 02/28/2023] Open
Abstract
We developed and assessed the performance of a new multiplex real-time PCR assay for the detection of all Chlamydia species and simultaneous differentiation of Chlamydia psittaci and Chlamydia pneumoniae-two important human respiratory pathogens-in human clinical specimens. Next-generation sequencing was used to identify unique targets to design real-time PCR assays targeting all Chlamydia species, C. psittaci, and C. pneumoniae. To validate the assay, we used a panel of 49 culture isolates comprising seven C. psittaci genotypes, eight C. pneumoniae isolates, seven other Chlamydia species, and 22 near-neighbor bacterial and viral isolates, along with 22 specimens from external quality assessment (EQA) panels and 34 nasopharyngeal and oropharyngeal swabs and cerebrospinal fluid, stool, and sputum specimens previously identified as positive or negative for C. psittaci or C. pneumoniae. The assays were 100% specific, with limits of detection of 7.64- 9.02 fg/μL. The assay results matched with historical assay results for all specimens, except for one owing to the increased sensitivity of the new C. psittaci assay; the results of the EQA specimens were 100% accurate. This assay may improve the timely and accurate clinical diagnosis of Chlamydia infections and provide a greater understanding of the burden of disease caused by these agents.
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Affiliation(s)
- Bernard J Wolff
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Anna Gaines
- Applied Bioinformatics Laboratory, Atlanta, GA, USA
| | | | - Emily Norris
- Applied Bioinformatics Laboratory, Atlanta, GA, USA
| | - Lavanya Rishishwar
- Applied Bioinformatics Laboratory, Atlanta, GA, USA.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Aroon T Chande
- Applied Bioinformatics Laboratory, Atlanta, GA, USA.,School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Eungi Yang
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Maureen H Diaz
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jonas M Winchell
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
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Connor NE, Islam MS, Mullany LC, Shang N, Bhutta ZA, Zaidi AKM, Soofi S, Nisar I, Panigrahi P, Panigrahi K, Satpathy R, Bose A, Isaac R, Baqui AH, Mitra DK, Sadeq-ur Rahman Q, Hossain T, Schrag SJ, Winchell JM, Arvay ML, Diaz MH, Waller JL, Weber MW, Hamer DH, Hibberd P, Nawshad Uddin Ahmed ASM, Islam M, Hossain MB, Qazi SA, El Arifeen S, Darmstadt GL, Saha SK. Risk factors for community-acquired bacterial infection among young infants in South Asia: a longitudinal cohort study with nested case-control analysis. BMJ Glob Health 2022; 7:bmjgh-2022-009706. [PMID: 36319031 PMCID: PMC9628539 DOI: 10.1136/bmjgh-2022-009706] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 09/24/2022] [Indexed: 11/07/2022] Open
Abstract
OBJECTIVE Risk factors predisposing infants to community-acquired bacterial infections during the first 2 months of life are poorly understood in South Asia. Identifying risk factors for infection could lead to improved preventive measures and antibiotic stewardship. METHODS Five sites in Bangladesh, India and Pakistan enrolled mother-child pairs via population-based pregnancy surveillance by community health workers. Medical, sociodemographic and epidemiological risk factor data were collected. Young infants aged 0-59 days with signs of possible serious bacterial infection (pSBI) and age-matched controls provided blood and respiratory specimens that were analysed by blood culture and real-time PCR. These tests were used to build a Bayesian partial latent class model (PLCM) capable of attributing the probable cause of each infant's infection in the ANISA study. The collected risk factors from all mother-child pairs were classified and analysed against the PLCM using bivariate and stepwise logistic multivariable regression modelling to determine risk factors of probable bacterial infection. RESULTS Among 63 114 infants born, 14 655 were assessed and 6022 had signs of pSBI; of these, 81% (4859) provided blood samples for culture, 71% (4216) provided blood samples for quantitative PCR (qPCR) and 86% (5209) provided respiratory qPCR samples. Risk factors associated with bacterial-attributed infections included: low (relative risk (RR) 1.73, 95% credible interval (CrI) 1.42 to 2.11) and very low birth weight (RR 5.77, 95% CrI 3.73 to 8.94), male sex (RR 1.27, 95% CrI 1.07 to 1.52), breathing problems at birth (RR 2.50, 95% CrI 1.96 to 3.18), premature rupture of membranes (PROMs) (RR 1.27, 95% CrI 1.03 to 1.58) and being in the lowest three socioeconomic status quintiles (first RR 1.52, 95% CrI 1.07 to 2.16; second RR 1.41, 95% CrI 1.00 to 1.97; third RR 1.42, 95% CrI 1.01 to 1.99). CONCLUSION Distinct risk factors: birth weight, male sex, breathing problems at birth and PROM were significantly associated with the development of bacterial sepsis across South Asian community settings, supporting refined clinical discernment and targeted use of antimicrobials.
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Affiliation(s)
- Nicholas E Connor
- Department of Microbiology, Child Health Research Foundation, Dhaka, Bangladesh,Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK
| | | | - Luke C Mullany
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Nong Shang
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Zulfiqar A Bhutta
- Centre for Global Child Health, The Hospital for Sick Children, Toronto, Ontario, Canada,Institute for Global Health and Development, The Aga Khan University, Karachi, Pakistan
| | - Anita K M Zaidi
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Sajid Soofi
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Imran Nisar
- Department of Pediatrics and Child Health, The Aga Khan University, Karachi, Pakistan
| | - Pinaki Panigrahi
- Department of Pediatrics, Georgetown University Medical Center, Washington, DC, USA
| | | | | | | | - Rita Isaac
- Christian Medical College, Vellore, India
| | - Abdullah H Baqui
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Dipak K Mitra
- Department of Public Health, North South University, Dhaka, Bangladesh
| | - Qazi Sadeq-ur Rahman
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Tanvir Hossain
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Stephanie J Schrag
- Division of Bacterial Diseases, 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
| | - Melissa L Arvay
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Maureen H Diaz
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jessica L Waller
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Martin W Weber
- Child and Adolescent Health and Development Division, WHO Regional Office for Europe, Copenhagen, Denmark
| | - Davidson H Hamer
- Department of Global Health, Boston University School of Public Health, Boston, Massachusetts, USA,Section of Infectious Diseases, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Patricia Hibberd
- Department of Global Health, Boston University School of Public Health, Boston, Massachusetts, USA,Section of Infectious Diseases, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | | | - Maksuda Islam
- Department of Microbiology, Child Health Research Foundation, Dhaka, Bangladesh
| | | | - Shamim A Qazi
- Consultant and Researcher, (Retired WHO staff), Geneva, Switzerland
| | - Shams El Arifeen
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Gary L Darmstadt
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California, USA
| | - Samir K Saha
- Department of Microbiology, Child Health Research Foundation, Dhaka, Bangladesh
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Ritter JM, Seixas JN, Walong E, Dawa J, Onyango C, Pimenta FC, da Gloria Carvalho M, Silva-Flannery L, Jenkinson T, Howard K, Bhatnagar J, Diaz M, Winchell JM, Zaki SR, Chaves SS, Martines RB. Histopathology Is Key to Interpreting Multiplex Molecular Test Results From Postmortem Minimally Invasive Tissue Samples. Clin Infect Dis 2021; 73:S351-S359. [PMID: 34910182 PMCID: PMC8672755 DOI: 10.1093/cid/ciab772] [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] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Minimally invasive tissue sampling (MITS) is an alternative to complete autopsy for determining causes of death. Multiplex molecular testing performed on MITS specimens poses challenges of interpretation, due to high sensitivity and indiscriminate detection of pathogenic, commensal, or contaminating microorganisms. METHODS MITS was performed on 20 deceased children with respiratory illness, at 10 timepoints up to 88 hours postmortem. Samples were evaluated by multiplex molecular testing on fresh tissues by TaqMan® Array Card (TAC) and by histopathology, special stains, immunohistochemistry (IHC), and molecular testing (PCR) on formalin-fixed, paraffin-embedded (FFPE) tissues. Results were correlated to determine overall pathologic and etiologic diagnoses and to guide interpretation of TAC results. RESULTS MITS specimens collected up to 3 days postmortem were adequate for histopathologic evaluation and testing. Seven different etiologic agents were detected by TAC in 10 cases. Three cases had etiologic agents detected by FFPE or other methods and not TAC; 2 were agents not present on TAC, and 2 were streptococci that may have been species other than those present on TAC. Result agreement was 43% for TAC and IHC or PCR, and 69% for IHC and PCR. Extraneous TAC results were common, especially when aspiration was present. CONCLUSIONS TAC can be performed on MITS up to 3 days after death with refrigeration and provides a sensitive method for detection of pathogens but requires careful interpretation in the context of clinicoepidemiologic and histopathologic findings. Interpretation of all diagnostic tests in aggregate to establish overall case diagnoses maximizes the utility of TAC in MITS.
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Affiliation(s)
- Jana M Ritter
- Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Josilene N Seixas
- Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Edwin Walong
- College of Health Sciences, University of Nairobi, Nairobi, Kenya
| | - Jeanette Dawa
- College of Health Sciences, University of Nairobi, Nairobi, Kenya
- Washington State University, Global Health Programs (Kenya office), Nairobi, Kenya
| | - Clayton Onyango
- Division of Global Health Protection, Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Fabiana C Pimenta
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Maria da Gloria Carvalho
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Luciana Silva-Flannery
- Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Tiffany Jenkinson
- Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Katie Howard
- Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Julu Bhatnagar
- Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Maureen Diaz
- Division of Bacterial Diseases, 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
| | - Sherif R Zaki
- Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Sandra S Chaves
- Influenza Program, Centers for Disease Control and Prevention, Nairobi, Kenya and Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Roosecelis B Martines
- Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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5
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Dawa J, Walong E, Onyango C, Mathaiya J, Muturi P, Bunei M, Ochieng W, Barake W, Seixas JN, Mayieka L, Ochieng M, Omballa V, Lidechi S, Hunsperger E, Otieno NA, Ritter JM, Widdowson MA, Diaz MH, Winchell JM, Martines RB, Zaki SR, Chaves SS. Effect of Time Since Death on Multipathogen Molecular Test Results of Postmortem Specimens Collected Using Minimally Invasive Tissue Sampling Techniques. Clin Infect Dis 2021; 73:S360-S367. [PMID: 34910183 PMCID: PMC8672767 DOI: 10.1093/cid/ciab810] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Background We used postmortem minimally invasive tissue sampling (MITS) to assess the effect of time since death on molecular detection of pathogens among respiratory illness–associated deaths. Methods Samples were collected from 20 deceased children (aged 1–59 months) hospitalized with respiratory illness from May 2018 through February 2019. Serial lung and/or liver and blood samples were collected using MITS starting soon after death and every 6 hours thereafter for up to 72 hours. Bodies were stored in the mortuary refrigerator for the duration of the study. All specimens were analyzed using customized multipathogen TaqMan® array cards (TACs). Results We identified a median of 3 pathogens in each child’s lung tissue (range, 1–8; n = 20), 3 pathogens in each child’s liver tissue (range, 1–4; n = 5), and 2 pathogens in each child’s blood specimen (range, 0–4; n = 5). Pathogens were not consistently detected across all collection time points; there was no association between postmortem interval and the number of pathogens detected (P = .43) and no change in TAC cycle threshold value over time for pathogens detected in lung tissue. Human ribonucleoprotein values indicated that specimens collected were suitable for testing throughout the study period. Conclusions Results suggest that lung, liver, and blood specimens can be collected using MITS procedures up to 4 days after death in adequately preserved bodies. However, inconsistent pathogen detection in samples needs careful consideration before drawing definitive conclusions on the etiologic causes of death.
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Affiliation(s)
- Jeanette Dawa
- Washington State University, Global Health Programs (Kenya Office), Nairobi, Kenya.,College of Health Sciences, University of Nairobi, Nairobi, Kenya
| | - Edwin Walong
- College of Health Sciences, University of Nairobi, Nairobi, Kenya
| | - Clayton Onyango
- Division of Global Health Protection, Centers for Disease Control and Prevention, Nairobi, Kenya
| | - John Mathaiya
- Department of Pathology, Thika Level 5 Hospital, Kiambu County, Kenya
| | - Peter Muturi
- Washington State University, Global Health Programs (Kenya Office), Nairobi, Kenya
| | - Milka Bunei
- Washington State University, Global Health Programs (Kenya Office), Nairobi, Kenya
| | | | - Walter Barake
- College of Health Sciences, University of Nairobi, Nairobi, Kenya
| | - Josilene N Seixas
- Infectious Diseases Pathology Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lillian Mayieka
- Centre for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Melvin Ochieng
- Centre for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Victor Omballa
- Centre for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Shirley Lidechi
- Centre for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Elizabeth Hunsperger
- Division of Global Health Protection, Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Nancy A Otieno
- Centre for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Jana M Ritter
- Infectious Diseases Pathology Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Marc-Alain Widdowson
- Division of Global Health Protection, Centers for Disease Control and Prevention, Nairobi, Kenya.,Institute of Tropical Medicine, Antwerp, Belgium
| | - Maureen H Diaz
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jonas M Winchell
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Roosecelis B Martines
- Infectious Diseases Pathology Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Sherif R Zaki
- Infectious Diseases Pathology Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Sandra S Chaves
- Influenza Program, Centers for Disease Control and Prevention, Nairobi, Kenya
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Shu B, Kirby MK, Davis WG, Warnes C, Liddell J, Liu J, Wu KH, Hassell N, Benitez AJ, Wilson MM, Keller MW, Rambo-Martin BL, Camara Y, Winter J, Kondor RJ, Zhou B, Spies S, Rose LE, Winchell JM, Limbago BM, Wentworth DE, Barnes JR. Multiplex Real-Time Reverse Transcription PCR for Influenza A Virus, Influenza B Virus, and Severe Acute Respiratory Syndrome Coronavirus 2. Emerg Infect Dis 2021; 27:1821-1830. [PMID: 34152951 PMCID: PMC8237866 DOI: 10.3201/eid2707.210462] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in late 2019, and the outbreak rapidly evolved into the current coronavirus disease pandemic. SARS-CoV-2 is a respiratory virus that causes symptoms similar to those caused by influenza A and B viruses. On July 2, 2020, the US Food and Drug Administration granted emergency use authorization for in vitro diagnostic use of the Influenza SARS-CoV-2 Multiplex Assay. This assay detects influenza A virus at 102.0, influenza B virus at 102.2, and SARS-CoV-2 at 100.3 50% tissue culture or egg infectious dose, or as few as 5 RNA copies/reaction. The simultaneous detection and differentiation of these 3 major pathogens increases overall testing capacity, conserves resources, identifies co-infections, and enables efficient surveillance of influenza viruses and SARS-CoV-2.
