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Bruxvoort K, Tenggardjaja CF, Slezak J, Gullett JC, Broder B, Park CH, Aragones M, Mercado C, Wong K, McLaren S, Jacobsen SJ. Variation in SARS-CoV-2 molecular test sensitivity by specimen types in a large sample of emergency department patients. Am J Emerg Med 2021; 50:381-387. [PMID: 34478943 PMCID: PMC8367656 DOI: 10.1016/j.ajem.2021.08.034] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 10/30/2022] Open
Abstract
BACKGROUND Provider-collected nasopharyngeal specimens for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) molecular testing are the standard of care in many clinical settings, but patient-collected saliva and anterior nares specimens are less invasive and more flexible alternatives. Prior studies comparing specimen types for SARS-CoV-2 molecular testing have been limited by small sample sizes and low pretest probability. We conducted a large observational study among symptomatic adults at 7 emergency departments of Kaiser Permanente Southern California to examine sensitivity of SARS-CoV-2 molecular tests by specimen type and patient characteristics. METHODS Provider-collected nasopharyngeal/oropharyngeal (NP/OP) specimens and patient-collected saliva and anterior nares specimens were collected at the same visit and analyzed with the Roche cobas® SARS-CoV-2 assay. Patients were considered truly positive for SARS-CoV-2 if any of the three specimens was positive and negative if all three specimens were negative. Factors associated with discordant and missed positive results were examined with multivariable logistic regression. RESULTS Of 2112 patients, 350 (16.6%) were positive for SARS-CoV-2. Sensitivity of NP/OP was 93.7% (95% confidence interval [CI] 90.6%-96.0%), sensitivity of saliva was 87.7% (83.8%-91.0%), and sensitivity of anterior nares was 85.4% (81.3%-89.0%). Patients ages 18-39 years versus ≥40 years were more likely to have discordant results [adjusted odds ratio (aOR) 1.97 (1.12-3.45)], as were patients with <4 symptoms versus ≥4 [aOR 2.43 (1.39-4.25)]. Cycle threshold values were higher for saliva and anterior nares than NP/OP specimens, as well as for specimens in discordant versus concordant sets and patients with fewer symptoms. CONCLUSION This study provides robust evidence that patient-collected saliva and anterior nares are sensitive for SARS-CoV-2 molecular testing in emergency department settings, particularly among adults ages ≥40 years and those with multiple symptoms. Higher sensitivity of provider-collected NP/OP specimens must be weighed against the benefits of patient-collected specimens in tailored strategies for SARS-CoV-2 testing.
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Affiliation(s)
- Katia Bruxvoort
- Department of Research & Evaluation, Kaiser Permanente Southern California, 100 South Los Robles Avenue, Pasadena, CA 91101, USA.
| | - Christopher F Tenggardjaja
- Department of Urology, Southern California Permanente Medical Group, 4867 Sunset Boulevard, Los Angeles, CA 90027, USA
| | - Jeff Slezak
- Department of Research & Evaluation, Kaiser Permanente Southern California, 100 South Los Robles Avenue, Pasadena, CA 91101, USA
| | - Jonathan C Gullett
- Regional Reference Laboratories, Southern California Permanente Medical Group, 11668 Sherman Way, North Hollywood, CA 91605, USA
| | - Benjamin Broder
- Department of Quality and Clinical Analysis, Southern California Permanente Medical Group, 393 East Walnut Street, Pasadena, CA 91188, USA
