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Wang Y, Xia W, Wang Y, Cui Y, Yu L, Liu C, Zhao D, Guan X, Wang Y, Wu S, Li J, Li Y, Hu J, Liu J. Multiplexed bacterial pathogen detection and clinical characteristics of orthopedic infection in hospitalized patients. Front Cell Infect Microbiol 2024; 14:1394352. [PMID: 38938882 PMCID: PMC11210349 DOI: 10.3389/fcimb.2024.1394352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 05/02/2024] [Indexed: 06/29/2024] Open
Abstract
Introduction Accurate identification of the etiology of orthopedic infection is very important for correct and timely clinical management, but it has been poorly studied. In the current study we explored the association of multiple bacterial pathogens with orthopedic infection. Methods Hospitalized orthopedic patients were enrolled in a rural hospital in Qingdao, China. Wound or exudate swab samples were collected and tested for twelve bacterial pathogens with both culture and multiplex real time PCR. Results and discussion A total of 349 hospitalized orthopedic patients were enrolled including 193 cases presenting infection manifestations upon admission and 156 with no sign of infection. Orthopedic infection patients were mainly male (72.5%) with more lengthy hospital stay (median 15 days). At least one pathogen was detected in 42.5% (82/193) of patients with infection while 7.1% (11/156) in the patients without infection (P < 0.001). S. aureus was the most prevalent causative pathogen (15.5%). Quantity dependent pathogen association with infection was observed, particularly for P. aeruginosa and K. pneumoniae, possibly indicating subclinical infection. Most of the patients with detected pathogens had a previous history of orthopedic surgery (odds ratio 2.8, P = 0.038). Pathogen specific clinical manifestations were characterized. Multiplex qPCR, because of its high sensitivity, superior specificity, and powerful quantification could be utilized in combination with culture to guide antimicrobial therapy and track the progression of orthopedic infection during treatment.
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Affiliation(s)
- Yani Wang
- School of Public Health, Qingdao University, Qingdao, China
| | - Wenbo Xia
- Department of Orthopedics, Qingdao Huangdao Traditional Chinese Medicine Hospital, Qingdao, China
| | - Ying Wang
- School of Public Health, Qingdao University, Qingdao, China
| | - Yanxiang Cui
- Department of Clinical Laboratory, Qingdao Huangdao Traditional Chinese Medicine Hospital, Qingdao, China
| | - Linhong Yu
- Qingdao Medical College, Qingdao University, Qingdao, China
| | - Chao Liu
- School of Public Health, Qingdao University, Qingdao, China
| | - Dan Zhao
- School of Public Health, Qingdao University, Qingdao, China
| | - Xiaoxuan Guan
- Department of Clinical Laboratory, Qingdao Huangdao Traditional Chinese Medicine Hospital, Qingdao, China
| | - Yingdi Wang
- School of Public Health, Qingdao University, Qingdao, China
| | - Shanrui Wu
- School of Public Health, Qingdao University, Qingdao, China
| | - Jie Li
- School of Public Health, Qingdao University, Qingdao, China
| | - Yisong Li
- School of Public Health, Qingdao University, Qingdao, China
| | - Jianqiang Hu
- Department of Orthopedics, Qingdao Huangdao Traditional Chinese Medicine Hospital, Qingdao, China
| | - Jie Liu
- School of Public Health, Qingdao University, Qingdao, China
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Tugume L, Ssebambulidde K, Kasibante J, Ellis J, Wake RM, Gakuru J, Lawrence DS, Abassi M, Rajasingham R, Meya DB, Boulware DR. Cryptococcal meningitis. Nat Rev Dis Primers 2023; 9:62. [PMID: 37945681 DOI: 10.1038/s41572-023-00472-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/09/2023] [Indexed: 11/12/2023]
Abstract
Cryptococcus neoformans and Cryptococcus gattii species complexes cause meningoencephalitis with high fatality rates and considerable morbidity, particularly in persons with deficient T cell-mediated immunity, most commonly affecting people living with HIV. Whereas the global incidence of HIV-associated cryptococcal meningitis (HIV-CM) has decreased over the past decade, cryptococcosis still accounts for one in five AIDS-related deaths globally due to the persistent burden of advanced HIV disease. Moreover, mortality remains high (~50%) in low-resource settings. The armamentarium to decrease cryptococcosis-associated mortality is expanding: cryptococcal antigen screening in the serum and pre-emptive azole therapy for cryptococcal antigenaemia are well established, whereas enhanced pre-emptive combination treatment regimens to improve survival of persons with cryptococcal antigenaemia are in clinical trials. Short courses (≤7 days) of amphotericin-based therapy combined with flucytosine are currently the preferred options for induction therapy of cryptococcal meningitis. Whether short-course induction regimens improve long-term morbidity such as depression, reduced neurocognitive performance and physical disability among survivors is the subject of further study. Here, we discuss underlying immunology, changing epidemiology, and updates on the management of cryptococcal meningitis with emphasis on HIV-associated disease.
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Affiliation(s)
- Lillian Tugume
- Infectious Diseases Institute, Makerere University, Kampala, Uganda.
| | - Kenneth Ssebambulidde
- Infectious Diseases Institute, Makerere University, Kampala, Uganda
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - John Kasibante
- Infectious Diseases Institute, Makerere University, Kampala, Uganda
| | - Jayne Ellis
- Infectious Diseases Institute, Makerere University, Kampala, Uganda
- Clinical Research Department, Faculty of Infectious and Tropical Diseases London School of Hygiene and Tropical Medicine, London, UK
| | - Rachel M Wake
- Institute for Infection and Immunity, St George's University of London, London, UK
| | - Jane Gakuru
- Infectious Diseases Institute, Makerere University, Kampala, Uganda
| | - David S Lawrence
- Clinical Research Department, Faculty of Infectious and Tropical Diseases London School of Hygiene and Tropical Medicine, London, UK
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Mahsa Abassi
- Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Radha Rajasingham
- Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - David B Meya
- Infectious Diseases Institute, Makerere University, Kampala, Uganda
- Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - David R Boulware
- Department of Medicine, University of Minnesota, Minneapolis, MN, USA
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Gulleen EA, Holte S, Zhang Y, Mbarusha I, Mubiru D, Pedun B, Keng M, Heysell SK, Omoding A, Moore CC, Phipps W. Etiology of Fever and Associated Outcomes Among Adults Receiving Chemotherapy for the Treatment of Solid Tumors in Uganda. Open Forum Infect Dis 2023; 10:ofad508. [PMID: 37953812 PMCID: PMC10633783 DOI: 10.1093/ofid/ofad508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 10/11/2023] [Indexed: 11/14/2023] Open
Abstract
Background Little is known about the microbiology and outcomes of chemotherapy-associated febrile illness among patients in sub-Saharan Africa. Understanding the microbiology of febrile illness could improve antibiotic selection and infection-related outcomes. Methods From September 2019 through June 2022, we prospectively enrolled adult inpatients at the Uganda Cancer Institute who had solid tumors and developed fever within 30 days of receiving chemotherapy. Evaluation included blood cultures, malaria rapid diagnostic tests, and urinary lipoarabinomannan testing for tuberculosis. Serum cryptococcal antigen was evaluated in participants with human immunodeficiency virus (HIV). The primary outcome was the mortality rate 40 days after fever onset, which we estimated using Cox proportional hazards models. Results A total of 104 febrile episodes occurred among 99 participants. Thirty febrile episodes (29%) had ≥1 positive microbiologic result. The most frequently identified causes of infection were tuberculosis (19%) and bacteremia (12%). The prevalence of tuberculosis did not differ by HIV status. The 40-day case fatality ratio was 25%. There was no difference in all-cause mortality based on HIV serostatus, presence of neutropenia, or positive microbiologic results. A universal vital assessment score of >4 was associated with all-cause mortality (hazard ratio, 14.5 [95% confidence interval, 5-42.7]). Conclusions The 40-day mortality rate among Ugandan patients with solid tumors who developed chemotherapy-associated febrile illness was high, and few had an identified source of infection. Tuberculosis and bacterial bloodstream infections were the leading diagnoses associated with fever. Tuberculosis should be included in the differential diagnosis for patients who develop fever after receiving chemotherapy in tuberculosis-endemic settings, regardless of HIV serostatus.
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Affiliation(s)
- Elizabeth A Gulleen
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Allergy and Infectious Diseases Division, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Sarah Holte
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Yuzheng Zhang
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | | | | | | | - Michael Keng
- Division of Oncology, Department of Medicine, University of Virginia, Charlottesville, USA
| | - Scott K Heysell
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia, USA
| | | | - Christopher C Moore
- Division of Oncology, Department of Medicine, University of Virginia, Charlottesville, USA
| | - Warren Phipps
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Allergy and Infectious Diseases Division, Department of Medicine, University of Washington, Seattle, Washington, USA
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Bastos-Moreira Y, Ouédraogo L, De Boevre M, Argaw A, de Kok B, Hanley-Cook GT, Deng L, Ouédraogo M, Compaoré A, Tesfamariam K, Ganaba R, Huybregts L, Toe LC, Lachat C, Kolsteren P, De Saeger S, Dailey-Chwalibóg T. A Multi-Omics and Human Biomonitoring Approach to Assessing the Effectiveness of Fortified Balanced Energy-Protein Supplementation on Maternal and Newborn Health in Burkina Faso: A Study Protocol. Nutrients 2023; 15:4056. [PMID: 37764838 PMCID: PMC10535470 DOI: 10.3390/nu15184056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/05/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Fortified balanced energy-protein (BEP) supplementation is a promising intervention for improving maternal health, birth outcomes and infant growth in low- and middle-income countries. This nested biospecimen sub-study aimed to evaluate the physiological effect of multi-micronutrient-fortified BEP supplementation on pregnant and lactating women and their infants. Pregnant women (15-40 years) received either fortified BEP and iron-folic acid (IFA) (intervention) or IFA only (control) throughout pregnancy. The same women were concurrently randomized to receive either a fortified BEP supplement during the first 6 months postpartum in combination with IFA for the first 6 weeks (i.e., intervention) or the postnatal standard of care, which comprised IFA alone for 6 weeks postpartum (i.e., control). Biological specimens were collected at different timepoints. Multi-omics profiles will be characterized to assess the mediating effect of BEP supplementation on the different trial arms and its effect on maternal health, as well as birth and infant growth outcomes. The mediating effect of the exposome in the relationship between BEP supplementation and maternal health, birth outcomes and infant growth were characterized via biomonitoring markers of air pollution, mycotoxins and environmental contaminants. The results will provide holistic insight into the granular physiological effects of prenatal and postnatal BEP supplementation.
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Affiliation(s)
- Yuri Bastos-Moreira
- Center of Excellence in Mycotoxicology and Public Health, MYTOXSOUTH Coordination Unit, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium; (M.D.B.); (S.D.S.)
- Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium; (L.O.); (A.A.); (B.d.K.); (G.T.H.-C.); (L.D.); (K.T.); (L.H.); (L.C.T.); (C.L.); (P.K.)
| | - Lionel Ouédraogo
- Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium; (L.O.); (A.A.); (B.d.K.); (G.T.H.-C.); (L.D.); (K.T.); (L.H.); (L.C.T.); (C.L.); (P.K.)
- Centre Muraz, Bobo-Dioulasso 01 BP 390, Burkina Faso
| | - Marthe De Boevre
- Center of Excellence in Mycotoxicology and Public Health, MYTOXSOUTH Coordination Unit, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium; (M.D.B.); (S.D.S.)
| | - Alemayehu Argaw
- Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium; (L.O.); (A.A.); (B.d.K.); (G.T.H.-C.); (L.D.); (K.T.); (L.H.); (L.C.T.); (C.L.); (P.K.)
| | - Brenda de Kok
- Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium; (L.O.); (A.A.); (B.d.K.); (G.T.H.-C.); (L.D.); (K.T.); (L.H.); (L.C.T.); (C.L.); (P.K.)
| | - Giles T. Hanley-Cook
- Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium; (L.O.); (A.A.); (B.d.K.); (G.T.H.-C.); (L.D.); (K.T.); (L.H.); (L.C.T.); (C.L.); (P.K.)
| | - Lishi Deng
- Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium; (L.O.); (A.A.); (B.d.K.); (G.T.H.-C.); (L.D.); (K.T.); (L.H.); (L.C.T.); (C.L.); (P.K.)
| | - Moctar Ouédraogo
- Agence de Formation de Recherche et d’Expertise en Santé pour l’Afrique (AFRICSanté), Bobo-Dioulasso 01 BP 298, Burkina Faso; (M.O.); (A.C.); (R.G.)
| | - Anderson Compaoré
- Agence de Formation de Recherche et d’Expertise en Santé pour l’Afrique (AFRICSanté), Bobo-Dioulasso 01 BP 298, Burkina Faso; (M.O.); (A.C.); (R.G.)
| | - Kokeb Tesfamariam
- Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium; (L.O.); (A.A.); (B.d.K.); (G.T.H.-C.); (L.D.); (K.T.); (L.H.); (L.C.T.); (C.L.); (P.K.)
| | - Rasmané Ganaba
- Agence de Formation de Recherche et d’Expertise en Santé pour l’Afrique (AFRICSanté), Bobo-Dioulasso 01 BP 298, Burkina Faso; (M.O.); (A.C.); (R.G.)
| | - Lieven Huybregts
- Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium; (L.O.); (A.A.); (B.d.K.); (G.T.H.-C.); (L.D.); (K.T.); (L.H.); (L.C.T.); (C.L.); (P.K.)
- Nutrition, Diets, and Health Unit, Department of Food and Nutrition Policy, International Food Policy Research Institute (IFPRI), Washington, DC 20005, USA
| | - Laeticia Celine Toe
- Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium; (L.O.); (A.A.); (B.d.K.); (G.T.H.-C.); (L.D.); (K.T.); (L.H.); (L.C.T.); (C.L.); (P.K.)
- Unité Nutrition et Maladies Métaboliques, Institut de Recherche en Sciences de la Santé (IRSS), Bobo-Dioulasso 01 BP 545, Burkina Faso
| | - Carl Lachat
- Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium; (L.O.); (A.A.); (B.d.K.); (G.T.H.-C.); (L.D.); (K.T.); (L.H.); (L.C.T.); (C.L.); (P.K.)
| | - Patrick Kolsteren
- Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium; (L.O.); (A.A.); (B.d.K.); (G.T.H.-C.); (L.D.); (K.T.); (L.H.); (L.C.T.); (C.L.); (P.K.)
| | - Sarah De Saeger
- Center of Excellence in Mycotoxicology and Public Health, MYTOXSOUTH Coordination Unit, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium; (M.D.B.); (S.D.S.)