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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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Althaus T, Thaipadungpanit J, Greer RC, Swe MMM, Dittrich S, Peerawaranun P, Smit PW, Wangrangsimakul T, Blacksell S, Winchell JM, Diaz MH, Day NPJ, Smithuis F, Turner P, Lubell Y. Causes of fever in primary care in Southeast Asia and the performance of C-reactive protein in discriminating bacterial from viral pathogens. Int J Infect Dis 2020; 96:334-342. [PMID: 32437937 PMCID: PMC7211754 DOI: 10.1016/j.ijid.2020.05.016] [Citation(s) in RCA: 3] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/01/2020] [Accepted: 05/03/2020] [Indexed: 12/23/2022] Open
Abstract
OBJECTIVES This study investigated causes of fever in the primary levels of care in Southeast Asia, and evaluated whether C-reactive protein (CRP) could distinguish bacterial from viral pathogens. METHODS Blood and nasopharyngeal swab specimens were taken from children and adults with fever (>37.5 °C) or history of fever (<14 days) in Thailand and Myanmar. RESULTS Of 773 patients with at least one blood or nasopharyngeal swab specimen collected, 227 (29.4%) had a target organism detected. Influenza virus type A was detected in 85/227 cases (37.5%), followed by dengue virus (30 cases, 13.2%), respiratory syncytial virus (24 cases, 10.6%) and Leptospira spp. (nine cases, 4.0%). Clinical outcomes were similar between patients with a bacterial or a viral organism, regardless of antibiotic prescription. CRP was higher among patients with a bacterial organism compared with those with a viral organism (median 18 mg/L, interquartile range [10-49] versus 10 mg/L [≤8-22], p = 0.003), with an area under the curve of 0.65 (95% CI 0.55-0.75). CONCLUSIONS Serious bacterial infections requiring antibiotics are an exception rather than the rule in the first line of care. CRP testing could assist in ruling out such cases in settings where diagnostic uncertainty is high and routine antibiotic prescription is common. The original CRP randomised controlled trial was registered with ClinicalTrials.gov, number NCT02758821.
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Affiliation(s)
- Thomas Althaus
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom.
| | - Janjira Thaipadungpanit
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Rachel C Greer
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Myo Maung Maung Swe
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Myanmar-Oxford Clinical Research Unit (MOCRU), Medical Action Myanmar (MAM), Yangon, Myanmar
| | - Sabine Dittrich
- Foundation for Innovative New Diagnostics (FIND), Geneva, Switzerland
| | - Pimnara Peerawaranun
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Pieter W Smit
- Maasstad Ziekenhuis Hospital, Department of Medical Microbiology, Rotterdam, The Netherlands; Public Health Laboratory (GGD), Amsterdam, The Netherlands
| | - Tri Wangrangsimakul
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Stuart Blacksell
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Jonas M Winchell
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Maureen H Diaz
- Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Nicholas P J Day
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Frank Smithuis
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom; Myanmar-Oxford Clinical Research Unit (MOCRU), Medical Action Myanmar (MAM), Yangon, Myanmar
| | - Paul Turner
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom; Cambodia-Oxford Medical Research Unit (COMRU), Angkor Hospital for Children, Siem Reap, Cambodia
| | - Yoel Lubell
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
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9
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Kutty PK, Jain S, Taylor TH, Bramley AM, Diaz MH, Ampofo K, Arnold SR, Williams DJ, Edwards KM, McCullers JA, Pavia AT, Winchell JM, Schrag SJ, Hicks LA. Mycoplasma pneumoniae Among Children Hospitalized With Community-acquired Pneumonia. Clin Infect Dis 2020; 68:5-12. [PMID: 29788037 DOI: 10.1093/cid/ciy419] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 05/14/2018] [Indexed: 12/22/2022] Open
Abstract
Background The epidemiology of Mycoplasma pneumoniae (Mp) among US children (<18 years) hospitalized with community-acquired pneumonia (CAP) is poorly understood. Methods In the Etiology of Pneumonia in the Community study, we prospectively enrolled 2254 children hospitalized with radiographically confirmed pneumonia from January 2010-June 2012 and tested nasopharyngeal/oropharyngeal swabs for Mp using real-time polymerase chain reaction (PCR). Clinical and epidemiological features of Mp PCR-positive and -negative children were compared using logistic regression. Macrolide susceptibility was assessed by genotyping isolates. Results One hundred and eighty two (8%) children were Mp PCR-positive (median age, 7 years); 12% required intensive care and 26% had pleural effusion. No in-hospital deaths occurred. Macrolide resistance was found in 4% (6/169) isolates. Of 178 (98%) Mp PCR-positive children tested for copathogens, 50 (28%) had ≥1 copathogen detected. Variables significantly associated with higher odds of Mp detection included age (10-17 years: adjusted odds ratio [aOR], 10.7 [95% confidence interval {CI}, 5.4-21.1] and 5-9 years: aOR, 6.4 [95% CI, 3.4-12.1] vs 2-4 years), outpatient antibiotics ≤5 days preadmission (aOR, 2.3 [95% CI, 1.5-3.5]), and copathogen detection (aOR, 2.1 [95% CI, 1.3-3.3]). Clinical characteristics were non-specific. Conclusions Usually considered as a mild respiratory infection, Mp was the most commonly detected bacteria among children aged ≥5 years hospitalized with CAP, one-quarter of whom had codetections. Although associated with clinically nonspecific symptoms, there was a need for intensive care in some cases. Mycoplasma pneumoniae should be included in the differential diagnosis for school-aged children hospitalized with CAP.
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Affiliation(s)
- Preeta K Kutty
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Seema Jain
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Thomas H Taylor
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Anna M Bramley
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Maureen H Diaz
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Krow Ampofo
- University of Utah Health Sciences Center, Salt Lake City
| | - Sandra R Arnold
- Le Bonheur Children's Hospital, Memphis.,University of Tennessee Health Science Center, Memphis
| | - Derek J Williams
- Vanderbilt University Medical Center, Nashville.,Monroe Carell Jr Children's Hospital at Vanderbilt, Nashville
| | - Kathryn M Edwards
- Vanderbilt University Medical Center, Nashville.,Monroe Carell Jr Children's Hospital at Vanderbilt, Nashville
| | - Jonathan A McCullers
- Le Bonheur Children's Hospital, Memphis.,University of Tennessee Health Science Center, Memphis.,St Jude Children's Research Hospital, Memphis, Tennessee
| | - Andrew T Pavia
- University of Utah Health Sciences Center, Salt Lake City
| | | | | | - Lauri A Hicks
- Centers for Disease Control and Prevention, Atlanta, Georgia
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10
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Diaz MH, Waller JL, Theodore MJ, Patel N, Wolff BJ, Benitez AJ, Morris T, Raghunathan PL, Breiman RF, Whitney CG, Blau DM, Winchell JM. Development and Implementation of Multiplex TaqMan Array Cards for Specimen Testing at Child Health and Mortality Prevention Surveillance Site Laboratories. Clin Infect Dis 2019; 69:S311-S321. [PMID: 31598666 PMCID: PMC7108207 DOI: 10.1093/cid/ciz571] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Child Health and Mortality Prevention Surveillance (CHAMPS) laboratories are employing a variety of laboratory methods to identify infectious agents contributing to deaths of children <5 years old and stillbirths in sub-Saharan Africa and South Asia. In support of this long-term objective, our team developed TaqMan Array Cards (TACs) for testing postmortem specimens (blood, cerebrospinal fluid, lung tissue, respiratory tract swabs, and rectal swabs) for >100 real-time polymerase chain reaction (PCR) targets in total (30-45 per card depending on configuration). Multipathogen panels were configured by syndrome and customized to include pathogens of significance in young children within the regions where CHAMPS is conducted, including bacteria (57 targets covering 30 genera), viruses (48 targets covering 40 viruses), parasites (8 targets covering 8 organisms), and fungi (3 targets covering 3 organisms). The development and application of multiplex real-time PCR reactions to the TAC microfluidic platform increased the number of targets in each panel while maintaining assay efficiency and replicates for heightened sensitivity. These advances represent a substantial improvement in the utility of this technology for infectious disease diagnostics and surveillance. We optimized all aspects of the CHAMPS molecular laboratory testing workflow including nucleic acid extraction, quality assurance, and data management to ensure comprehensive molecular testing of specimens and high-quality data. Here we describe the development and implementation of multiplex TACs and associated laboratory protocols for specimen processing, testing, and data management at CHAMPS site laboratories.
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Affiliation(s)
- Maureen H Diaz
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jessica L Waller
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | | | - Bernard J Wolff
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Alvaro J Benitez
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Timothy Morris
- Public Health Informatics Institute, The Task Force for Global Health, Atlanta, Georgia, USA
| | - Pratima L Raghunathan
- Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Robert F Breiman
- Emory Global Health Institute, Emory University, Atlanta, Georgia, USA
| | - Cynthia G Whitney
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Dianna M Blau
- Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jonas M Winchell
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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11
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Nyawanda BO, Njuguna HN, Onyango CO, Makokha C, Lidechi S, Fields B, Winchell JM, Katieno JS, Nyaundi J, Ade F, Emukule GO, Mott JA, Otieno N, Widdowson MA, Chaves SS. Comparison of respiratory pathogen yields from Nasopharyngeal/Oropharyngeal swabs and sputum specimens collected from hospitalized adults in rural Western Kenya. Sci Rep 2019; 9:11237. [PMID: 31375774 PMCID: PMC6677726 DOI: 10.1038/s41598-019-47713-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 05/13/2019] [Accepted: 07/16/2019] [Indexed: 11/13/2022] Open
Abstract
Molecular diagnostic methods are becoming increasingly available for assessment of acute lower respiratory illnesses (ALRI). However, nasopharyngeal/oropharyngeal (NP/OP) swabs may not accurately reflect etiologic agents from the lower respiratory tract where sputum specimens are considered as a more representative sample. The pathogen yields from NP/OP against sputum specimens have not been extensively explored, especially in tropical countries. We compared pathogen yields from NP/OP swabs and sputum specimens from patients ≥18 years hospitalized with ALRI in rural Western Kenya. Specimens were tested for 30 pathogens using TaqMan Array Cards (TAC) and results compared using McNemar's test. The agreement for pathogen detection between NP/OP and sputum specimens ranged between 85-100%. More viruses were detected from NP/OP specimens whereas Klebsiella pneumoniae and Mycobacterium tuberculosis were more common in sputum specimens. There was no clear advantage in using sputum over NP/OP specimens to detect pathogens of ALRI in adults using TAC in the context of this tropical setting.
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Affiliation(s)
- Bryan O Nyawanda
- Kenya Medical Research Institute - Center for Global Health Research, Kisumu, Kenya.
| | - Henry N Njuguna
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Clayton O Onyango
- Division of Global Health Protection, Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Caroline Makokha
- Kenya Medical Research Institute - Center for Global Health Research, Kisumu, Kenya
| | - Shirley Lidechi
- Kenya Medical Research Institute - Center for Global Health Research, Kisumu, Kenya
| | - Barry Fields
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Jim S Katieno
- Kenya Medical Research Institute - Center for Global Health Research, Kisumu, Kenya
| | - Jeremiah Nyaundi
- Kenya Medical Research Institute - Center for Global Health Research, Kisumu, Kenya
| | - Fredrick Ade
- Kenya Medical Research Institute - Center for Global Health Research, Kisumu, Kenya
| | - Gideon O Emukule
- Influenza Program, Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Joshua A Mott
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Nancy Otieno
- Kenya Medical Research Institute - Center for Global Health Research, Kisumu, Kenya
| | - Marc-Alain Widdowson
- Division of Global Health Protection, Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Sandra S Chaves
- Centers for Disease Control and Prevention, Atlanta, GA, USA
- Influenza Program, Centers for Disease Control and Prevention, Nairobi, Kenya
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12
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Novosad SA, Basavaraju SV, Annambhotla P, Mohr M, Halpin AL, Foy L, Chmielewski R, Winchell JM, Benitez AJ, Morrison SS, Johnson T, Crabb DM, Ratliff AE, Waites K, Kuehnert MJ. Mycoplasma hominis Infections Transmitted Through Amniotic Tissue Product. Clin Infect Dis 2019; 65:1152-1158. [PMID: 28575162 DOI: 10.1093/cid/cix507] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 05/30/2017] [Indexed: 11/14/2022] Open
Abstract
Background Mycoplasma hominis is a commensal genitourinary tract organism that can cause infections outside the genitourinary tract. We investigated a cluster of M. hominis surgical site infections in patients who underwent spine surgery, all associated with amniotic tissue linked to a common donor. Methods Laboratory tests of tissue product from the donor, including culture, quantitative real-time polymerase chain reaction (qPCR), and whole-genome sequencing were performed. Use of this amniotic tissue product was reviewed. A multistate investigation to identify additional cases and locate any unused products was conducted. Results Twenty-seven tissue product vials from a donor were distributed to facilities in 7 states; at least 20 vials from this donor were used in 14 patients. Of these, 4 of 14 (29%) developed surgical site infections, including 2 M. hominis infections. Mycoplasma hominis was detected by culture and qPCR in 2 unused vials from the donor. Sequencing indicated >99% similarity between patient and unopened vial isolates. For 5 of 27 (19%) vials, the final disposition could not be confirmed. Conclusions Mycoplasma hominis was transmitted through amniotic tissue from a single donor to 2 recipients. Current routine donor screening and product testing does not detect all potential pathogens. Clinicians should be aware that M. hominis can cause surgical site infections, and may not be detected by routine clinical cultures. The lack of a standardized system to track tissue products in healthcare facilities limits the ability of public health agencies to respond to outbreaks and investigate other adverse events associated with these products.
