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Kimambo AH, Vuhahula EA, Philipo GS, Mushi BP, Mmbaga EJ, Van Loon K, Ng DL. Rapid Onsite Evaluation for Specimen Adequacy and Triage of Breast Masses in a Low-Resource Setting. Arch Pathol Lab Med 2024; 148:e9-e17. [PMID: 37327201 PMCID: PMC10728347 DOI: 10.5858/arpa.2022-0398-oa] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2023] [Indexed: 06/18/2023]
Abstract
CONTEXT.— Rapid onsite evaluation (ROSE) is critical in determining sample adequacy and triaging cytology samples. Although fine-needle aspiration biopsy (FNAB) is the primary method of initial tissue sampling in Tanzania, ROSE is not practiced. OBJECTIVE.— To investigate the performance of ROSE in determining cellular adequacy and providing preliminary diagnoses in breast FNAB in a low-resource setting. DESIGN.— Patients with breast masses were recruited prospectively from the FNAB clinic at Muhimbili National Hospital. Each FNAB was evaluated by ROSE for overall specimen adequacy, cellularity, and preliminary diagnosis. The preliminary interpretation was compared to the final cytologic diagnosis and histologic diagnosis, when available. RESULTS.— Fifty FNAB cases were evaluated, and all were adequate for diagnosis on ROSE and final interpretation. Overall percentage of agreement (OPA) between preliminary and final cytologic diagnosis was 84%, positive percentage of agreement (PPA) was 33%, and negative percentage of agreement (NPA) was 100% (κ = 0.4, P < .001). Twenty-one cases had correlating surgical resections. OPA between preliminary cytologic and histologic diagnoses was 67%, PPA was 22%, and NPA was 100% (κ = 0.2, P = .09). OPA between final cytologic and histologic diagnoses was 95%, PPA was 89%, and NPA was 100% (κ = 0.9, P = <.001). CONCLUSIONS.— False-positive rates of ROSE diagnoses for breast FNAB are low. While preliminary cytologic diagnoses had a high false-negative rate, final cytologic diagnoses had overall high concordance with histologic diagnoses. Therefore, the role of ROSE for preliminary diagnosis should be considered carefully in low-resource settings, and it may need to be paired with additional interventions to improve pathologic diagnosis.
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Affiliation(s)
- Asteria H Kimambo
- From the Departments of Pathology (Kimambo, Vuhahula) and Epidemiology and Biostatistics (Philipo, Mushi, Mmbaga), Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Edda A Vuhahula
- From the Departments of Pathology (Kimambo, Vuhahula) and Epidemiology and Biostatistics (Philipo, Mushi, Mmbaga), Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Godfrey S Philipo
- From the Departments of Pathology (Kimambo, Vuhahula) and Epidemiology and Biostatistics (Philipo, Mushi, Mmbaga), Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Beatrice P Mushi
- From the Departments of Pathology (Kimambo, Vuhahula) and Epidemiology and Biostatistics (Philipo, Mushi, Mmbaga), Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Elia J Mmbaga
- From the Departments of Pathology (Kimambo, Vuhahula) and Epidemiology and Biostatistics (Philipo, Mushi, Mmbaga), Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- the Department of Community Medicine and Global Health, University of Oslo, Oslo, Norway (Mmbaga)
| | - Katherine Van Loon
- the Division of Hematology and Oncology in the Department of Medicine (Van Loon), the Helen Diller Family Comprehensive Cancer Center (Van Loon, Ng)
| | - Dianna L Ng
- the Division of Hematology and Oncology in the Department of Medicine (Van Loon), the Helen Diller Family Comprehensive Cancer Center (Van Loon, Ng)
- the Department of Pathology (Ng), University of California, San Francisco
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Van Loon K, Mmbaga EJ, Mushi BP, Selekwa M, Mwanga A, Akoko LO, Mwaiselage J, Mosha I, Ng DL, Wu W, Silverstein J, Mulima G, Kaimila B, Gopal S, Snell JM, Benz SC, Vaske C, Sanborn Z, Sedgewick AJ, Radenbaugh A, Newton Y, Collisson EA. A Genomic Analysis of Esophageal Squamous Cell Carcinoma in Eastern Africa. Cancer Epidemiol Biomarkers Prev 2023; 32:1411-1420. [PMID: 37505926 DOI: 10.1158/1055-9965.epi-22-0775] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 04/19/2023] [Accepted: 07/26/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND Esophageal squamous cell carcinoma (ESCC) comprises 90% of all esophageal cancer cases globally and is the most common histology in low-resource settings. Eastern Africa has a disproportionately high incidence of ESCC. METHODS We describe the genomic profiles of 61 ESCC cases from Tanzania and compare them to profiles from an existing cohort of ESCC cases from Malawi. We also provide a comparison to ESCC tumors in The Cancer Genome Atlas (TCGA). RESULTS We observed substantial transcriptional overlap with other squamous histologies via comparison with TCGA PanCan dataset. DNA analysis revealed known mutational patterns, both genome-wide as well as in genes known to be commonly mutated in ESCC. TP53 mutations were the most common somatic mutation in tumors from both Tanzania and Malawi but were detected at lower frequencies than previously reported in ESCC cases from other settings. In a combined analysis, two unique transcriptional clusters were identified: a proliferative/epithelial cluster and an invasive/migrative/mesenchymal cluster. Mutational signature analysis of the Tanzanian cohort revealed common signatures associated with aging and cytidine deaminase activity (APOBEC) and an absence of signature 29, which was previously reported in the Malawi cohort. CONCLUSIONS This study defines the molecular characteristics of ESCC in Tanzania, and enriches the Eastern African dataset, with findings of overall similarities but also some heterogeneity across two unique sites. IMPACT Despite a high burden of ESCC in Eastern Africa, investigations into the genomics in this region are nascent. This represents the largest comprehensive genomic analysis ESCC from sub-Saharan Africa to date.
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Affiliation(s)
- Katherine Van Loon
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California
| | - Elia J Mmbaga
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Beatrice P Mushi
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Msiba Selekwa
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Ally Mwanga
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Larry O Akoko
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | | | | | - Dianna L Ng
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California
| | - Wei Wu
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California
| | - Jordyn Silverstein
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California
| | | | | | - Satish Gopal
- UNC Project-Malawi, Lilongwe, Malawi
- University of North Carolina, Chapel Hill, North Carolina
| | - Jeff M Snell
- University of North Carolina, Chapel Hill, North Carolina
| | | | | | - Zack Sanborn
- NantOmics/NantHealth, Inc., El Segundo, California
| | | | | | - Yulia Newton
- NantOmics/NantHealth, Inc., El Segundo, California
| | - Eric A Collisson
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, California
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Zhao X, Ersoy E, Ng DL. Comparison of low-cost phantoms for ultrasound-guided fine-needle aspiration biopsy training. J Am Soc Cytopathol 2023; 12:275-283. [PMID: 37085429 PMCID: PMC10330098 DOI: 10.1016/j.jasc.2023.03.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 01/04/2023] [Revised: 03/20/2023] [Accepted: 03/22/2023] [Indexed: 04/23/2023]
Abstract
INTRODUCTION Phantoms and simulators are widely accepted methods to gain valuable experience and confidence for inexperienced trainees prior to seeing their patient and for refining their skills. A phantom model that is durable, simple, and inexpensive to produce and use would be ideal to train practitioners in ultrasound-guided fine-needle aspiration biopsy (USFNA) technique. MATERIALS AND METHODS In this study, we systematically compared several low-cost phantom models including gelatin, extra firm tofu, canned cooked pork, ballistics gel, and chicken breast for their haptic properties, echogenicity, teaching utility, and overall performance based on a Likert scale (1-5; 5 = best). Nine cytopathologists and cytopathology fellows who perform FNA regularly evaluated these models and completed the survey. RESULTS The gelatin phantom, with a gelatin to water ratio of 1:8 by weight, was found to be the best for USFNA practice and overall performance, followed by the 1:10 gelatin phantom. Tofu and chicken breast phantoms were also good low-cost alternatives that needed only a few minutes of total preparation time. CONCLUSIONS Low-cost, homemade phantoms can serve as excellent alternatives to commercial phantoms for practicing and teaching USFNA.
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Affiliation(s)
- Xiaofeng Zhao
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Esma Ersoy
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Dianna L Ng
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York.
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Donat SM, Sonoda Y, Al-Ahmadie H, Murali R, Ng DL, Funt SA, Park KJ. Evaluation of Women With a Positive Urine Cytology and no Demonstrable Disease in the Urinary Tract. Urology 2023; 173:10-16. [PMID: 36621649 PMCID: PMC10406391 DOI: 10.1016/j.urology.2022.12.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/08/2022] [Accepted: 12/26/2022] [Indexed: 01/07/2023]
Abstract
Urinary cytology is indispensable both for the evaluation of gross hematuria and surveillance of patients with urothelial neoplasms. A positive urine cytology usually indicates the presence of urothelial carcinoma somewhere in the urinary tract. However, in women, it may also signal urothelial carcinoma involvement of the lower gynecologic tract or be the presenting sign for a primary cancer of the lower gynecologic tract or rectum. Guidelines for the evaluation of women with a positive cytology and normal urinary tract are lacking. We present a review of the current literature with case scenarios to bring clinicians attention to this diagnostic dilemma.
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Affiliation(s)
- Sherri M Donat
- Urology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY; Weill Cornell Medical College, New York, NY.
| | - Yukio Sonoda
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY; Weill Cornell Medical College, New York, NY
| | - Hikmat Al-Ahmadie
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Rajmohan Murali
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Dianna L Ng
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Samuel A Funt
- Genitourinary Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY; Weill Cornell Medical College, New York, NY
| | - Kay J Park
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
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Nomburg J, Bullman S, Nasrollahzadeh D, Collisson EA, Abedi-Ardekani B, Akoko LO, Atkins JR, Buckle GC, Gopal S, Hu N, Kaimila B, Khoshnia M, Malekzadeh R, Menya D, Mmbaga BT, Moody S, Mulima G, Mushi BP, Mwaiselage J, Mwanga A, Newton Y, Ng DL, Radenbaugh A, Rwakatema DS, Selekwa M, Schüz J, Taylor PR, Vaske C, Goldstein A, Stratton MR, McCormack V, Brennan P, DeCaprio JA, Meyerson M, Mmbaga EJ, Van Loon K. An international report on bacterial communities in esophageal squamous cell carcinoma. Int J Cancer 2022; 151:1947-1959. [PMID: 35837755 DOI: 10.1002/ijc.34212] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 12/14/2021] [Revised: 03/23/2022] [Accepted: 04/11/2022] [Indexed: 11/09/2022]
Abstract
The incidence of esophageal squamous cell carcinoma (ESCC) is disproportionately high in the eastern corridor of Africa and parts of Asia. Emerging research has identified a potential association between poor oral health and ESCC. One possible link between poor oral health and ESCC involves the alteration of the microbiome. We performed an integrated analysis of four independent sequencing efforts of ESCC tumors from patients from high- and low-incidence regions of the world. Using whole genome sequencing (WGS) and RNA sequencing (RNAseq) of ESCC tumors from 61 patients in Tanzania, we identified a community of bacteria, including members of the genera Fusobacterium, Selenomonas, Prevotella, Streptococcus, Porphyromonas, Veillonella and Campylobacter, present at high abundance in ESCC tumors. We then characterized the microbiome of 238 ESCC tumor specimens collected in two additional independent sequencing efforts consisting of patients from other high-ESCC incidence regions (Tanzania, Malawi, Kenya, Iran, China). This analysis revealed similar ESCC-associated bacterial communities in these cancers. Because these genera are traditionally considered members of the oral microbiota, we next explored whether there was a relationship between the synchronous saliva and tumor microbiomes of ESCC patients in Tanzania. Comparative analyses revealed that paired saliva and tumor microbiomes were significantly similar with a specific enrichment of Fusobacterium and Prevotella in the tumor microbiome. Together, these data indicate that cancer-associated oral bacteria are associated with ESCC tumors at the time of diagnosis and support a model in which oral bacteria are present in high abundance in both saliva and tumors of some ESCC patients.