- Department of Biotechnology and Food Technology, Faculty of Science, University of Johannesburg, Doornfontein Campus, Gauteng 2028, South Africa
| | - Trenton Dailey-Chwalibóg
- Department of Food Technology, Safety and Health, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium; (L.O.); (A.A.); (B.d.K.); (G.T.H.-C.); (L.D.); (K.T.); (L.H.); (L.C.T.); (C.L.); (P.K.)
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Lehman A, Ellis J, Nalintya E, Bahr NC, Loyse A, Rajasingham R. Advanced HIV disease: A review of diagnostic and prophylactic strategies. HIV Med 2023; 24:859-876. [PMID: 37041113 PMCID: PMC10642371 DOI: 10.1111/hiv.13487] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 03/13/2023] [Indexed: 04/13/2023]
Abstract
BACKGROUND Despite expanded access to antiretroviral therapy (ART) and the rollout of the World Health Organization's (WHO) 'test-and-treat' strategy, the proportion of people with HIV (PWH) presenting with advanced HIV disease (AHD) remains unchanged at approximately 30%. Fifty percent of persons with AHD report prior engagement to care. ART failure and insufficient retention in HIV care are major causes of AHD. People living with AHD are at high risk for opportunistic infections and death. In 2017, the WHO published guidelines for the management of AHD that included a comprehensive package of care for screening and prophylaxis of major opportunistic infections (OIs). In the interim, ART regimens have evolved: integrase inhibitors are first-line therapy globally, and the diagnostic landscape is evolving. The objective of this review is to highlight novel point-of-care (POC) diagnostics and treatment strategies that can facilitate OI screening and prophylaxis for persons with AHD. METHODS We reviewed the WHO guidelines for recommendations for persons with AHD. We summarized the scientific literature on current and emerging diagnostics, along with emerging treatment strategies for persons with AHD. We also highlight the key research and implementation gaps together with potential solutions. RESULTS While POC CD4 testing is being rolled out in order to identify persons with AHD, this alone is insufficient; implementation of the Visitect CD4 platform has been challenging given operational and test interpretation issues. Numerous non-sputum POC TB diagnostics are being evaluated, many with limited sensitivity. Though imperfect, these tests are designed to provide rapid results (within hours) and are relatively affordable for resource-poor settings. While novel POC diagnostics are being developed for cryptococcal infection, histoplasmosis and talaromycosis, implementation science studies are urgently needed to understand the clinical benefit of these tests in the routine care. CONCLUSIONS Despite progress with HIV treatment and prevention, a persistent 20%-30% of PWH present to care with AHD. Unfortunately, these persons with AHD continue to carry the burden of HIV-related morbidity and mortality. Investment in the development of additional POC or near-bedside CD4 platforms is urgently needed. Implementation of POC diagnostics theoretically could improve HIV retention in care and thereby reduce mortality by overcoming delays in laboratory testing and providing patients and healthcare workers with timely same-day results. However, in real-world scenarios, people with AHD have multiple comorbidities and imperfect follow-up. Pragmatic clinical trials are needed to understand whether these POC diagnostics can facilitate timely diagnosis and treatment, thereby improving clinical outcomes such as HIV retention in care.
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Affiliation(s)
- Alice Lehman
- Division of Infectious Diseases and International Medicine, University of Minnesota, Minneapolis, Minnesota, USA
| | - Jayne Ellis
- London School of Hygiene and Tropical Medicine, London, UK
| | | | - Nathan C. Bahr
- Division of Infectious Diseases, University of Kansas, Kansas City, Kansas, USA
| | - Angela Loyse
- Division of Infection and Immunity Research Institute, St George’s University of London, London, UK
| | - Radha Rajasingham
- Division of Infectious Diseases and International Medicine, University of Minnesota, Minneapolis, Minnesota, USA
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Peñataro Yori P, Paredes Olórtegui M, Schiaffino F, Colston JM, Pinedo Vasquez T, Garcia Bardales PF, Shapiama Lopez V, Zegarra Paredes LF, Perez K, Curico G, Flynn T, Zhang J, Ramal Asayag C, Meza Sanchez G, Silva Delgado H, Casapia Morales M, Casanova W, Jiu B, Oberhelman R, Munayco Escate C, Silver R, Henao O, Cooper KK, Liu J, Houpt ER, Kosek MN. Etiology of acute febrile illness in the peruvian amazon as determined by modular formatted quantitative PCR: a protocol for RIVERA, a health facility-based case-control study. BMC Public Health 2023; 23:674. [PMID: 37041550 PMCID: PMC10088183 DOI: 10.1186/s12889-023-15619-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 04/06/2023] [Indexed: 04/13/2023] Open
Abstract
BACKGROUND The study of the etiology of acute febrile illness (AFI) has historically been designed as a prevalence of pathogens detected from a case series. This strategy has an inherent unrealistic assumption that all pathogen detection allows for causal attribution, despite known asymptomatic carriage of the principal causes of acute febrile illness in most low- and middle-income countries (LMICs). We designed a semi-quantitative PCR in a modular format to detect bloodborne agents of acute febrile illness that encompassed common etiologies of AFI in the region, etiologies of recent epidemics, etiologies that require an immediate public health response and additional pathogens of unknown endemicity. We then designed a study that would delineate background levels of transmission in the community in the absence of symptoms to provide corrected estimates of attribution for the principal determinants of AFI. METHODS A case-control study of acute febrile illness in patients ten years or older seeking health care in Iquitos, Loreto, Peru, was planned. Upon enrollment, we will obtain blood, saliva, and mid-turbinate nasal swabs at enrollment with a follow-up visit on day 21-28 following enrollment to attain vital status and convalescent saliva and blood samples, as well as a questionnaire including clinical, socio-demographic, occupational, travel, and animal contact information for each participant. Whole blood samples are to be simultaneously tested for 32 pathogens using TaqMan array cards. Mid-turbinate samples will be tested for SARS-CoV-2, Influenza A and Influenza B. Conditional logistic regression models will be fitted treating case/control status as the outcome and with pathogen-specific sample positivity as predictors to attain estimates of attributable pathogen fractions for AFI. DISCUSSION The modular PCR platforms will allow for reporting of all primary results of respiratory samples within 72 h and blood samples within one week, allowing for results to influence local medical practice and enable timely public health responses. The inclusion of controls will allow for a more accurate estimate of the importance of specific prevalent pathogens as a cause of acute illness. STUDY REGISTRATION Project 1791, Registro de Proyectos de Investigación en Salud Pública (PRISA), Instituto Nacional de Salud, Perú.
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Affiliation(s)
- Pablo Peñataro Yori
- Division of Infectious Disease and International Health, School of Medicine, University of Virginia, Charlottesville, VA, USA
- Asociación Benefica PRISMA, Iquitos, Loreto, Peru
| | | | - Francesca Schiaffino
- Division of Infectious Disease and International Health, School of Medicine, University of Virginia, Charlottesville, VA, USA
- Faculty of Veterinary Medicine, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Josh M Colston
- Division of Infectious Disease and International Health, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | | | | | | | | | - Karin Perez
- Asociación Benefica PRISMA, Iquitos, Loreto, Peru
| | | | - Thomas Flynn
- Division of Infectious Disease and International Health, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Jixian Zhang
- Division of Infectious Disease and International Health, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Cesar Ramal Asayag
- Universidad Nacional de La Amazonia Peruana, Loreto, Peru
- Hospital Regional de Loreto, Iquitos, Loreto, Peru
| | - Graciela Meza Sanchez
- Universidad Nacional de La Amazonia Peruana, Loreto, Peru
- Direccion Regional de Salud, Loreto, Peru
| | | | - Martin Casapia Morales
- Universidad Nacional de La Amazonia Peruana, Loreto, Peru
- Hospital Regional de Loreto, Iquitos, Loreto, Peru
| | - Wilma Casanova
- Universidad Nacional de La Amazonia Peruana, Loreto, Peru
| | - Bruce Jiu
- Laboratorio de Referencia en Salud Publica de la Direccion Regional de Salud- Diresa, Loreto, Peru
| | - Richard Oberhelman
- Tulane School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - Cesar Munayco Escate
- Centro Nacional de Epidemiologia, Prevencion, y Control de Enfermedades, Ministerio de Salud de Peru, Jesus Maria, Peru
| | - Rachel Silver
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Olga Henao
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Kerry K Cooper
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, USA
| | - Jie Liu
- School of Public Health, Qingdao University, Qingdao, China
| | - Eric R Houpt
- Division of Infectious Disease and International Health, School of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Margaret N Kosek
- Division of Infectious Disease and International Health, School of Medicine, University of Virginia, Charlottesville, VA, USA.
- Asociación Benefica PRISMA, Iquitos, Loreto, Peru.
- Division of Infectious Diseases and International Health, Public Health Sciences, 345 Crispell Dr, Rm 2525, Charlottesville, USA.
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7
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Peñataro Yori P, Paredes Olórtegui M, Schiaffino F, Perez K, Curico Huansi G, Flynn T, Zhang J, Ramal Asayag C, Meza Sanchez G, Silva Delgado H, Casapia Morales M, Casanova W, Jiu B, Munayco Escate C, Silver R, Henao O, Cooper KK, Liu J, Houpt E, Kosek MN, Colston JM, Oberhelman R, Pinedo Vasquez T, Garcia Bardales PF, Shapiama Lopez WV, Zegarra Paredes LF. Etiology of Acute Febrile Illness in the Peruvian Amazon as determined by modular formatted quantitative PCR: A Protocol for RIVERA, a Health Facility-Based Case-Control Study. RESEARCH SQUARE 2023:rs.3.rs-2635774. [PMID: 37034707 PMCID: PMC10081374 DOI: 10.21203/rs.3.rs-2635774/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Background The study of the etiology of acute febrile illness (AFI) has historically been designed as a prevalence of pathogens detected from a case series. This strategy has an inherent unrealistic assumption that all pathogen detection allows for causal attribution, despite known asymptomatic carriage of the principal causes of acute febrile illness in most low- and middle-income countries (LMICs). We designed a semi-quantitative PCR in a modular format to detect bloodborne agents of acute febrile illness that encompassed common etiologies of AFI in the region, etiologies of recent epidemics, etiologies that require an immediate public health response and additional pathogens of unknown endemicity. We then designed a study that would delineate background levels of transmission in the community in the absence of symptoms to provide corrected estimates of attribution for the principal determinants of AFI. Methods A case-control study of acute febrile illness in patients ten years or older seeking health care in Iquitos, Loreto, Peru, was planned. Upon enrollment, we will obtain blood, saliva, and mid-turbinate nasal swabs at enrollment with a follow-up visit on day 21-28 following enrollment to attain vital status and convalescent saliva and blood samples, as well as a questionnaire including clinical, socio-demographic, occupational, travel, and animal contact information for each participant. Whole blood samples are to be simultaneously tested for 32 pathogens using TaqMan array cards. Mid-turbinate samples will be tested for SARS-CoV-2, Influenza A and Influenza B. Conditional logistic regression models will be fitted treating case/control status as the outcome and with pathogen-specific sample positivity as predictors to attain estimates of attributable pathogen fractions for AFI. Discussion The modular PCR platforms will allow for reporting of all primary results of respiratory samples within 72 hours and blood samples within one week, allowing for results to influence local medical practice and enable timely public health responses. The inclusion of controls will allow for a more accurate estimate of the importance of specific, prevalent pathogens as a cause of acute illness. Study Registration Project 1791, Registro de Proyectos de Investigación en Salud Pública (PRISA), Instituto Nacional de Salud, Perú.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Cesar Munayco Escate
- Centro de Epidemiologia, Prevencion, y Control de Enfermedades, Ministerio de Salud
| | | | - Olga Henao
- Centers for Disease Control and Prevention
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Grundy BS, Parikh H, Jacob S, Banura P, Moore CC, Liu J, Houpt ER. Pathogen Detection Using Metagenomic Next-Generation Sequencing of Plasma Samples from Patients with Sepsis in Uganda. Microbiol Spectr 2023; 11:e0431222. [PMID: 36625651 PMCID: PMC9927450 DOI: 10.1128/spectrum.04312-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 12/16/2022] [Indexed: 01/11/2023] Open
Abstract
Metagenomic sequencing is a promising new method for pathogen detection. We aimed to detect pathogens from archived plasma using metagenomic sequencing in a previously well-characterized cohort of 254 predominantly HIV-infected patients with sepsis in Uganda. We used Illumina sequencing and the Chan Zuckerberg ID metagenomics platform to sequence and identify pathogens. On average, each plasma sample yielded 3,404,737 ± 2,201,997 reads (mean ± standard deviation), of which 220,032 ± 416,691 (6.3% ± 8.6%) were identified as nonhuman reads. Using a background model filter, 414 genus-specific pathogen identifications were found in the 254 samples. Nineteen pathogens were previously detected positive by quantitative PCR (qPCR), compared to sequencing, which demonstrated 30.2% sensitivity and 99.5% specificity. Sensitivity was higher for viral pathogens than nonviral pathogens (37% versus 5%). For example, HIV viremia was detected in 69% of samples using qPCR, and sequencing revealed 70% sensitivity and 92% specificity. There were 75 genus-specific potential pathogens identified by sequencing in this cohort, including hepatitis B and Epstein-Barr virus (EBV), among several others. qPCR showed a prevalence of hepatitis B and EBV viremia of 17% and 45%, respectively. In-hospital mortality was associated with a lower qPCR threshold cycle value for EBV (adjusted odds ratio, 0.85; P < .001) but not for hepatitis B or HIV. In conclusion, a broad range of potential pathogens were identified by metagenomic sequencing in patients with sepsis in Uganda. Unexpectedly high rates of hepatitis B and EBV viremia were found. Whether these viral infections in HIV patients with sepsis are clinically important requires further study. IMPORTANCE The use of next-generation sequencing (NGS) in blood samples is an emerging technology for clinical microbiology labs. In this work, we performed NGS on plasma samples from a well-characterized cohort, where all samples had been previously tested by PCR for 43 pathogens. Therefore, we could compare sequencing performance against that of PCR and identify clinical correlates. A broad range of potential pathogens were identified by metagenomic sequencing in patients with sepsis in Uganda, particularly viruses, which we confirmed by PCR. In addition to HIV viremia, unexpectedly high rates of hepatitis B and EBV viremia were found, which may have important clinical implications.