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Affiliation(s)
- Shannon A Novosad
- Epidemic Intelligence Service, and.,Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Sridhar V Basavaraju
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Pallavi Annambhotla
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | - Alison Laufer Halpin
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Linda Foy
- St Vincent Charity Medical Center, Cleveland, Ohio
| | | | - Jonas M Winchell
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia; and
| | - Alvaro J Benitez
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia; and
| | - Shatavia S Morrison
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia; and
| | - Taccara Johnson
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia; and
| | | | | | | | - Matthew J Kuehnert
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
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13
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Beall SG, Cantera J, Diaz MH, Winchell JM, Lillis L, White H, Kalnoky M, Gallarda J, Boyle DS. Performance and workflow assessment of six nucleic acid extraction technologies for use in resource limited settings. PLoS One 2019; 14:e0215753. [PMID: 30998749 PMCID: PMC6472818 DOI: 10.1371/journal.pone.0215753] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 02/16/2019] [Indexed: 01/20/2023] Open
Abstract
Infectious disease nucleic acid amplification technologies (NAAT) have superior sensitivity, specificity, and rapid time to result compared to traditional microbiological methods. Recovery of concentrated, high quality pathogen nucleic acid (NA) from complex specimen matrices is required for optimal performance of several NA amplification/detection technologies such as polymerase chain reaction (PCR). Fully integrated NAAT platforms that enable rapid sample-to-result workflows with minimal user input are generally restricted to larger reference lab settings, and their complexity and cost are prohibitive to widespread implementation in resource limited settings (RLS). Identification of component technologies for incorporation of reliable and affordable sample preparation with pathogen NA amplification/detection into an integrated platform suitable for RLS, is a necessary first step toward achieving the overarching goal of reducing infectious disease-associated morbidity and mortality globally. In the current study, we evaluate the performance of six novel NA extraction technologies from different developers using blinded panels of stool, sputum and blood spiked with variable amounts of quality-controlled DNA- and/or RNA-based microbes. The extraction efficiencies were semi-quantitatively assessed using validated real-time reverse transcription (RT)-PCR assays specific for each microbe and comparing target-specific RT-PCR results to those obtained with reference NA extraction methods. The technologies were ranked based on overall diagnostic accuracy (analytical sensitivity and specificity). Sample input and output volumes, total processing time, user-required manual steps and cost estimates were also examined for suitability in RLS. Together with the performance analysis, these metrics were used to select the more suitable candidate technologies for further optimization of integrated NA amplification and detection technologies for RLS.
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Affiliation(s)
- Shivani G. Beall
- Centers for Disease Control and Prevention, Division of Bacterial Diseases, Respiratory Diseases Branch, Atlanta, Georgia, United States of America
| | | | - Maureen H. Diaz
- Centers for Disease Control and Prevention, Division of Bacterial Diseases, Respiratory Diseases Branch, Atlanta, Georgia, United States of America
| | - Jonas M. Winchell
- Centers for Disease Control and Prevention, Division of Bacterial Diseases, Respiratory Diseases Branch, Atlanta, Georgia, United States of America
| | | | | | | | - James Gallarda
- Bill and Melinda Gates Foundation, Seattle, Washington, United States of America
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14
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Velaphi SC, Westercamp M, Moleleki M, Pondo T, Dangor Z, Wolter N, von Gottberg A, Shang N, Demirjian A, Winchell JM, Diaz MH, Nakwa F, Okudo G, Wadula J, Cutland C, Schrag SJ, Madhi SA. Surveillance for incidence and etiology of early-onset neonatal sepsis in Soweto, South Africa. PLoS One 2019; 14:e0214077. [PMID: 30970036 PMCID: PMC6457488 DOI: 10.1371/journal.pone.0214077] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Accepted: 03/06/2019] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Globally, over 400,000 neonatal deaths in 2015 were attributed to sepsis, however, the incidence and etiologies of these infections are largely unknown in low-middle income countries. We aimed to determine incidence and etiology of community-acquired early-onset (<72 hours age) sepsis (EOS) using culture and molecular diagnostics. METHODS This was a prospective observational study, in which we conducted a surveillance for pathogens using a combination of blood culture and a polymerase chain reaction (PCR)-based test. Blood culture was performed on all neonates with suspected EOS. Among the subset fulfilling criteria for protocol-defined EOS, blood and nasopharyngeal (NP) respiratory swabs were tested by quantitative real-time reverse-transcriptase PCR using a Taqman Array Card (TAC) with 15 bacterial and 12 viral targets. Blood and NP samples from 312 healthy newborns were also tested by TAC to estimate background positivity rates. We used variant latent-class methods to attribute etiologies and calculate pathogen-specific proportions and incidence rates. RESULTS We enrolled 2,624 neonates with suspected EOS and from these 1,231 newborns met criteria for protocol-defined EOS (incidence- 39.3/1,000 live-births). Using the partially latent-class modelling, only 26.7% cases with protocol-defined EOS had attributable etiology, and the largest pathogen proportion were Ureaplasma spp. (5.4%; 95%CI: 3.6-8.0) and group B Streptococcus (GBS) (4.8%; 95%CI: 4.1-5.8), and no etiology was attributable for 73.3% of cases. Blood cultures were positive in 99/1,231 (8.0%) with protocol-defined EOS (incidence- 3.2/1,000 live-births). Leading pathogens on blood culture included GBS (35%) and viridans streptococci (24%). Ureaplasma spp. was the most common organism identified on TAC among cases with protocol-defined EOS. CONCLUSION Using a combination of blood culture and a PCR-based test the common pathogens isolated in neonates with sepsis were Ureaplasma spp. and GBS. Despite documenting higher rates of protocol-defined EOS and using a combination of tests, the etiology for EOS remains elusive.
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Affiliation(s)
- Sithembiso C. Velaphi
- Department of Pediatrics, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Matthew Westercamp
- Centers for Disease Control and Prevention, Atlanta, United States of America
| | - Malefu Moleleki
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service (NHLS), and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Tracy Pondo
- Centers for Disease Control and Prevention, Atlanta, United States of America
| | - Ziyaad Dangor
- Department of Pediatrics, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nicole Wolter
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service (NHLS), and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service (NHLS), and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nong Shang
- Centers for Disease Control and Prevention, Atlanta, United States of America
| | - Alicia Demirjian
- Centers for Disease Control and Prevention, Atlanta, United States of America
| | - Jonas M. Winchell
- Centers for Disease Control and Prevention, Atlanta, United States of America
| | - Maureen H. Diaz
- Centers for Disease Control and Prevention, Atlanta, United States of America
| | - Firdose Nakwa
- Department of Pediatrics, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Grace Okudo
- Department of Pediatrics, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jeannette Wadula
- Department of Clinical Microbiology and Infectious Diseases, NHLS, South Africa and School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Clare Cutland
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Stephanie J. Schrag
- Centers for Disease Control and Prevention, Atlanta, United States of America
| | - Shabir A. Madhi
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Science and Technology/National Research Foundation: South African Research Chair Initiative in Vaccine Preventable Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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15
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Raphael BH, Huynh T, Brown E, Smith JC, Ruberto I, Getsinger L, White S, Winchell JM. Culture of Clinical Specimens Reveals Extensive Diversity of Legionella pneumophila Strains in Arizona. mSphere 2019; 4:e00649-18. [PMID: 30814318 PMCID: PMC6393729 DOI: 10.1128/msphere.00649-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 11/19/2018] [Accepted: 01/27/2019] [Indexed: 11/23/2022] Open
Abstract
Between 2000 and 2017, a total of 236 Legionella species isolates from Arizona were submitted to the CDC for reference testing. Most of these isolates were recovered from bronchoalveolar lavage specimens. Although the incidence of legionellosis in Arizona is less than the overall U.S. incidence, Arizona submits the largest number of isolates to the CDC for testing compared to those from other states. In addition to a higher proportion of culture confirmation of legionellosis cases in Arizona than in other states, all Legionellapneumophila isolates are forwarded to the CDC for confirmatory testing. Compared to that from other states, a higher proportion of isolates from Arizona were identified as belonging to L. pneumophila serogroups 6 (28.2%) and 8 (8.9%). Genome sequencing was conducted on 113 L. pneumophila clinical isolates not known to be associated with outbreaks in order to understand the genomic diversity of strains causing legionellosis in Arizona. Whole-genome multilocus sequence typing (wgMLST) revealed 17 clusters of isolates sharing at least 99% identical allele content. Only two of these clusters contained isolates from more than one individual with exposure at the same facility. Additionally, wgMLST analysis revealed a group of 31 isolates predominantly belonging to serogroup 6 and containing isolates from three separate clusters. Single nucleotide polymorphism (SNP) and pangenome analysis were used to further resolve genome sequences belonging to a subset of isolates. This study demonstrates that culture of clinical specimens for Legionella spp. reveals a highly diverse population of strains causing legionellosis in Arizona which could be underappreciated using other diagnostic approaches.IMPORTANCE Culture of clinical specimens from patients with Legionnaires' disease is rarely performed, restricting our understanding of the diversity and ecology of Legionella Culture of Legionella from patient specimens in Arizona revealed a greater proportion of non-serogroup 1 Legionellapneumophila isolates than in other U.S. isolates examined. Disease caused by such isolates may go undetected using other diagnostic methods. Moreover, genome sequence analysis revealed that these isolates were genetically diverse, and understanding these populations may help in future environmental source attribution studies.
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Affiliation(s)
- Brian H Raphael
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Trung Huynh
- Arizona Department of Health Services, Phoenix, Arizona, USA
| | - Ellen Brown
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jessica C Smith
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Irene Ruberto
- Arizona Department of Health Services, Phoenix, Arizona, USA
| | - Linda Getsinger
- Arizona Department of Health Services, Phoenix, Arizona, USA
| | - Stacy White
- Arizona Department of Health Services, Phoenix, Arizona, USA
| | - Jonas M Winchell
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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16
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Carrim M, Wolter N, Benitez AJ, Tempia S, du Plessis M, Walaza S, Moosa F, Diaz MH, Wolff BJ, Treurnicht FK, Hellferscee O, Dawood H, Variava E, Cohen C, Winchell JM, von Gottberg A. Epidemiology and Molecular Identification and Characterization of Mycoplasma pneumoniae, South Africa, 2012-2015. Emerg Infect Dis 2019; 24:506-513. [PMID: 29460736 PMCID: PMC5823326 DOI: 10.3201/eid2403.162052] [Citation(s) in RCA: 21] [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: 11/19/2022] Open
Abstract
During 2012-2015, we tested respiratory specimens from patients with severe respiratory illness (SRI), patients with influenza-like illness (ILI), and controls in South Africa by real-time PCR for Mycoplasma pneumoniae, followed by culture and molecular characterization of positive samples. M. pneumoniae prevalence was 1.6% among SRI patients, 0.7% among ILI patients, and 0.2% among controls (p<0.001). Age <5 years (adjusted odd ratio 7.1; 95% CI 1.7-28.7) and HIV infection (adjusted odds ratio 23.8; 95% CI 4.1-138.2) among M. pneumonia-positive persons were associated with severe disease. The detection rate attributable to illness was 93.9% (95% CI 74.4%-98.5%) in SRI patients and 80.7% (95% CI 16.7%-95.6%) in ILI patients. The hospitalization rate was 28 cases/100,000 population. We observed the macrolide-susceptible M. pneumoniae genotype in all cases and found P1 types 1, 2, and a type 2 variant with multilocus variable number tandem repeat types 3/6/6/2, 3/5/6/2, and 4/5/7/2.
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17
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Mercante JW, Caravas JA, Ishaq MK, Kozak-Muiznieks NA, Raphael BH, Winchell JM. Genomic heterogeneity differentiates clinical and environmental subgroups of Legionella pneumophila sequence type 1. PLoS One 2018; 13:e0206110. [PMID: 30335848 PMCID: PMC6193728 DOI: 10.1371/journal.pone.0206110] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [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: 06/18/2018] [Accepted: 10/05/2018] [Indexed: 11/19/2022] Open
Abstract
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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Affiliation(s)
- Jeffrey W. Mercante
- Pneumonia Response and Surveillance Laboratory, Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Jason A. Caravas
- Pneumonia Response and Surveillance Laboratory, Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Maliha K. Ishaq
- Pneumonia Response and Surveillance Laboratory, Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Natalia A. Kozak-Muiznieks
- Pneumonia Response and Surveillance Laboratory, Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Brian H. Raphael
- Pneumonia Response and Surveillance Laboratory, Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Jonas M. Winchell
- Pneumonia Response and Surveillance Laboratory, Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
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Saha SK, Schrag SJ, El Arifeen S, Mullany LC, Shahidul Islam M, Shang N, Qazi SA, Zaidi AKM, Bhutta ZA, Bose A, Panigrahi P, Soofi SB, Connor NE, Mitra DK, Isaac R, Winchell JM, Arvay ML, Islam M, Shafiq Y, Nisar I, Baloch B, Kabir F, Ali M, Diaz MH, Satpathy R, Nanda P, Padhi BK, Parida S, Hotwani A, Hasanuzzaman M, Ahmed S, Belal Hossain M, Ariff S, Ahmed I, Ibne Moin SM, Mahmud A, Waller JL, Rafiqullah I, Quaiyum MA, Begum N, Balaji V, Halen J, Nawshad Uddin Ahmed ASM, Weber MW, Hamer DH, Hibberd PL, Sadeq-Ur Rahman Q, Mogan VR, Hossain T, McGee L, Anandan S, Liu A, Panigrahi K, Abraham AM, Baqui AH. Causes and incidence of community-acquired serious infections among young children in south Asia (ANISA): an observational cohort study. Lancet 2018; 392:145-159. [PMID: 30025808 PMCID: PMC6053599 DOI: 10.1016/s0140-6736(18)31127-9] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 05/08/2018] [Accepted: 05/15/2018] [Indexed: 12/11/2022]
Abstract
BACKGROUND More than 500 000 neonatal deaths per year result from possible serious bacterial infections (pSBIs), but the causes are largely unknown. We investigated the incidence of community-acquired infections caused by specific organisms among neonates in south Asia. METHODS From 2011 to 2014, we identified babies through population-based pregnancy surveillance at five sites in Bangladesh, India, and Pakistan. Babies were visited at home by community health workers up to ten times from age 0 to 59 days. Illness meeting the WHO definition of pSBI and randomly selected healthy babies were referred to study physicians. The primary objective was to estimate proportions of specific infectious causes by blood culture and Custom TaqMan Array Cards molecular assay (Thermo Fisher, Bartlesville, OK, USA) of blood and respiratory samples. FINDINGS 6022 pSBI episodes were identified among 63 114 babies (95·4 per 1000 livebirths). Causes were attributed in 28% of episodes (16% bacterial and 12% viral). Mean incidence of bacterial infections was 13·2 (95% credible interval [CrI] 11·2-15·6) per 1000 livebirths and of viral infections was 10·1 (9·4-11·6) per 1000 livebirths. The leading pathogen was respiratory syncytial virus (5·4, 95% CrI 4·8-6·3 episodes per 1000 livebirths), followed by Ureaplasma spp (2·4, 1·6-3·2 episodes per 1000 livebirths). Among babies who died, causes were attributed to 46% of pSBI episodes, among which 92% were bacterial. 85 (83%) of 102 blood culture isolates were susceptible to penicillin, ampicillin, gentamicin, or a combination of these drugs. INTERPRETATION Non-attribution of a cause in a high proportion of patients suggests that a substantial proportion of pSBI episodes might not have been due to infection. The predominance of bacterial causes among babies who died, however, indicates that appropriate prevention measures and management could substantially affect neonatal mortality. Susceptibility of bacterial isolates to first-line antibiotics emphasises the need for prudent and limited use of newer-generation antibiotics. Furthermore, the predominance of atypical bacteria we found and high incidence of respiratory syncytial virus indicated that changes in management strategies for treatment and prevention are needed. Given the burden of disease, prevention of respiratory syncytial virus would have a notable effect on the overall health system and achievement of Sustainable Development Goal. FUNDING Bill & Melinda Gates Foundation.