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Affiliation(s)
- Jason Nomburg
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Harvard Program in Virology, Harvard Medical School, Boston, Massachusetts, USA
| | - Susan Bullman
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Dariush Nasrollahzadeh
- Digestive Oncology Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Shariati Hospital, Tehran, Iran
- International Agency for Research on Cancer (IARC), Genomic Epidemiology Branch, Lyon, France
| | - Eric A Collisson
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, California, USA
- Division of Hematology/Oncology, Department of Medicine, UCSF, San Francisco, California, USA
| | - Behnoush Abedi-Ardekani
- International Agency for Research on Cancer (IARC), Genomic Epidemiology Branch, Lyon, France
| | - Larry O Akoko
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Joshua R Atkins
- International Agency for Research on Cancer (IARC), Genomic Epidemiology Branch, Lyon, France
| | - Geoffrey C Buckle
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, California, USA
- Division of Hematology/Oncology, Department of Medicine, UCSF, San Francisco, California, USA
| | - Satish Gopal
- University of North Carolina (UNC), Chapel Hill, North Carolina, USA
| | - Nan Hu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | | | - Masoud Khoshnia
- Digestive Oncology Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Shariati Hospital, Tehran, Iran
| | - Reza Malekzadeh
- Digestive Oncology Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Shariati Hospital, Tehran, Iran
| | - Diana Menya
- School of Public Health, Moi University, Eldoret, Kenya
| | - Blandina T Mmbaga
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Center, Moshi, Tanzania
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Sarah Moody
- The Cancer, Ageing and Somatic Mutation Programme, Wellcome Trust Sanger Institute, Cambridgeshire, UK
| | | | - Beatrice P Mushi
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | | | - Ally Mwanga
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Yulia Newton
- NantOmics/NantHealth, Inc., El Segundo, California, USA
| | - Dianna L Ng
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, California, USA
- Department of Pathology, UCSF, San Francisco, California, USA
| | | | - Deogratias S Rwakatema
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Center, Moshi, Tanzania
- Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Msiba Selekwa
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Joachim Schüz
- International Agency for Research on Cancer (IARC/WHO), Environment and Lifestyle Epidemiology Branch, Lyon, France
| | - Philip R Taylor
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Charles Vaske
- NantOmics/NantHealth, Inc., El Segundo, California, USA
| | - Alisa Goldstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, USA
| | - Michael R Stratton
- The Cancer, Ageing and Somatic Mutation Programme, Wellcome Trust Sanger Institute, Cambridgeshire, UK
| | - Valerie McCormack
- International Agency for Research on Cancer (IARC/WHO), Environment and Lifestyle Epidemiology Branch, Lyon, France
| | - Paul Brennan
- International Agency for Research on Cancer (IARC), Genomic Epidemiology Branch, Lyon, France
| | - James A DeCaprio
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Harvard Program in Virology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Elia J Mmbaga
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Department of Community Medicine and Global Health, University of Oslo, Oslo, Norway
| | - Katherine Van Loon
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, California, USA
- Division of Hematology/Oncology, Department of Medicine, UCSF, San Francisco, California, USA
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Ngaiza A, Vuhahula E, Yahaya J, Ndayisaba MC, Kawishe GJ, Grenert JP, Zhang L, Van Loon K, Ng DL. Evaluation of Human Epidermal Growth Factor Receptor 2 Expression in Gastric and Gastroesophageal Cancers in Tanzania. Arch Pathol Lab Med 2022; 146:1523-1529. [PMID: 35344993 PMCID: PMC9515243 DOI: 10.5858/arpa.2021-0394-oa] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/28/2021] [Indexed: 11/06/2022]
Abstract
CONTEXT.— The incidence of human epidermal growth factor receptor 2 (HER2) positivity in gastric cancers differs widely across various populations and is unknown in many low-resource settings. OBJECTIVE.— To evaluate the rates of HER2 positivity in gastric and gastroesophageal adenocarcinoma at a national referral hospital in East Africa. We also assessed the association between HER2 overexpression and patient clinicopathologic characteristics. DESIGN.— A retrospective review of cases diagnosed as either gastric or gastroesophageal adenocarcinoma between 2013 and 2017 was performed at Muhimbili National Hospital in Dar es Salaam, Tanzania. Of 1205 specimens meeting inclusion criteria, stratified random sampling was conducted to select 150 cases for HER2 immunohistochemistry and clinicopathologic analysis. RESULTS.— The median age of patients was 56.5 years, with 65.3% (98 of 150) of the cohort composed of male patients, and 34.7% (52 of 150) of female patients. HER2 overexpression was identified in 6.0% (9 of 150) of cases. Approximately half of the tumors (51.3%; 77 of 150) were intestinal-type gastric adenocarcinoma, and 36.0% (54 of 150) were moderately differentiated. Intestinal-type (P = .01) and well-differentiated tumors (P = .001) were associated with HER2 overexpression. CONCLUSIONS.— HER2 overexpression was primarily seen in intestinal-type and well-differentiated tumors. Therefore, prioritizing HER2 testing for patients with intestinal-type, well-differentiated, or moderately differentiated gastric and gastroesophageal adenocarcinomas may be appropriate in Tanzania in efforts to allocate testing for patients who are most likely to benefit from trastuzumab therapy.
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Affiliation(s)
- Advera Ngaiza
- From the Department of Pathology, Muhimbili National Hospital, Dar es Salaam, Tanzania (Ngaiza, Vuhahula)
| | - Edda Vuhahula
- From the Department of Pathology, Muhimbili National Hospital, Dar es Salaam, Tanzania (Ngaiza, Vuhahula)
- The Department of Pathology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania (Vuhahula)
| | - James Yahaya
- The Department of Histopathology and Morbid Anatomy, University of Dodoma, Dodoma, Tanzania (Yahaya)
| | - Marie Claire Ndayisaba
- The Department of Pathology, University Teaching Hospital of Kigali, Kigali, Rwanda (Ndayisaba)
| | - Gerald J Kawishe
- The Department of Molecular Biology and Biotechnology, University of Dar es Salaam, Dar es Salaam, Tanzania (Kawishe)
| | - James P Grenert
- The Department of Pathology (Grenert, Ng), University of California, San Francisco
| | - Li Zhang
- The Department of Epidemiology and Biostatistics (Zhang), University of California, San Francisco
- The Division of Hematology/Oncology, Department of Medicine (Zhang, Van Loon), University of California, San Francisco
- The Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (Ng, Zhang, Van Loon)
| | - Katherine Van Loon
- The Division of Hematology/Oncology, Department of Medicine (Zhang, Van Loon), University of California, San Francisco
- The Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (Ng, Zhang, Van Loon)
| | - Dianna L Ng
- The Department of Pathology (Grenert, Ng), University of California, San Francisco
- The Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (Ng, Zhang, Van Loon)
- Ng is currently affiliated with the Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
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Philipo GS, Vuhahula E, Kimambo A, Mmbaga EJ, Van Loon K, Ng DL. Feasibility of Fine-Needle Aspiration Biopsy and Rapid On-Site Evaluation for Immediate Triage in Breast Cancer Screening in Tanzania. JCO Glob Oncol 2021; 7:146-152. [PMID: 33493018 PMCID: PMC8081537 DOI: 10.1200/go.20.00279] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
PURPOSE Clinical breast examination (CBE) is one of the most common methods used for early detection of breast cancer in low- and middle-income countries. CBE alone is limited by lack of specificity and may result in unnecessary diagnostic procedures. We evaluated the feasibility of integrating CBE, fine-needle aspiration biopsy (FNAB), and rapid on-site evaluation (ROSE) in triaging palpable breast masses for specialized cancer care. MATERIALS AND METHODS An intensive breast cancer screening event was conducted at a national trade fair by a multidisciplinary team of care providers targeting a healthy population in Dar es Salaam, Tanzania. All adults age ≥ 18 years were invited to participate. CBE was performed by oncologists and/or pathologists. FNAB was performed by a pathologist on palpable masses that were then categorized as benign, indeterminate, or suspicious for malignancy or definitively malignant based on ROSE. RESULTS A total of 208 individuals (207 females, one male; median age, 36 years; range, 18-68 years) were screened. Most (90.8%, 189 of 208) had normal findings, whereas 7.2% (15 of 208), 1% (2 of 208), and 1% (2 of 208) had a palpable mass, breast pain, and nipple discharge, respectively. Two participants had lesions too small for palpation-guided biopsy and clinically consistent with fibroadenomas; the participants were counseled, and observation was recommended. FNAB was performed on 13 breast masses, with 9 of 13 (69%) categorized as benign and 4 of 13 (31%) suspicious for malignancy. Final cytopathologic review of referred patients confirmed one case to be breast adenocarcinoma, one was suggestive of fibroadenoma, and two showed inflammations. CONCLUSION Integration of CBE with ROSE and FNAB was feasible in a breast cancer screening program in Tanzania. In settings with constrained resources for cancer care, this may be an effective method for triaging patients with breast masses.