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Affiliation(s)
- Brian S. Grundy
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Hardik Parikh
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Shevin Jacob
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Patrick Banura
- Ministry of Health, National Disease Control Department, Kampala, Uganda
| | - Chris C. Moore
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Jie Liu
- School of Public Health, Qingdao University, Qingdao, China
| | - Eric R. Houpt
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
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9
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Obiero CW, Gumbi W, Mwakio S, Mwangudzah H, Seale AC, Taniuchi M, Liu J, Houpt E, Berkley JA. Detection of pathogens associated with early-onset neonatal sepsis in cord blood at birth using quantitative PCR. Wellcome Open Res 2022; 7:3. [PMID: 35600002 PMCID: PMC9114825 DOI: 10.12688/wellcomeopenres.17386.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/03/2022] [Indexed: 11/10/2022] Open
Abstract
Background: Early onset neonatal sepsis (EONS) typically begins prior to, during or soon after birth and may be rapidly fatal. There is paucity of data on the aetiology of EONS in sub-Saharan Africa due to limited diagnostic capacity in this region, despite the associated significant mortality and long-term neurological impairment. Methods: We compared pathogens detected in cord blood samples between neonates admitted to hospital with possible serious bacterial infection (pSBI) in the first 48 hours of life (cases) and neonates remaining well (controls). Cord blood was systematically collected at Kilifi County Hospital (KCH) from 2011-2016, and later tested for 21 bacterial, viral and protozoal targets using multiplex PCR via TaqMan Array Cards (TAC). Results: Among 603 cases (101 [17%] of whom died), 179 (30%) tested positive for ≥1 target and 37 (6.1%) tested positive for multiple targets. Klebsiella oxytoca, Escherichia coli/Shigella spp., Pseudomonas aeruginosa, and Streptococcus pyogenes were commonest. Among 300 controls, 79 (26%) tested positive for ≥1 target, 11 (3.7%) were positive for multiple targets, and K. oxytoca and P. aeruginosa were most common. Cumulative odds ratios across controls: cases (survived): cases (died) were E. coli/Shigella spp. 2.6 (95%CI 1.6-4.4); E. faecalis 4.0 (95%CI 1.1-15); S. agalactiae 4.5 (95%CI 1.6-13); Ureaplasma spp. 2.9 (95%CI 1.3-6.4); Enterovirus 9.1 (95%CI 2.3-37); and Plasmodium spp. 2.9 (95%CI 1.4-6.2). Excluding K. oxytoca and P. aeruginosa as likely contaminants, aetiology was attributed in 9.4% (95%CI 5.1-13) cases using TAC. Leading pathogen attributions by TAC were E. coli/Shigella spp. (3.5% (95%CI 1.7-5.3)) and Ureaplasma spp. (1.7% (95%CI 0.5-3.0)). Conclusions: Cord blood sample may be useful in describing EONS pathogens at birth, but more specific tests are needed for individual diagnosis. Careful sampling of cord blood using aseptic techniques is crucial to minimize contamination. In addition to culturable bacteria, Ureaplasma and Enterovirus were causes of EONS.
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Affiliation(s)
- Christina W. Obiero
- Clinical research, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Global health, Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Wilson Gumbi
- Bioscience department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Stella Mwakio
- Clinical research, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Hope Mwangudzah
- Clinical research, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Anna C. Seale
- Clinical research, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
- College of Health and Medical Sciences, Haramaya University, Harar, Ethiopia
| | - Mami Taniuchi
- Division of Infectious Diseases and International Health, University of Virginia, Virginia, USA
| | - Jie Liu
- Division of Infectious Diseases and International Health, University of Virginia, Virginia, USA
| | - Eric Houpt
- Division of Infectious Diseases and International Health, University of Virginia, Virginia, USA
| | - James A. Berkley
- Clinical research, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine, University of Oxford, Oxford, UK
- The Childhood Acute Illness & Nutrition (CHAIN) Network, Nairobi, Kenya
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10
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Liu X, Du X, Huang Y, Pang B, Zhang M, Ma Y, Wang X, Song X, Li J, Li J. Rapid detection of four pathogens in bloodstream infection by antimicrobial peptide capture combined with multiplex PCR and capillary electrophoresis. Microchem J 2022. [DOI: 10.1016/j.microc.2022.108199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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11
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Skipper CP, Hullsiek KH, Cresswell FV, Tadeo KK, Okirwoth M, Blackstad M, Hernandez-Alvarado N, Fernández-Alarcón C, Walukaga S, Martyn E, Ellis J, Ssebambulidde K, Tugume L, Nuwagira E, Rhein J, Meya DB, Boulware DR, Schleiss MR. Cytomegalovirus viremia as a risk factor for mortality in HIV-associated cryptococcal and tuberculous meningitis. Int J Infect Dis 2022; 122:785-792. [PMID: 35843498 PMCID: PMC9653033 DOI: 10.1016/j.ijid.2022.07.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/22/2022] [Accepted: 07/11/2022] [Indexed: 11/16/2022] Open
Abstract
OBJECTIVES CMV viremia is associated with increased mortality in persons with HIV. We previously demonstrated that CMV viremia was a risk factor for 10-week mortality in antiretroviral therapy (ART)-naïve persons with cryptococcal meningitis. We investigated whether similar observations existed over a broader cohort of patients with HIV-associated meningitis at 18 weeks. METHODS We prospectively enrolled Ugandans with cryptococcal or TB meningitis into clinical trials in 2015-2019. We quantified CMV DNA concentrations from stored baseline plasma or serum samples from 340 participants. We compared 18-week survival between those with and without CMV viremia. RESULTS We included 308 persons with cryptococcal meningitis and 32 with TB meningitis, of whom 121 (36%) had detectable CMV DNA. Baseline CD4+ T-cell counts (14 vs. 24 cells/µl; P = 0.07) and antiretroviral exposure (47% vs. 45%; P = 0.68) did not differ between persons with and without CMV viremia. The 18-week mortality was 50% (61/121) in those with CMV viremia versus 34% (74/219) in those without (P = 0.003). Detectable CMV viremia (adjusted hazard ratio [aHR] 1.60; 95% confidence interval [CI] 1.13-2.25; P = 0.008) and greater viral load (aHR 1.22 per log10 IU/ml increase; 95% CI 1.09-1.35; P <0.001) were positively associated with all-cause mortality through 18 weeks. CONCLUSION CMV viremia at baseline was associated with a higher risk of death at 18 weeks among persons with HIV-associated cryptococcal or TB meningitis, and the risk increased as the CMV viral load increased. Further investigation is warranted to determine whether CMV is a modifiable risk contributing to deaths in HIV-associated meningitis or is a biomarker of immune dysfunction.
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Affiliation(s)
- Caleb P Skipper
- University of Minnesota Medical School, Minneapolis, USA; Infectious Diseases Institute, Makerere University, Kampala, Uganda.
| | | | - Fiona V Cresswell
- Infectious Diseases Institute, Makerere University, Kampala, Uganda; Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK; Global Health and Infection, Brighton and Sussex Medical School, Brighton, UK
| | - Kiiza K Tadeo
- Infectious Diseases Institute, Makerere University, Kampala, Uganda
| | - Michael Okirwoth
- Infectious Diseases Institute, Makerere University, Kampala, Uganda
| | - Mark Blackstad
- University of Minnesota Medical School, Minneapolis, USA
| | | | | | | | - Emily Martyn
- Infectious Diseases Institute, Makerere University, Kampala, Uganda; Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Jayne Ellis
- Infectious Diseases Institute, Makerere University, Kampala, Uganda; Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | | | - Lillian Tugume
- Infectious Diseases Institute, Makerere University, Kampala, Uganda
| | - Edwin Nuwagira
- Infectious Diseases Institute, Makerere University, Kampala, Uganda; Department of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Joshua Rhein
- University of Minnesota Medical School, Minneapolis, USA
| | - David B Meya
- University of Minnesota Medical School, Minneapolis, USA; Infectious Diseases Institute, Makerere University, Kampala, Uganda
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Long-Term Infection and Pathogenesis in a Novel Mouse Model of Human Respiratory Syncytial Virus. Viruses 2022; 14:v14081740. [PMID: 36016362 PMCID: PMC9415064 DOI: 10.3390/v14081740] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 07/30/2022] [Accepted: 08/03/2022] [Indexed: 11/24/2022] Open
Abstract
Intensive efforts have been made to develop models of hRSV infection or disease using various animals. However, the limitations such as semi-permissiveness and short duration of infection have impeded their applications in both the pathogenesis of hRSV and therapeutics development. Here, we present a mouse model based on a Rag2 gene knockout using CRISPR/Cas9 technology. Rag2−/− mice sustained high viral loads upon intranasal inoculation with hRSV. The average peak titer rapidly reached 1 × 109.8 copies/g and 1c106 TCID50 in nasal cavity, as well as 1 × 108 copies/g and 1 × 105 TCID50 in the lungs up to 5 weeks. Mild interstitial pneumonia, severe bronchopneumonia, elevated cytokines and NK cells were seen in Rag2−/− mice. A humanized monoclonal antibody showed strong antiviral activity in this animal model, implying that Rag2−/− mice that support long-term stable infection are a useful tool for studying the transmission and pathogenesis of human RSV, as well as evaluating therapeutics.
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13
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Byashalira K, Chamba N, Alkabab Y, Mbelele P, Mpolya E, Ntinginya N, Shayo PJ, Ramaiya KL, Lillebaek T, Heysell SK, Mmbaga BT, Bygbjerg IC, Mpagama S, Christensen DL. Impact of early diagnosis of impaired glucose regulation in tuberculosis: Comparison of clinical outcomes in people with tuberculosis in Tanzania. Trop Med Int Health 2022; 27:815-822. [DOI: 10.1111/tmi.13806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Kenneth Byashalira
- Kilimanjaro Christian Medical University College Moshi Tanzania
- Kibong'oto Infectious Diseases Hospital Kilimanjaro Tanzania
| | - Nyasatu Chamba
- Kilimanjaro Christian Medical University College Moshi Tanzania
- Kilimanjaro Christian Medical Centre Moshi Tanzania
| | - Yosra Alkabab
- Division of Infectious Diseases and International Health University of Virginia USA
| | - Peter Mbelele
- Kibong'oto Infectious Diseases Hospital Kilimanjaro Tanzania
| | - Emmanuel Mpolya
- Department of Global Health and Bio‐Medical Sciences Nelson Mandela African Institution of Science
| | - Nyanda Ntinginya
- National Institute of Medical Research, Mbeya Medical Research Centre Mbeya Tanzania
| | | | | | - Troels Lillebaek
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut Copenhagen Denmark
- Global Health Section, Department of Public Health University of Copenhagen Denmark
| | - Scott K. Heysell
- Division of Infectious Diseases and International Health University of Virginia USA
| | - Blandina T. Mmbaga
- Kilimanjaro Christian Medical University College Moshi Tanzania
- Kilimanjaro Christian Medical Centre Moshi Tanzania
- Kilimanjaro Clinical Research Institute, Kilimanjaro Christian Medical Centre Moshi Tanzania
| | - Ib C. Bygbjerg
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut Copenhagen Denmark
| | - Stellah Mpagama
- Kilimanjaro Christian Medical University College Moshi Tanzania
- Kibong'oto Infectious Diseases Hospital Kilimanjaro Tanzania
| | - Dirk L. Christensen
- Global Health Section, Department of Public Health University of Copenhagen Denmark
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Brinkworth JF, Shaw JG. On race, human variation, and who gets and dies of sepsis. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2022. [PMCID: PMC9544695 DOI: 10.1002/ajpa.24527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jessica F. Brinkworth
- Department of Anthropology University of Illinois Urbana‐Champaign Urbana Illinois USA
- Carl R. Woese Institute for Genomic Biology University of Illinois at Urbana‐Champaign Urbana Illinois USA
- Department of Evolution, Ecology and Behavior University of Illinois Urbana‐Champaign Urbana Illinois USA
| | - J. Grace Shaw
- Department of Anthropology University of Illinois Urbana‐Champaign Urbana Illinois USA
- Carl R. Woese Institute for Genomic Biology University of Illinois at Urbana‐Champaign Urbana Illinois USA
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15
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Towards Improved Management of Tuberculous Bloodstream Infections: Pharmacokinetic Considerations with Suggestions for Better Treatment Outcomes. Antibiotics (Basel) 2022; 11:antibiotics11070895. [PMID: 35884149 PMCID: PMC9311525 DOI: 10.3390/antibiotics11070895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/09/2022] [Accepted: 04/11/2022] [Indexed: 11/17/2022] Open
Abstract
Mycobacterium tuberculosis is the leading cause of sepsis among HIV-infected adults, yet effective treatment remains a challenge. Efficacy of antituberculous drugs is optimized by high Area Under Curve to Minimum Inhibitory Concentration (AUC/MIC) ratios, suggesting that both the drug concentration at the disease site and time above MIC are critical to treatment outcomes. We elaborate on sepsis pathophysiology and show how it adversely affects antituberculous drug kinetics. Expanding distribution volumes secondary to an increased vascular permeability prevents the attainment of target Cmax concentrations for nearly all drugs. Furthermore, sepsis-induced metabolic acidosis promotes protonation, which increases renal clearance of basic drugs such as isoniazid and ethambutol, and hence AUCs are substantially reduced. Compared with the treatment of non-sepsis TB disease, these distorted kinetics underlie the poor treatment outcomes observed with bloodstream infections. In addition to aggressive hemodynamic management, an increase in both the dose and frequency of drug administration are warranted, at least in the early phase of treatment.
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16
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Tsere DB, Shirima GM, Grundy BS, Heysell SK, Mpagama SG, Mziray SR, Mbelele PM. Multiple pathogens contribute to human immunodeficiency virus-related sepsis in addition to Mycobacterium tuberculosis: A prospective cohort in Tanzania. Int J Mycobacteriol 2022; 11:241-248. [PMID: 36260441 PMCID: PMC9582297 DOI: 10.4103/ijmy.ijmy_80_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Background Mortality from tuberculosis (TB) sepsis is common among patients living with human immunodeficiency virus (PLHIV). We aimed to detect M. tuberculosis (MTB) and additional sepsis etiologies, and mortality determinants in PLHIV. Methods This prospective cohort study consented and followed-up PLHIV for 28 days in northern Tanzania. From May through December 2021, patients provided urine and sputum for TB testing in lateral-flow lipoarabinomannan (LF-LAM) and Xpert® MTB/RIF. Bacterial blood culture, cryptococcal antigen, malaria rapid diagnostic, C-reactive-protein (CRP), and international normalized ratio (INR) tests were also performed. Sepsis severity was clinically measured by Karnofsky and modified early warning signs (MEWS) scores. Anti-TB, broad-spectrum antibiotics, and antimalarial and antifungal agents were prescribed in accordance with Tanzania treatment guideline. An independent t-test and Chi-square or Fisher's exact tests compared means and proportions, respectively. P < 0.05 was statistically significant. Results Among 98 patients, 59 (60.2%) were female. Their mean (standard deviation) age was 44 (12.9) years. TB detection increased from 24 (24.5%) by Xpert® MTB/RIF to 36 (36.7%) when LF-LAM was added. In total, 23 (23.5%) patients had other than TB etiologies of sepsis, including Staphylococcus aureus, Streptococcus pneumoniae, Cryptococcus spp., and Plasmodium spp. Twenty-four (94.4%) of 36 patients with TB had higher CRP (≥10 mg/l) compared to 25 (40.3%) non-TB patients (P < 0.001). Nine (9.2%) patients died and almost all had INR ≥1.8 (n = 8), Karnofsky score <50% (n = 9), MEWS score >6 (n = 8), and malnutrition (n = 9). Conclusions MTB and other microbes contributed to sepsis in PLHIV. Adding non-TB tests informed clinical decisions. Mortality was predicted by conventional sepsis and severity scoring, malnutrition, and elevated INR.