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Affiliation(s)
- Samir K Saha
- Department of Microbiology, Child Health Research Foundation, Dhaka Shishu Hospital, Sher-E-Bangla Nagar, Dhaka, Bangladesh.
| | - Stephanie J Schrag
- Centers for Disease Control and Prevention, Respiratory Diseases Branch, Atlanta, GA, USA
| | - Shams El Arifeen
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Luke C Mullany
- Johns Hopkins Bloomberg, School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Mohammad Shahidul Islam
- Department of Microbiology, Child Health Research Foundation, Dhaka Shishu Hospital, Sher-E-Bangla Nagar, Dhaka, Bangladesh
| | - Nong Shang
- Centers for Disease Control and Prevention, Respiratory Diseases Branch, Atlanta, GA, USA
| | - Shamim A Qazi
- Department of Child and Adolescent Health and Development, World Health Organization, Geneva, Switzerland
| | - Anita K M Zaidi
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Zulfiqar A Bhutta
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | | | - Pinaki Panigrahi
- Center for Global Health and Development, College of Public Health, University of Nebraska Medical Center, Omaha, NE, USA
| | - Sajid B Soofi
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Nicholas E Connor
- Department of Microbiology, Child Health Research Foundation, Dhaka Shishu Hospital, Sher-E-Bangla Nagar, Dhaka, Bangladesh
| | - Dipak K Mitra
- Maternal and Child Health Division, icddr,b, Dhaka, Bangladesh
| | - Rita Isaac
- Christian Medical College, Bagayam, Vellore, India
| | - Jonas M Winchell
- Centers for Disease Control and Prevention, Respiratory Diseases Branch, Atlanta, GA, USA
| | - Melissa L Arvay
- Centers for Disease Control and Prevention, Respiratory Diseases Branch, Atlanta, GA, USA
| | - Maksuda Islam
- Department of Microbiology, Child Health Research Foundation, Dhaka Shishu Hospital, Sher-E-Bangla Nagar, Dhaka, Bangladesh
| | - Yasir Shafiq
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Imran Nisar
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Benazir Baloch
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Furqan Kabir
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Murtaza Ali
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Maureen H Diaz
- Centers for Disease Control and Prevention, Respiratory Diseases Branch, Atlanta, GA, USA
| | | | - Pritish Nanda
- Asian Institute of Public Health, Bhubaneswar, India
| | | | | | - Aneeta Hotwani
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - M Hasanuzzaman
- Department of Microbiology, Child Health Research Foundation, Dhaka Shishu Hospital, Sher-E-Bangla Nagar, Dhaka, Bangladesh
| | - Sheraz Ahmed
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Mohammad Belal Hossain
- Department of Microbiology, Child Health Research Foundation, Dhaka Shishu Hospital, Sher-E-Bangla Nagar, Dhaka, Bangladesh
| | - Shabina Ariff
- Department of Microbiology, Child Health Research Foundation, Dhaka Shishu Hospital, Sher-E-Bangla Nagar, Dhaka, Bangladesh
| | - Imran Ahmed
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Syed Mamun Ibne Moin
- Johns Hopkins Bloomberg, School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Arif Mahmud
- Johns Hopkins Bloomberg, School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Jessica L Waller
- Centers for Disease Control and Prevention, Respiratory Diseases Branch, Atlanta, GA, USA
| | - Iftekhar Rafiqullah
- Department of Microbiology, Child Health Research Foundation, Dhaka Shishu Hospital, Sher-E-Bangla Nagar, Dhaka, Bangladesh
| | | | - Nazma Begum
- Johns Hopkins Bloomberg, School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | | | - Jasmin Halen
- Christian Medical College, Bagayam, Vellore, India
| | - A S M Nawshad Uddin Ahmed
- Department of Microbiology, Child Health Research Foundation, Dhaka Shishu Hospital, Sher-E-Bangla Nagar, Dhaka, Bangladesh
| | - Martin W Weber
- Child and Adolescent Health and Development Division, World Health Organization Regional Office for Europe, Copenhagen, Denmark
| | - Davidson H Hamer
- Department of Global Health and Center for Global Health and Development, Boston University School of Public Health, Boston, MA, USA
| | - Patricia L Hibberd
- Department of Global Health and Center for Global Health and Development, Boston University School of Public Health, Boston, MA, USA
| | | | | | - Tanvir Hossain
- Maternal and Child Health Division, icddr,b, Dhaka, Bangladesh
| | - Lesley McGee
- Centers for Disease Control and Prevention, Respiratory Diseases Branch, Atlanta, GA, USA
| | | | - Anran Liu
- Centers for Disease Control and Prevention, Respiratory Diseases Branch, Atlanta, GA, USA
| | - Kalpana Panigrahi
- Center for Global Health and Development, College of Public Health, University of Nebraska Medical Center, Omaha, NE, USA
| | | | - Abdullah H Baqui
- Johns Hopkins Bloomberg, School of Public Health, Johns Hopkins University, Baltimore, MD, USA
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Wolff BJ, Morrison SS, Winchell JM. Development of a multiplex TaqMan real-time PCR assay for the detection of Chlamydia psittaci and Chlamydia pneumoniae in human clinical specimens. Diagn Microbiol Infect Dis 2018; 90:167-170. [DOI: 10.1016/j.diagmicrobio.2017.11.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 11/16/2017] [Accepted: 11/20/2017] [Indexed: 02/06/2023]
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20
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Kozak-Muiznieks NA, Morrison SS, Mercante JW, Ishaq MK, Johnson T, Caravas J, Lucas CE, Brown E, Raphael BH, Winchell JM. Comparative genome analysis reveals a complex population structure of Legionella pneumophila subspecies. Infect Genet Evol 2018; 59:172-185. [PMID: 29427765 DOI: 10.1016/j.meegid.2018.02.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 02/05/2018] [Accepted: 02/06/2018] [Indexed: 10/18/2022]
Abstract
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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Affiliation(s)
- Natalia A Kozak-Muiznieks
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Shatavia S Morrison
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Jeffrey W Mercante
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Maliha K Ishaq
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Taccara Johnson
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Jason Caravas
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Claressa E Lucas
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Ellen Brown
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Brian H Raphael
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Jonas M Winchell
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States.
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21
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Llewellyn AC, Lucas CE, Roberts SE, Brown EW, Nayak BS, Raphael BH, Winchell JM. Distribution of Legionella and bacterial community composition among regionally diverse US cooling towers. PLoS One 2017; 12:e0189937. [PMID: 29261791 PMCID: PMC5738086 DOI: 10.1371/journal.pone.0189937] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [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: 08/02/2017] [Accepted: 12/05/2017] [Indexed: 11/19/2022] Open
Abstract
Cooling towers (CTs) are a leading source of outbreaks of Legionnaires' disease (LD), a severe form of pneumonia caused by inhalation of aerosols containing Legionella bacteria. Accordingly, proper maintenance of CTs is vital for the prevention of LD. The aim of this study was to determine the distribution of Legionella in a subset of regionally diverse US CTs and characterize the associated microbial communities. Between July and September of 2016, we obtained aliquots from water samples collected for routine Legionella testing from 196 CTs located in eight of the nine continental US climate regions. After screening for Legionella by PCR, positive samples were cultured and the resulting Legionella isolates were further characterized. Overall, 84% (164) were PCR-positive, including samples from every region studied. Of the PCR-positive samples, Legionella spp were isolated from 47% (78), L. pneumophila was isolated from 32% (53), and L. pneumophila serogroup 1 (Lp1) was isolated from 24% (40). Overall, 144 unique Legionella isolates were identified; 53% (76) of these were Legionella pneumophila. Of the 76 L. pneumophila isolates, 51% (39) were Lp1. Legionella were isolated from CTs in seven of the eight US regions examined. 16S rRNA amplicon sequencing was used to compare the bacterial communities of CT waters with and without detectable Legionella as well as the microbiomes of waters from different climate regions. Interestingly, the microbial communities were homogenous across climate regions. When a subset of seven CTs sampled in April and July were compared, there was no association with changes in corresponding CT microbiomes over time in the samples that became culture-positive for Legionella. Legionella species and Lp1 were detected frequently among the samples examined in this first large-scale study of Legionella in US CTs. Our findings highlight that, under the right conditions, there is the potential for CT-related LD outbreaks to occur throughout the US.
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Affiliation(s)
- Anna C. Llewellyn
- Laboratory Leadership Service, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
- Pneumonia Response and Surveillance Laboratory, Respiratory Disease Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Claressa E. Lucas
- Pneumonia Response and Surveillance Laboratory, Respiratory Disease Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Sarah E. Roberts
- Pneumonia Response and Surveillance Laboratory, Respiratory Disease Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Ellen W. Brown
- Pneumonia Response and Surveillance Laboratory, Respiratory Disease Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Bina S. Nayak
- Water Quality Division, Pinellas County Utilities, Largo, FL, United States of America
| | - Brian H. Raphael
- Pneumonia Response and Surveillance Laboratory, Respiratory Disease Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Jonas M. Winchell
- Pneumonia Response and Surveillance Laboratory, Respiratory Disease Branch, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
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Patel JC, George J, Vuong J, Potts CC, Bozio C, Clark TA, Thomas J, Schier J, Chang A, Waller JL, Diaz MH, Whaley M, Jenkins LT, Fuller S, Williams DE, Redd JT, Arthur RR, Taweh F, Vera Walker Y, Hardy P, Freeman M, Katawera V, Gwesa G, Gbanya MZ, Clement P, Kohar H, Stone M, Fallah M, Nyenswah T, Winchell JM, Wang X, McNamara LA, Dokubo EK, Fox LM. Rapid Laboratory Identification of Neisseria meningitidis Serogroup C as the Cause of an Outbreak - Liberia, 2017. MMWR Morb Mortal Wkly Rep 2017; 66:1144-1147. [PMID: 29073124 PMCID: PMC5689101 DOI: 10.15585/mmwr.mm6642a5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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23
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Diaz MH, Desai HP, Morrison SS, Benitez AJ, Wolff BJ, Caravas J, Read TD, Dean D, Winchell JM. Correction: Comprehensive bioinformatics analysis of Mycoplasma pneumoniae genomes to investigate underlying population structure and type-specific determinants. PLoS One 2017; 12:e0186030. [PMID: 28977025 PMCID: PMC5627953 DOI: 10.1371/journal.pone.0186030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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24
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Diaz MH, Desai HP, Morrison SS, Benitez AJ, Wolff BJ, Caravas J, Read TD, Dean D, Winchell JM. Comprehensive bioinformatics analysis of Mycoplasma pneumoniae genomes to investigate underlying population structure and type-specific determinants. PLoS One 2017; 12:e0174701. [PMID: 28410368 PMCID: PMC5391922 DOI: 10.1371/journal.pone.0174701] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 03/13/2017] [Indexed: 11/28/2022] Open
Abstract
Mycoplasma pneumoniae is a significant cause of respiratory illness worldwide. Despite a minimal and highly conserved genome, genetic diversity within the species may impact disease. We performed whole genome sequencing (WGS) analysis of 107 M. pneumoniae isolates, including 67 newly sequenced using the Pacific BioSciences RS II and/or Illumina MiSeq sequencing platforms. Comparative genomic analysis of 107 genomes revealed >3,000 single nucleotide polymorphisms (SNPs) in total, including 520 type-specific SNPs. Population structure analysis supported the existence of six distinct subgroups, three within each type. We developed a predictive model to classify an isolate based on whole genome SNPs called against the reference genome into the identified subtypes, obviating the need for genome assembly. This study is the most comprehensive WGS analysis for M. pneumoniae to date, underscoring the power of combining complementary sequencing technologies to overcome difficult-to-sequence regions and highlighting potential differential genomic signatures in M. pneumoniae.