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Affiliation(s)
- Godfrey S Philipo
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Edda Vuhahula
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Asteria Kimambo
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Elia J Mmbaga
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Katherine Van Loon
- Department of Pathology, University of California San Francisco, San Francisco, CA
| | - Dianna L Ng
- Department of Pathology, University of California San Francisco, San Francisco, CA
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Abstract
Background: Prior studies evaluating thyroid fine needle aspiration biopsies (FNABs) have limited the calculation of risk of malignancy (ROM) to cytologic specimens with corresponding histologic specimens, and clinical follow-up for those patients who do not undergo immediate surgery has been largely disregarded. Moreover, there is marked variability in how researchers have approached thyroid FNAB statistical analyses. This study addresses the urgent need for information from a large cohort of patients with long-term clinical follow-up to more accurately determine the performance of thyroid FNAB and ROM for each diagnostic category. Methods: A retrospective review of the University of California, San Francisco (UCSF), pathology database for thyroid FNABs from January 1, 1997, to December 31, 2004, was performed. Diagnoses were coded using the 2017 The Bethesda System for Reporting Thyroid Cytopathology (TBSRTC), and patients were matched to both the UCSF cancer registry and California Cancer Registry. Data were analyzed using the Kaplan-Meier method, and stratified by TBSRTC diagnostic category. Kaplan-Meier curves were used to estimate incidence rates of malignancy, stratified by FNAB category. Cox proportional hazards models were used to determine the instantaneous ROM. Results: Initial FNABs from 2207 patients were included. Median follow-up period after the first thyroid FNAB was 13.9 years (range: 10.5-18.4 years). During follow-up, there were 279 confirmed diagnoses of thyroid malignancy. Estimates derived from Kaplan-Meier curves demonstrated that the risk of having a thyroid malignancy was low for nondiagnostic and benign categories, intermediate for atypia of undetermined significance (AUS), follicular lesion of undetermined significance (FLUS), AUS/FLUS combined, and follicular neoplasm, and high for suspicious and malignant categories. A total of 52/1575 false-negative cases (3.2%) were identified. Excluding papillary microcarcinomas, the false-negative rate was 1.5% (23/1575). No patients with a false-negative diagnosis died of thyroid cancer during the follow-up period. Conclusions: Asymptomatic patients with low-risk clinical and radiologic features and initially benign or unsatisfactory biopsy are unlikely to develop thyroid malignancy and highly unlikely to die of thyroid cancer. FNAB is highly accurate in detecting malignancy. Additional studies evaluating similar large data sets after the adoption of TBSRTC and the integration of molecular testing are needed.
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Affiliation(s)
- Dianna L. Ng
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, USA
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Annemieke van Zante
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Ann Griffin
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, USA
| | - Nancy K. Hills
- Department of Epidemiology and Biostatistics, and University of California, San Francisco, San Francisco, California, USA
- Department of Neurology, University of California, San Francisco, San Francisco, California, USA
| | - Britt-Marie Ljung
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, USA
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Butler D, Mozsary C, Meydan C, Foox J, Rosiene J, Shaiber A, Danko D, Afshinnekoo E, MacKay M, Sedlazeck FJ, Ivanov NA, Sierra M, Pohle D, Zietz M, Gisladottir U, Ramlall V, Sholle ET, Schenck EJ, Westover CD, Hassan C, Ryon K, Young B, Bhattacharya C, Ng DL, Granados AC, Santos YA, Servellita V, Federman S, Ruggiero P, Fungtammasan A, Chin CS, Pearson NM, Langhorst BW, Tanner NA, Kim Y, Reeves JW, Hether TD, Warren SE, Bailey M, Gawrys J, Meleshko D, Xu D, Couto-Rodriguez M, Nagy-Szakal D, Barrows J, Wells H, O'Hara NB, Rosenfeld JA, Chen Y, Steel PAD, Shemesh AJ, Xiang J, Thierry-Mieg J, Thierry-Mieg D, Iftner A, Bezdan D, Sanchez E, Campion TR, Sipley J, Cong L, Craney A, Velu P, Melnick AM, Shapira S, Hajirasouliha I, Borczuk A, Iftner T, Salvatore M, Loda M, Westblade LF, Cushing M, Wu S, Levy S, Chiu C, Schwartz RE, Tatonetti N, Rennert H, Imielinski M, Mason CE. Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions. Nat Commun 2021; 12:1660. [PMID: 33712587 PMCID: PMC7954844 DOI: 10.1038/s41467-021-21361-7] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [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: 09/03/2020] [Accepted: 01/25/2021] [Indexed: 02/08/2023] Open
Abstract
In less than nine months, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) killed over a million people, including >25,000 in New York City (NYC) alone. The COVID-19 pandemic caused by SARS-CoV-2 highlights clinical needs to detect infection, track strain evolution, and identify biomarkers of disease course. To address these challenges, we designed a fast (30-minute) colorimetric test (LAMP) for SARS-CoV-2 infection from naso/oropharyngeal swabs and a large-scale shotgun metatranscriptomics platform (total-RNA-seq) for host, viral, and microbial profiling. We applied these methods to clinical specimens gathered from 669 patients in New York City during the first two months of the outbreak, yielding a broad molecular portrait of the emerging COVID-19 disease. We find significant enrichment of a NYC-distinctive clade of the virus (20C), as well as host responses in interferon, ACE, hematological, and olfaction pathways. In addition, we use 50,821 patient records to find that renin-angiotensin-aldosterone system inhibitors have a protective effect for severe COVID-19 outcomes, unlike similar drugs. Finally, spatial transcriptomic data from COVID-19 patient autopsy tissues reveal distinct ACE2 expression loci, with macrophage and neutrophil infiltration in the lungs. These findings can inform public health and may help develop and drive SARS-CoV-2 diagnostic, prevention, and treatment strategies.
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Affiliation(s)
- Daniel Butler
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Christopher Mozsary
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Joel Rosiene
- New York Genome Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Alon Shaiber
- New York Genome Center, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine and the Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - David Danko
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Ebrahim Afshinnekoo
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Matthew MacKay
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Nikolay A Ivanov
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Clinical & Translational Science Center, Weill Cornell Medicine, New York, NY, USA
| | - Maria Sierra
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Diana Pohle
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Tuebingen, Germany
| | - Michael Zietz
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, Columbia, NY, USA
| | - Undina Gisladottir
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, Columbia, NY, USA
| | - Vijendra Ramlall
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, Columbia, NY, USA
- Department of Cellular, Molecular Physiology & Biophysics, Columbia University, Columbia, NY, USA
| | - Evan T Sholle
- Information Technologies & Services Department, Weill Cornell Medicine, New York, NY, USA
| | - Edward J Schenck
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Craig D Westover
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Ciaran Hassan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Krista Ryon
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Benjamin Young
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | | | - Dianna L Ng
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Andrea C Granados
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Yale A Santos
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Venice Servellita
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Scot Federman
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Phyllis Ruggiero
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | | | | | | | | | | | | | | | | | | | | | - Justyna Gawrys
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Dmitry Meleshko
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Tri-Institutional Computational Biology & Medicine Program, Weill Cornell Medicine, New York, NY, USA
| | - Dong Xu
- Genomics Resources Core Facility, Weill Cornell Medicine, New York, NY, USA
| | | | - Dorottya Nagy-Szakal
- Biotia, Inc., New York, NY, USA
- Department of Cell Biology, SUNY Downstate Health Sciences University, New York, NY, USA
| | | | | | - Niamh B O'Hara
- Biotia, Inc., New York, NY, USA
- Department of Cell Biology, SUNY Downstate Health Sciences University, New York, NY, USA
| | - Jeffrey A Rosenfeld
- Rutgers Cancer Institute of New Jersey, New York, NJ, USA
- Department of Pathology, Robert Wood Johnson Medical School, New York, NJ, USA
| | - Ying Chen
- Rutgers Cancer Institute of New Jersey, New York, NJ, USA
| | - Peter A D Steel
- Department of Emergency Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Amos J Shemesh
- Department of Emergency Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Jenny Xiang
- Genomics Resources Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Jean Thierry-Mieg
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Danielle Thierry-Mieg
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Angelika Iftner
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Tuebingen, Germany
| | - Daniela Bezdan
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Tuebingen, Germany
| | | | - Thomas R Campion
- Information Technologies & Services Department, Weill Cornell Medicine, New York, NY, USA
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | - John Sipley
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Lin Cong
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Arryn Craney
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Priya Velu
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Ari M Melnick
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Sagi Shapira
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, Columbia, NY, USA
| | - Iman Hajirasouliha
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine and the Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Alain Borczuk
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Thomas Iftner
- Institute of Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Tuebingen, Germany
| | - Mirella Salvatore
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Population Health Sciences, Weill Cornell Medicine, New York, NY, USA
| | - Massimo Loda
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Lars F Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Melissa Cushing
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Shixiu Wu
- Hangzhou Cancer Institute, Hangzhou Cancer Hospital, Hangzhou, China
- Department of Radiation Oncology, Hangzhou Cancer Hospital, Hangzhou, China
| | - Shawn Levy
- HudsonAlpha Discovery Institute, Huntsville, AL, USA
| | - Charles Chiu
- Department of Laboratory Medicine, University of California, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, CA, USA
| | | | - Nicholas Tatonetti
- Department of Biomedical Informatics, Department of Systems Biology, Department of Medicine, Institute for Genomic Medicine, Columbia University, Columbia, NY, USA.
| | - Hanna Rennert
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.
| | - Marcin Imielinski
- New York Genome Center, New York, NY, USA.
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.
- Englander Institute for Precision Medicine and the Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA.
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA.
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10
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Ng DL, Granados AC, Santos YA, Servellita V, Goldgof GM, Meydan C, Sotomayor-Gonzalez A, Levine AG, Balcerek J, Han LM, Akagi N, Truong K, Neumann NM, Nguyen DN, Bapat SP, Cheng J, Martin CSS, Federman S, Foox J, Gopez A, Li T, Chan R, Chu CS, Wabl CA, Gliwa AS, Reyes K, Pan CY, Guevara H, Wadford D, Miller S, Mason CE, Chiu CY. A diagnostic host response biosignature for COVID-19 from RNA profiling of nasal swabs and blood. Sci Adv 2021; 7:eabe5984. [PMID: 33536218 PMCID: PMC7857687 DOI: 10.1126/sciadv.abe5984] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 12/15/2020] [Indexed: 05/05/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease-19 (COVID-19), has emerged as the cause of a global pandemic. We used RNA sequencing to analyze 286 nasopharyngeal (NP) swab and 53 whole-blood (WB) samples from 333 patients with COVID-19 and controls. Overall, a muted immune response was observed in COVID-19 relative to other infections (influenza, other seasonal coronaviruses, and bacterial sepsis), with paradoxical down-regulation of several key differentially expressed genes. Hospitalized patients and outpatients exhibited up-regulation of interferon-associated pathways, although heightened and more robust inflammatory responses were observed in hospitalized patients with more clinically severe illness. Two-layer machine learning-based host classifiers consisting of complete (>1000 genes), medium (<100), and small (<20) gene biomarker panels identified COVID-19 disease with 85.1-86.5% accuracy when benchmarked using an independent test set. SARS-CoV-2 infection has a distinct biosignature that differs between NP swabs and WB and can be leveraged for COVID-19 diagnosis.
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Affiliation(s)
- Dianna L Ng
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Andrea C Granados
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Yale A Santos
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Venice Servellita
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Gregory M Goldgof
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Alicia Sotomayor-Gonzalez
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Andrew G Levine
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Joanna Balcerek
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Lucy M Han
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Naomi Akagi
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Kent Truong
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Neil M Neumann
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - David N Nguyen
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Sagar P Bapat
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA
| | - Jing Cheng
- Department of Preventive and Restorative Dental Sciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Claudia Sanchez-San Martin
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Scot Federman
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA
| | - Allan Gopez
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Tony Li
- Department of Medicine, Division of Hematology and Oncology, University of California, San Francisco, San Francisco, CA, USA
| | - Ray Chan
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Cynthia S Chu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Chiara A Wabl
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Amelia S Gliwa
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Kevin Reyes
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Chao-Yang Pan
- Viral and Rickettsial Disease Laboratory, California Department of Health, Richmond, CA, USA
| | - Hugo Guevara
- Viral and Rickettsial Disease Laboratory, California Department of Health, Richmond, CA, USA
| | - Debra Wadford
- Viral and Rickettsial Disease Laboratory, California Department of Health, Richmond, CA, USA
| | - Steve Miller
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- New York Genome Center, New York, NY, USA
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA.