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Affiliation(s)
- Donatus Bonphace Tsere
- Department of medical services, Kibong’oto Infectious Diseases Hospital, Siha, Tanzania
- Department of Global Health and Biomedical Sciences, School of Life Sciences and Bioengineering, Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | - Gabriel Mkilema Shirima
- Department of Global Health and Biomedical Sciences, School of Life Sciences and Bioengineering, Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | - Brian S. Grundy
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Scott K. Heysell
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Stellah G. Mpagama
- Department of medical services, Kibong’oto Infectious Diseases Hospital, Siha, Tanzania
| | - Shabani Ramadhani Mziray
- Department of medical services, Kibong’oto Infectious Diseases Hospital, Siha, Tanzania
- Department of Biochemistry and Molecular Biology, Kilimanjaro Christian Medical University College, Moshi, Kilimanjaro, Tanzania
| | - Peter M. Mbelele
- Department of medical services, Kibong’oto Infectious Diseases Hospital, Siha, Tanzania
- Department of Global Health and Biomedical Sciences, School of Life Sciences and Bioengineering, Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
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Obiero CW, Gumbi W, Mwakio S, Mwangudzah H, Seale AC, Taniuchi M, Liu J, Houpt E, Berkley JA. Detection of pathogens associated with early-onset neonatal sepsis in cord blood at birth using quantitative PCR. Wellcome Open Res 2022; 7:3. [PMID: 35600002 PMCID: PMC9114825 DOI: 10.12688/wellcomeopenres.17386.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/04/2022] [Indexed: 11/20/2022] Open
Abstract
Background: Early onset neonatal sepsis (EONS) typically begins prior to, during or soon after birth and may be rapidly fatal. There is paucity of data on the aetiology of EONS in sub-Saharan Africa due to limited diagnostic capacity in this region, despite the associated significant mortality and long-term neurological impairment. Methods: We compared pathogens detected in cord blood samples between neonates admitted to hospital with possible serious bacterial infection (pSBI) in the first 48 hours of life (cases) and neonates remaining well (controls). Cord blood was systematically collected at Kilifi County Hospital (KCH) from 2011-2016, and later tested for 21 bacterial, viral and protozoal targets using multiplex PCR via TaqMan Array Cards (TAC). Results: Among 603 cases (101 [17%] of whom died), 179 (30%) tested positive for ≥1 target and 37 (6.1%) tested positive for multiple targets. Klebsiella oxytoca, Escherichia coli/Shigella spp., Pseudomonas aeruginosa, and Streptococcus pyogenes were commonest. Among 300 controls, 79 (26%) tested positive for ≥1 target, 11 (3.7%) were positive for multiple targets, and K. oxytoca and P. aeruginosa were most common. Cumulative odds ratios across controls: cases (survived): cases (died) were E. coli/Shigella spp. 2.6 (95%CI 1.6-4.4); E. faecalis 4.0 (95%CI 1.1-15); S. agalactiae 4.5 (95%CI 1.6-13); Ureaplasma spp. 2.9 (95%CI 1.3-6.4); Enterovirus 9.1 (95%CI 2.3-37); and Plasmodium spp. 2.9 (95%CI 1.4-6.2). Excluding K. oxytoca and P. aeruginosa as likely contaminants, aetiology was attributed in 9.4% (95%CI 5.1-13) cases using TAC. Leading pathogen attributions by TAC were E. coli/Shigella spp. (3.5% (95%CI 1.7-5.3)) and Ureaplasma spp. (1.7% (95%CI 0.5-3.0)). Conclusions: Cord blood sample may be useful in describing EONS pathogens at birth, but more specific tests are needed for individual diagnosis. Careful sampling of cord blood using aseptic techniques is crucial to minimize contamination. In addition to culturable bacteria, Ureaplasma and Enterovirus were causes of EONS.
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Affiliation(s)
- Christina W. Obiero
- Clinical research, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Global health, Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Wilson Gumbi
- Bioscience department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Stella Mwakio
- Clinical research, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Hope Mwangudzah
- Clinical research, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Anna C. Seale
- Clinical research, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
- College of Health and Medical Sciences, Haramaya University, Harar, Ethiopia
| | - Mami Taniuchi
- Division of Infectious Diseases and International Health, University of Virginia, Virginia, USA
| | - Jie Liu
- Division of Infectious Diseases and International Health, University of Virginia, Virginia, USA
| | - Eric Houpt
- Division of Infectious Diseases and International Health, University of Virginia, Virginia, USA
| | - James A. Berkley
- Clinical research, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine, University of Oxford, Oxford, UK
- The Childhood Acute Illness & Nutrition (CHAIN) Network, Nairobi, Kenya
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Lappan R, Jirapanjawat T, Williamson DA, Lange S, Chown SL, Greening C. Simultaneous detection of multiple pathogens with the TaqMan Array Card. MethodsX 2022; 9:101707. [PMID: 35518918 PMCID: PMC9062751 DOI: 10.1016/j.mex.2022.101707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 04/12/2022] [Indexed: 02/07/2023] Open
Abstract
Quantitative polymerase chain reaction (qPCR) is a gold standard method for the detection and quantification of pathogenic organisms. Standard qPCR is inexpensive, sensitive and highly specific to the pathogen of interest. While qPCR assays can be multiplexed to allow the detection of multiple organisms in one reaction, it is prohibitively labour intensive to screen large numbers of samples for several pathogens at the same time. The TaqMan Array Card (TAC) is a cost-effective and accurate technique that expands the number of assays that can be simultaneously performed on a sample, with no increase in set-up time and only small reductions in sensitivity. This approach is highly beneficial in settings where there is a need to monitor a large panel of pathogens. We illustrate the application of TAC to the monitoring of gastrointestinal pathogens, which span viral, bacterial, protist and helminth taxa. This protocol outlines the laboratory set-up of a TaqMan Array Card, and some recommended data processing steps to aid in accurate interpretation of the results. A video protocol is additionally provided to assist in the use of the technique.•The TAC is designed primarily for gene expression assays, but has recently been utilised in several studies for pathogen detection in human clinical samples.•We expand the use of TAC for pathogen detection across human, animal and environmental sample types, and have developed a protocol and guidelines for the processing and interpretation of results that circumvents issues with the automated outputs.•This technique is applicable to pathogen or organism detection in any context, if quality nucleic acid extracts can be obtained from the sample type of interest.
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Affiliation(s)
- Rachael Lappan
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Thanavit Jirapanjawat
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Deborah A Williamson
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Sigrid Lange
- Department of Microbiology and Immunology, University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Steven L Chown
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
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Gulleen EA, Lubwama M, Komakech A, Krantz EM, Liu C, Phipps W. Knowledge and perceptions of antimicrobial resistance and antimicrobial stewardship among staff at a national cancer referral center in Uganda. ANTIMICROBIAL STEWARDSHIP & HEALTHCARE EPIDEMIOLOGY : ASHE 2022; 2:e54. [PMID: 36483337 PMCID: PMC9726558 DOI: 10.1017/ash.2022.28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/24/2022] [Accepted: 01/27/2022] [Indexed: 06/17/2023]
Abstract
OBJECTIVES As access to cancer care has improved throughout sub-Saharan Africa, treatment-associated infections have increased. Assessing healthcare worker knowledge of antimicrobial stewardship and identifying the barriers to infection management will inform the development of contextually appropriate antimicrobial stewardship programs, improving cancer outcomes in sub-Saharan Africa. DESIGN Cross-sectional survey. SETTING The Uganda Cancer Institute (UCI), a national cancer referral center in Kampala, Uganda. PARTICIPANTS We surveyed 61 UCI staff: 29 nurses, 7 pharmacists, and 25 physicians. METHODS The survey contained 25 questions and 1 ranking exercise. We examined differences in responses by staff role. RESULTS All 60 respondents who answered the question had heard the term "antimicrobial resistance." Only 44 (73%) had heard the term "antimicrobial stewardship." Nurses were less likely than pharmacists or physicians to be familiar with either term. Also, 41 respondents (68%) felt that loss of antibiotic susceptibility is a major issue at UCI. Regarding barriers to diagnosing infections, 54 (93%) of 58 thought that it was difficult to obtain blood cultures and 48 (86%) of 56 thought that it was difficult to regularly measure temperatures. CONCLUSIONS Although most recognized the term "antimicrobial resistance," fewer were familiar with the term "antimicrobial stewardship." Inappropriate antibiotic use was recognized as a contributor to antimicrobial resistance, but hand hygiene was underrecognized as a contributing factor. We identified numerous barriers to diagnosing infections, including the ability to obtain blood cultures and consistently monitor temperatures. Educating staff regarding antimicrobial selection, allocating resources for blood cultures, and implementing strategies to enhance fever detection will improve infection management.
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Affiliation(s)
- Elizabeth A. Gulleen
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States
- Allergy and Infectious Diseases Division, Department of Medicine, University of Washington, Seattle, Washington, United States
- Seattle Cancer Care Alliance, Seattle, Washington, United States
| | - Margaret Lubwama
- Department of Medical Microbiology, Makerere University, Kampala, Uganda
| | - Alfred Komakech
- Department of Pharmacy, Uganda Cancer Institute, Kampala, Uganda
| | - Elizabeth M. Krantz
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States
| | - Catherine Liu
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States
- Allergy and Infectious Diseases Division, Department of Medicine, University of Washington, Seattle, Washington, United States
- Seattle Cancer Care Alliance, Seattle, Washington, United States
| | - Warren Phipps
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States
- Allergy and Infectious Diseases Division, Department of Medicine, University of Washington, Seattle, Washington, United States
- Seattle Cancer Care Alliance, Seattle, Washington, United States
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20
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Mduma E, Halidou T, Kaboré B, Walongo T, Lompo P, Museveni J, Gidabayda J, Gratz J, Guga G, Kimathi C, Liu J, Mdoe P, Moshiro R, Petzold M, Singlovic J, Guillerm M, Gomes MF, Houpt ER, Halleux CM. Etiology of severe invasive infections in young infants in rural settings in sub-Saharan Africa. PLoS One 2022; 17:e0264322. [PMID: 35213629 PMCID: PMC8880396 DOI: 10.1371/journal.pone.0264322] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 02/08/2022] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Serious invasive infections in newborns are a major cause of death. Lack of data on etiological causes hampers progress towards reduction of mortality. This study aimed to identify pathogens responsible for such infections in young infants in sub-Saharan Africa and to describe their antibiotics resistance profile. METHODS Between September 2016 and April 2018 we implemented an observational study in two rural sites in Burkina Faso and Tanzania enrolling young infants aged 0-59 days old with serious invasive infection. Blood samples underwent blood culture and molecular biology. RESULTS In total 634 infants with clinical diagnosis of serious invasive infection were enrolled and 4.2% of the infants had a positive blood culture. The most frequent pathogens identified by blood culture were Klebsiella pneumonia and Staphylococcus aureus, followed by Escherichia coli. Gram-negative isolates were only partially susceptible to first line WHO recommended treatment for neonatal sepsis at community level. A total of 18.6% of the infants were PCR positive for at least one pathogen and Escherichia coli and Staphylococcus aureus were the most common bacteria detected. Among infants enrolled, 60/634 (9.5%) died. Positive blood culture but not positive PCR was associated with risk of death. For most deaths, no pathogen was identified either by blood culture or molecular testing, and hence a causal agent remained unclear. Mortality was associated with low body temperature, tachycardia, respiratory symptoms, convulsions, history of difficult feeding, movement only when stimulated or reduced level of consciousness, diarrhea and/or vomiting. CONCLUSION While Klebsiella pneumonia and Staphylococcus aureus, as well as Escherichia coli were pathogens most frequently identified in infants with clinical suspicion of serious invasive infections, most cases remain without definite diagnosis, making more accurate diagnostic tools urgently needed. Antibiotics resistance to first line antibiotics is an increasing challenge even in rural Africa.