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Affiliation(s)
- Maureen H. Diaz
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Heta P. Desai
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Shatavia S. Morrison
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Alvaro J. Benitez
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Bernard J. Wolff
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Jason Caravas
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Timothy D. Read
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Deborah Dean
- Center for Immunobiology and Vaccine Research, University of California San Francisco Benioff Children’s Hospital Oakland Research Institute, Oakland, California, United States of America
- Joint Graduate Program in Bioengineering, University of California San Francisco and University of California Berkeley, Oakland, California, United States of America
| | - Jonas M. Winchell
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- * E-mail:
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25
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Harris AM, Bramley AM, Jain S, Arnold SR, Ampofo K, Self WH, Williams DJ, Anderson EJ, Grijalva CG, McCullers JA, Pavia AT, Wunderink RG, Edwards KM, Winchell JM, Hicks LA. Influence of Antibiotics on the Detection of Bacteria by Culture-Based and Culture-Independent Diagnostic Tests in Patients Hospitalized With Community-Acquired Pneumonia. Open Forum Infect Dis 2017; 4:ofx014. [PMID: 28480285 DOI: 10.1093/ofid/ofx014] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [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: 11/08/2016] [Accepted: 01/26/2017] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Specimens collected after antibiotic exposure may reduce culture-based bacterial detections. The impact on culture-independent diagnostic tests is unclear. We assessed the effect of antibiotic exposure on both of these test results among patients hospitalized with community-acquired pneumonia (CAP). METHODS Culture-based bacterial testing included blood cultures and high-quality sputum or endotracheal tube (ET) aspirates; culture-independent testing included urinary antigen testing (adults) for Streptococcus pneumoniae and Legionella pneumophila and polymerase chain reaction (PCR) on nasopharyngeal and oropharyngeal (NP/OP) swabs for Mycoplasma pneumoniae and Chlamydia pneumoniae. The proportion of bacterial detections was compared between specimens collected before and after either any antibiotic exposure (prehospital and/or inpatient) or only prehospital antibiotics and increasing time after initiation of inpatient antibiotics. RESULTS Of 4678 CAP patients, 4383 (94%) received antibiotics: 3712 (85%) only inpatient, 642 (15%) both inpatient and prehospital, and 29 (<1%) only prehospital. There were more bacterial detections in specimens collected before antibiotics for blood cultures (5.2% vs 2.6%; P < .01) and sputum/ET cultures (50.0% vs 26.8%; P < .01) but not urine antigen (7.0% vs 5.7%; P = .53) or NP/OP PCR (6.7% vs 5.4%; P = .31). For all diagnostic testing, bacterial detections declined with increasing time between inpatient antibiotic administration and specimen collection. CONCLUSIONS Bacteria were less frequently detected in culture-based tests collected after antibiotics and in culture-independent tests that had longer intervals between antibiotic exposure and specimen collection. Bacterial yield could improve if specimens were collected promptly, preferably before antibiotics, providing data for improved antibiotic selection.
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Affiliation(s)
- Aaron M Harris
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Anna M Bramley
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Seema Jain
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Sandra R Arnold
- Le Bonheur Children's Hospital, Memphis, Tennessee.,University of Tennessee Health Science Center, Memphis
| | - Krow Ampofo
- University of Utah Health Sciences Center, Salt Lake City
| | - Wesley H Self
- Vanderbilt University School of Medicine, Nashville, Tennessee
| | | | | | | | - Jonathan A McCullers
- Le Bonheur Children's Hospital, Memphis, Tennessee.,University of Tennessee Health Science Center, Memphis.,St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Andrew T Pavia
- University of Utah Health Sciences Center, Salt Lake City
| | | | | | | | - Lauri A Hicks
- 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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Mercante JW, Morrison SS, Desai HP, Raphael BH, Winchell JM. Genomic Analysis Reveals Novel Diversity among the 1976 Philadelphia Legionnaires' Disease Outbreak Isolates and Additional ST36 Strains. PLoS One 2016; 11:e0164074. [PMID: 27684472 PMCID: PMC5042515 DOI: 10.1371/journal.pone.0164074] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [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: 06/29/2016] [Accepted: 09/19/2016] [Indexed: 11/18/2022] Open
Abstract
Legionella pneumophila was first recognized as a cause of severe and potentially fatal pneumonia during a large-scale outbreak of Legionnaires’ disease (LD) at a Pennsylvania veterans’ convention in Philadelphia, 1976. The ensuing investigation and recovery of four clinical isolates launched the fields of Legionella epidemiology and scientific research. Only one of the original isolates, “Philadelphia-1”, has been widely distributed or extensively studied. Here we describe the whole-genome sequencing (WGS), complete assembly, and comparative analysis of all Philadelphia LD strains recovered from that investigation, along with L. pneumophila isolates sharing the Philadelphia sequence type (ST36). Analyses revealed that the 1976 outbreak was due to multiple serogroup 1 strains within the same genetic lineage, differentiated by an actively mobilized, self-replicating episome that is shared with L. pneumophila str. Paris, and two large, horizontally-transferred genomic loci, among other polymorphisms. We also found a completely unassociated ST36 strain that displayed remarkable genetic similarity to the historical Philadelphia isolates. This similar strain implies the presence of a potential clonal population, and suggests important implications may exist for considering epidemiological context when interpreting phylogenetic relationships among outbreak-associated isolates. Additional extensive archival research identified the Philadelphia isolate associated with a non-Legionnaire case of “Broad Street pneumonia”, and provided new historical and genetic insights into the 1976 epidemic. This retrospective analysis has underscored the utility of fully-assembled WGS data for Legionella outbreak investigations, highlighting the increased resolution that comes from long-read sequencing and a sequence type-matched genomic data set.
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Affiliation(s)
- Jeffrey W. Mercante
- Pneumonia Response and Surveillance Laboratory, Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Shatavia S. Morrison
- Pneumonia Response and Surveillance Laboratory, Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Heta P. Desai
- Pneumonia Response and Surveillance Laboratory, Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Brian H. Raphael
- Pneumonia Response and Surveillance Laboratory, Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Jonas M. Winchell
- Pneumonia Response and Surveillance Laboratory, Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- * E-mail:
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Wolter N, Carrim M, Cohen C, Tempia S, Walaza S, Sahr P, de Gouveia L, Treurnicht F, Hellferscee O, Cohen AL, Benitez AJ, Dawood H, Variava E, Winchell JM, von Gottberg A. Legionnaires' Disease in South Africa, 2012-2014. Emerg Infect Dis 2016; 22:131-3. [PMID: 26692504 PMCID: PMC4696697 DOI: 10.3201/eid2201.150972] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [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: 11/23/2022] Open
Abstract
During June 2012–September 2014, we tested patients with severe respiratory illness for Legionella spp. infection and conducted a retrospective epidemiologic investigation. Of 1,805 patients tested, Legionella was detected in samples of 21 (1.2%); most were adults who had HIV or tuberculosis infections and were inappropriately treated for Legionella.
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Ku DN, Ku SK, Helfman B, McCarty NA, Wolff BJ, Winchell JM, Anderson LJ. Ability of device to collect bacteria from cough aerosols generated by adults with cystic fibrosis. F1000Res 2016; 5:1920. [PMID: 27781088 PMCID: PMC5054809 DOI: 10.12688/f1000research.9251.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/27/2016] [Indexed: 12/02/2022] Open
Abstract
Background: Identifying lung pathogens and acute spikes in lung counts remain a challenge in the treatment of patients with cystic fibrosis (CF). Bacteria from the deep lung may be sampled from aerosols produced during coughing. Methods: A new device was used to collect and measure bacteria levels from cough aerosols of patients with CF. Sputum and oral specimens were also collected and measured for comparison. Pseudomonas aeruginosa, Staphylococcus aureus, Klebsiella pneumoniae, and Streptococcus mitis were detected in specimens using Real-Time Polymerase Chain Reaction (RT-PCR) molecular assays. Results: Twenty adult patients with CF and 10 healthy controls participated. CF related bacteria (CFRB) were detected in 13/20 (65%) cough specimens versus 15/15 (100%) sputum specimens. Commensal S. mitis was present in 0/17 (0%, p=0.0002) cough specimens and 13/14 (93%) sputum samples. In normal controls, no bacteria were collected in cough specimens but 4/10 (40%) oral specimens were positive for CFRB. Conclusions: Non-invasive cough aerosol collection may detect lower respiratory pathogens in CF patients, with similar specificity and sensitivity to rates detected by BAL, without contamination by oral CFRB or commensal bacteria.
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Affiliation(s)
- David N. Ku
- Georgia Institute of Technology, Atlanta, GA, 30332, USA
- MD Innovate, Inc, Decatur, GA, 30030, USA
| | | | - Beth Helfman
- Emory Children’s Center for Cystic Fibrosis Research, Emory University, Atlanta, GA, 30322, USA
- Department of Pediatrics, Emory University, Atlanta, 30322, USA
| | - Nael A. McCarty
- Emory Children’s Center for Cystic Fibrosis Research, Emory University, Atlanta, GA, 30322, USA
- Department of Pediatrics, Emory University, Atlanta, 30322, USA
| | - Bernard J. Wolff
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - Jonas M. Winchell
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, 30333, USA
| | - Larry J. Anderson
- Division of Infectious Diseases, Department of Pediatrics, Emory University and Children’s Healthcare of Atlanta, Atlanta, GA, 30322, USA
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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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Cross KE, Mercante JW, Benitez AJ, Brown EW, Diaz MH, Winchell JM. Simultaneous detection of Legionella species and L. anisa, L. bozemanii, L. longbeachae and L. micdadei using conserved primers and multiple probes in a multiplex real-time PCR assay. Diagn Microbiol Infect Dis 2016; 85:295-301. [PMID: 27107536 PMCID: PMC5505572 DOI: 10.1016/j.diagmicrobio.2016.03.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 03/03/2016] [Accepted: 03/29/2016] [Indexed: 10/27/2022]
Abstract
Legionnaires' disease is a severe respiratory disease that is estimated to cause between 8,000 and 18,000 hospitalizations each year, though the exact burden is unknown due to under-utilization of diagnostic testing. Although Legionella pneumophila is the most common species detected in clinical cases (80-90%), other species have also been reported to cause disease. However, little is known about Legionnaires' disease caused by these non-pneumophila species. We designed a multiplex real-time PCR assay for detection of all Legionella spp. and simultaneous specific identification of four clinically-relevant Legionella species, L. anisa, L. bozemanii, L. longbeachae, and L. micdadei, using 5'-hydrolysis probe real-time PCR. The analytical sensitivity for detection of nucleic acid from each target species was ≤50fg per reaction. We demonstrated the utility of this assay in spiked human sputum specimens. This assay could serve as a tool for understanding the scope and impact of non-pneumophila Legionella species in human disease.
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Affiliation(s)
- Kristen E Cross
- Pneumonia Response and Surveillance Laboratory, Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Atlanta, GA, 30329, USA
| | - Jeffrey W Mercante
- Pneumonia Response and Surveillance Laboratory, Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Atlanta, GA, 30329, USA
| | - Alvaro J Benitez
- Pneumonia Response and Surveillance Laboratory, Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Atlanta, GA, 30329, USA
| | - Ellen W Brown
- Pneumonia Response and Surveillance Laboratory, Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Atlanta, GA, 30329, USA
| | - Maureen H Diaz
- Pneumonia Response and Surveillance Laboratory, Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Atlanta, GA, 30329, USA
| | - Jonas M Winchell
- Pneumonia Response and Surveillance Laboratory, Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Atlanta, GA, 30329, USA.
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32
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Diaz MH, Cross KE, Benitez AJ, Hicks LA, Kutty P, Bramley AM, Chappell JD, Hymas W, Patel A, Qi C, Williams DJ, Arnold SR, Ampofo K, Self WH, Grijalva CG, Anderson EJ, McCullers JA, Pavia AT, Wunderink RG, Edwards KM, Jain S, Winchell JM. Identification of Bacterial and Viral Codetections With Mycoplasma pneumoniae Using the TaqMan Array Card in Patients Hospitalized With Community-Acquired Pneumonia. Open Forum Infect Dis 2016; 3:ofw071. [PMID: 27191004 PMCID: PMC4867659 DOI: 10.1093/ofid/ofw071] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 03/28/2016] [Indexed: 12/13/2022] Open
Abstract
Mycoplasma pneumoniae was detected in a number of patients with community-acquired pneumonia in a recent prospective study. To assess whether other pathogens were also detected in these patients, TaqMan Array Cards were used to test 216 M pneumoniae-positive respiratory specimens for 25 additional viral and bacterial respiratory pathogens. It is interesting to note that 1 or more codetections, predominantly bacterial, were identified in approximately 60% of specimens, with codetections being more common in children.