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA
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11
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Ruiz-Cordero R, Ng DL. Neurotrophic receptor tyrosine kinase (NTRK) fusions and their role in cancer. Cancer Cytopathol 2020; 128:775-779. [PMID: 33002320 DOI: 10.1002/cncy.22350] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 08/04/2020] [Indexed: 12/14/2022]
Abstract
Neurotrophic receptor tyrosine kinase (NTRK) fusions are rare, therapeutically actionable, and, in some cases, diagnostic oncogenic events that can occur in a variety of adult and pediatric cancers. Cytopathologists need to be a familiar with the types of tumors that can harbor NTRK fusions to triage specimens accordingly for testing.
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12
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Kimambo AH, Vuhahula EA, Mwakigonja AR, Ljung BM, Zhang L, Van Loon K, Ng DL. Evaluating Estrogen Receptor Immunohistochemistry on Cell Blocks From Breast Cancer Patients in a Low-Resource Setting. Arch Pathol Lab Med 2020; 145:834-841. [PMID: 33053150 DOI: 10.5858/arpa.2020-0086-oa] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2020] [Indexed: 12/24/2022]
Abstract
CONTEXT.— Breast cancer biomarker assessment is critical in determining treatment and prognosis. In Tanzania, immunohistochemistry (IHC) is limited to surgical specimens and core biopsies. However, performing IHC on fine-needle aspiration biopsy cell blocks would offer numerous advantages. OBJECTIVE.— To compare the performance between estrogen receptor (ER) IHC performed at Muhimbili National Hospital (MNH) in Tanzania and ER IHC performed at University of California, San Francisco (UCSF), to demonstrate feasibility of performing IHC using cell blocks in Tanzania. DESIGN.— Patients with breast masses were recruited prospectively from the fine-needle aspiration biopsy clinic at MNH. Estrogen receptor IHC results on cell blocks, performed at both MNH and UCSF, and corresponding tissue blocks, performed at MNH, were compared to determine concordance. RESULTS.— Eighty-six cell blocks were evaluated by ER IHC at MNH, with 41 of 86 (47.7%) positive and 45 of 86 (52.3%) negative. Among 65 UCSF and MNH cell block pairs, overall ER IHC concordance was 93.8% (61 of 65) and positive concordance was 93.5% (29 of 31) (κ = 0.88, P > .99). Among 43 paired UCSF cell blocks and MNH tissue blocks, overall ER IHC concordance was 88.3% (38 of 43) and positive concordance was 90.5% (19 of 21) (κ = 0.77, P > .99). We compared 62 MNH cell block and tissue block pairs. Overall ER IHC concordance was 90.3% and positive concordance was 87.9% (κ = 0.81, P = .69). CONCLUSIONS.— Pairwise comparisons between ER IHC at MNH, on cell blocks and tissue blocks, with ER IHC at UCSF on cell blocks showed excellent concordance. We demonstrate that ER IHC on fine-needle aspiration biopsy specimens can be implemented in resource-constrained settings.
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Affiliation(s)
- Asteria H Kimambo
- From the Department of Pathology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania (Kimambo, Vuhahula, Mwakigonja)
| | - Edda A Vuhahula
- From the Department of Pathology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania (Kimambo, Vuhahula, Mwakigonja)
| | - Amos R Mwakigonja
- From the Department of Pathology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania (Kimambo, Vuhahula, Mwakigonja)
| | - Britt-Marie Ljung
- The Department of Pathology (Ljung, Ng), San Francisco Medical Center, San Francisco
| | - Li Zhang
- Department of Epidemiology and Biostatistics (Zhang), San Francisco Medical Center, San Francisco.,The Department of Medicine, Division of Hematology and Oncology (Zhang, Van Loon), San Francisco Medical Center, San Francisco
| | - Katherine Van Loon
- The Department of Medicine, Division of Hematology and Oncology (Zhang, Van Loon), San Francisco Medical Center, San Francisco
| | - Dianna L Ng
- The Helen Diller Family Comprehensive Cancer Center (Zhang, Van Loon, Ng), San Francisco Medical Center, San Francisco.,University of California, San Francisco Medical Center, San Francisco. Ng is now at the Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
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13
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Whitman JD, Hiatt J, Mowery CT, Shy BR, Yu R, Yamamoto TN, Rathore U, Goldgof GM, Whitty C, Woo JM, Gallman AE, Miller TE, Levine AG, Nguyen DN, Bapat SP, Balcerek J, Bylsma SA, Lyons AM, Li S, Wong AWY, Gillis-Buck EM, Steinhart ZB, Lee Y, Apathy R, Lipke MJ, Smith JA, Zheng T, Boothby IC, Isaza E, Chan J, Acenas DD, Lee J, Macrae TA, Kyaw TS, Wu D, Ng DL, Gu W, York VA, Eskandarian HA, Callaway PC, Warrier L, Moreno ME, Levan J, Torres L, Farrington LA, Loudermilk RP, Koshal K, Zorn KC, Garcia-Beltran WF, Yang D, Astudillo MG, Bernstein BE, Gelfand JA, Ryan ET, Charles RC, Iafrate AJ, Lennerz JK, Miller S, Chiu CY, Stramer SL, Wilson MR, Manglik A, Ye CJ, Krogan NJ, Anderson MS, Cyster JG, Ernst JD, Wu AHB, Lynch KL, Bern C, Hsu PD, Marson A. Evaluation of SARS-CoV-2 serology assays reveals a range of test performance. Nat Biotechnol 2020; 38:1174-1183. [PMID: 32855547 PMCID: PMC7740072 DOI: 10.1038/s41587-020-0659-0] [Citation(s) in RCA: 198] [Impact Index Per Article: 49.5] [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: 06/09/2020] [Accepted: 07/29/2020] [Indexed: 12/18/2022]
Abstract
Appropriate use and interpretation of serological tests for assessments of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exposure, infection and potential immunity require accurate data on assay performance. We conducted a head-to-head evaluation of ten point-of-care-style lateral flow assays (LFAs) and two laboratory-based enzyme-linked immunosorbent assays to detect anti-SARS-CoV-2 IgM and IgG antibodies in 5-d time intervals from symptom onset and studied the specificity of each assay in pre-coronavirus disease 2019 specimens. The percent of seropositive individuals increased with time, peaking in the latest time interval tested (>20 d after symptom onset). Test specificity ranged from 84.3% to 100.0% and was predominantly affected by variability in IgM results. LFA specificity could be increased by considering weak bands as negative, but this decreased detection of antibodies (sensitivity) in a subset of SARS-CoV-2 real-time PCR-positive cases. Our results underline the importance of seropositivity threshold determination and reader training for reliable LFA deployment. Although there was no standout serological assay, four tests achieved more than 80% positivity at later time points tested and more than 95% specificity.
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Affiliation(s)
- Jeffrey D Whitman
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Joseph Hiatt
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Cody T Mowery
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Brian R Shy
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Ruby Yu
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Tori N Yamamoto
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Ujjwal Rathore
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Gregory M Goldgof
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Caroline Whitty
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Jonathan M Woo
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Antonia E Gallman
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, USA
| | - Tyler E Miller
- Department of Pathology, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Andrew G Levine
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - David N Nguyen
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA
| | - Sagar P Bapat
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Joanna Balcerek
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Sophia A Bylsma
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA
| | - Ana M Lyons
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Stacy Li
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Allison Wai-Yi Wong
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
| | - Eva Mae Gillis-Buck
- Department of Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Zachary B Steinhart
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Youjin Lee
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Ryan Apathy
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Mitchell J Lipke
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Jennifer Anne Smith
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Tina Zheng
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Ian C Boothby
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
- Department of Dermatology, University of California, San Francisco, San Francisco, CA, USA
| | - Erin Isaza
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
- Program in Quantitative Biology, University of California, San Francisco, San Francisco, CA, USA
| | - Jackie Chan
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Dante D Acenas
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Jinwoo Lee
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
- School of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Trisha A Macrae
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
- School of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Than S Kyaw
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - David Wu
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Dianna L Ng
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Wei Gu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Vanessa A York
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Haig Alexander Eskandarian
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Perri C Callaway
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Infectious Diseases and Immunity Graduate Group, University of California, Berkeley, Berkeley, CA, USA
| | - Lakshmi Warrier
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Mary E Moreno
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Justine Levan
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Leonel Torres
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Lila A Farrington
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Rita P Loudermilk
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Kanishka Koshal
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Kelsey C Zorn
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | | | - Diane Yang
- Department of Pathology, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Michael G Astudillo
- Department of Pathology, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Bradley E Bernstein
- Department of Pathology, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Jeffrey A Gelfand
- Division of Infectious Diseases, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Edward T Ryan
- Division of Infectious Diseases, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Richelle C Charles
- Division of Infectious Diseases, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - A John Iafrate
- Department of Pathology, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Jochen K Lennerz
- Department of Pathology, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Steve Miller
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Susan L Stramer
- Scientific Affairs, American Red Cross, Gaithersburg, MD, USA
| | - Michael R Wilson
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA, USA
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Aashish Manglik
- Department of Anesthesia and Perioperative Care, University of California, San Francisco, San Francisco, CA, USA
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Chun Jimmie Ye
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Institute of Computational Health Sciences, University of California, San Francisco, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Nevan J Krogan
- J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Mark S Anderson
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA
| | - Jason G Cyster
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, USA
| | - Joel D Ernst
- Division of Experimental Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Alan H B Wu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Kara L Lynch
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Caryn Bern
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA.
| | - Patrick D Hsu
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
- Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA.
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA.
| | - Alexander Marson
- J. David Gladstone Institutes, San Francisco, CA, USA.
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
- Diabetes Center, University of California, San Francisco, San Francisco, CA, USA.