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Affiliation(s)
- Estomih Mduma
- Haydom Research Center, Haydom Lutheran Hospital, Haydom, United Republic of Tanzania
| | - Tinto Halidou
- Institut de Recherche en Sciences de la Santé (IRSS), Clinical Research Unit of Nanoro (CRUN), Nanoro, Burkina Faso
| | - Berenger Kaboré
- Institut de Recherche en Sciences de la Santé (IRSS), Clinical Research Unit of Nanoro (CRUN), Nanoro, Burkina Faso
| | - Thomas Walongo
- Haydom Research Center, Haydom Lutheran Hospital, Haydom, United Republic of Tanzania
| | - Palpouguini Lompo
- Institut de Recherche en Sciences de la Santé (IRSS), Clinical Research Unit of Nanoro (CRUN), Nanoro, Burkina Faso
| | - Justine Museveni
- Haydom Research Center, Haydom Lutheran Hospital, Haydom, United Republic of Tanzania
| | - Joshua Gidabayda
- Haydom Research Center, Haydom Lutheran Hospital, Haydom, United Republic of Tanzania
| | - Jean Gratz
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, United States of America
| | - Godfrey Guga
- Haydom Research Center, Haydom Lutheran Hospital, Haydom, United Republic of Tanzania
| | - Caroline Kimathi
- Haydom Research Center, Haydom Lutheran Hospital, Haydom, United Republic of Tanzania
| | - Jie Liu
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, United States of America
| | - Paschal Mdoe
- Haydom Research Center, Haydom Lutheran Hospital, Haydom, United Republic of Tanzania
| | - Robert Moshiro
- Haydom Research Center, Haydom Lutheran Hospital, Haydom, United Republic of Tanzania
| | - Max Petzold
- School of Public Health and Community Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Jan Singlovic
- UNICEF/UNDP/WB/WHO Special Program for Research & Training in Tropical Diseases (TDR), World Health Organization, Geneva, Switzerland
| | - Martine Guillerm
- UNICEF/UNDP/WB/WHO Special Program for Research & Training in Tropical Diseases (TDR), World Health Organization, Geneva, Switzerland
| | - Melba F. Gomes
- UNICEF/UNDP/WB/WHO Special Program for Research & Training in Tropical Diseases (TDR), World Health Organization, Geneva, Switzerland
| | - Eric R. Houpt
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, United States of America
| | - Christine M. Halleux
- UNICEF/UNDP/WB/WHO Special Program for Research & Training in Tropical Diseases (TDR), World Health Organization, Geneva, Switzerland
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21
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Ravindranath TM. Viral sepsis: underrated and under diagnosed entity in clinical arena. Future Virol 2022. [DOI: 10.2217/fvl-2021-0189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Thyyar M Ravindranath
- Department of Pediatrics, Division of Pediatric Critical Care Medicine, Morgan Stanley Children’s Hospital, NewYork-Presbyterian Hospital, Columbia University Irving Medical Center, Vagelos College of Physicians & Surgeons, 630 West 168th Street, New York, NY 10032, USA
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22
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Obiero CW, Gumbi W, Mwakio S, Mwangudzah H, Seale AC, Taniuchi M, Liu J, Houpt E, Berkley JA. Detection of pathogens associated with early-onset neonatal sepsis in cord blood at birth using quantitative PCR. Wellcome Open Res 2022; 7:3. [PMID: 35600002 PMCID: PMC9114825 DOI: 10.12688/wellcomeopenres.17386.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/08/2021] [Indexed: 12/20/2022] Open
Abstract
Background: Early onset neonatal sepsis (EONS) typically begins prior to, during or soon after birth and may be rapidly fatal. There is paucity of data on the aetiology of EONS in sub-Saharan Africa due to limited diagnostic capacity in this region, despite the associated significant mortality and long-term neurological impairment. Methods: We compared pathogens detected in cord blood samples between neonates admitted to hospital with possible serious bacterial infection (pSBI) in the first 48 hours of life (cases) and neonates remaining well (controls). Cord blood was systematically collected at Kilifi County Hospital (KCH) from 2011-2016, and later tested for 21 bacterial, viral and protozoal targets using multiplex PCR via TaqMan Array Cards (TAC). Results: Among 603 cases (101 [17%] of whom died), 179 (30%) tested positive for ≥1 target and 37 (6.1%) tested positive for multiple targets. Klebsiella oxytoca, Escherichia coli/Shigella spp., Pseudomonas aeruginosa, and Streptococcus pyogenes were commonest. Among 300 controls, 79 (26%) tested positive for ≥1 target, 11 (3.7%) were positive for multiple targets, and K. oxytoca and P. aeruginosa were most common. Cumulative odds ratios across controls: cases (survived): cases (died) were E. coli/Shigella spp. 2.6 (95%CI 1.6-4.4); E. faecalis 4.0 (95%CI 1.1-15); S. agalactiae 4.5 (95%CI 1.6-13); Ureaplasma spp. 2.9 (95%CI 1.3-6.4); Enterovirus 9.1 (95%CI 2.3-37); and Plasmodium spp. 2.9 (95%CI 1.4-6.2). Excluding K. oxytoca and P. aeruginosa as likely contaminants, aetiology was attributed in 9.4% (95%CI 5.1-13) cases using TAC. Leading pathogen attributions by TAC were E. coli/Shigella spp. (3.5% (95%CI 1.7-5.3)) and Ureaplasma spp. (1.7% (95%CI 0.5-3.0)). Conclusions: Cord blood sample may be useful in describing EONS pathogens at birth, but more specific tests are needed for individual diagnosis. Careful sampling of cord blood using aseptic techniques is crucial to minimize contamination. In addition to culturable bacteria, Ureaplasma and Enterovirus were causes of EONS.
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Affiliation(s)
- Christina W. Obiero
- Clinical research, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Global health, Academic Medical Center of the University of Amsterdam, Amsterdam, The Netherlands
| | - Wilson Gumbi
- Bioscience department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Stella Mwakio
- Clinical research, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Hope Mwangudzah
- Clinical research, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Anna C. Seale
- Clinical research, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
- College of Health and Medical Sciences, Haramaya University, Harar, Ethiopia
| | - Mami Taniuchi
- Division of Infectious Diseases and International Health, University of Virginia, Virginia, USA
| | - Jie Liu
- Division of Infectious Diseases and International Health, University of Virginia, Virginia, USA
| | - Eric Houpt
- Division of Infectious Diseases and International Health, University of Virginia, Virginia, USA
| | - James A. Berkley
- Clinical research, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine, University of Oxford, Oxford, UK
- The Childhood Acute Illness & Nutrition (CHAIN) Network, Nairobi, Kenya
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23
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Abstract
Supplemental Digital Content is available in the text. OBJECTIVES: To identify the epidemiology and outcome of adults and children with and without sepsis in a rural sub-Sahara African setting. DESIGN: A priori planned substudy of a prospective, before-and-after trial. SETTING: Rural, sub-Sahara African hospital. PATIENTS: One-thousand four-hundred twelve patients (adults, n = 491; children, n = 921) who were admitted to hospital because of an acute infection. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: Demographic, clinical, laboratory data, danger signs, and the presence of sepsis (defined as a quick Sequential Organ Failure Assessment score count ≥ 2) at admission were extracted. Sepsis was observed in 69 adults (14.1%) and 248 children (26.9%). Sepsis patients differed from subjects without sepsis in several demographic and clinical aspects. Malaria was the most frequent type of infection in adults (66.7%) and children (63.7%) with sepsis, followed by suspected bacterial and parasitic infections other than malaria. Adults with sepsis more frequently developed respiratory failure (8.7% vs 2.1%; p = 0.01), had a higher in-hospital mortality (17.4% vs 8.3%; p < 0.001), were less often discharged home (81.2% vs 92.2%; p = 0.007), and had higher median (interquartile range) costs of care (30,300 [19,400–49,900] vs 42,500 Rwandan Francs [27,000–64,400 Rwandan Francs]; p = 0.004) than adults without sepsis. Children with sepsis were less frequently discharged home than children without sepsis (93.1% vs 96.4%; p = 0.046). Malaria and respiratory tract infections claimed the highest absolute numbers of lives. The duration of symptoms before hospital admission did not differ between survivors and nonsurvivors in adults (72 [24–168] vs 96 hr [72–168 hr]; p = 0.27) or children (48 [24–72] vs 36 [24–108 hr]; p = 0.8). Respiratory failure and coma were the most common causes of in-hospital death. CONCLUSIONS: In addition to suspected bacterial, viral, and fungal infections, malaria and other parasitic infections are common and important causes of sepsis in adults and children admitted to a rural hospital in sub-Sahara Africa. The in-hospital mortality associated with sepsis is substantial, primarily in adults.
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24
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Chen K, Malik AA, Sheng YJ, Ahmed S, Sun C, Deng CL, Ojha SC. Clinical Utility of Molecular Tests for Guiding Therapeutic Decisions in Bloodstream Staphylococcal Infections: A Meta-Analysis. Front Pediatr 2021; 9:713447. [PMID: 34422731 PMCID: PMC8374148 DOI: 10.3389/fped.2021.713447] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 07/12/2021] [Indexed: 12/14/2022] Open
Abstract
Background: Treatment of bloodstream staphylococcal infections (BSI) necessitates the prompt initiation of appropriate antimicrobial agents and the rapid de-escalation of excessive broad-spectrum coverage to reduce the risk of mortality. We, therefore, aimed to demonstrate the diagnostic accuracy of nucleic acid amplification tests (NAAT) for the identification of methicillin-resistant S. aureus (MRSA) and methicillin-sensitive S. aureus (MSSA) in clinically suspected patients. Methods: Until November 23, 2020, databases including PubMed, Scopus, Embase, and Web of Science were scanned for eligible studies. A bivariate random-effects model was used for meta-analysis of the 33 included studies obtained from 1606 citations, and pooled summary estimates with 95% confidence intervals (CI) were generated. Results: Twenty-three studies (n = 8,547) assessed NAAT accuracy for MSSA detection, while three studies (n = 479) evaluated MRSA detection in adults. The pooled NAAT sensitivity and specificity for MRSA in adults was higher [sensitivity: 0.83 (95% CI 0.59-0.96), specificity: 0.99 (95% CI 0.98-1.0)] as compared to MSSA [sensitivity: 0.76 (95% CI 0.69-0.82), specificity: 0.98 (95% CI 0.98-0.99)]. Similarly, eight studies (n = 4,089) investigating MSSA in pediatric population reported higher NAAT accuracy [sensitivity: 0.89 (95% CI 0.76-0.96), specificity: 0.98 (95% CI 0.97-0.98)] compared to adults. Among NAA tests, SeptiFast (real-time PCR, commercial) was frequently applied, and its diagnostic accuracy corresponded well to the overall summary estimates. A meta-regression and subgroup analysis of study design, sample condition, and patient selection method could not explain the heterogeneity (P > 0.05) in the diagnostic efficiency. Conclusions: NAAT could be applied as the preferred initial tests for timely diagnosis and BSI management.
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Affiliation(s)
- Ke Chen
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Southwest Medical University, Luzhou, China
| | - Aijaz Ahmad Malik
- Faculty of Medical Technology, Center of Data Mining and Biomedical Informatics, Mahidol University, Bangkok, Thailand
| | - Yun-Jian Sheng
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Southwest Medical University, Luzhou, China
| | - Sarfraz Ahmed
- Department of Basic Sciences, University of Veterinary and Animal Sciences Lahore, Narowal, Pakistan
| | - Changfeng Sun
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Southwest Medical University, Luzhou, China
| | - Cun-Liang Deng
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Suvash Chandra Ojha
- Department of Infectious Diseases, The Affiliated Hospital of Southwest Medical University, Luzhou, China
- Southwest Medical University, Luzhou, China
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25
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Antibiotic-Resistant Acinetobacter baumannii in Low-Income Countries (2000-2020): Twenty-One Years and Still below the Radar, Is It Not There or Can They Not Afford to Look for It? Antibiotics (Basel) 2021; 10:antibiotics10070764. [PMID: 34201723 PMCID: PMC8300836 DOI: 10.3390/antibiotics10070764] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 12/30/2022] Open
Abstract
Acinetobacter baumannii is an emerging pathogen, and over the last three decades it has proven to be particularly difficult to treat by healthcare services. It is now regarded as a formidable infectious agent with a genetic setup for prompt development of resistance to most of the available antimicrobial agents. Yet, it is noticed that there is a gap in the literature covering this pathogen especially in countries with limited resources. In this review, we provide a comprehensive updated overview of the available data about A. baumannii, the multi-drug resistant (MDR) phenotype spread, carbapenem-resistance, and the associated genetic resistance determinants in low-income countries (LIICs) since the beginning of the 21st century. The coverage included three major databases; PubMed, Scopus, and Web of Science. Only 52 studies were found to be relevant covering only 18 out of the 29 countries included in the LIC group. Studies about two countries, Syria and Ethiopia, contributed ~40% of the studies. Overall, the survey revealed a wide spread of MDR and alarming carbapenem-resistance profiles. Yet, the total number of studies is still very low compared to those reported about countries with larger economies. Accordingly, a discussion about possible reasons and recommendations to address the issue is presented. In conclusion, our analyses indicated that the reported studies of A. baumannii in the LICs is far below the expected numbers based on the prevailing circumstances in these countries. Lack of proper surveillance systems due to inadequate financial resources could be a major contributor to these findings.
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26
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Paulson JN, Williams BL, Hehnly C, Mishra N, Sinnar SA, Zhang L, Ssentongo P, Mbabazi-Kabachelor E, Wijetunge DSS, von Bredow B, Mulondo R, Kiwanuka J, Bajunirwe F, Bazira J, Bebell LM, Burgoine K, Couto-Rodriguez M, Ericson JE, Erickson T, Ferrari M, Gladstone M, Guo C, Haran M, Hornig M, Isaacs AM, Kaaya BN, Kangere SM, Kulkarni AV, Kumbakumba E, Li X, Limbrick DD, Magombe J, Morton SU, Mugamba J, Ng J, Olupot-Olupot P, Onen J, Peterson MR, Roy F, Sheldon K, Townsend R, Weeks AD, Whalen AJ, Quackenbush J, Ssenyonga P, Galperin MY, Almeida M, Atkins H, Warf BC, Lipkin WI, Broach JR, Schiff SJ. Paenibacillus infection with frequent viral coinfection contributes to postinfectious hydrocephalus in Ugandan infants. Sci Transl Med 2021; 12:12/563/eaba0565. [PMID: 32998967 DOI: 10.1126/scitranslmed.aba0565] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 05/06/2020] [Indexed: 12/14/2022]
Abstract
Postinfectious hydrocephalus (PIH), which often follows neonatal sepsis, is the most common cause of pediatric hydrocephalus worldwide, yet the microbial pathogens underlying this disease remain to be elucidated. Characterization of the microbial agents causing PIH would enable a shift from surgical palliation of cerebrospinal fluid (CSF) accumulation to prevention of the disease. Here, we examined blood and CSF samples collected from 100 consecutive infant cases of PIH and control cases comprising infants with non-postinfectious hydrocephalus in Uganda. Genomic sequencing of samples was undertaken to test for bacterial, fungal, and parasitic DNA; DNA and RNA sequencing was used to identify viruses; and bacterial culture recovery was used to identify potential causative organisms. We found that infection with the bacterium Paenibacillus, together with frequent cytomegalovirus (CMV) coinfection, was associated with PIH in our infant cohort. Assembly of the genome of a facultative anaerobic bacterial isolate recovered from cultures of CSF samples from PIH cases identified a strain of Paenibacillus thiaminolyticus This strain, designated Mbale, was lethal when injected into mice in contrast to the benign reference Paenibacillus strain. These findings show that an unbiased pan-microbial approach enabled characterization of Paenibacillus in CSF samples from PIH cases, and point toward a pathway of more optimal treatment and prevention for PIH and other proximate neonatal infections.