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Affiliation(s)
| | | | | | | | | | - Anna M Bramley
- Influenza Division , Centers for Disease Control, and Prevention , Atlanta, Georgia
| | | | - Weston Hymas
- University of Utah Health Sciences Center , Salt Lake City
| | - Anami Patel
- Le Bonheur Children's Hospital, Memphis, Tennessee; University of Tennessee Health Science Center, Memphis
| | - Chao Qi
- Northwestern University Feinberg School of Medicine , Chicago, Illinois
| | - Derek J Williams
- Vanderbilt University School of Medicine, Nashville, Tennessee; Vanderbilt Vaccine Research Program, Nashville, Tennessee
| | - Sandra R Arnold
- Le Bonheur Children's Hospital, Memphis, Tennessee; University of Tennessee Health Science Center, Memphis
| | - Krow Ampofo
- University of Utah Health Sciences Center , Salt Lake City
| | - Wesley H Self
- Vanderbilt University School of Medicine , Nashville, Tennessee
| | | | | | - Jonathan A McCullers
- Le Bonheur Children's Hospital, Memphis, Tennessee; University of Tennessee Health Science Center, Memphis; St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Andrew T Pavia
- University of Utah Health Sciences Center , Salt Lake City
| | | | - Kathryn M Edwards
- Vanderbilt University School of Medicine, Nashville, Tennessee; Vanderbilt Vaccine Research Program, Nashville, Tennessee
| | - Seema Jain
- Influenza Division , Centers for Disease Control, and Prevention , Atlanta, Georgia
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33
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Tomczyk S, Arriola CS, Beall B, Benitez A, Benoit SR, Berman L, Bresee J, da Gloria Carvalho M, Cohn A, Cross K, Diaz MH, Francois Watkins LK, Gierke R, Hagan JE, Harris AM, Jain S, Kim L, Kobayashi M, Lindstrom S, McGee L, McMorrow M, Metcalf BL, Moore MR, Moura I, Nix WA, Nyangoma E, Oberste MS, Olsen SJ, Pimenta F, Socias C, Thurman K, Waller J, Waterman SH, Westercamp M, Wharton M, Whitney CG, Winchell JM, Wolff B, Kim C. Multistate Outbreak of Respiratory Infections Among Unaccompanied Children, June 2014-July 2014. Clin Infect Dis 2016; 63:48-56. [PMID: 27001799 DOI: 10.1093/cid/ciw147] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [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: 12/10/2015] [Accepted: 03/07/2016] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND From January 2014-July 2014, more than 46 000 unaccompanied children (UC) from Central America crossed the US-Mexico border. In June-July, UC aged 9-17 years in 4 shelters and 1 processing center in 4 states were hospitalized with acute respiratory illness. We conducted a multistate investigation to interrupt disease transmission. METHODS Medical charts were abstracted for hospitalized UC. Nonhospitalized UC with influenza-like illness were interviewed, and nasopharyngeal and oropharyngeal swabs were collected to detect respiratory pathogens. Nasopharyngeal swabs were used to assess pneumococcal colonization in symptomatic and asymptomatic UC. Pneumococcal blood isolates from hospitalized UC and nasopharyngeal isolates were characterized by serotyping and whole-genome sequencing. RESULTS Among 15 hospitalized UC, 4 (44%) of 9 tested positive for influenza viruses, and 6 (43%) of 14 with blood cultures grew pneumococcus, all serotype 5. Among 48 nonhospitalized children with influenza-like illness, 1 or more respiratory pathogens were identified in 46 (96%). Among 774 nonhospitalized UC, 185 (24%) yielded pneumococcus, and 70 (38%) were serotype 5. UC transferring through the processing center were more likely to be colonized with serotype 5 (odds ratio, 3.8; 95% confidence interval, 2.1-6.9). Analysis of core pneumococcal genomes detected 2 related, yet independent, clusters. No pneumococcus cases were reported after pneumococcal and influenza immunization campaigns. CONCLUSIONS This respiratory disease outbreak was due to multiple pathogens, including Streptococcus pneumoniae serotype 5 and influenza viruses. Pneumococcal and influenza vaccinations prevented further transmission. Future efforts to prevent similar outbreaks will benefit from use of both vaccines.
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Affiliation(s)
- Sara Tomczyk
- Epidemic Intelligence Service Respiratory Diseases Branch
| | | | | | | | | | | | | | | | | | | | | | | | | | - Jose E Hagan
- Epidemic Intelligence Service Global Immunizations Division, Centers for Disease Control and Prevention, Atlanta, Georgia US Public Health Service, Rockville, Maryland
| | - Aaron M Harris
- Respiratory Diseases Branch US Public Health Service, Rockville, Maryland
| | | | - Lindsay Kim
- Respiratory Diseases Branch US Public Health Service, Rockville, Maryland
| | | | | | | | | | | | - Matthew R Moore
- Respiratory Diseases Branch US Public Health Service, Rockville, Maryland
| | | | - W Allan Nix
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Edith Nyangoma
- Epidemic Intelligence Service Division of Global Migration and Quarantine
| | - M Steven Oberste
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | | | - Christina Socias
- Epidemic Intelligence Service National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, West Virginia
| | | | | | | | | | | | - Cynthia G Whitney
- Respiratory Diseases Branch US Public Health Service, Rockville, Maryland
| | | | | | - Curi Kim
- US Public Health Service, Rockville, Maryland Office of Refugee Resettlement, Administration for Children and Families, Washington D.C
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Diaz MH, Winchell JM. The Evolution of Advanced Molecular Diagnostics for the Detection and Characterization of Mycoplasma pneumoniae. Front Microbiol 2016; 7:232. [PMID: 27014191 PMCID: PMC4781879 DOI: 10.3389/fmicb.2016.00232] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 02/15/2016] [Indexed: 12/12/2022] Open
Abstract
Over the past decade there have been significant advancements in the methods used for detecting and characterizing Mycoplasma pneumoniae, a common cause of respiratory illness and community-acquired pneumonia worldwide. The repertoire of available molecular diagnostics has greatly expanded from nucleic acid amplification techniques (NAATs) that encompass a variety of chemistries used for detection, to more sophisticated characterizing methods such as multi-locus variable-number tandem-repeat analysis (MLVA), Multi-locus sequence typing (MLST), matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS), single nucleotide polymorphism typing, and numerous macrolide susceptibility profiling methods, among others. These many molecular-based approaches have been developed and employed to continually increase the level of discrimination and characterization in order to better understand the epidemiology and biology of M. pneumoniae. This review will summarize recent molecular techniques and procedures and lend perspective to how each has enhanced the current understanding of this organism and will emphasize how Next Generation Sequencing may serve as a resource for researchers to gain a more comprehensive understanding of the genomic complexities of this insidious pathogen.
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Affiliation(s)
| | - Jonas M. Winchell
- Pneumonia Response and Surveillance Laboratory, Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, AtlantaGA, USA
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35
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Benitez AJ, Winchell JM. Rapid detection and typing of pathogenic nonpneumophila Legionella spp. isolates using a multiplex real-time PCR assay. Diagn Microbiol Infect Dis 2016; 84:298-303. [PMID: 26867966 DOI: 10.1016/j.diagmicrobio.2016.01.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [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: 10/23/2015] [Revised: 01/05/2016] [Accepted: 01/09/2016] [Indexed: 11/26/2022]
Abstract
We developed a single tube multiplex real-time PCR assay that allows for the rapid detection and typing of 9 nonpneumophila Legionella spp. isolates that are clinically relevant. The multiplex assay is capable of simultaneously detecting and discriminating L. micdadei, L. bozemanii, L. dumoffii, L. longbeachae, L. feeleii, L. anisa, L. parisiensis, L. tucsonensis serogroup (sg) 1 and 3, and L. sainthelensis sg 1 and 2 isolates. Evaluation of the assay with nucleic acid from each of these species derived from both clinical and environmental isolates and typing strains demonstrated 100% sensitivity and 100% specificity when tested against 43 other Legionella spp. Typing of L. anisa, L. parisiensis, and L. tucsonensis sg 1 and 3 isolates was accomplished by developing a real-time PCR assay followed by high-resolution melt (HRM) analysis targeting the ssrA gene. Further typing of L. bozemanii, L. longbeachae, and L. feeleii isolates to the serogroup level was accomplished by developing a real-time PCR assay followed by HRM analysis targeting the mip gene. When used in conjunction with other currently available diagnostic tests, these assays may aid in rapidly identifying specific etiologies associated with Legionella outbreaks, clusters, sporadic cases, and potential environmental sources.
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Affiliation(s)
- Alvaro J Benitez
- Pneumonia Response and Surveillance Laboratory, Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jonas M Winchell
- Pneumonia Response and Surveillance Laboratory, Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
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36
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Harvey JJ, Chester S, Burke SA, Ansbro M, Aden T, Gose R, Sciulli R, Bai J, DesJardin L, Benfer JL, Hall J, Smole S, Doan K, Popowich MD, St George K, Quinlan T, Halse TA, Li Z, Pérez-Osorio AC, Glover WA, Russell D, Reisdorf E, Whyte T, Whitaker B, Hatcher C, Srinivasan V, Tatti K, Tondella ML, Wang X, Winchell JM, Mayer LW, Jernigan D, Mawle AC. Comparative analytical evaluation of the respiratory TaqMan Array Card with real-time PCR and commercial multi-pathogen assays. J Virol Methods 2015; 228:151-7. [PMID: 26640122 PMCID: PMC7113746 DOI: 10.1016/j.jviromet.2015.11.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 11/19/2015] [Accepted: 11/25/2015] [Indexed: 12/24/2022]
Abstract
Viral and bacterial real-time PCR oligonucleotides were spotted on TaqMan Array Cards. Analytical sensitivity was compared with standalone laboratory PCR assays. TaqMan Array Card sensitivity was generally one log lower. Reproducibility across six independent testing sites was within one log.
In this study, a multicenter evaluation of the Life Technologies TaqMan® Array Card (TAC) with 21 custom viral and bacterial respiratory assays was performed on the Applied Biosystems ViiA™ 7 Real-Time PCR System. The goal of the study was to demonstrate the analytical performance of this platform when compared to identical individual pathogen specific laboratory developed tests (LDTs) designed at the Centers for Disease Control and Prevention (CDC), equivalent LDTs provided by state public health laboratories, or to three different commercial multi-respiratory panels. CDC and Association of Public Health Laboratories (APHL) LDTs had similar analytical sensitivities for viral pathogens, while several of the bacterial pathogen APHL LDTs demonstrated sensitivities one log higher than the corresponding CDC LDT. When compared to CDC LDTs, TAC assays were generally one to two logs less sensitive depending on the site performing the analysis. Finally, TAC assays were generally more sensitive than their counterparts in three different commercial multi-respiratory panels. TAC technology allows users to spot customized assays and design TAC layout, simplify assay setup, conserve specimen, dramatically reduce contamination potential, and as demonstrated in this study, analyze multiple samples in parallel with good reproducibility between instruments and operators.
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Affiliation(s)
- John J Harvey
- Battelle Technical On-Site Professional Services, Atlanta, GA, 30329 USA; Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, GA, 30329-4027 USA.
| | - Stephanie Chester
- Association of Public Health Laboratories, Silver Spring, MD, 20904 USA
| | - Stephen A Burke
- Battelle Technical On-Site Professional Services, Atlanta, GA, 30329 USA; Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, GA, 30329-4027 USA
| | - Marisela Ansbro
- Battelle Technical On-Site Professional Services, Atlanta, GA, 30329 USA; Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, GA, 30329-4027 USA
| | - Tricia Aden
- Battelle Technical On-Site Professional Services, Atlanta, GA, 30329 USA; Association of Public Health Laboratories, Silver Spring, MD, 20904 USA
| | - Remedios Gose
- Hawaii Department of Health State Laboratories, Pearl City, HI, 96782 USA
| | - Rebecca Sciulli
- Hawaii Department of Health State Laboratories, Pearl City, HI, 96782 USA
| | - Jing Bai
- Iowa State Hygienic Laboratory, Coralville, IA, 52241 USA
| | - Lucy DesJardin
- Iowa State Hygienic Laboratory, Coralville, IA, 52241 USA
| | | | - Joshua Hall
- William A. Hinton State Laboratory Institute, Jamaica Plain, MA, 02130 USA
| | - Sandra Smole
- William A. Hinton State Laboratory Institute, Jamaica Plain, MA, 02130 USA
| | - Kimberly Doan
- William A. Hinton State Laboratory Institute, Jamaica Plain, MA, 02130 USA
| | - Michael D Popowich
- Wadsworth Center, New York State Department of Health, Albany, NY, 12201-0509 USA
| | - Kirsten St George
- Wadsworth Center, New York State Department of Health, Albany, NY, 12201-0509 USA
| | - Tammy Quinlan
- Wadsworth Center, New York State Department of Health, Albany, NY, 12201-0509 USA
| | - Tanya A Halse
- Wadsworth Center, New York State Department of Health, Albany, NY, 12201-0509 USA
| | - Zhen Li
- Washington State Public Health Laboratories, Shoreline, WA, 98155-7224 USA
| | | | - William A Glover
- Washington State Public Health Laboratories, Shoreline, WA, 98155-7224 USA
| | - Denny Russell
- Washington State Public Health Laboratories, Shoreline, WA, 98155-7224 USA
| | - Erik Reisdorf
- Wisconsin State Laboratory of Hygiene, Madison, WI, USA
| | - Thomas Whyte
- Wisconsin State Laboratory of Hygiene, Madison, WI, USA
| | - Brett Whitaker
- Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, GA, 30329-4027 USA
| | - Cynthia Hatcher
- Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, GA, 30329-4027 USA
| | - Velusamy Srinivasan
- Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, GA, 30329-4027 USA
| | - Kathleen Tatti
- Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, GA, 30329-4027 USA
| | - Maria Lucia Tondella
- Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, GA, 30329-4027 USA
| | - Xin Wang
- Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, GA, 30329-4027 USA
| | - Jonas M Winchell
- Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, GA, 30329-4027 USA
| | - Leonard W Mayer
- Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, GA, 30329-4027 USA
| | - Daniel Jernigan
- Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, GA, 30329-4027 USA
| | - Alison C Mawle
- Centers for Disease Control and Prevention, U.S. Department of Health and Human Services, Atlanta, GA, 30329-4027 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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Olson D, Watkins LKF, Demirjian A, Lin X, Robinson CC, Pretty K, Benitez AJ, Winchell JM, Diaz MH, Miller LA, Foo TA, Mason MD, Lauper UL, Kupfer O, Kennedy J, Glodé MP, Kutty PK, Dominguez SR. Outbreak of Mycoplasma pneumoniae-Associated Stevens-Johnson Syndrome. Pediatrics 2015; 136. [PMID: 26216320 PMCID: PMC4516944 DOI: 10.1542/peds.2015-0278] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Stevens-Johnson syndrome (SJS) is an uncommon, sporadic disease and outbreaks are rare. In November 2013, an outbreak of SJS was identified at Children's Hospital Colorado. METHODS Outbreak cases were children aged 5-21 with a discharge diagnosis of SJS admitted from September 1 to November 30, 2013. Medical charts were reviewed using standardized data collection forms. Respiratory specimens were tested for viruses and Mycoplasma pneumoniae (Mp) by polymerase chain reaction (PCR). We conducted a separate 4-year retrospective case-control study comparing hospitalized SJS cases with and without evidence of Mp infection. RESULTS During the outbreak, 8 children met SJS criteria. Median age was 11.5 years (range 8-16 years); 5 (63%) were boys and 5 (63%) were Mp-PCR-positive. Of the 5 PCR-positive children, none had preceding medication exposure, and all had radiographic pneumonia. All outbreak Mp isolates were macrolide susceptible. The retrospective case-control analysis showed that Mp-associated SJS episodes (n = 17) were more likely to have pneumonia (odds ratio [OR] 7.5, confidence interval [CI] 1.6–35.1), preceding respiratory symptoms (OR 30.0, CI 3.3–269.4) [corrected] an erythrocyte sedimentation rate ≥35 mg/dL (OR 22.8, CI 2.1-244.9), and ≤3 affected skin sites (OR 4.5, CI 1.2-17.4) than non-Mp-associated SJS episodes (n = 23). CONCLUSIONS We report the largest outbreak of SJS in children, which was also predominately associated with Mp infection. Mp-associated SJS was associated with a distinct clinical presentation that included less extensive skin disease, an elevated erythrocyte sedimentation rate, and evidence of a preceding respiratory infection.