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
- Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
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14
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Ng DL, Goldgof GM, Shy BR, Levine AG, Balcerek J, Bapat SP, Prostko J, Rodgers M, Coller K, Pearce S, Franz S, Du L, Stone M, Pillai SK, Sotomayor-Gonzalez A, Servellita V, Martin CSS, Granados A, Glasner DR, Han LM, Truong K, Akagi N, Nguyen DN, Neumann NM, Qazi D, Hsu E, Gu W, Santos YA, Custer B, Green V, Williamson P, Hills NK, Lu CM, Whitman JD, Stramer SL, Wang C, Reyes K, Hakim JMC, Sujishi K, Alazzeh F, Pham L, Thornborrow E, Oon CY, Miller S, Kurtz T, Simmons G, Hackett J, Busch MP, Chiu CY. SARS-CoV-2 seroprevalence and neutralizing activity in donor and patient blood. Nat Commun 2020; 11:4698. [PMID: 32943630 PMCID: PMC7499171 DOI: 10.1038/s41467-020-18468-8] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [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: 06/19/2020] [Accepted: 08/18/2020] [Indexed: 01/08/2023] Open
Abstract
Given the limited availability of serological testing to date, the seroprevalence of SARS-CoV-2-specific antibodies in different populations has remained unclear. Here, we report very low SARS-CoV-2 seroprevalence in two San Francisco Bay Area populations. Seroreactivity was 0.26% in 387 hospitalized patients admitted for non-respiratory indications and 0.1% in 1,000 blood donors in early April 2020. We additionally describe the longitudinal dynamics of immunoglobulin-G (IgG), immunoglobulin-M (IgM), and in vitro neutralizing antibody titers in COVID-19 patients. The median time to seroconversion ranged from 10.3-11.0 days for these 3 assays. Neutralizing antibodies rose in tandem with immunoglobulin titers following symptom onset, and positive percent agreement between detection of IgG and neutralizing titers was >93%. These findings emphasize the importance of using highly accurate tests for surveillance studies in low-prevalence populations, and provide evidence that seroreactivity using SARS-CoV-2 anti-nucleocapsid protein IgG and anti-spike IgM assays are generally predictive of in vitro neutralizing capacity.
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Affiliation(s)
- Dianna L Ng
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Gregory M Goldgof
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Brian R Shy
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Andrew G Levine
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Joanna Balcerek
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Sagar P Bapat
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - John Prostko
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL, USA
| | - Mary Rodgers
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL, USA
| | - Kelly Coller
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL, USA
| | - Sandra Pearce
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL, USA
| | - Sergej Franz
- Vitalant Research Institute, San Francisco, CA, USA
| | - Li Du
- Vitalant Research Institute, San Francisco, CA, USA
| | - Mars Stone
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Vitalant Research Institute, San Francisco, CA, USA
| | | | - Alicia Sotomayor-Gonzalez
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Venice Servellita
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Claudia Sanchez San Martin
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Andrea Granados
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Dustin R Glasner
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Lucy M Han
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Kent Truong
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Naomi Akagi
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - David N Nguyen
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA
| | - Neil M Neumann
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Daniel Qazi
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Elaine Hsu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Wei Gu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Yale A Santos
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Brian Custer
- Vitalant Research Institute, San Francisco, CA, USA
| | | | | | - Nancy K Hills
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Chuanyi M Lu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Laboratory Medicine Service, San Francisco VA Health Care System, San Francisco, CA, USA
| | - Jeffrey D Whitman
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | | | - Candace Wang
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Kevin Reyes
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Jill M C Hakim
- Department of Medicine at ZSFG, The Division of HIV, ID & Global Medicine, San Francisco, CA, USA
| | - Kirk Sujishi
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Fariba Alazzeh
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Lori Pham
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Edward Thornborrow
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Ching-Ying Oon
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Steve Miller
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Theodore Kurtz
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Graham Simmons
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Vitalant Research Institute, San Francisco, CA, USA
| | - John Hackett
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL, USA
| | - Michael P Busch
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Vitalant Research Institute, San Francisco, CA, USA
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA.
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA.
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA.
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15
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Ng DL, Goldgof GM, Shy BR, Levine AG, Balcerek J, Bapat SP, Prostko J, Rodgers M, Coller K, Pearce S, Franz S, Du L, Stone M, Pillai SK, Sotomayor-Gonzalez A, Servellita V, Martin CSS, Granados A, Glasner DR, Han LM, Truong K, Akagi N, Nguyen DN, Neumann NM, Qazi D, Hsu E, Gu W, Santos YA, Custer B, Green V, Williamson P, Hills NK, Lu CM, Whitman JD, Stramer S, Wang C, Reyes K, Hakim JM, Sujishi K, Alazzeh F, Pham L, Oon CY, Miller S, Kurtz T, Hackett J, Simmons G, Busch MP, Chiu CY. SARS-CoV-2 seroprevalence and neutralizing activity in donor and patient blood from the San Francisco Bay Area. medRxiv 2020:2020.05.19.20107482. [PMID: 32511477 PMCID: PMC7273245 DOI: 10.1101/2020.05.19.20107482] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We report very low SARS-CoV-2 seroprevalence in two San Francisco Bay Area populations. Seropositivity was 0.26% in 387 hospitalized patients admitted for non-respiratory indications and 0.1% in 1,000 blood donors. We additionally describe the longitudinal dynamics of immunoglobulin-G, immunoglobulin-M, and in vitro neutralizing antibody titers in COVID-19 patients. Neutralizing antibodies rise in tandem with immunoglobulin levels following symptom onset, exhibiting median time to seroconversion within one day of each other, and there is >93% positive percent agreement between detection of immunoglobulin-G and neutralizing titers.
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Affiliation(s)
- Dianna L. Ng
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Gregory M. Goldgof
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Brian R. Shy
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Andrew G. Levine
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Joanna Balcerek
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Sagar P. Bapat
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - John Prostko
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL, USA
| | - Mary Rodgers
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL, USA
| | - Kelly Coller
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL, USA
| | - Sandy Pearce
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL, USA
| | - Sergej Franz
- Vitalant Research Institute, San Francisco, CA, USA
| | - Li Du
- Vitalant Research Institute, San Francisco, CA, USA
| | - Mars Stone
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Vitalant Research Institute, San Francisco, CA, USA
| | | | - Alicia Sotomayor-Gonzalez
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Venice Servellita
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Claudia Sanchez San Martin
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Andrea Granados
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Dustin R. Glasner
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Lucy M. Han
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Kent Truong
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Naomi Akagi
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - David N. Nguyen
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA
| | - Neil M. Neumann
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Daniel Qazi
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Elaine Hsu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Wei Gu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Yale A. Santos
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Brian Custer
- Vitalant Research Institute, San Francisco, CA, USA
| | | | | | - Nancy K. Hills
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Chuanyi M. Lu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Lab Medicine Service, San Francisco VA Healthcare System
| | - Jeffrey D. Whitman
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | | | - Candace Wang
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Kevin Reyes
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Jill M.C. Hakim
- Department of Medicine at ZSFG, the Division of HIV, ID & Global Medicine
| | - Kirk Sujishi
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Fariba Alazzeh
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Lori Pham
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Ching-Ying Oon
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Steve Miller
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | - Theodore Kurtz
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - John Hackett
- Applied Research and Technology, Abbott Diagnostics, Abbott Park, IL, USA
| | - Graham Simmons
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Vitalant Research Institute, San Francisco, CA, USA
| | - Michael P. Busch
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Vitalant Research Institute, San Francisco, CA, USA
| | - Charles Y. Chiu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA, USA
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16
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Whitman JD, Hiatt J, Mowery CT, Shy BR, Yu R, Yamamoto TN, Rathore U, Goldgof GM, Whitty C, Woo JM, Gallman AE, Miller TE, Levine AG, Nguyen DN, Bapat SP, Balcerek J, Bylsma SA, Lyons AM, Li S, Wong AWY, Gillis-Buck EM, Steinhart ZB, Lee Y, Apathy R, Lipke MJ, Smith JA, Zheng T, Boothby IC, Isaza E, Chan J, Acenas DD, Lee J, Macrae TA, Kyaw TS, Wu D, Ng DL, Gu W, York VA, Eskandarian HA, Callaway PC, Warrier L, Moreno ME, Levan J, Torres L, Farrington LA, Loudermilk R, Koshal K, Zorn KC, Garcia-Beltran WF, Yang D, Astudillo MG, Bernstein BE, Gelfand JA, Ryan ET, Charles RC, Iafrate AJ, Lennerz JK, Miller S, Chiu CY, Stramer SL, Wilson MR, Manglik A, Ye CJ, Krogan NJ, Anderson MS, Cyster JG, Ernst JD, Wu AHB, Lynch KL, Bern C, Hsu PD, Marson A. Test performance evaluation of SARS-CoV-2 serological assays. medRxiv 2020. [PMID: 32511497 PMCID: PMC7273265 DOI: 10.1101/2020.04.25.20074856] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Background: Serological tests are crucial tools for assessments of SARS-CoV-2 exposure, infection and potential immunity. Their appropriate use and interpretation require accurate assay performance data. Method: We conducted an evaluation of 10 lateral flow assays (LFAs) and two ELISAs to detect anti-SARS-CoV-2 antibodies. The specimen set comprised 128 plasma or serum samples from 79 symptomatic SARS-CoV-2 RT-PCR-positive individuals; 108 pre-COVID-19 negative controls; and 52 recent samples from individuals who underwent respiratory viral testing but were not diagnosed with Coronavirus Disease 2019 (COVID-19). Samples were blinded and LFA results were interpreted by two independent readers, using a standardized intensity scoring system. Results: Among specimens from SARS-CoV-2 RT-PCR-positive individuals, the percent seropositive increased with time interval, peaking at 81.8–100.0% in samples taken >20 days after symptom onset. Test specificity ranged from 84.3–100.0% in pre-COVID-19 specimens. Specificity was higher when weak LFA bands were considered negative, but this decreased sensitivity. IgM detection was more variable than IgG, and detection was highest when IgM and IgG results were combined. Agreement between ELISAs and LFAs ranged from 75.7–94.8%. No consistent cross-reactivity was observed. Conclusion: Our evaluation showed heterogeneous assay performance. Reader training is key to reliable LFA performance, and can be tailored for survey goals. Informed use of serology will require evaluations covering the full spectrum of SARS-CoV-2 infections, from asymptomatic and mild infection to severe disease, and later convalescence. Well-designed studies to elucidate the mechanisms and serological correlates of protective immunity will be crucial to guide rational clinical and public health policies.