| | - Claire H Park
- Department of Research & Evaluation, Kaiser Permanente Southern California, 100 South Los Robles Avenue, Pasadena, CA 91101, USA; Currently with the Acute Communicable Disease Control Program, Los Angeles County Department of Public Health, 313 North Figueroa Street, Los Angeles, California 90012, USA
| | - Michael Aragones
- Department of Research & Evaluation, Kaiser Permanente Southern California, 100 South Los Robles Avenue, Pasadena, CA 91101, USA
| | - Cheryl Mercado
- Department of Research & Evaluation, Kaiser Permanente Southern California, 100 South Los Robles Avenue, Pasadena, CA 91101, USA
| | - Katherine Wong
- Department of Research & Evaluation, Kaiser Permanente Southern California, 100 South Los Robles Avenue, Pasadena, CA 91101, USA
| | - Steven McLaren
- Regional Reference Laboratories, Southern California Permanente Medical Group, 11668 Sherman Way, North Hollywood, CA 91605, USA
| | - Steven J Jacobsen
- Department of Research & Evaluation, Kaiser Permanente Southern California, 100 South Los Robles Avenue, Pasadena, CA 91101, USA
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Blicharz L, Michalak M, Szymanek-Majchrzak K, Młynarczyk G, Skowroński K, Rudnicka L, Samochocki Z. The Propensity to Form Biofilm in vitro by Staphylococcus aureus Strains Isolated from the Anterior Nares of Patients with Atopic Dermatitis: Clinical Associations. Dermatology 2020; 237:528-534. [PMID: 33113538 DOI: 10.1159/000511182] [Citation(s) in RCA: 4] [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: 05/23/2020] [Accepted: 08/26/2020] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Atopic dermatitis is a chronic inflammatory dermatosis with complex pathogenesis. The skin microbiome in atopic dermatitis is dominated by Staphylococcus aureus which shows the ability to produce biofilm. OBJECTIVES The aim of this work was to assess the influence of S. aureus biofilm on the course of atopic dermatitis. METHODS Disease severity was evaluated based on the SCORAD index in 56 adult patients with atopic dermatitis. Microtiter plate assay of the propensity to form biofilm was performed on S. aureus strains isolated from the anterior nares, lesional skin, and nonlesional skin. Microbiological results were correlated to the clinical parameters and total IgE concentration. RESULTS Biofilm-producing strains of S. aureus were identified in 76.3% (29/38) and 79.1% (34/43) of samples from the anterior nares and lesional skin, respectively (p > 0.05), and in 48.5% (16/33) of samples from nonlesional skin (p < 0.03). Patients colonized by biofilm-producing strains of S. aureus within the anterior nares showed statistically higher mean values of total and objective SCORAD and its components (extent, dryness), and of the largest extent of skin lesions during the flares in the last year when compared to patients colonized by non-biofilm-producing strains. Carriage of biofilm-producing S. aureus on lesional skin was associated with higher mean values of the extent of skin lesions during stable periods of the disease. CONCLUSIONS The results of this study may suggest a relationship between the production of biofilm by S. aureus strains colonizing the anterior nares and the course of atopic dermatitis. Biofilm seems crucial for dispersal and persistent colonization of large areas of the skin by this pathogen. Destruction of S. aureus biofilm could positively affect the course of atopic dermatitis.