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Affiliation(s)
| | - Louise K. Francois Watkins
- Centers for Disease Control and Prevention, Atlanta, Georgia;,Epidemic Intelligence Service Program, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Alicia Demirjian
- Centers for Disease Control and Prevention, Atlanta, Georgia;,Epidemic Intelligence Service Program, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Xia Lin
- Centers for Disease Control and Prevention, Atlanta, Georgia;,Epidemic Intelligence Service Program, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Christine C. Robinson
- Department of Pathology and Laboratory Medicine, Children's Hospital Colorado, Aurora, Colorado
| | - Kristin Pretty
- Department of Pathology and Laboratory Medicine, Children's Hospital Colorado, Aurora, Colorado
| | | | | | - Maureen H. Diaz
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Lisa A. Miller
- Colorado Department of Public Health and Environment, Denver, Colorado
| | - Teresa A. Foo
- University of Colorado School of Medicine, Aurora, Colorado
| | | | | | | | | | | | - Preeta K. Kutty
- Centers for Disease Control and Prevention, Atlanta, Georgia
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Jain S, Self WH, Wunderink RG, Fakhran S, Balk R, Bramley AM, Reed C, Grijalva CG, Anderson EJ, Courtney DM, Chappell JD, Qi C, Hart EM, Carroll F, Trabue C, Donnelly HK, Williams DJ, Zhu Y, Arnold SR, Ampofo K, Waterer GW, Levine M, Lindstrom S, Winchell JM, Katz JM, Erdman D, Schneider E, Hicks LA, McCullers JA, Pavia AT, Edwards KM, Finelli L. Community-Acquired Pneumonia Requiring Hospitalization among U.S. Adults. N Engl J Med 2015; 373:415-27. [PMID: 26172429 PMCID: PMC4728150 DOI: 10.1056/nejmoa1500245] [Citation(s) in RCA: 1491] [Impact Index Per Article: 165.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND Community-acquired pneumonia is a leading infectious cause of hospitalization and death among U.S. adults. Incidence estimates of pneumonia confirmed radiographically and with the use of current laboratory diagnostic tests are needed. METHODS We conducted active population-based surveillance for community-acquired pneumonia requiring hospitalization among adults 18 years of age or older in five hospitals in Chicago and Nashville. Patients with recent hospitalization or severe immunosuppression were excluded. Blood, urine, and respiratory specimens were systematically collected for culture, serologic testing, antigen detection, and molecular diagnostic testing. Study radiologists independently reviewed chest radiographs. We calculated population-based incidence rates of community-acquired pneumonia requiring hospitalization according to age and pathogen. RESULTS From January 2010 through June 2012, we enrolled 2488 of 3634 eligible adults (68%). Among 2320 adults with radiographic evidence of pneumonia (93%), the median age of the patients was 57 years (interquartile range, 46 to 71); 498 patients (21%) required intensive care, and 52 (2%) died. Among 2259 patients who had radiographic evidence of pneumonia and specimens available for both bacterial and viral testing, a pathogen was detected in 853 (38%): one or more viruses in 530 (23%), bacteria in 247 (11%), bacterial and viral pathogens in 59 (3%), and a fungal or mycobacterial pathogen in 17 (1%). The most common pathogens were human rhinovirus (in 9% of patients), influenza virus (in 6%), and Streptococcus pneumoniae (in 5%). The annual incidence of pneumonia was 24.8 cases (95% confidence interval, 23.5 to 26.1) per 10,000 adults, with the highest rates among adults 65 to 79 years of age (63.0 cases per 10,000 adults) and those 80 years of age or older (164.3 cases per 10,000 adults). For each pathogen, the incidence increased with age. CONCLUSIONS The incidence of community-acquired pneumonia requiring hospitalization was highest among the oldest adults. Despite current diagnostic tests, no pathogen was detected in the majority of patients. Respiratory viruses were detected more frequently than bacteria. (Funded by the Influenza Division of the National Center for Immunizations and Respiratory Diseases.).
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Affiliation(s)
- Seema Jain
- From the Centers for Disease Control and Prevention, Atlanta (S.J., A.M.B., C.R., M.L., S.L., J.M.W., J.M.K., D.E., E.S., L.A.H., L.F.); Vanderbilt University School of Medicine (W.H.S., C.G.G., J.D.C., F.C., D.J.W., Y.Z., K.M.E.) and University of Tennessee Health Science Center-Saint Thomas Health (C.T.), Nashville, and Le Bonheur Children's Hospital (S.R.A., J.A.M.), University of Tennessee Health Science Center (S.R.A., J.A.M.), and St. Jude Children's Research Hospital (J.A.M.), Memphis - all in Tennessee; Northwestern University Feinberg School of Medicine (R.G.W., E.J.A., D.M.C., C.Q., E.M.H., H.K.D., G.W.W.), John H. Stroger, Jr., Hospital of Cook County (S.F.), and Rush University Medical Center (R.B.) - all in Chicago; University of Utah Health Sciences Center, Salt Lake City (K.A., A.T.P.); and University of Western Australia, Perth (G.W.W.)
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Diaz MH, Benitez AJ, Cross KE, Hicks LA, Kutty P, Bramley AM, Chappell JD, Hymas W, Patel A, Qi C, Williams DJ, Arnold SR, Ampofo K, Self WH, Grijalva CG, Anderson EJ, McCullers JA, Pavia AT, Wunderink RG, Edwards KM, Jain S, Winchell JM. Molecular Detection and Characterization of Mycoplasma pneumoniae Among Patients Hospitalized With Community-Acquired Pneumonia in the United States. Open Forum Infect Dis 2015; 2:ofv106. [PMID: 26284257 PMCID: PMC4536330 DOI: 10.1093/ofid/ofv106] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 07/06/2015] [Indexed: 11/24/2022] Open
Abstract
We report molecular characteristics of M. pneumoniae in respiratory specimens from children and adults hospitalized with CAP. The P1 type 1 genotype and MLVA type 4/5/7/2 predominated, but proportions of types differed between children and adults. Macrolide resistance was rare. Background. Mycoplasma pneumoniae is a common cause of community-acquired pneumonia (CAP). The molecular characteristics of M pneumoniae detected in patients hospitalized with CAP in the United States are poorly described. Methods. We performed molecular characterization of M pneumoniae in nasopharyngeal/oropharyngeal swabs from children and adults hospitalized with CAP in the Centers for Disease Control and Prevention Etiology of Pneumonia in the Community (EPIC) study, including P1 typing, multilocus variable-number tandem-repeat analysis (MLVA), and macrolide susceptibility genotyping. Results. Of 216 M pneumoniae polymerase chain reaction-positive specimens, 40 (18.5%) were obtained from adults and 176 (81.5%) from children. P1 type distribution differed between adults (64% type 1 and 36% type 2) and children (84% type 1, 13% type 2, and 3% variant) (P < .05) and among sites (P < .01). Significant differences in the proportions of MLVA types 4/5/7/2 and 3/5/6/2 were also observed by age group (P < .01) and site (P < .01). A macrolide-resistant genotype was identified in 7 (3.5%) specimens, 5 of which were from patients who had recently received macrolide therapy. No significant differences in clinical characteristics were identified among patients with various strain types or between macrolide-resistant and -sensitive M pneumoniae infections. Conclusions. The P1 type 1 genotype and MLVA type 4/5/7/2 predominated, but there were differences between children and adults and among sites. Macrolide resistance was rare. Differences in strain types did not appear to be associated with differences in clinical outcomes. Whole genome sequencing of M pneumoniae may help identify better ways to characterize strains.
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Affiliation(s)
| | | | | | | | | | - Anna M Bramley
- Influenza Division , Centers for Disease Control and Prevention , Atlanta, Georgia
| | | | - Weston Hymas
- University of Utah Health Sciences Center , Salt Lake City
| | - Anami Patel
- Le Bonheur Children's Hospital ; University of Tennessee Health Science Center
| | - Chao Qi
- Northwestern University Feinberg School of Medicine , Chicago, Illinois
| | - Derek J Williams
- Vanderbilt University School of Medicine , Nashville, Tennessee ; Vanderbilt Vaccine Research Program , Nashville
| | - Sandra R Arnold
- Le Bonheur Children's Hospital ; University of Tennessee Health Science Center
| | - Krow Ampofo
- University of Utah Health Sciences Center , Salt Lake City
| | - Wesley H Self
- Vanderbilt University School of Medicine , Nashville, Tennessee
| | | | | | - Jonathan A McCullers
- Le Bonheur Children's Hospital ; University of Tennessee Health Science Center ; St. Jude Children's Research Hospital , Memphis, Tennessee
| | - Andrew T Pavia
- University of Utah Health Sciences Center , Salt Lake City
| | | | - Kathryn M Edwards
- Vanderbilt University School of Medicine , Nashville, Tennessee ; Vanderbilt Vaccine Research Program , Nashville
| | - Seema Jain
- Influenza Division , Centers for Disease Control and Prevention , Atlanta, Georgia
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Wolff BJ, Morrison SS, Pesti D, Ganakammal SR, Srinivasamoorthy G, Changayil S, Weil MR, MacCannell D, Rowe L, Frace M, Ritchie BW, Dean D, Winchell JM. Chlamydia psittaci comparative genomics reveals intraspecies variations in the putative outer membrane and type III secretion system genes. Microbiology (Reading) 2015; 161:1378-91. [PMID: 25887617 PMCID: PMC4635502 DOI: 10.1099/mic.0.000097] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Chlamydia psittaci is an obligate intracellular bacterium that can cause significant disease among a broad range of hosts. In humans, this organism may cause psittacosis, a respiratory disease that can spread to involve multiple organs, and in rare untreated cases may be fatal. There are ten known genotypes based on sequencing the major outer-membrane protein gene, ompA, of C. psittaci. Each genotype has overlapping host preferences and virulence characteristics. Recent studies have compared C. psittaci among other members of the Chlamydiaceae family and showed that this species frequently switches hosts and has undergone multiple genomic rearrangements. In this study, we sequenced five genomes of C. psittaci strains representing four genotypes, A, B, D and E. Due to the known association of the type III secretion system (T3SS) and polymorphic outer-membrane proteins (Pmps) with host tropism and virulence potential, we performed a comparative analysis of these elements among these five strains along with a representative genome from each of the remaining six genotypes previously sequenced. We found significant genetic variation in the Pmps and tbl3SS genes that may partially explain differences noted in C. psittaci host infection and disease.
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Affiliation(s)
- Bernard J Wolff
- 1Infectious Diseases Laboratory, College of Veterinary Medicine, University of Georgia, Athens, GA, USA 2Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Shatavia S Morrison
- 2Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Denise Pesti
- 1Infectious Diseases Laboratory, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Satishkumar Ranganathan Ganakammal
- 3The National Center for Emerging and Zoonotic Infectious Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Ganesh Srinivasamoorthy
- 3The National Center for Emerging and Zoonotic Infectious Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Shankar Changayil
- 3The National Center for Emerging and Zoonotic Infectious Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - M Ryan Weil
- 3The National Center for Emerging and Zoonotic Infectious Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Duncan MacCannell
- 3The National Center for Emerging and Zoonotic Infectious Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Lori Rowe
- 3The National Center for Emerging and Zoonotic Infectious Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Michael Frace
- 3The National Center for Emerging and Zoonotic Infectious Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Branson W Ritchie
- 1Infectious Diseases Laboratory, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Deborah Dean
- 4Children's Hospital Oakland Research Institute, Oakland, CA 5UCSF and UC Berkeley Joint Graduate Program in Bioengineering, Oakland, CA
| | - Jonas M Winchell
- 2Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, GA, USA
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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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43
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Jain S, Williams DJ, Arnold SR, Ampofo K, Bramley AM, Reed C, Stockmann C, Anderson EJ, Grijalva CG, Self WH, Zhu Y, Patel A, Hymas W, Chappell JD, Kaufman RA, Kan JH, Dansie D, Lenny N, Hillyard DR, Haynes LM, Levine M, Lindstrom S, Winchell JM, Katz JM, Erdman D, Schneider E, Hicks LA, Wunderink RG, Edwards KM, Pavia AT, McCullers JA, Finelli L. Community-acquired pneumonia requiring hospitalization among U.S. children. N Engl J Med 2015; 372:835-45. [PMID: 25714161 PMCID: PMC4697461 DOI: 10.1056/nejmoa1405870] [Citation(s) in RCA: 1062] [Impact Index Per Article: 118.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
BACKGROUND Incidence estimates of hospitalizations for community-acquired pneumonia among children in the United States that are based on prospective data collection are limited. Updated estimates of pneumonia that has been confirmed radiographically and with the use of current laboratory diagnostic tests are needed. METHODS We conducted active population-based surveillance for community-acquired pneumonia requiring hospitalization among children younger than 18 years of age in three hospitals in Memphis, Nashville, and Salt Lake City. We excluded children with recent hospitalization or severe immunosuppression. Blood and respiratory specimens were systematically collected for pathogen detection with the use of multiple methods. Chest radiographs were reviewed independently by study radiologists. RESULTS From January 2010 through June 2012, we enrolled 2638 of 3803 eligible children (69%), 2358 of whom (89%) had radiographic evidence of pneumonia. The median age of the children was 2 years (interquartile range, 1 to 6); 497 of 2358 children (21%) required intensive care, and 3 (<1%) died. Among 2222 children with radiographic evidence of pneumonia and with specimens available for bacterial and viral testing, a viral or bacterial pathogen was detected in 1802 (81%), one or more viruses in 1472 (66%), bacteria in 175 (8%), and both bacterial and viral pathogens in 155 (7%). The annual incidence of pneumonia was 15.7 cases per 10,000 children (95% confidence interval [CI], 14.9 to 16.5), with the highest rate among children younger than 2 years of age (62.2 cases per 10,000 children; 95% CI, 57.6 to 67.1). Respiratory syncytial virus was more common among children younger than 5 years of age than among older children (37% vs. 8%), as were adenovirus (15% vs. 3%) and human metapneumovirus (15% vs. 8%). Mycoplasma pneumoniae was more common among children 5 years of age or older than among younger children (19% vs. 3%). CONCLUSIONS The burden of hospitalization for children with community-acquired pneumonia was highest among the very young, with respiratory viruses the most commonly detected causes of pneumonia. (Funded by the Influenza Division of the National Center for Immunization and Respiratory Diseases.).