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Affiliation(s)
- Jeffrey D Whitman
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Joseph Hiatt
- Medical Scientist Training Program, University of California, San Francisco, CA 94143, USA.,Biomedical Sciences Graduate Program, University of California, San Francisco, CA 94143, USA.,J. David Gladstone Institutes, San Francisco, CA 94158, USA.,Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA.,Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA.,Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Cody T Mowery
- Medical Scientist Training Program, University of California, San Francisco, CA 94143, USA.,Biomedical Sciences Graduate Program, University of California, San Francisco, CA 94143, USA.,Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA.,Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA.,Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Brian R Shy
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ruby Yu
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA.,Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Tori N Yamamoto
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA.,Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA.,Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ujjwal Rathore
- J. David Gladstone Institutes, San Francisco, CA 94158, USA.,Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA.,Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA.,Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Gregory M Goldgof
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Caroline Whitty
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.,Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA.,Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jonathan M Woo
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA.,Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA.,Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Antonia E Gallman
- Medical Scientist Training Program, University of California, San Francisco, CA 94143, USA.,Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA.,Howard Hughes Medical Institute, University of California, San Francisco
| | - Tyler E Miller
- Department of Pathology, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Andrew G Levine
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - David N Nguyen
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA.,Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA.,Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sagar P Bapat
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.,Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA.,Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Joanna Balcerek
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sophia A Bylsma
- Department of Bioengineering, University of California, Berkeley, Berkeley CA 94720 USA
| | - Ana M Lyons
- Department of Integrative Biology, University of California, Berkeley, Berkeley CA 94720 USA
| | - Stacy Li
- Department of Integrative Biology, University of California, Berkeley, Berkeley CA 94720 USA
| | - Allison Wai-Yi Wong
- Medical Scientist Training Program, University of California, San Francisco, CA 94143, USA
| | - Eva Mae Gillis-Buck
- Department of Surgery, University of California, San Francisco, CA 94143, USA
| | - Zachary B Steinhart
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA.,Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Youjin Lee
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA
| | - Ryan Apathy
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA.,Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA.,Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Mitchell J Lipke
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA.,Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jennifer Anne Smith
- Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA.,Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Tina Zheng
- Medical Scientist Training Program, University of California, San Francisco, CA 94143, USA.,Biomedical Sciences Graduate Program, University of California, San Francisco, CA 94143, USA.,Department of Neurology, University of California, San Francisco, CA 94158, USA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Ian C Boothby
- Medical Scientist Training Program, University of California, San Francisco, CA 94143, USA.,Department of Dermatology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Erin Isaza
- Medical Scientist Training Program, University of California, San Francisco, CA 94143, USA.,Program in Quantitative Biology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jackie Chan
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA
| | - Dante D Acenas
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA
| | - Jinwoo Lee
- Medical Scientist Training Program, University of California, San Francisco, CA 94143, USA.,School of Medicine, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Trisha A Macrae
- Medical Scientist Training Program, University of California, San Francisco, CA 94143, USA.,School of Medicine, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Than S Kyaw
- Medical Scientist Training Program, University of California, San Francisco, CA 94143, USA.,Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA
| | - David Wu
- Medical Scientist Training Program, University of California, San Francisco, CA 94143, USA.,Biomedical Sciences Graduate Program, University of California, San Francisco, CA 94143, USA
| | - Dianna L Ng
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA.,Department of Pathology, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Wei Gu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Vanessa A York
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco CA, USA
| | - Haig Alexander Eskandarian
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco CA, USA
| | - Perri C Callaway
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco CA, USA.,Infectious Diseases and Immunity Graduate Group, University of California Berkeley, Berkeley, CA, USA
| | - Lakshmi Warrier
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco CA, USA
| | - Mary E Moreno
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco CA, USA
| | - Justine Levan
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco CA, USA
| | - Leonel Torres
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco CA, USA
| | - Lila A Farrington
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco CA, USA
| | - Rita Loudermilk
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA
| | - Kanishka Koshal
- Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA
| | - Kelsey C Zorn
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | | | - Diane Yang
- Department of Pathology, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Michael G Astudillo
- Department of Pathology, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Bradley E Bernstein
- Department of Pathology, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Jeffrey A Gelfand
- Division of Infectious Diseases, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Edward T Ryan
- Division of Infectious Diseases, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Richelle C Charles
- Division of Infectious Diseases, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - A John Iafrate
- Department of Pathology, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Jochen K Lennerz
- Department of Pathology, Massachusetts General Hospital/Harvard Medical School, Boston, MA, USA
| | - Steve Miller
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.,Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, San Francisco, CA 94143, USA.,UCSF-Abbott Viral Diagnostics and Discovery Center, San Francisco, CA, USA
| | | | - Michael R Wilson
- Biomedical Sciences Graduate Program, University of California, San Francisco, CA 94143, USA.,Weill Institute for Neurosciences, Department of Neurology, University of California, San Francisco, San Francisco, CA
| | - Aashish Manglik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158
| | - Chun Jimmie Ye
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA.,Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.,Division of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.,Institute of Computational Health Sciences, University of California, San Francisco, San Francisco, CA, USA.,Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Nevan J Krogan
- J. David Gladstone Institutes, San Francisco, CA 94158, USA.,Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA.,Quantitative Biosciences Institute, University of California, San Francisco, CA 94158, USA
| | - Mark S Anderson
- Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jason G Cyster
- Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA.,Howard Hughes Medical Institute, University of California, San Francisco
| | - Joel D Ernst
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco CA, USA
| | - Alan H B Wu
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Kara L Lynch
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Caryn Bern
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Patrick D Hsu
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA.,Department of Bioengineering, University of California, Berkeley, Berkeley CA 94720 USA
| | - Alexander Marson
- J. David Gladstone Institutes, San Francisco, CA 94158, USA.,Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA.,Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA.,Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA.,Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158, USA.,Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA.,Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
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Eslami A, Can NT, Ng DL. Infectious disease diagnosed by fine needle aspiration biopsy. J Am Soc Cytopathol 2020; 9:152-158. [PMID: 32173403 DOI: 10.1016/j.jasc.2020.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/22/2020] [Accepted: 01/24/2020] [Indexed: 01/22/2023]
Abstract
INTRODUCTION Fine needle aspiration biopsies (FNABs) have become increasingly important in the assessment of infectious diseases. We assess the ability of cytopathology to predict the presence of a pathogen and review how often neoplasia occurs concurrently with infection. MATERIALS AND METHODS A 3-year retrospective review of FNABs with concurrent culture results was performed at the Zuckerberg San Francisco General Hospital and Trauma Center. Rapid onsite evaluation was performed for all cases by a pathologist. The results of the special and immunohistochemical stains and polymerase chain reaction testing were correlated, when available. RESULTS A total of 231 samples from 11 different tissue sites were submitted for microbial culture, of which 49 (21%) were positive for pathogenic organisms. Only 2 false-negative cases by cytology were found in immunosuppressed patients. A total of 38 patients had a diagnosis of neoplasia, with 2 (5%) having concurrent infection. Overall, the sensitivity and specificity of cytology in predicting the presence of infection was 96% (95% confidence interval, 86%-100%) and 42% (95% confidence interval, 34%-50%), respectively. Molecular testing was performed in 11 cases, 2 of which were positive for Mycobacterium tuberculosis complex and had cytologic findings of necrosis. Polymerase chain reaction and other ancillary tests were unable to further characterize 2 cases with acid-fast bacilli. CONCLUSIONS Our study has shown that FNABs have high sensitivity in detecting infection and that negative cytology findings will correlate with a negative infectious workup. Although infection in the setting of neoplasia is uncommon, it should be considered if clinical data are available to suggest infection.
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Affiliation(s)
- Arash Eslami
- Department of Pathology, University of California, San Francisco, Medical Center, San Francisco, California
| | - Nhu Thuy Can
- Department of Pathology, University of California, San Francisco, Medical Center, San Francisco, California
| | - Dianna L Ng
- Department of Pathology, University of California, San Francisco, Medical Center, San Francisco, California.
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18
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Balassanian R, Ng DL, van Zante A. Stop using expired plasma for cell blocks. Cancer Cytopathol 2019; 127:737-738. [PMID: 31756044 DOI: 10.1002/cncy.22204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 10/14/2019] [Accepted: 10/16/2019] [Indexed: 11/08/2022]
Affiliation(s)
- Ronald Balassanian
- Department of Pathology, University of California San Francisco, San Francisco, California
| | - Dianna L Ng
- Department of Pathology, University of California San Francisco, San Francisco, California
| | - Annemieke van Zante
- Department of Pathology, University of California San Francisco, San Francisco, California
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19
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Ng DL, Balassanian R. Granulomatous inflammation diagnosed by fine-needle aspiration biopsy. J Am Soc Cytopathol 2019; 8:317-323. [PMID: 31636024 DOI: 10.1016/j.jasc.2019.07.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 05/02/2019] [Revised: 07/26/2019] [Accepted: 07/29/2019] [Indexed: 11/18/2022]
Abstract
INTRODUCTION Fine-needle aspiration biopsy (FNAB) is a minimally invasive biopsy technique and an important tool for diagnosing infectious diseases. Rapid onsite evaluation allows for triage for ancillary testing, including microbiologic cultures. We aimed to determine the etiology of granulomatous inflammation diagnosed by FNAB by correlating with culture results and clinical history. MATERIALS AND METHODS A 16-year retrospective review of cases diagnosed as "granulomatous inflammation" or "granuloma" was performed at the Departments of Pathology at the Zuckerberg San Francisco General Hospital and Trauma Center and University of California, San Francisco. RESULTS A total of 339 FNABs diagnosed as granulomatous inflammation were identified. Necrotizing granulomatous inflammation was present in 117 of 339 cases (34.5%) and non-necrotizing granulomatous inflammation was present in 222 of 339 cases (65.5%). A pathogen was detected in 100 of 339 (29.5%) FNABs by either cytomorphology, special stains, or culture, or a combination of more than one test. Of the 100 pathogen-positive cases, necrotizing granulomatous inflammation was seen in 50 of 100 (50%) and non-necrotizing granulomatous inflammation was identified in 50 of 100 (50%) cases. Culture results were available in 239 cases and positive in 70 (29%). Positive culture results included 40 of 239 (17%) cases with Mycobacterium tuberculosis complex, 15 of 239 (6.3%) with atypical mycobacterial species, 6 of 239 (3%) with Coccidioides immitis, 2 of 239 (<1%) with Histoplasma capsulatum, and 2 of 239 with Talaromyces marneffei (<1%). CONCLUSIONS Granulomatous inflammation is a nonspecific finding and suggests a broad range of disease processes, ranging from infection to malignancy. FNAB is an excellent minimally invasive technique that allows for ancillary testing critical for definitive diagnosis.
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Affiliation(s)
- Dianna L Ng
- Department of Pathology, University of California, San Francisco, California.
| | - Ronald Balassanian
- Department of Pathology, University of California, San Francisco, California
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20
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Ng DL, Vuhahula E, Zhang L, Waterhouse EG, White KL, Mushi BP, Nyeriga MS, Philipo GS, Mmbaga EJ, Sheth S, Van Loon K, Lee AY, Balassanian R. Efficacy of an Intensive, Ultrasound-Guided Fine-Needle Aspiration Biopsy Training Workshop in Tanzania. J Glob Oncol 2019; 4:1-9. [PMID: 30372401 PMCID: PMC7010453 DOI: 10.1200/jgo.18.00134] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Background Fine-needle aspiration biopsy (FNAB) is a minimally invasive, cost-effective diagnostic tool that can be used in low-resource settings. However, adequacy and accuracy of FNAB is highly dependent on the skills of the operator and requires specialized training. Poor technique can preclude definitive diagnoses because of insufficient quality or quantity of FNAB samples. We evaluated the efficacy of an intensive training experience in Tanzania on improving ultrasound-guided FNAB techniques. Methods A 2-day workshop offered didactic lectures, demonstrations, and hands-on practicum on fundamentals of ultrasound imaging and FNAB technique. A prospective interventional study design was used with pre- and postintervention surveys and assessments to measure the effect of the workshop on specific skills related to slide smearing and ultrasound-guidance among participants. Results Twenty-six pathologists and radiologists, including trainees in each specialty, participated in the workshop. Pre- and postworkshop assessments demonstrated that most participants improved significantly in nearly all technical skills for slide smearing and ultrasound-guided FNAB. After the workshop, most participants demonstrated substantial improvements in ability to prepare the ultrasound equipment, measure the lesion in three dimensions by ultrasound, target lesions in one pass using both parallel and perpendicular approaches, and prepare high-quality aspirate smears. Conclusion An in-country 2-day workshop in Tanzania was efficacious in transferring basic skills in FNAB smear preparation and ultrasound-guided FNAB, resulting in skills enhancement among participating pathologists and radiologists. Although mastery of skills was not the goal of this short workshop, participants demonstrated proficiency in most technical elements after workshop completion, and the workshop generated interest among select participants to pursue additional intensive training in cytopathology.