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Affiliation(s)
- Leszek Blicharz
- Department of Dermatology, Medical University of Warsaw, Warsaw, Poland
| | - Maryla Michalak
- Department of Medical Microbiology, Medical University of Warsaw, Warsaw, Poland
| | | | - Grażyna Młynarczyk
- Department of Medical Microbiology, Medical University of Warsaw, Warsaw, Poland
| | | | - Lidia Rudnicka
- Department of Dermatology, Medical University of Warsaw, Warsaw, Poland,
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Caputo M, Zoch-Lesniak B, Karch A, Vital M, Meyer F, Klawonn F, Baillot A, Pieper DH, Mikolajczyk RT. Bacterial community structure and effects of picornavirus infection on the anterior nares microbiome in early childhood. BMC Microbiol 2019; 19:1. [PMID: 30616583 PMCID: PMC6322332 DOI: 10.1186/s12866-018-1372-8] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 12/11/2018] [Indexed: 11/13/2022] Open
Abstract
Background Little is known regarding the nasal microbiome in early childhood and the impact of respiratory infection on the infants’ nasal microbial composition. Here we investigated the temporal dynamics and diversity of the bacterial composition in the anterior nares in children attending daycare centers. Results For our investigation, we considered 76 parental-taken nasal swabs of 26 children (aged 13 to 36 months) collected over a study period of 3 months. Overall, there was no significant age-specific effect or seasonal shift in the nasal bacterial community structure. In a sub-sample of 14 healthy children the relative abundance of individual taxa as well as the overall diversity did not reveal relevant changes, indicating a stable community structure over the entire study period. Moreover, the nasal bacterial profiles clustered subject-specific with Bray-Curtis similarities being elevated in intra-subject calculations compared to between-subject calculations. The remaining subset of 12 children provided samples taken during picornavirus infection (PVI) and either before or after a PVI. We detected an association between the relative abundance of members of the genus Streptococcus and PV when comparing both (i) samples taken during PVI with samples out of 14 healthy children and (ii) samples taken during PVI with samples taken after PVI within the same individual. In addition, the diversity was higher during PVI than after infection. Conclusions Our findings suggest that a personalized structure of the nasal bacterial community is established already in early childhood and could be detected over a timeframe of 3 months. Studies following infants over a longer time with frequent swab sampling would allow investigating whether certain parameter of the bacterial community, such as the temporal variability, could be related to viral infection. Electronic supplementary material The online version of this article (10.1186/s12866-018-1372-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mahrrouz Caputo
- Department of Epidemiology, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Braunschweig, Germany.,PhD Programme "Epidemiology", Braunschweig, Germany.,PhD Programme "Epidemiology", Hannover, Germany
| | - Beate Zoch-Lesniak
- Department of Epidemiology, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Braunschweig, Germany.,PhD Programme "Epidemiology", Braunschweig, Germany.,PhD Programme "Epidemiology", Hannover, Germany
| | - André Karch
- Department of Epidemiology, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Braunschweig, Germany.,German Centre for Infection Research (DZIF), Hannover-Braunschweig site, Inhoffenstraße 7, 38124, Braunschweig, Germany.,Institute for Epidemiology and Social Medicine, University of Münster, Domagkstraße 3, 48149, Münster, Germany
| | - Marius Vital
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Braunschweig, Germany
| | - Frederic Meyer
- Microbial Communication Research Group, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Braunschweig, Germany
| | - Frank Klawonn
- Biostatistics Research Group, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Braunschweig, Germany.,Institute of Information Engineering, Ostfalia University, Salzdahlumer Str. 46/48, 38302, Wolfenbüttel, Germany
| | - Armin Baillot
- Governmental Institute of Public Health of Lower Saxony, Roesebeckstraße 4-6, 30449, Hannover, Germany
| | - Dietmar H Pieper
- Microbial Interactions and Processes Research Group, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Braunschweig, Germany
| | - Rafael T Mikolajczyk
- German Centre for Infection Research (DZIF), Hannover-Braunschweig site, Inhoffenstraße 7, 38124, Braunschweig, Germany. .,Institute for Medical Epidemiology, Biometrics, and Informatics (IMEBI), Medical Faculty of the Martin Luther University Halle-Wittenberg, Magdeburger Str. 8, 06110, Halle (Saale), Germany.