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Affiliation(s)
- Seema Jain
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Derek J. Williams
- Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt Vaccine Research Program, Nashville, TN, USA
| | - Sandra R. Arnold
- Le Bonheur Children's Hospital, Memphis, TN, USA
- University of Tennessee Health Science Center, Memphis, TN, USA
| | - Krow Ampofo
- University of Utah Health Sciences Center, Salt Lake City, UT, USA
| | - Anna M. Bramley
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Carrie Reed
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Chris Stockmann
- University of Utah Health Sciences Center, Salt Lake City, UT, USA
| | - Evan J. Anderson
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | | | - Wesley H. Self
- Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Yuwei Zhu
- Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Anami Patel
- Le Bonheur Children's Hospital, Memphis, TN, USA
- University of Tennessee Health Science Center, Memphis, TN, USA
| | - Weston Hymas
- University of Utah Health Sciences Center, Salt Lake City, UT, USA
| | | | - Robert A. Kaufman
- University of Tennessee Health Science Center, Memphis, TN, USA
- St. Jude Children's Research Hospital, Memphis, TN, USA
| | - J. Herman Kan
- Vanderbilt University School of Medicine, Nashville, TN, USA
| | - David Dansie
- University of Utah Health Sciences Center, Salt Lake City, UT, USA
| | - Noel Lenny
- Le Bonheur Children's Hospital, Memphis, TN, USA
- University of Tennessee Health Science Center, Memphis, TN, USA
| | | | - Lia M. Haynes
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Min Levine
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | | | | | - Dean Erdman
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Lauri A. Hicks
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Kathryn M. Edwards
- Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt Vaccine Research Program, Nashville, TN, USA
| | - Andrew T. Pavia
- University of Utah Health Sciences Center, Salt Lake City, UT, USA
| | - Jonathan A. McCullers
- Le Bonheur Children's Hospital, Memphis, TN, USA
- University of Tennessee Health Science Center, Memphis, TN, USA
- St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Lyn Finelli
- Centers for Disease Control and Prevention, Atlanta, GA, USA
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Abstract
Legionnaires' disease (LD) is an often severe and potentially fatal form of bacterial pneumonia caused by an extensive list of Legionella species. These ubiquitous freshwater and soil inhabitants cause human respiratory disease when amplified in man-made water or cooling systems and their aerosols expose a susceptible population. Treatment of sporadic cases and rapid control of LD outbreaks benefit from swift diagnosis in concert with discriminatory bacterial typing for immediate epidemiological responses. Traditional culture and serology were instrumental in describing disease incidence early in its history; currently, diagnosis of LD relies almost solely on the urinary antigen test, which captures only the dominant species and serogroup, Legionella pneumophila serogroup 1 (Lp1). This has created a diagnostic "blind spot" for LD caused by non-Lp1 strains. This review focuses on historic, current, and emerging technologies that hold promise for increasing LD diagnostic efficiency and detection rates as part of a coherent testing regimen. The importance of cooperation between epidemiologists and laboratorians for a rapid outbreak response is also illustrated in field investigations conducted by the CDC with state and local authorities. Finally, challenges facing health care professionals, building managers, and the public health community in combating LD are highlighted, and potential solutions are discussed.
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Affiliation(s)
- Jeffrey W Mercante
- Pneumonia Response and Surveillance Laboratory, Respiratory Diseases Branch, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jonas M Winchell
- Pneumonia Response and Surveillance Laboratory, Respiratory Diseases Branch, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Diaz MH, Benitez AJ, Winchell JM. Investigations of Mycoplasma pneumoniae infections in the United States: trends in molecular typing and macrolide resistance from 2006 to 2013. J Clin Microbiol 2015; 53:124-30. [PMID: 25355769 PMCID: PMC4290910 DOI: 10.1128/jcm.02597-14] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [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: 09/09/2014] [Accepted: 10/22/2014] [Indexed: 11/20/2022] Open
Abstract
Mycoplasma pneumoniae is a leading cause of respiratory infections, including community-acquired pneumonia (CAP). Currently, pathogen-specific testing is not routinely performed in the primary care setting, and the United States lacks a systematic surveillance program for M. pneumoniae. Documentation of individual cases and clusters typically occurs only when severe illness and/or failure to improve with empirical antibiotic therapy is observed. Outbreaks, some lasting for extended periods and involving a large number of cases, occur regularly. However, many more likely go unrecognized due to the lack of diagnostic testing and structured reporting. We reviewed data from 17 investigations of cases, small clusters, and outbreaks of M. pneumoniae infections that were supported by the Centers for Disease Control and Prevention (CDC) between 2006 and 2013. We examined 199 M. pneumoniae-positive specimens collected during this time period in order to identify trends in antimicrobial resistance and circulating types. Overall, macrolide resistance was identified in approximately 10% of M. pneumoniae infections occurring during this time period. Typing of strains revealed cocirculation of multiple multilocus variable-number tandem-repeat analysis (MLVA) and P1 types throughout this period, including diversity in types detected within individual outbreaks. Three MLVA types (4572, 3562, and 3662) accounted for 97% of the infections during the study period. A systematic surveillance program is necessary to understand the burden of M. pneumoniae disease in the United States, facilitate case and outbreak identification, and inform appropriate therapeutic and infection control strategies.
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Affiliation(s)
- Maureen H Diaz
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Alvaro J Benitez
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jonas M Winchell
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Olson D, Watkins LF, Demirjian A, Lin X, Robinson CC, Pretty K, Benitez A, Winchell JM, Diaz M, Miller L, Foo T, Mason M, Lauper U, Kupfer O, Kennedy J, Glode M, Kutty P, Dominguez SR. 121Clinical Characteristics of an outbreak of Mycoplasma pneumoniae-Associated Stevens - Johnson syndrome (SJS) in Children, Colorado, 2013. Open Forum Infect Dis 2014. [PMCID: PMC5781697 DOI: 10.1093/ofid/ofu051.29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Affiliation(s)
- Daniel Olson
- Pediatric Infectious Diseases, University of Colorado - Denver, Aurora, CO
| | | | | | - Xia Lin
- Centers for Disease Control and Prevention, Atlanta, GA
| | | | | | | | | | - Mauren Diaz
- Centers for Disease Control and Prevention, Atlanta, GA
| | - Lisa Miller
- Colorado Department of Public Health and Environment, Denver, CO
| | - Teresa Foo
- University of Colorado General Preventative Medicine and Public Health Residency, Aurora, CO
| | | | | | - Oren Kupfer
- Pediatrics, University of Colorado - Denver, Aurora, CO
| | | | - Mary Glode
- Pediatric Infectious Diseases, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, CO
| | - Preeta Kutty
- Centers for Disease Control and Prevention, Atlanta, GA
| | - Samuel R. Dominguez
- Department of Infectious Disease, Children's Hospital Colorado/University of Colorado School of Medicine, Aurora, CO
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Waller JL, Diaz MH, Petrone BL, Benitez AJ, Wolff BJ, Edison L, Tobin-D'Angelo M, Moore A, Martyn A, Dishman H, Drenzek CL, Turner K, Hicks LA, Winchell JM. Detection and characterization of Mycoplasma pneumoniae during an outbreak of respiratory illness at a university. J Clin Microbiol 2014; 52:849-53. [PMID: 24371236 PMCID: PMC3957776 DOI: 10.1128/jcm.02810-13] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [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: 11/04/2013] [Accepted: 12/20/2013] [Indexed: 01/14/2023] Open
Abstract
An outbreak at a university in Georgia was identified after 83 cases of probable pneumonia were reported among students. Respiratory specimens were obtained from 21 students for the outbreak investigation. The TaqMan array card (TAC), a quantitative PCR (qPCR)-based multipathogen detection technology, was used to initially identify Mycoplasma pneumoniae as the causative agent in this outbreak. TAC demonstrated 100% diagnostic specificity and sensitivity compared to those of the multiplex qPCR assay for this agent. All M. pneumoniae specimens (n=12) and isolates (n=10) were found through genetic analysis to be susceptible to macrolide antibiotics. The strain diversity of M. pneumoniae associated with this outbreak setting was identified using a variety of molecular typing procedures, resulting in two P1 genotypes (types 1 [60%] and 2 [40%]) and seven different multilocus variable-number tandem-repeat analysis (MLVA) profiles. Continued molecular typing of this organism, particularly during outbreaks, may enhance the current understanding of the epidemiology of M. pneumoniae and may ultimately lead to a more effective public health response.
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Affiliation(s)
- Jessica L. Waller
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Maureen H. Diaz
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Brianna L. Petrone
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Alvaro J. Benitez
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Bernard J. Wolff
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Laura Edison
- Georgia Department of Public Health, Atlanta, Georgia, USA
- Epidemiology Workforce Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Ashley Moore
- Georgia Department of Public Health, Atlanta, Georgia, USA
| | - Audrey Martyn
- Georgia Department of Public Health, Atlanta, Georgia, USA
| | - Hope Dishman
- Georgia Department of Public Health, Atlanta, Georgia, USA
| | | | - Kim Turner
- Fulton County Department of Health and Wellness, Atlanta, Georgia, USA
| | - Lauri A. Hicks
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jonas M. Winchell
- Respiratory Diseases Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Kozak-Muiznieks NA, Lucas CE, Brown E, Pondo T, Taylor TH, Frace M, Miskowski D, Winchell JM. 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; 52:201-11. [PMID: 24197883 PMCID: PMC3911437 DOI: 10.1128/jcm.01973-13] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [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: 07/26/2013] [Accepted: 10/28/2013] [Indexed: 11/20/2022] Open
Abstract
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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Affiliation(s)
- Natalia A. Kozak-Muiznieks
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Claressa E. Lucas
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Ellen Brown
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Tracy Pondo
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Thomas H. Taylor
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Michael Frace
- Biotechnology Core Facility Branch, Division of Scientific Resources, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | - Jonas M. Winchell
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Watkins LF, Olson D, Diaz M, Benitez A, Winchell JM, Robinson CC, Demirjian A, Lin X, Foo T, Lauper U, Mason M, Dominguez SR, Glode M, Kutty P, Miller L. 804Epidemiology and Molecular Characteristics of Mycoplasma pneumoniae (Mp) during an Outbreak of Mp-Associated Stevens-Johnson Syndrome, Colorado, 2013. Open Forum Infect Dis 2014. [DOI: 10.1093/ofid/ofu052.512] [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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Diaz MH, Waller JL, Napoliello RA, Islam MS, Wolff BJ, Burken DJ, Holden RL, Srinivasan V, Arvay M, McGee L, Oberste MS, Whitney CG, Schrag SJ, Winchell JM, Saha SK. Optimization of Multiple Pathogen Detection Using the TaqMan Array Card: Application for a Population-Based Study of Neonatal Infection. PLoS One 2013; 8:e66183. [PMID: 23805203 PMCID: PMC3689704 DOI: 10.1371/journal.pone.0066183] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [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: 03/29/2013] [Accepted: 05/02/2013] [Indexed: 12/01/2022] Open
Abstract
Identification of etiology remains a significant challenge in the diagnosis of infectious diseases, particularly in resource-poor settings. Viral, bacterial, and fungal pathogens, as well as parasites, play a role for many syndromes, and optimizing a single diagnostic system to detect a range of pathogens is challenging. The TaqMan Array Card (TAC) is a multiple-pathogen detection method that has previously been identified as a valuable technique for determining etiology of infections and holds promise for expanded use in clinical microbiology laboratories and surveillance studies. We selected TAC for use in the Aetiology of Neonatal Infection in South Asia (ANISA) study for identifying etiologies of severe disease in neonates in Bangladesh, India, and Pakistan. Here we report optimization of TAC to improve pathogen detection and overcome technical challenges associated with use of this technology in a large-scale surveillance study. Specifically, we increased the number of assay replicates, implemented a more robust RT-qPCR enzyme formulation, and adopted a more efficient method for extraction of total nucleic acid from blood specimens. We also report the development and analytical validation of ten new assays for use in the ANISA study. Based on these data, we revised the study-specific TACs for detection of 22 pathogens in NP/OP swabs and 12 pathogens in blood specimens as well as two control reactions (internal positive control and human nucleic acid control) for each specimen type. The cumulative improvements realized through these optimization studies will benefit ANISA and perhaps other studies utilizing multiple-pathogen detection approaches. These lessons may also contribute to the expansion of TAC technology to the clinical setting.
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Affiliation(s)
- Maureen H. Diaz
- Respiratory Diseases Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Jessica L. Waller
- Respiratory Diseases Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Rebecca A. Napoliello
- Respiratory Diseases Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Md. Shahidul Islam
- Department of Microbiology, Bangladesh Institute of Child Health, Child Health Research Foundation, Dhaka Shishu Hospital, Dhaka, Bangladesh
| | - Bernard J. Wolff
- Respiratory Diseases Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Daniel J. Burken
- Respiratory Diseases Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Rhiannon L. Holden
- Respiratory Diseases Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Velusamy Srinivasan
- Respiratory Diseases Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Melissa Arvay
- Division of Preparedness and Emerging Infections, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Lesley McGee
- Respiratory Diseases Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - M. Steven Oberste
- Polio and Picornavirus Laboratory Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Cynthia G. Whitney
- Respiratory Diseases Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Stephanie J. Schrag
- Respiratory Diseases Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Jonas M. Winchell
- Respiratory Diseases Branch, Division of Bacterial Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- * E-mail:
| | - Samir K. Saha
- Department of Microbiology, Bangladesh Institute of Child Health, Child Health Research Foundation, Dhaka Shishu Hospital, Dhaka, Bangladesh
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