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Affiliation(s)
- Dianna L Ng
- Dianna L. Ng, Li Zhang, Emily G. Waterhouse, Kristie L. White, Sujay Sheth, Katherine Van Loon, Amie Y. Lee, and Ronald Balassanian, University of California, San Francisco, San Francisco, CA; Edda Vuhahula, Beatrice Paul Mushi, Msiba Selekwa Nyeriga, Godfrey Sama Philipo, and Elia J. Mmbaga, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Edda Vuhahula
- Dianna L. Ng, Li Zhang, Emily G. Waterhouse, Kristie L. White, Sujay Sheth, Katherine Van Loon, Amie Y. Lee, and Ronald Balassanian, University of California, San Francisco, San Francisco, CA; Edda Vuhahula, Beatrice Paul Mushi, Msiba Selekwa Nyeriga, Godfrey Sama Philipo, and Elia J. Mmbaga, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Li Zhang
- Dianna L. Ng, Li Zhang, Emily G. Waterhouse, Kristie L. White, Sujay Sheth, Katherine Van Loon, Amie Y. Lee, and Ronald Balassanian, University of California, San Francisco, San Francisco, CA; Edda Vuhahula, Beatrice Paul Mushi, Msiba Selekwa Nyeriga, Godfrey Sama Philipo, and Elia J. Mmbaga, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Emily G Waterhouse
- Dianna L. Ng, Li Zhang, Emily G. Waterhouse, Kristie L. White, Sujay Sheth, Katherine Van Loon, Amie Y. Lee, and Ronald Balassanian, University of California, San Francisco, San Francisco, CA; Edda Vuhahula, Beatrice Paul Mushi, Msiba Selekwa Nyeriga, Godfrey Sama Philipo, and Elia J. Mmbaga, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Kristie L White
- Dianna L. Ng, Li Zhang, Emily G. Waterhouse, Kristie L. White, Sujay Sheth, Katherine Van Loon, Amie Y. Lee, and Ronald Balassanian, University of California, San Francisco, San Francisco, CA; Edda Vuhahula, Beatrice Paul Mushi, Msiba Selekwa Nyeriga, Godfrey Sama Philipo, and Elia J. Mmbaga, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Beatrice Paul Mushi
- Dianna L. Ng, Li Zhang, Emily G. Waterhouse, Kristie L. White, Sujay Sheth, Katherine Van Loon, Amie Y. Lee, and Ronald Balassanian, University of California, San Francisco, San Francisco, CA; Edda Vuhahula, Beatrice Paul Mushi, Msiba Selekwa Nyeriga, Godfrey Sama Philipo, and Elia J. Mmbaga, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Msiba Selekwa Nyeriga
- Dianna L. Ng, Li Zhang, Emily G. Waterhouse, Kristie L. White, Sujay Sheth, Katherine Van Loon, Amie Y. Lee, and Ronald Balassanian, University of California, San Francisco, San Francisco, CA; Edda Vuhahula, Beatrice Paul Mushi, Msiba Selekwa Nyeriga, Godfrey Sama Philipo, and Elia J. Mmbaga, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Godfrey Sama Philipo
- Dianna L. Ng, Li Zhang, Emily G. Waterhouse, Kristie L. White, Sujay Sheth, Katherine Van Loon, Amie Y. Lee, and Ronald Balassanian, University of California, San Francisco, San Francisco, CA; Edda Vuhahula, Beatrice Paul Mushi, Msiba Selekwa Nyeriga, Godfrey Sama Philipo, and Elia J. Mmbaga, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Elia J Mmbaga
- Dianna L. Ng, Li Zhang, Emily G. Waterhouse, Kristie L. White, Sujay Sheth, Katherine Van Loon, Amie Y. Lee, and Ronald Balassanian, University of California, San Francisco, San Francisco, CA; Edda Vuhahula, Beatrice Paul Mushi, Msiba Selekwa Nyeriga, Godfrey Sama Philipo, and Elia J. Mmbaga, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Sujay Sheth
- Dianna L. Ng, Li Zhang, Emily G. Waterhouse, Kristie L. White, Sujay Sheth, Katherine Van Loon, Amie Y. Lee, and Ronald Balassanian, University of California, San Francisco, San Francisco, CA; Edda Vuhahula, Beatrice Paul Mushi, Msiba Selekwa Nyeriga, Godfrey Sama Philipo, and Elia J. Mmbaga, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Katherine Van Loon
- Dianna L. Ng, Li Zhang, Emily G. Waterhouse, Kristie L. White, Sujay Sheth, Katherine Van Loon, Amie Y. Lee, and Ronald Balassanian, University of California, San Francisco, San Francisco, CA; Edda Vuhahula, Beatrice Paul Mushi, Msiba Selekwa Nyeriga, Godfrey Sama Philipo, and Elia J. Mmbaga, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Amie Y Lee
- Dianna L. Ng, Li Zhang, Emily G. Waterhouse, Kristie L. White, Sujay Sheth, Katherine Van Loon, Amie Y. Lee, and Ronald Balassanian, University of California, San Francisco, San Francisco, CA; Edda Vuhahula, Beatrice Paul Mushi, Msiba Selekwa Nyeriga, Godfrey Sama Philipo, and Elia J. Mmbaga, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Ronald Balassanian
- Dianna L. Ng, Li Zhang, Emily G. Waterhouse, Kristie L. White, Sujay Sheth, Katherine Van Loon, Amie Y. Lee, and Ronald Balassanian, University of California, San Francisco, San Francisco, CA; Edda Vuhahula, Beatrice Paul Mushi, Msiba Selekwa Nyeriga, Godfrey Sama Philipo, and Elia J. Mmbaga, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
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Muehlenbachs A, Bollweg BC, Schulz TJ, Forrester JD, DeLeon Carnes M, Molins C, Ray GS, Cummings PM, Ritter JM, Blau DM, Andrew TA, Prial M, Ng DL, Prahlow JA, Sanders JH, Shieh WJ, Paddock CD, Schriefer ME, Mead P, Zaki SR. Cardiac Tropism of Borrelia burgdorferi: An Autopsy Study of Sudden Cardiac Death Associated with Lyme Carditis. Am J Pathol 2016; 186:1195-205. [PMID: 26968341 DOI: 10.1016/j.ajpath.2015.12.027] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Revised: 11/23/2015] [Accepted: 12/15/2015] [Indexed: 12/17/2022]
Abstract
Fatal Lyme carditis caused by the spirochete Borrelia burgdorferi rarely is identified. Here, we describe the pathologic, immunohistochemical, and molecular findings of five case patients. These sudden cardiac deaths associated with Lyme carditis occurred from late summer to fall, ages ranged from young adult to late 40s, and four patients were men. Autopsy tissue samples were evaluated by light microscopy, Warthin-Starry stain, immunohistochemistry, and PCR for B. burgdorferi, and immunohistochemistry for complement components C4d and C9, CD3, CD79a, and decorin. Post-mortem blood was tested by serology. Interstitial lymphocytic pancarditis in a relatively characteristic road map distribution was present in all cases. Cardiomyocyte necrosis was minimal, T cells outnumbered B cells, plasma cells were prominent, and mild fibrosis was present. Spirochetes in the cardiac interstitium associated with collagen fibers and co-localized with decorin. Rare spirochetes were seen in the leptomeninges of two cases by immunohistochemistry. Spirochetes were not seen in other organs examined, and joint tissue was not available for evaluation. Although rare, sudden cardiac death caused by Lyme disease might be an under-recognized entity and is characterized by pancarditis and marked tropism of spirochetes for cardiac tissues.
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Affiliation(s)
- Atis Muehlenbachs
- Infectious Diseases Pathology Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia.
| | - Brigid C Bollweg
- Infectious Diseases Pathology Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | - Joseph D Forrester
- Bacterial Diseases Branch, Division of Vector Borne Infectious Diseases, Centers for Disease Control and Prevention, Ft. Collins, Colorado
| | - Marlene DeLeon Carnes
- Infectious Diseases Pathology Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Claudia Molins
- Bacterial Diseases Branch, Division of Vector Borne Infectious Diseases, Centers for Disease Control and Prevention, Ft. Collins, Colorado
| | | | | | - Jana M Ritter
- Infectious Diseases Pathology Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Dianna M Blau
- Infectious Diseases Pathology Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Thomas A Andrew
- Office of the Chief Medical Examiner, Concord, New Hampshire
| | | | - Dianna L Ng
- Infectious Diseases Pathology Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Joseph A Prahlow
- The Medical Foundation, South Bend, Indiana; Indiana University School of Medicine-South Bend, South Bend, Indiana
| | - Jeanine H Sanders
- Infectious Diseases Pathology Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Wun Ju Shieh
- Infectious Diseases Pathology Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Christopher D Paddock
- Rickettsial Zoonotic Diseases Branch, Division of Vector Borne Infectious Diseases, Atlanta, Georgia
| | - Martin E Schriefer
- Bacterial Diseases Branch, Division of Vector Borne Infectious Diseases, Centers for Disease Control and Prevention, Ft. Collins, Colorado
| | - Paul Mead
- Bacterial Diseases Branch, Division of Vector Borne Infectious Diseases, Centers for Disease Control and Prevention, Ft. Collins, Colorado
| | - Sherif R Zaki
- Infectious Diseases Pathology Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia
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22
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Ng DL, Al Hosani F, Keating MK, Gerber SI, Jones TL, Metcalfe MG, Tong S, Tao Y, Alami NN, Haynes LM, Mutei MA, Abdel-Wareth L, Uyeki TM, Swerdlow DL, Barakat M, Zaki SR. Clinicopathologic, Immunohistochemical, and Ultrastructural Findings of a Fatal Case of Middle East Respiratory Syndrome Coronavirus Infection in the United Arab Emirates, April 2014. Am J Pathol 2016; 186:652-8. [PMID: 26857507 PMCID: PMC7093852 DOI: 10.1016/j.ajpath.2015.10.024] [Citation(s) in RCA: 285] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 09/24/2015] [Accepted: 10/30/2015] [Indexed: 12/15/2022]
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) infection causes an acute respiratory illness and is associated with a high case fatality rate; however, the pathogenesis of severe and fatal MERS-CoV infection is unknown. We describe the histopathologic, immunohistochemical, and ultrastructural findings from the first autopsy performed on a fatal case of MERS-CoV in the world, which was related to a hospital outbreak in the United Arab Emirates in April 2014. The main histopathologic finding in the lungs was diffuse alveolar damage. Evidence of chronic disease, including severe peripheral vascular disease, patchy cardiac fibrosis, and hepatic steatosis, was noted in the other organs. Double staining immunoassays that used anti–MERS-CoV antibodies paired with immunohistochemistry for cytokeratin and surfactant identified pneumocytes and epithelial syncytial cells as important targets of MERS-CoV antigen; double immunostaining with dipeptidyl peptidase 4 showed colocalization in scattered pneumocytes and syncytial cells. No evidence of extrapulmonary MERS-CoV antigens were detected, including the kidney. These results provide critical insights into the pathogenesis of MERS-CoV in humans.