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Affiliation(s)
- Joseph N Paulson
- Department of Biostatistics, Product Development, Genentech Inc., South San Francisco, CA 94080, USA
| | - Brent L Williams
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA.,Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY 10032, USA
| | - Christine Hehnly
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Nischay Mishra
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA.,Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY 10032, USA
| | - Shamim A Sinnar
- Center for Neural Engineering, Pennsylvania State University, University Park, PA 16802, USA.,Department of Medicine, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Lijun Zhang
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Paddy Ssentongo
- Center for Neural Engineering, Pennsylvania State University, University Park, PA 16802, USA.,Department of Engineering Science and Mechanics, Pennsylvania State University, University Park, PA 16802, USA.,Department of Public Health Sciences, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | | | - Dona S S Wijetunge
- Department of Pathology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Benjamin von Bredow
- Department of Pathology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Ronnie Mulondo
- CURE Children's Hospital of Uganda, Plot 97-105, Bugwere Road, P.O. Box 903 Mbale, Uganda
| | - Julius Kiwanuka
- Department of Pediatrics, Mbarara University of Science and Technology, P.O. Box 1410 Mbarara, Uganda
| | - Francis Bajunirwe
- Department of Epidemiology, Mbarara University of Science and Technology, P.O. Box 1410, Mbarara, Uganda
| | - Joel Bazira
- Department of Microbiology, Mbarara University of Science and Technology, P.O. Box 1410 Mbarara, Uganda
| | - Lisa M Bebell
- Division of Infectious Disease, Massachusetts Genereal Hospital, Harvard Medical School, 55 Fruit St, GRJ-504, Boston, MA 02114, USA
| | - Kathy Burgoine
- Neonatal Unit, Department of Paediatrics and Child Health, Mbale Regional Referral Hospital, Plot 29-33 Pallisa Road, P.O. Box 1966, Mbale, Uganda.,Mbale Clinical Research Institute, Mbale Regional Referral Hospital, Plot 29-33 Pallisa Road, P.O. Box 1966 Mbale, Uganda.,University of Liverpool, Liverpool, L69 3BX, UK
| | - Mara Couto-Rodriguez
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA.,Biotia, 100 6th avenue, New York, NY 10013, USA
| | - Jessica E Ericson
- Division of Pediatric Infectious Disease, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Tim Erickson
- CURE Children's Hospital of Uganda, Plot 97-105, Bugwere Road, P.O. Box 903 Mbale, Uganda
| | - Matthew Ferrari
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA 16802, USA.,Department of Biology, Pennsylvania State University, University Park, PA 16802, USA.,Department of Statistics, Pennsylvania State University, University Park, PA 16802, USA
| | - Melissa Gladstone
- Institute for Translational Medicine, University of Liverpool, Liverpool, L12 2AP, UK
| | - Cheng Guo
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Murali Haran
- Department of Statistics, Pennsylvania State University, University Park, PA 16802, USA
| | - Mady Hornig
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY 10032, USA
| | - Albert M Isaacs
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63130, USA
| | - Brian Nsubuga Kaaya
- CURE Children's Hospital of Uganda, Plot 97-105, Bugwere Road, P.O. Box 903 Mbale, Uganda
| | - Sheila M Kangere
- CURE Children's Hospital of Uganda, Plot 97-105, Bugwere Road, P.O. Box 903 Mbale, Uganda
| | - Abhaya V Kulkarni
- Division of Neurosurgery, Hospital for Sick Children, University of Toronto, Toronto, Ontario, M5G 1X8, Canada
| | - Elias Kumbakumba
- Department of Pediatrics, Mbarara University of Science and Technology, P.O. Box 1410 Mbarara, Uganda
| | - Xiaoxiao Li
- Institute for Translational Medicine, University of Liverpool, Liverpool, L12 2AP, UK
| | - David D Limbrick
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO 63130, USA
| | - Joshua Magombe
- CURE Children's Hospital of Uganda, Plot 97-105, Bugwere Road, P.O. Box 903 Mbale, Uganda
| | - Sarah U Morton
- Division of Newborn Medicine, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston MA 02115, USA
| | - John Mugamba
- CURE Children's Hospital of Uganda, Plot 97-105, Bugwere Road, P.O. Box 903 Mbale, Uganda
| | - James Ng
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Peter Olupot-Olupot
- Mbale Clinical Research Institute, Mbale Regional Referral Hospital, Plot 29-33 Pallisa Road, P.O. Box 1966 Mbale, Uganda.,Busitema University, Mbale Campus, Plot 29-33 Pallisa Road, P.O. Box 1966, Mbale, Uganda
| | - Justin Onen
- CURE Children's Hospital of Uganda, Plot 97-105, Bugwere Road, P.O. Box 903 Mbale, Uganda
| | - Mallory R Peterson
- Center for Neural Engineering, Pennsylvania State University, University Park, PA 16802, USA.,Department of Engineering Science and Mechanics, Pennsylvania State University, University Park, PA 16802, USA
| | - Farrah Roy
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Kathryn Sheldon
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Reid Townsend
- Department of Medicine, Washington University School of Medicine , St. Louis, MO 63130, USA
| | - Andrew D Weeks
- Sanyu Research Unit, Liverpool Women's Hospital, University of Liverpool, Liverpool L8 7SS, UK
| | - Andrew J Whalen
- Department of Mechanical Engineering, Pennsylvania State University, University Park, PA 16802, USA
| | - John Quackenbush
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Peter Ssenyonga
- CURE Children's Hospital of Uganda, Plot 97-105, Bugwere Road, P.O. Box 903 Mbale, Uganda
| | - Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Mathieu Almeida
- Université Paris-Saclay, INRAE, MGP, Jouy-en-Josas, 78350, France
| | - Hannah Atkins
- Department of Comparative Medicine, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Benjamin C Warf
- Department of Neurosurgery, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA.,Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY 10032, USA
| | - James R Broach
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Steven J Schiff
- Center for Neural Engineering, Pennsylvania State University, University Park, PA 16802, USA. .,Department of Engineering Science and Mechanics, Pennsylvania State University, University Park, PA 16802, USA.,Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA 16802, USA.,Department of Neurosurgery, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA.,Department of Physics, Pennsylvania State University, University Park, PA 16802, USA
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Rao PS, Moore CC, Mbonde AA, Nuwagira E, Orikiriza P, Nyehangane D, Al-Shaer MH, Peloquin CA, Gratz J, Pholwat S, Arinaitwe R, Boum Y, Mwanga-Amumpaire J, Houpt ER, Kagan L, Heysell SK, Muzoora C. Population Pharmacokinetics and Significant Under-Dosing of Anti-Tuberculosis Medications in People with HIV and Critical Illness. Antibiotics (Basel) 2021; 10:antibiotics10060739. [PMID: 34207312 PMCID: PMC8235594 DOI: 10.3390/antibiotics10060739] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/12/2021] [Accepted: 06/15/2021] [Indexed: 12/18/2022] Open
Abstract
Critical illness from tuberculosis (TB) bloodstream infection results in a high case fatality rate for people living with human immunodeficiency virus (HIV). Critical illness can lead to altered pharmacokinetics and suboptimal drug exposures. We enrolled adults living with HIV and hospitalized with sepsis, with and without meningitis, in Mbarara, Uganda that were starting first-line anti-TB therapy. Serum was collected two weeks after enrollment at 1-, 2-, 4-, and 6-h post-dose and drug concentrations quantified by validated LC-MS/MS methods. Non-compartmental analyses were used to determine total drug exposure, and population pharmacokinetic modeling and simulations were performed to determine optimal dosages. Eighty-one participants were enrolled. Forty-nine completed pharmacokinetic testing: 18 (22%) died prior to testing, 13 (16%) were lost to follow-up and one had incomplete testing. Isoniazid had the lowest serum attainment, with only 4.1% achieving a target exposure over 24 h (AUC0–24) of 52 mg·h/L despite appropriate weight-based dosing. Simulations to reach target AUC0–24 found necessary doses of rifampin of 1800 mg, pyrazinamide of 2500–3000 mg, and for isoniazid 900 mg or higher. Given the high case fatality ratio of TB-related critical illness in this population, an early higher dose anti-TB therapy should be trialed.
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Affiliation(s)
- Prakruti S. Rao
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA 22908, USA; (P.S.R.); (C.C.M.); (J.G.); (S.P.); (E.R.H.)
| | - Christopher C. Moore
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA 22908, USA; (P.S.R.); (C.C.M.); (J.G.); (S.P.); (E.R.H.)
| | - Amir A. Mbonde
- Faculty of Medicine, Mbarara University of Science and Technology, Mbarara 1410, Uganda; (A.A.M.); (E.N.); (R.A.); (J.M.-A.); (C.M.)
| | - Edwin Nuwagira
- Faculty of Medicine, Mbarara University of Science and Technology, Mbarara 1410, Uganda; (A.A.M.); (E.N.); (R.A.); (J.M.-A.); (C.M.)
| | - Patrick Orikiriza
- Department of Microbiology, University of Global Health Equity, Kigali 6955, Rwanda;
| | - Dan Nyehangane
- Epicentre Mbarara Research Center, Mbarara 1956, Uganda; (D.N.); (Y.B.)
| | - Mohammad H. Al-Shaer
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA; (M.H.A.-S.); (C.A.P.)
| | - Charles A. Peloquin
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, University of Florida, Gainesville, FL 32610, USA; (M.H.A.-S.); (C.A.P.)
| | - Jean Gratz
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA 22908, USA; (P.S.R.); (C.C.M.); (J.G.); (S.P.); (E.R.H.)
| | - Suporn Pholwat
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA 22908, USA; (P.S.R.); (C.C.M.); (J.G.); (S.P.); (E.R.H.)
| | - Rinah Arinaitwe
- Faculty of Medicine, Mbarara University of Science and Technology, Mbarara 1410, Uganda; (A.A.M.); (E.N.); (R.A.); (J.M.-A.); (C.M.)
- Epicentre Mbarara Research Center, Mbarara 1956, Uganda; (D.N.); (Y.B.)
| | - Yap Boum
- Epicentre Mbarara Research Center, Mbarara 1956, Uganda; (D.N.); (Y.B.)
| | - Juliet Mwanga-Amumpaire
- Faculty of Medicine, Mbarara University of Science and Technology, Mbarara 1410, Uganda; (A.A.M.); (E.N.); (R.A.); (J.M.-A.); (C.M.)
- Epicentre Mbarara Research Center, Mbarara 1956, Uganda; (D.N.); (Y.B.)
| | - Eric R. Houpt
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA 22908, USA; (P.S.R.); (C.C.M.); (J.G.); (S.P.); (E.R.H.)
| | - Leonid Kagan
- Department of Pharmaceutics and Center of Excellence for Pharmaceutical Translational Research and Education, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA;
| | - Scott K. Heysell
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA 22908, USA; (P.S.R.); (C.C.M.); (J.G.); (S.P.); (E.R.H.)
- Correspondence:
| | - Conrad Muzoora
- Faculty of Medicine, Mbarara University of Science and Technology, Mbarara 1410, Uganda; (A.A.M.); (E.N.); (R.A.); (J.M.-A.); (C.M.)
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Lappan R, Henry R, Chown SL, Luby SP, Higginson EE, Bata L, Jirapanjawat T, Schang C, Openshaw JJ, O'Toole J, Lin A, Tela A, Turagabeci A, Wong THF, French MA, Brown RR, Leder K, Greening C, McCarthy D. Monitoring of diverse enteric pathogens across environmental and host reservoirs with TaqMan array cards and standard qPCR: a methodological comparison study. Lancet Planet Health 2021; 5:e297-e308. [PMID: 33964239 PMCID: PMC8116308 DOI: 10.1016/s2542-5196(21)00051-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 02/22/2021] [Accepted: 03/03/2021] [Indexed: 05/25/2023]
Abstract
BACKGROUND Multiple bacteria, viruses, protists, and helminths cause enteric infections that greatly impact human health and wellbeing. These enteropathogens are transmited via several pathways through human, animal, and environmental reservoirs. Individual qPCR assays have been extensively used to detect enteropathogens within these types of samples, whereas the TaqMan array card (TAC), which allows simultaneous detection of multiple enteropathogens, has only previously been validated in human clinical samples. METHODS In this methodological comparison study, we compared the performance of a custom 48-singleplex TAC relative to standard qPCR. We established the sensitivity and specificity of each method for the detection of eight enteric targets, by using spiked samples with varying levels of PCR inhibition. We then tested the prevalence and abundance of pathogens in wastewater from Melbourne (Australia), and human, animal, and environmental samples from informal settlements in Suva, Fiji using both TAC and qPCR. FINDINGS Both methods exhibited similarly h specificity (TAC 100%, qPCR 94%), sensitivity (TAC 92%, qPCR 100%), and quantitation accuracy (TAC 91%, qPCR 99%) in non-inhibited sample matrices with spiked gene fragments. PCR inhibitors substantially affected detection via TAC, though this issue was alleviated by ten-fold sample dilution. Among samples from informal settlements, the two techniques performed similarly for detection (89% agreement) and quantitation (R2 0·82) for the eight enteropathogen targets. The TAC additionally included 38 other enteric targets, enabling detection of diverse faecal pathogens and extensive environmental contamination that would be prohibitively labour intensive to assay by standard qPCR. INTERPRETATION The two techniques produced similar results across diverse sample types, with qPCR prioritising greater sensitivity and quantitation accuracy, and TAC trading small reductions in these for a cost-effective larger enteropathogen panel enabling a greater number of enteric pathogens to be analysed concurrently, which is beneficial given the abundance and variety of enteric pathogens in environments such as urban informal settlements. The ability to monitor multiple enteric pathogens across diverse reservoirs could allow better resolution of pathogen exposure pathways, and the design and monitoring of interventions to reduce pathogen load. FUNDING Wellcome Trust Our Planet, Our Health programme.
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Affiliation(s)
- Rachael Lappan
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Rebekah Henry
- Department of Civil Engineering, Monash University, Clayton, VIC, Australia
| | - Steven L Chown
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Stephen P Luby
- Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA
| | - Ellen E Higginson
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
| | - Lamiya Bata
- Department of Civil Engineering, Monash University, Clayton, VIC, Australia
| | - Thanavit Jirapanjawat
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - Christelle Schang
- Department of Civil Engineering, Monash University, Clayton, VIC, Australia
| | - John J Openshaw
- Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA
| | - Joanne O'Toole
- School of Public Health and Preventive Medicine, Monash University, Clayton, VIC, Australia
| | - Audrie Lin
- Division of Epidemiology and Biostatistics, School of Public Health, University of California Berkeley, CA, USA
| | - Autiko Tela
- School of Public Health, Fiji National University, Suva, Fiji
| | | | - Tony H F Wong
- Water Sensitive Cities Institute, Monash University, Clayton, VIC, Australia
| | - Matthew A French
- Monash Sustainable Development Institute, Monash University, Clayton, VIC, Australia
| | - Rebekah R Brown
- Monash Sustainable Development Institute, Monash University, Clayton, VIC, Australia
| | - Karin Leder
- School of Public Health and Preventive Medicine, Monash University, Clayton, VIC, Australia
| | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
| | - David McCarthy
- Department of Civil Engineering, Monash University, Clayton, VIC, Australia
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Marks F, Liu J, Soura AB, Gasmelseed N, Operario D, Grundy B, Wieser J, Gratz J, Meyer CG, Im J, Lim JK, von Kalckreuth V, Cruz Espinoza LM, Konings F, Jeon HJ, Rakotozandrindrainy R, Zhang J, Panzner U, Houpt E. Pathogens causing acute febrile illness among children and adolescents in Burkina Faso, Madagascar and Sudan. Clin Infect Dis 2021; 73:1338-1345. [PMID: 33822011 PMCID: PMC8528393 DOI: 10.1093/cid/ciab289] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 04/01/2021] [Indexed: 11/13/2022] Open
Abstract
Background The etiology and optimal clinical management of acute febrile illness (AFI) is poorly understood. Methods Blood samples taken from study participants with acute fever (≥37.5°C) or a history of fever and recruited into the previous Typhoid Fever Surveillance in Africa (TSAP) study were evaluated using a polymerase chain reaction (PCR)-based TaqMan-Array Card designed to detect a panel of bacterial, viral, and parasitic pathogens. Clinical metadata were also assessed. Results A total of 615 blood samples available for analysis originated from Burkina Faso (n = 53), Madagascar (n = 364), and Sudan (n = 198) and were taken from participants ranging in age from 0–19 years. Through the TaqMan-Array Card, at least 1 pathogen was detected in 62% (33 of 53), 24% (86 of 364), and 60% (118 of 198) of specimens from Burkina Faso, Madagascar, and Sudan, respectively. The leading identified pathogen overall was Plasmodium spp., accounting for 47% (25 of 53), 2.2% (8 of 364), and 45% (90 of 198) of AFI at the respective sites. In Madagascar, dengue virus was the most prevalent pathogen (10.2%). Overall, 69% (357 of 516) of patients with clinical diagnoses of malaria, respiratory infection, or gastrointestinal infection were prescribed a World Health Organization guideline-recommended empiric antibiotic, whereas only 45% (106 of 237) of patients with pathogens detected were treated with an antibiotic exerting likely activity. Conclusions A PCR approach for identifying multiple bacterial, viral, and parasitic pathogens in whole blood unveiled a diversity of previously undetected pathogens in AFI cases and carries implications for the appropriate management of this common syndrome.