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Luna PN, Hasegawa K, Ajami NJ, Espinola JA, Henke DM, Petrosino JF, Piedra PA, Sullivan AF, Camargo CA, Shaw CA, Mansbach JM. The association between anterior nares and nasopharyngeal microbiota in infants hospitalized for bronchiolitis. Microbiome 2018; 6:2. [PMID: 29298732 PMCID: PMC5751828 DOI: 10.1186/s40168-017-0385-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 12/14/2017] [Indexed: 05/09/2023]
Abstract
BACKGROUND The airway microbiome is a subject of great interest for the study of respiratory disease. Anterior nare samples are more accessible than samples from deeper within the nasopharynx. However, the correlation between the microbiota found in the anterior nares and the microbiota found within the nasopharynx is unknown. We assessed the anterior nares and nasopharyngeal microbiota to determine (1) the relation of the microbiota from these two upper airway sites and (2) if associations were maintained between the microbiota from these two sites and two bronchiolitis severity outcomes. RESULTS Among 815 infants hospitalized at 17 US centers for bronchiolitis with optimal 16S rRNA gene sequence reads from both nasal swab and nasopharyngeal aspirate samples, there were strong intra-individual correlations in the microbial communities between the two sample types, especially relating to Haemophilus and Moraxella genera. By contrast, we found a high abundance of Staphylococcus genus in the nasal swabs-a pattern not found in the nasopharyngeal samples and not informative when predicting the dominant nasopharyngeal genera. While these disparities may have been due to sample processing differences (i.e., nasal swabs were mailed at ambient temperature to emulate processing of future parent collected swabs while nasopharyngeal aspirates were mailed on dry ice), a previously reported association between Haemophilus-dominant nasopharyngeal microbiota and the increased severity of bronchiolitis was replicated utilizing the nasal swab microbiota and the same outcome measures: intensive care use (adjusted OR 6.43; 95% CI 2.25-20.51; P < 0.001) and hospital length-of-stay (adjusted OR 4.31; 95% CI, 1.73-11.11; P = 0.002). Additionally, Moraxella-dominant nasopharyngeal microbiota was previously identified as protective against intensive care use, a result that was replicated when analyzing the nasal swab microbiota (adjusted OR 0.30; 95% CI, 0.11-0.64; P = 0.01). CONCLUSIONS While the microbiota of the anterior nares and the nasopharynx are distinct, there is considerable overlap between the bacterial community compositions from these two anatomic sites. Despite processing differences between the samples, these results indicate that microbiota severity associations from the nasopharynx are recapitulated in the anterior nares, suggesting that nasal swab samples not only are effective sample types, but also can be used to detect microbial risk markers.
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Affiliation(s)
- Pamela N Luna
- Department of Statistics, Rice University, Houston, TX, USA
| | - Kohei Hasegawa
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Nadim J Ajami
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Janice A Espinola
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - David M Henke
- Department of Molecular and Human Genetics MS 225, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Joseph F Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Pedro A Piedra
- Department of Molecular Virology and Microbiology and Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Ashley F Sullivan
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Carlos A Camargo
- Department of Emergency Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Chad A Shaw
- Department of Statistics, Rice University, Houston, TX, USA.
- Department of Molecular and Human Genetics MS 225, Baylor College of Medicine, Houston, TX, 77030, USA.
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Mullen A, Wieland HJ, Wieser ES, Spannhake EW, Marinos RS. Perioperative participation of orthopedic patients and surgical staff in a nasal decolonization intervention to reduce Staphylococcus spp surgical site infections. Am J Infect Control 2017; 45:554-556. [PMID: 28189415 DOI: 10.1016/j.ajic.2016.12.021] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 12/29/2016] [Accepted: 12/29/2016] [Indexed: 11/30/2022]
Abstract
With the goal of reducing rates of surgical site infections in our spine patients, we initiated a trial to investigate the impact of adding perisurgical nasal decolonization involving patients and surgical and nursing staff. We combined immediate presurgical application of a nonantibiotic alcohol-based nasal antiseptic with existing chlorhexidine bath or wipes in a comprehensive pre- and postoperative decolonization protocol. Mean infection rates were significantly decreased by 81% from 1.76 to 0.33 per 100 surgeries during the 15-month trial, when compared with the prior 9-month baseline.
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Affiliation(s)
- Anildaliz Mullen
- Baylor Orthopedic and Spine Hospital at Arlington, Arlington, TX.
| | - Helen J Wieland
- Baylor Orthopedic and Spine Hospital at Arlington, Arlington, TX
| | - Eric S Wieser
- Baylor Orthopedic and Spine Hospital at Arlington, Arlington, TX
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