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Affiliation(s)
- Dianna L Ng
- Infectious Diseases Pathology Branch, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Farida Al Hosani
- Communicable Diseases Department, Abu Dhabi, United Arab Emirates
| | - M Kelly Keating
- Infectious Diseases Pathology Branch, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Susan I Gerber
- Epidemiology Branch, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Tara L Jones
- Infectious Diseases Pathology Branch, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Maureen G Metcalfe
- Infectious Diseases Pathology Branch, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Suxiang Tong
- Gastroenteritis and Respiratory Virus Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Ying Tao
- Gastroenteritis and Respiratory Virus Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Negar N Alami
- Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, Georgia; International Research and Programs Branch, National Center for HIV/AIDS, Viral Hepatitis, STD and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Lia M Haynes
- Office of the Director, Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | - Laila Abdel-Wareth
- Pathology and Laboratory Medicine Institute, Cleveland Clinic, Abu Dhabi, United Arab Emirates
| | - Timothy M Uyeki
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - David L Swerdlow
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Maha Barakat
- Health Authority-Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Sherif R Zaki
- Infectious Diseases Pathology Branch, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia.
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23
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Martines RB, Ng DL, Greer PW, Rollin PE, Zaki SR. Tissue and cellular tropism, pathology and pathogenesis of Ebola and Marburg viruses. J Pathol 2015; 235:153-74. [PMID: 25297522 DOI: 10.1002/path.4456] [Citation(s) in RCA: 201] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 09/30/2014] [Accepted: 10/01/2014] [Indexed: 12/19/2022]
Abstract
Ebola viruses and Marburg viruses include some of the most virulent and fatal pathogens known to humans. These viruses cause severe haemorrhagic fevers, with case fatality rates in the range 25-90%. The diagnosis of filovirus using formalin-fixed tissues from fatal cases poses a significant challenge. The most characteristic histopathological findings are seen in the liver; however, the findings overlap with many other viral and non-viral haemorrhagic diseases. The need to distinguish filovirus infections from other haemorrhagic fevers, particularly in areas with multiple endemic viral haemorrhagic agents, is of paramount importance. In this review we discuss the current state of knowledge of filovirus infections and their pathogenesis, including histopathological findings, epidemiology, modes of transmission and filovirus entry and spread within host organisms. The pathogenesis of filovirus infections is complex and involves activation of the mononuclear phagocytic system, with release of pro-inflammatory cytokines, chemokines and growth factors, endothelial dysfunction, alterations of the innate and adaptive immune systems, direct organ and endothelial damage from unrestricted viral replication late in infection, and coagulopathy. Although our understanding of the pathogenesis of filovirus infections has rapidly increased in the past few years, many questions remain unanswered.
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Affiliation(s)
- Roosecelis Brasil Martines
- Infectious Diseases Pathology Branch, Division of High Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, GA, USA
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Abstract
BACKGROUND The only treatment for coeliac disease is lifelong adherence to a rigorous gluten-free diet. The present study aimed to evaluate the influence of coeliac disease on the social aspects of daily life of individuals in the U.S.A. METHODS The present study used a self-administered survey including the standard Quality of Life questionnaire (12-item short-form) with validated disease-specific questions. sas statistical software 2010 (SAS Institute, Cary, NC, U.S.A.) was used to calculate the mean (SD). RESULTS Individuals with coeliac disease overall had a low positive health perception. Validated diet and disease-specific questions revealed a significant negative impact on quality of life in social settings. Specifically, the areas of travel, dining out and family life are most affected. The negative impact of diet significantly decreased over time, although it did not resolve for the domains of dining out of the home and travel. Those diagnosed in childhood and maintained on the diet had less of an impact on the quality of life as an adult. CONCLUSIONS Individuals with coeliac disease in the U.S.A. have a diminished quality of life, especially in the social aspects of life.
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Affiliation(s)
- A R Lee
- Department of Medicine, Celiac Disease Center, Columbia University Medical Center, New York, NY, USA.
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25
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Lee AR, Ng DL, Dave E, Ciaccio EJ, Green PHR. The effect of substituting alternative grains in the diet on the nutritional profile of the gluten-free diet. J Hum Nutr Diet 2009; 22:359-63. [PMID: 19519750 DOI: 10.1111/j.1365-277x.2009.00970.x] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
BACKGROUND The only treatment for coeliac disease is lifelong adherence to a gluten-free diet. Several studies have reported nutritional deficiencies in individuals on a gluten-free diet. The present study aimed to determine whether the nutritional profile of gluten-free diet could be improved through the use of alternative grains. METHODS A retrospective review of diet history records by a celiac specialist dietitian were used to establish a 'standard' gluten-free dietary pattern. An 'alternative' gluten-free dietary pattern was developed that substituted naturally gluten-free grains or gluten-free products made from 'alternative' flours (oats, high fibre gluten-free bread and quinoa) in the standard pattern. A paired t-test was performed to identify statistical significance between the 'alternative' and standard gluten-free dietary pattern. RESULTS Analysis of standard pattern indicated that 38% of meals and snacks contained no grain or starch choice. Of those meals that contained a grain or starch component, rice was the grain chosen 44% of the time. The inclusion of alternative grains or grain products provided a higher nutrient profile compared to the standard gluten-free dietary pattern (P = 0.002). Several nutrients; protein (20.6 g versus 11 g), iron (18.4 mg versus 1.4 mg), calcium (182 mg versus 0 mg) and fibre (12.7 g versus 5 g) were significantly increased by changing the grain or starch component in the dietary pattern. The B vitamin content (riboflavin, niacin and folate) was improved, although this was not statistically significant (P = 0.125). DISCUSSION The inclusion of alternative grain-based products increased the nutrient profile of the gluten-free dietary pattern significantly.
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Affiliation(s)
- A R Lee
- Celiac Disease Center, Department of Medicine, Columbia University, New York, NY, USA.
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26
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Abstract
BACKGROUND Coeliac disease is a common, autoimmune disorder, for which the only treatment is lifelong adherence to a gluten-free diet. This study evaluates the economic burden of adhering to a gluten-free diet. METHODS A market basket of products identified by name brand, weight or package size for both regular wheat-based products and gluten-free counterparts was developed. The differences in price between purchase venues, both type of store (general grocery store, an upscale grocery store and a health food store and four internet-based grocery sites) and region was also analysed. RESULTS Availability of gluten-free products varied between the different venues, regular grocery stores carried 36%, while upscale markets carried 41%, and health food stores 94%, compared with 100% availability on the internet. Overall, every gluten-free product was more expensive than their wheat-based counterpart (P <or= 0.05). Bread and pasta was twice as expensive as their wheat-based counterparts. Cost was affected more by shopping venue than geographic location. CONCLUSIONS This study demonstrated that gluten-free foods have poor availability and are more expensive than their gluten-containing counterparts. The impact of these findings on dietary compliance and the quality of life needs to be addressed.
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Affiliation(s)
- A R Lee
- Celiac Disease Center, Columbia University, New York, NY 10032, USA.
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27
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Heng BH, Goh KT, Ng DL, Ling AE. Surveillance of legionellosis and Legionella bacteria in the built environment in Singapore. Ann Acad Med Singap 1997; 26:557-65. [PMID: 9494658] [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] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
During the period 1986 to 1996, a total of 258 sporadic cases of community-acquired legionellosis was reported, giving a mean annual morbidity rate of 0.9 per 100,000 population. Majority of the cases (91.5%) was serologically diagnosed by the indirect fluorescent antibody (IFA) test against Legionella pneumophila based on single sera with a titre of > or = 1:1024. The others were confirmed by a four-fold increase in IFA titre to a minimum of 1:128 (7.4%) and by culture (1.1%). Cases were reported predominantly among males, ethnic Indians, the elderly and those with concurrent medical conditions. The overall case-fatality rate was 14.7%, with the rate significantly higher among those aged > or = 45 years (21%), smokers (20.4%) and those with concurrent medical conditions (22.5%). Seroepidemiological studies among the healthy population based on an IFA titre of > or = 1:32 showed a prevalence of between 10.3% and 21.9%. Of the various occupational groups investigated, high seroprevalence rates were found in foreign construction workers (52.6%) and occupants of a building investigated for an unusual building-related illness (76.1%). Environmental surveillance of Legionella bacteria showed that 36% of cooling towers, 15% to 19% of decorative fountains and waterfalls and 2% of spa pools were positive. The majority (85%) of environmental isolates was identified as Legionella pneumophila: 54.8% of serogroup 1 and 5% of Pontiac subtype.
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Affiliation(s)
- B H Heng
- Quarantine & Epidemiology Department, Ministry of the Environment, Singapore
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28
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Ng DL, Koh BB, Tay L, Heng BH. Comparison of polymerase chain reaction and conventional culture for the detection of legionellae in cooling tower waters in Singapore. Lett Appl Microbiol 1997; 24:214-6. [PMID: 9080703 DOI: 10.1046/j.1472-765x.1997.00382.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A total of 80 cooling tower water samples were investigated for legionellae using both cultural and polymerase chain reaction (PCR) methods. PCR was performed with the Perkin Elmer EnviroAmp Legionella kit. Forty-seven samples (58.8%) were found positive by both methods; 29 samples (36.3%) were positive by PCR only, while four samples (5%) showed PCR inhibition despite the adoption of the more stringent sample preparation protocol especially designed to eliminate inhibitors.
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Affiliation(s)
- D L Ng
- Department of Pathology, Singapore General Hospital, Singapore
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29
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Dutt MC, Lo DS, Ng DL, Woo SO. Gas chromatographic study of the urinary codeine-to-morphine ratios in controlled codeine consumption and in mass screening for opiate drugs. J Chromatogr A 1983; 267:117-24. [PMID: 6630365 DOI: 10.1016/s0021-9673(01)90825-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The urinary codeine-to-morphine ratios in fifteen volunteers administered codeine tablets at intervals were studied by gas chromatography (GC) and compared with one month's GC results for enzyme multiplied immunoassay technique (EMIT)-screened urine specimens in a mass-screening programme for abuse of opiate drugs, particularly heroin. It appears that when M less than 2 and C/M greater than 0 or when M greater than 2 and C/M greater than 0.5, where C and M are codeine and morphine concentrations in micrograms per 10 ml of urine, codeine consumption has to be presumed.
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