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Affiliation(s)
- Florian Marks
- International Vaccine Institute, Seoul, Republic of Korea.,University of Antananarivo, Antananarivo, Madagascar.,Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | - Jie Liu
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | | | - Nagla Gasmelseed
- Faculty of Medicine at the University of Gezira, Wad Medani, Sudan
| | - Darwin Operario
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Brian Grundy
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - John Wieser
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Jean Gratz
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Christian G Meyer
- Faculty of Medicine, Duy Tan University, Da Nang, Vietnam.,Institute of Tropical Medicine, Eberhard Karls University, Tübingen, Germany
| | - Justin Im
- International Vaccine Institute, Seoul, Republic of Korea
| | | | | | | | - Frank Konings
- International Vaccine Institute, Seoul, Republic of Korea
| | - Hyon Jin Jeon
- International Vaccine Institute, Seoul, Republic of Korea.,Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, UK
| | | | - Jixian Zhang
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Ursula Panzner
- International Vaccine Institute, Seoul, Republic of Korea.,Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Eric Houpt
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
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30
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Gu X, Zhou F, Wang Y, Fan G, Cao B. Respiratory viral sepsis: epidemiology, pathophysiology, diagnosis and treatment. Eur Respir Rev 2020; 29:200038. [PMID: 32699026 PMCID: PMC9489194 DOI: 10.1183/16000617.0038-2020] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 04/04/2020] [Indexed: 12/11/2022] Open
Abstract
According to the Third International Consensus Definition for Sepsis and Septic Shock, sepsis is a life-threatening organ dysfunction resulting from dysregulated host responses to infection. Epidemiological data about sepsis from the 2017 Global Burden of Diseases, Injuries and Risk Factor Study showed that the global burden of sepsis was greater than previously estimated. Bacteria have been shown to be the predominant pathogen of sepsis among patients with pathogens detected, while sepsis caused by viruses is underdiagnosed worldwide. The coronavirus disease that emerged in 2019 in China and now in many other countries has brought viral sepsis back into the vision of physicians and researchers worldwide. Although the current understanding of the pathophysiology of sepsis has improved, the differences between viral and bacterial sepsis at the level of pathophysiology are not well understood. Diagnosis methods that can broadly differentiate between bacterial and viral sepsis at the initial stage after the development of sepsis are limited. New treatments that can be applied at clinics for sepsis are scarce and this situation is not consistent with the growing understanding of pathophysiology. This review aims to give a brief summary of current knowledge of the epidemiology, pathophysiology, diagnosis and treatment of viral sepsis.
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Affiliation(s)
- Xiaoying Gu
- Dept of Pulmonary and Critical Care Medicine, National Clinical Research Center of Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Science, Beijing, China
- Institute of Clinical Medical Sciences, China-Japan Friendship Hospital, Beijing, China
| | - Fei Zhou
- Dept of Pulmonary and Critical Care Medicine, National Clinical Research Center of Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Science, Beijing, China
| | - Yeming Wang
- Dept of Pulmonary and Critical Care Medicine, National Clinical Research Center of Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Science, Beijing, China
| | - Guohui Fan
- Dept of Pulmonary and Critical Care Medicine, National Clinical Research Center of Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Science, Beijing, China
- Institute of Clinical Medical Sciences, China-Japan Friendship Hospital, Beijing, China
| | - Bin Cao
- Dept of Pulmonary and Critical Care Medicine, National Clinical Research Center of Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Science, Beijing, China
- Dept of Respiratory Medicine, Capital Medical University, Beijing, China
- Tsinghua University-Peking University Joint Center for Life Sciences, Beijing, China
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Boyd AT, Oboho I, Paulin H, Ali H, Godfrey C, Date A, Sean Cavanaugh J. Addressing advanced HIV disease and mortality in global HIV programming. AIDS Res Ther 2020; 17:40. [PMID: 32650797 PMCID: PMC7348123 DOI: 10.1186/s12981-020-00296-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 07/02/2020] [Indexed: 11/10/2022] Open
Abstract
INTRODUCTION The US President's Emergency Plan for AIDS Relief (PEPFAR) was launched to increase access to antiretroviral treatment (ART) among people living with HIV (PLHIV) and to prevent new HIV infections globally. As new infections have decreased in many PEPFAR-supported countries, PEPFAR is increasingly focusing on understanding and decreasing mortality among PLHIV, specifically by addressing advanced HIV disease (AHD) and its attendant opportunistic infections (OIs). Several developments in identifying AHD, in preventing, diagnosing, and treating selected OIs, and in PEPFAR's support for mortality surveillance make this an opportune moment for PEPFAR to address HIV-related mortality. DISCUSSION AHD upon diagnosis or re-engagement in HIV care is not uncommon, and it substantially increases risk of death from OIs. The World Health Organization provides evidence-based guidelines for a package of interventions for preventing, diagnosing, and treating common OIs, including tuberculosis (TB), cryptococcal meningitis, and severe bacterial infections. PEPFAR facilitates implementation of these guidelines. To identify PLHIV with low CD4, PEPFAR plans to support expanded access to CD4 testing, including a point-of-care assay that differentiates CD4 cell count as a binary of greater than or less than 200 cells/µL. To prevent AHD-related mortality, PEPFAR supports rapid ART initiation with integrase inhibitor-based regimens and implementation and documentation of TB preventive treatment. To diagnose selected OIs, PEPFAR is implementing urine lateral flow lipoarabinomannan use to identify TB among PLHIV who have a CD4 cell count < 200 cells/µL. To treat selected OIs, PEPFAR has focused on improving patient-centered care in TB/HIV co-infection services and scaling up implementation of new drug regimens for cryptococcal meningitis. To better understand mortality, PEPFAR has introduced an indicator, TX_ML, to routinely and systematically categorize outcomes, including deaths, among PLHIV on ART. CONCLUSIONS PEPFAR is increasing its efforts to identify AHD; to prevent, diagnose, and treat OIs; and to track mortality in its programs. These ongoing efforts, done in collaboration with other stakeholders, seek to decrease mortality among PLHIV.
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Kwambana-Adams BA, Liu J, Okoi C, Mwenda JM, Mohammed NI, Tsolenyanu E, Renner LA, Ansong D, Tagbo BN, Bashir MF, Hama MK, Sonko MA, Gratz J, Worwui A, Ndow P, Cohen AL, Serhan F, Mihigo R, Antonio M, Houpt E, On Behalf Of The Paediatric Bacterial Meningitis Surveillance Network In West Africa. Etiology of Pediatric Meningitis in West Africa Using Molecular Methods in the Era of Conjugate Vaccines against Pneumococcus, Meningococcus, and Haemophilus influenzae Type b. Am J Trop Med Hyg 2020; 103:696-703. [PMID: 32458777 PMCID: PMC7410464 DOI: 10.4269/ajtmh.19-0566] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Despite the implementation of effective conjugate vaccines against the three main bacterial pathogens that cause meningitis, Streptococcus pneumoniae, Haemophilus influenzae type b (Hib), and Neisseria meningitidis serogroup A, the burden of meningitis in West Africa remains high. The relative importance of other bacterial, viral, and parasitic pathogens in central nervous system infections is poorly characterized. Cerebrospinal fluid (CSF) specimens were collected from children younger than 5 years with suspected meningitis, presenting at pediatric teaching hospitals across West Africa in five countries including Senegal, Ghana, Togo, Nigeria, and Niger. Cerebrospinal fluid specimens were initially tested using bacteriologic culture and a triplex real-time polymerase chain reaction (PCR) assay for N. meningitidis, S. pneumoniae, and H. influenzae used in routine meningitis surveillance. A custom TaqMan Array Card (TAC) assay was later used to detect 35 pathogens including 15 bacteria, 17 viruses, one fungus, and two protozoans. Among 711 CSF specimens tested, the pathogen positivity rates were 2% and 20% by the triplex real-time PCR (three pathogens) and TAC (35 pathogens), respectively. TAC detected 10 bacterial pathogens, eight viral pathogens, and Plasmodium. Overall, Escherichia coli was the most prevalent (4.8%), followed by S. pneumoniae (3.5%) and Plasmodium (3.5%). Multiple pathogens were detected in 4.4% of the specimens. Children with human immunodeficiency virus (HIV) and Plasmodium detected in CSF had high mortality. Among 220 neonates, 17% had at least one pathogen detected, dominated by gram-negative bacteria. The meningitis TAC enhanced the detection of pathogens in children with meningitis and may be useful for case-based meningitis surveillance.
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Affiliation(s)
- Brenda A Kwambana-Adams
- Division of Infection and Immunity, NIHR Global Health Research Unit on Mucosal Pathogens, University College London, London, United Kingdom.,WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Jie Liu
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia
| | - Catherine Okoi
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Jason M Mwenda
- World Health Organization (WHO), Regional Office for Africa, Brazzaville, Congo
| | - Nuredin I Mohammed
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Enyonam Tsolenyanu
- Department of Paediatrics, Sylvanus Olympio Teaching Hospital, Lomé, Togo
| | - Lorna Awo Renner
- University of Ghana School of Medicine and Dentistry, Accra, Ghana
| | | | - Beckie N Tagbo
- Department of Paediatrics, University of Nigeria Teaching Hospital Ituku-Ozalla, Enug, Nigeria.,Institute of Child Health, University of Nigeria Teaching Hospital, Enug, Nigeria
| | - Muhammad F Bashir
- Department of Paediatrics, Abubakar Tafawa Balewa University Teaching Hospital, Bauchi, Nigeria
| | | | | | - Jean Gratz
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia
| | - Archibald Worwui
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Peter Ndow
- WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | | | | | - Richard Mihigo
- World Health Organization (WHO), Regional Office for Africa, Brazzaville, Congo
| | - Martin Antonio
- Division of Microbiology and Immunity, Warwick Medical School, University of Warwick, Coventry, United Kingdom.,WHO Collaborating Centre for New Vaccines Surveillance, Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia.,Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Eric Houpt
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia
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Byashalira K, Mbelele P, Semvua H, Chilongola J, Semvua S, Liyoyo A, Mmbaga B, Mfinanga S, Moore C, Heysell S, Mpagama S. Clinical outcomes of new algorithm for diagnosis and treatment of Tuberculosis sepsis in HIV patients. Int J Mycobacteriol 2020; 8:313-319. [PMID: 31793499 DOI: 10.4103/ijmy.ijmy_135_19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Background Despite effort to diagnose tuberculosis (TB) in the Human Immunodeficiency Virus (HIV) infected population, 45% of adults with HIV that had a previously unknown reason for death, demonstrated TB was the cause by autopsy examination. We aimed to assess the clinical outcomes of implementation a new algorithm for diagnosis and treatment of tuberculosis (TB) related sepsis among PLHIV presenting with life-threatening illness. Methods This study is a prospective cohort conducted in three-referral hospitals in Kilimanjaro, recruited 97 PLHIV from February through June 2018. Patients provided urine and sputum samples for testing lateral flow - lipoarabinomannan (LF-LAM) and Xpert Mycobacterium tuberculosis (MTB)/rifampicin (RIF) assays, respectively. Anti-TB was prescribed to patients with positive LF-LAM or Xpert MTB/RIF or received broad-spectrum antibiotics but deteriorated. Results Of 97 patients, 84 (87%) provided urine and sputa, and 13 (13%) provided only urine. The mean age (95% confidence interval) was 40 (38-43) years and 52 (54%) were female. In 84 patients, LF-LAM increased TB detection from 26 (31%) by Xpert MTB/RIF to 41 (55%) by both tests. Of 97 patients, 69 (71%) prescribed anti-TB, 67% (46/69) and 33% (23/69) had definitive and probable TB respectively. Sixteen (16.5%) patients died, of which one died before treatment, 73% (11/15) died within 7 days of admission. The 30-day survival was similar in both treatment groups (log rank = 0.1574). Mortality was significantly higher among hospitalized patients compared to outpatients (P ≤ 0.027). Conclusion Implementation of new algorithm increased TB case detection in patients that could have been missed by Xpert MTB/RIF assay. Survival of PLHIV with confirmed or probable TB was comparable to those of PLHIV that were treated with broad-spectrum antibiotics alone. Further work should focus on the optimal timing and content of the immediate antimicrobial regimen for sepsis among PLHIV in TB-endemic settings.
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Affiliation(s)
- Kenneth Byashalira
- Kilimanjaro Christian Medical University College; Kibong'oto Infectious Diseases Hospital, Tanzania
| | | | - Hadija Semvua
- Kilimanjaro Christian Medical University College; Kilimanjaro Clinical Research Institute, Tanzania
| | - Jaffu Chilongola
- Kilimanjaro Christian Medical University College; Kilimanjaro Clinical Research Institute, Tanzania
| | - Seleman Semvua
- Kilimanjaro Christian Medical University College, Tanzania
| | | | - Blandina Mmbaga
- Kilimanjaro Christian Medical University College; Kilimanjaro Clinical Research Institute, Tanzania
| | - Sayoki Mfinanga
- National Institute for Medical Research-Muhimbili Medical Research Centre, Tanzania
| | - Christopher Moore
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Scott Heysell
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, Virginia, USA
| | - Stellah Mpagama
- Kilimanjaro Christian Medical University College; Kibong'oto Infectious Diseases Hospital, Tanzania
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Chaka W, Berger C, Huo S, Robertson V, Tachiona C, Magwenzi M, Magombei T, Mpamhanga C, Katzenstein D, Metcalfe J. Presentation and outcome of suspected sepsis in a high-HIV burden, high antiretroviral coverage setting. Int J Infect Dis 2020; 96:276-283. [PMID: 32289564 PMCID: PMC8040698 DOI: 10.1016/j.ijid.2020.04.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 03/31/2020] [Accepted: 04/01/2020] [Indexed: 12/17/2022] Open
Abstract
Objective: To define sepsis syndromes in high-HIV burden settings in the antiretroviral therapy (ART) era. Methods: We characterized a prospective cohort of adults presenting to a tertiary emergency department in Harare, Zimbabwe with suspected community-acquired sepsis using blood and urine cultures, urine tuberculosis lipoarabinomannan (TB LAM), and serum cryptococcal antigen (CrAg) testing. The primary outcome was 30-day all-cause mortality. Results: Of 142 patients enrolled 68% (n = 96/142, 95% confidence interval (CI) [60–75%]) were HIV-positive, 41% (n = 39/96, 95% CI [31–50%]) of whom were ART-naïve. Among HIV-positive patients, both opportunistic pathogens (TB LAM-positivity, 36%, 95% CI [24–48%]; CrAg-positivity, 15%, 95% CI [7–23%]) and severe non-AIDS infections (S. pneumoniae urine antigen-positivity 12%, 95% CI [4–20%]; bacteraemia 17% (n = 16/96, 95% CI [9–24%]), of which 56% (n = 9/16, 95% CI [30–80%]) were gram-negative organisms) were common. Klebsiella pneumoniae recovered from blood and urine was uniformly resistant to ceftriaxone, as were most Escherichia coli isolates. Acknowledging the power limitations of our study, we conclude that relative to HIV-negative patients, HIV-positive patients had modestly higher 30-day mortality (adjusted hazard ratio (HR) 1.88, 95% CI [0.78–4.55]; p = 0.16, and 3.59, 95% CI [1.27–10.16], p = 0.02) among those with and without viral suppression, respectively. Conclusion: Rapid point-of-care assays provide substantial clinically actionable information in the setting of suspected sepsis, even in areas with high ART coverage. Antimicrobial resistance to first-line antibiotics in high burden settings is a growing threat.
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Affiliation(s)
- Wendy Chaka
- University of Zimbabwe College of Health Sciences, Department of Medical Microbiology, Box A178 Avondale, Harare, Zimbabwe
| | - Christopher Berger
- Zuckerberg San Francisco General Hospital, Division of Pulmonary and Critical Care Medicine, University of California, San Francisco, USA
| | - Stella Huo
- Zuckerberg San Francisco General Hospital, Division of Pulmonary and Critical Care Medicine, University of California, San Francisco, USA
| | - Valerie Robertson
- University of Zimbabwe College of Health Sciences, Department of Medical Microbiology, Box A178 Avondale, Harare, Zimbabwe
| | - Chipo Tachiona
- University of Zimbabwe College of Health Sciences, Department of Medical Microbiology, Box A178 Avondale, Harare, Zimbabwe
| | - Marcelyn Magwenzi
- University of Zimbabwe College of Health Sciences, Department of Medical Microbiology, Box A178 Avondale, Harare, Zimbabwe
| | - Trish Magombei
- University of Zimbabwe College of Health Sciences, Department of Medical Microbiology, Box A178 Avondale, Harare, Zimbabwe
| | - Chengetai Mpamhanga
- Parirenyatwa Group of Hospitals, Public Health Microbiology Laboratory, Mazowe Street, Harare, Zimbabwe
| | - David Katzenstein
- Stanford University Department of Medicine/Infectious Diseases, Stanford, CA 94305-5107, USA
| | - John Metcalfe
- Zuckerberg San Francisco General Hospital, Division of Pulmonary and Critical Care Medicine, University of California, San Francisco, USA.
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Cytomegalovirus in Pediatric Sepsis: Should We Care? Pediatr Crit Care Med 2020; 21:396-397. [PMID: 32251188 DOI: 10.1097/pcc.0000000000002209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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36
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Sinkov VV, Ogarkov OB, Plotnikov AO, Gogoleva NE, Zhdanova SN, Pervanchuk VL, Belkova NL, Koshcheev ME, Thomas TA, Liu J, Zorkaltseva EY, Heysell SK. Metagenomic analysis of mycobacterial transrenal DNA in patients with HIV and tuberculosis coinfection. INFECTION GENETICS AND EVOLUTION 2019; 77:104057. [PMID: 31629083 DOI: 10.1016/j.meegid.2019.104057] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 09/23/2019] [Accepted: 09/29/2019] [Indexed: 10/25/2022]
Abstract
The existence of "transrenal" DNA (tr-DNA), i.e. cell-free DNA that has distributed through the renal barrier to the urine, was first shown from a pathogen in 2000 (Botezatu et al., 2000). However, a targeted search for tr-DNA from Mycobacterium tuberculosis (MBT) started relatively recently (Cannas et al., 2008; Green et al., 2009). While other MBT cellular components found in the urine, e.g. lipoarabinomannan, have been used as an enhanced diagnostic tool, tr-DNA has the potential for strain specific identification or a more persistent biomarker during treatment of active disease. We therefore sought to identify by high-throughput next generation sequencing (NGS) MBT genome fragments in the urine of people with human immunodeficiency virus and tuberculosis (HIV-TB) co-infection living in a co-epidemic setting, and to evaluate whether these DNA targets are suitable for the development a quantitative TaqMan polymerase chain reaction with real-time detection (rt-PCR). Selection and mapping to the reference MBT genome of strain H37Rv (NC_000962) revealed 158 fragments of mycobacterial DNA with length from 19 to 44 base pairs (bp) repeated in different DNA samples. Five targets were chosen for design of rt-PCR primers and probes. Comparative analysis of the newly developed tests that were based on the results of NGS did not reveal a significant increase in sensitivity and specificity relative to the previous empirically designed targets. Howver, highly reproducible NGS reads of mycobacterial tr-DNA were obtained. rt-PCR test development suitable for more practical clinical use was likely limited by the small size of the secreted DNA fragments. It is necessary to develop further molecular approaches for the detection of mycobacterial tr-DNA or rely on NGS techniques with inherent bioinformatics requirements.
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Affiliation(s)
- Viacheslav V Sinkov
- Department of Epidemiology and Microbiology, "Scientific Centre for Family Health and Human Reproduction Problems", Irkutsk, Russia
| | - Oleg B Ogarkov
- Department of Epidemiology and Microbiology, "Scientific Centre for Family Health and Human Reproduction Problems", Irkutsk, Russia; Irkutsk State Medical Academy of Continuing Education, Irkutsk, Russia.
| | - Andrey O Plotnikov
- Center of Shared Scientific Equipment "Persistence of microorganisms", Institute for Cellular and Intracellular Symbiosis, Ural Branch of Russian Academy of Sciences, Orenburg, Russia
| | - Natalya E Gogoleva
- Center of Shared Scientific Equipment "Persistence of microorganisms", Institute for Cellular and Intracellular Symbiosis, Ural Branch of Russian Academy of Sciences, Orenburg, Russia; Kazan Institute of Biochemistry and Biophysics, Russian Academy of Sciences, Kazan, Russia
| | - Svetlana N Zhdanova
- Department of Epidemiology and Microbiology, "Scientific Centre for Family Health and Human Reproduction Problems", Irkutsk, Russia
| | | | - Natalia L Belkova
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | | | - Tania A Thomas
- Division of Infectious Diseases and International Health, University of Virginia, Virginia, USA
| | - Jie Liu
- Division of Infectious Diseases and International Health, University of Virginia, Virginia, USA
| | | | - Scott K Heysell
- Division of Infectious Diseases and International Health, University of Virginia, Virginia, USA
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Diaz MH, Waller JL, Theodore MJ, Patel N, Wolff BJ, Benitez AJ, Morris T, Raghunathan PL, Breiman RF, Whitney CG, Blau DM, Winchell JM. Development and Implementation of Multiplex TaqMan Array Cards for Specimen Testing at Child Health and Mortality Prevention Surveillance Site Laboratories. Clin Infect Dis 2019; 69:S311-S321. [PMID: 31598666 PMCID: PMC7108207 DOI: 10.1093/cid/ciz571] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Child Health and Mortality Prevention Surveillance (CHAMPS) laboratories are employing a variety of laboratory methods to identify infectious agents contributing to deaths of children <5 years old and stillbirths in sub-Saharan Africa and South Asia. In support of this long-term objective, our team developed TaqMan Array Cards (TACs) for testing postmortem specimens (blood, cerebrospinal fluid, lung tissue, respiratory tract swabs, and rectal swabs) for >100 real-time polymerase chain reaction (PCR) targets in total (30-45 per card depending on configuration). Multipathogen panels were configured by syndrome and customized to include pathogens of significance in young children within the regions where CHAMPS is conducted, including bacteria (57 targets covering 30 genera), viruses (48 targets covering 40 viruses), parasites (8 targets covering 8 organisms), and fungi (3 targets covering 3 organisms). The development and application of multiplex real-time PCR reactions to the TAC microfluidic platform increased the number of targets in each panel while maintaining assay efficiency and replicates for heightened sensitivity. These advances represent a substantial improvement in the utility of this technology for infectious disease diagnostics and surveillance. We optimized all aspects of the CHAMPS molecular laboratory testing workflow including nucleic acid extraction, quality assurance, and data management to ensure comprehensive molecular testing of specimens and high-quality data. Here we describe the development and implementation of multiplex TACs and associated laboratory protocols for specimen processing, testing, and data management at CHAMPS site laboratories.
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Affiliation(s)
- Maureen H Diaz
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jessica L Waller
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | | | | | - Bernard J Wolff
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Alvaro J Benitez
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Timothy Morris
- Public Health Informatics Institute, The Task Force for Global Health, Atlanta, Georgia, USA
| | - Pratima L Raghunathan
- Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Robert F Breiman
- Emory Global Health Institute, Emory University, Atlanta, Georgia, USA
| | - Cynthia G Whitney
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Dianna M Blau
- Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jonas M Winchell
- Respiratory Diseases Branch, Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Lewis JM, Feasey NA, Rylance J. Aetiology and outcomes of sepsis in adults in sub-Saharan Africa: a systematic review and meta-analysis. CRITICAL CARE : THE OFFICIAL JOURNAL OF THE CRITICAL CARE FORUM 2019; 23:212. [PMID: 31186062 PMCID: PMC6558702 DOI: 10.1186/s13054-019-2501-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 05/29/2019] [Indexed: 12/29/2022]
Abstract
Background Aetiology and outcomes of sepsis in sub-Saharan Africa (sSA) are poorly described; we performed a systematic review and meta-analysis to summarise the available data. Methods Systematic searches of PubMed and Scopus were undertaken to identify prospective studies recruiting adults (> 13 years) with community-acquired sepsis in sSA post-2000. Random effects meta-analysis of in-hospital and 30-day mortality was undertaken and available aetiology data also summarised by random effects meta-analysis. Results Fifteen studies of 2800 participants were identified. Inclusion criteria were heterogeneous. The majority of patients were HIV-infected, and Mycobacterium tuberculosis was the most common cause of blood stream infection where sought. Pooled in-hospital mortality for Sepsis-2-defined sepsis and severe sepsis was 19% (95% CI 12–29%) and 39% (95% CI 30–47%) respectively, and sepsis mortality was associated with the proportion of HIV-infected participants. Mortality and morbidity data beyond 30 days were absent. Conclusions Sepsis in sSA is dominated by HIV and tuberculosis, with poor outcomes. Optimal antimicrobial strategies, including the role of tuberculosis treatment, are unclear. Long-term outcome data are lacking. Standardised sepsis diagnostic criteria that are easily applied in low-resource settings are needed to establish an evidence base for sepsis management in sSA. Electronic supplementary material The online version of this article (10.1186/s13054-019-2501-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joseph M Lewis
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK. .,Malawi Liverpool Wellcome Clinical Research Programme, Blantyre, Malawi.
| | - Nicholas A Feasey
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK.,Malawi Liverpool Wellcome Clinical Research Programme, Blantyre, Malawi
| | - Jamie Rylance
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK.,Malawi Liverpool Wellcome Clinical Research Programme, Blantyre, Malawi
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Hazard RH, Kagina P, Kitayimbwa R, Male K, McShane M, Mubiru D, Welikhe E, Moore CC, Abdallah A. Effect of Empiric Anti- Mycobacterium tuberculosis Therapy on Survival Among Human Immunodeficiency Virus-Infected Adults Admitted With Sepsis to a Regional Referral Hospital in Uganda. Open Forum Infect Dis 2019; 6:ofz140. [PMID: 31024977 PMCID: PMC6475587 DOI: 10.1093/ofid/ofz140] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 03/13/2019] [Indexed: 11/26/2022] Open
Abstract
Background Mycobacterium tuberculosis is the leading cause of bloodstream infection among human immunodeficiency virus (HIV)–infected patients with sepsis in sub-Saharan Africa and is associated with high mortality rates. Methods We conducted a retrospective study of HIV-infected adults with sepsis at the Mbarara Regional Referral Hospital in Uganda to measure the proportion who received antituberculosis therapy and to determine the relationship between antituberculosis therapy and 28-day survival. Results Of the 149 patients evaluated, 74 (50%) had severe sepsis and 48 (32%) died. Of the 55 patients (37%) who received antituberculosis therapy, 19 (35%) died, compared with 29 of 94 (31%) who did not receive such therapy (odds ratio, 1.34; 95% confidence interval [CI], .56–3.18; P = .64). The 28-day survival rates did not differ significantly between these 2 groups (log-rank test, P = .21). Among the 74 patients with severe sepsis, 9 of 26 (35%) who received antituberculosis therapy died, versus 23 of 48 (48%) who did not receive such therapy (odds ratio, 0.58; 95% CI, .21–1.52; P = .27). In patients with severe sepsis, antituberculosis therapy was associated with an improved 28-day survival rate (log-rank test P = .01), and with a reduced mortality rate in a Cox proportional hazards model (hazard ratio, 0.32; 95% CI, .13–.80; P = .03). Conclusions Empiric antituberculosis therapy was associated with improved survival rates among patients with severe sepsis, but not among all patients with sepsis.
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Affiliation(s)
- Riley H Hazard
- University of Melbourne, School of Population and Global Health, Australia
| | - Peninah Kagina
- Mbarara University of Science and Technology, Department of Medicine, Uganda
| | - Richard Kitayimbwa
- Mbarara University of Science and Technology, Department of Medicine, Uganda
| | - Keneth Male
- Mbarara University of Science and Technology, Department of Medicine, Uganda
| | - Melissa McShane
- Temple University, Department of Medicine, Division of Hematology and Oncology, Philadelphia, Pennsylvania.,University of Virginia, Department of Medicine, Division of Infectious Diseases, Charlottesville
| | - Dennis Mubiru
- Mbarara University of Science and Technology, Department of Medicine, Uganda
| | - Emma Welikhe
- Mbarara University of Science and Technology, Department of Medicine, Uganda
| | - Christopher C Moore
- Mbarara University of Science and Technology, Department of Medicine, Uganda.,University of Virginia, Department of Medicine, Division of Infectious Diseases, Charlottesville
| | - Amir Abdallah
- Mbarara University of Science and Technology, Department of Medicine, Uganda.,Mayo Clinic Phoenix, Department of Neurology, Arizona
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