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Khun PA, Phi LD, Bui HTT, Collins DA, Riley TV. Clostridioides (Clostridium) difficile in adults with diarrhoea in Vietnam. Anaerobe 2023:102741. [PMID: 37244476 DOI: 10.1016/j.anaerobe.2023.102741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/18/2023] [Accepted: 05/20/2023] [Indexed: 05/29/2023]
Abstract
BACKGROUND Clostridioides (Clostridium) difficile causes antimicrobial-associated diarrhoea, however, presentations may range from asymptomatic carriage to severe diarrhoea, life-threatening toxic megacolon and even death. Reports on C. difficile infection (CDI) in Vietnam remain limited. The objectives of this study were to evaluate the epidemiology, molecular characteristics, and antimicrobial susceptibility of C. difficile isolated from adults with diarrhoea in Vietnam. METHODS Diarrhoeal stool samples from adult patients aged ≥17 years old were collected at Thai Binh General Hospital in northern Vietnam between 1st March 2021 and 28th February2022. All samples were transported to The University of Western Australia, Perth, Western Australia for C. difficile culture, toxin gene profiling, PCR ribotyping and antimicrobial susceptibility testing. RESULTS A total of 205 stool samples were collected from patients aged from 17 to 101 years old. The overall prevalence of C. difficile was 15.1% (31/205) with the recovery of toxigenic and non-toxigenic isolates 9.8% (20/205) and 6.3% (13/205), respectively. Thus 33 isolates were recovered comprising 18 known ribotypes (RTs) and one novel RT (two samples contained two different RTs in each sample). The most prevalent strains were RT 012 (five strains) and RTs 014/020, 017 and QX 070 three strains each. All C. difficile were susceptible to amoxicillin/clavulanate, fidaxomicin, metronidazole, moxifloxacin and vancomycin, while resistance to varying degrees was seen to clindamycin, erythromycin, tetracycline and rifaximin, 78.8% (26/33), 51.5% (17/33), 27.3% (9/33) and 6.1% (2/33), respectively. The prevalence of multidrug resistance was 27.3% (9/33) and multidrug resistance was most common in toxigenic RT 012 and non-toxigenic RT 038 strains. CONCLUSION The prevalence of C. difficile in adults with diarrhoea and multidrug resistance in C. difficile isolates was relatively high. A clinical assessment to differentiate between CDI/disease and colonisation is required.
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Affiliation(s)
- Peng An Khun
- School of Biomedical Sciences, The University of Western Australia, Western Australia, Australia
| | - Long Duc Phi
- Thai Binh University of Medicine and Pharmacy, Thai Binh, Viet Nam
| | | | - Deirdre A Collins
- School of Medical & Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Thomas V Riley
- School of Biomedical Sciences, The University of Western Australia, Western Australia, Australia; School of Medical & Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia; Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, Western Australia, Australia; Department of Microbiology, PathWest Laboratory Medicine, Nedlands, Western Australia, Australia.
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Delahoy MJ, Hubbard S, Mattioli M, Culquichicón C, Knee J, Brown J, Cabrera L, Barr DB, Ryan PB, Lescano AG, Gilman RH, Levy K. High Prevalence of Chemical and Microbiological Drinking Water Contaminants in Households with Infants Enrolled in a Birth Cohort-Piura, Peru, 2016. Am J Trop Med Hyg 2022; 107:881-892. [PMID: 35970283 PMCID: PMC9651523 DOI: 10.4269/ajtmh.22-0098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 06/06/2022] [Indexed: 11/07/2022] Open
Abstract
Chemical and microbiological drinking water contaminants pose risks to child health but are not often evaluated concurrently. At two consecutive visits to 96 households in Piura, Peru, we collected drinking water samples, administered health and exposure questionnaires, and collected infant stool samples. Standard methods were used to quantify heavy metals/metalloids, pesticides, and Escherichia coli concentrations in water samples. Stool samples were assayed for bacterial, viral, and parasitic enteropathogens. The primary drinking water source was indoor piped water for 70 of 96 households (73%); 36 households (38%) stored drinking water from the primary source in containers in the home. We found high prevalence of chemical and microbiological contaminants in household drinking water samples: arsenic was detected in 50% of 96 samples, ≥ 1 pesticide was detected in 65% of 92 samples, and E. coli was detected in 37% of 319 samples. Drinking water samples that had been stored in containers had higher odds of E. coli detection (adjusted odds ratio [aOR]: 4.50; 95% CI: 2.04-9.95) and pesticide detection (OR: 6.55; 95% CI: 2.05-21.0) compared with samples collected directly from a tap. Most infants (68%) had ≥ 1 enteropathogen detected in their stool. Higher odds of enteropathogen infection at the second visit were observed among infants from households where pesticides were detected in drinking water at the first visit (aOR: 2.93; 95% CI: 1.13-7.61). Results show concurrent risks of exposure to microbiological and chemical contaminants in drinking water in a low-income setting, despite high access to piped drinking water.
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Affiliation(s)
- Miranda J. Delahoy
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, United States
| | - Sydney Hubbard
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, United States
| | - Mia Mattioli
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, United States
| | - Carlos Culquichicón
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, United States
- Emerge, Emerging Diseases and Climate Change Research Unit, School of Public Health and Administration, Universidad Peruana Cayetano Heredia, Lima, Peru
- School of Health Sciences, Universidad Nacional de Piura, Piura, Peru
| | - Jackie Knee
- Disease Control Department, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Joe Brown
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States
| | | | - Dana Boyd Barr
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, United States
| | - P. Barry Ryan
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, United States
| | - Andres G. Lescano
- Emerge, Emerging Diseases and Climate Change Research Unit, School of Public Health and Administration, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Robert H. Gilman
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States
| | - Karen Levy
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia, United States
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, Washington, United States
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Khun PA, Riley TV. Epidemiology of Clostridium (Clostridioides) difficile Infection in Southeast Asia. Am J Trop Med Hyg 2022; 107:tpmd211167. [PMID: 35940201 PMCID: PMC9490644 DOI: 10.4269/ajtmh.21-1167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 03/27/2022] [Indexed: 11/07/2022] Open
Abstract
This review describes the current understanding of Clostridium (Clostridioides) difficile infection (CDI) in southeast Asia regarding the prevalence of CDI, C. difficile detection methods, antimicrobial susceptibility profiles, and the potential significance of a One Health approach to prevention and control. Our initial focus had been the Indochina region, however, due to limited studies/surveillance of CDI in Indochina, other studies in southeast Asian countries and neighboring Chinese provinces are presented here for comparison. Clostridium (Clostridioides) difficile infection is one of the most common causes of hospital-acquired gastroenteritis worldwide. Since its discovery as a cause of pseudomembranous colitis in 1978, C. difficile-related disease has been more prevalent in high-income rather than low-income countries. This may be because of a lack of knowledge and awareness about the significance of C. difficile and CDI, resulting in underreporting of true rates. Moreover, the abuse of antimicrobials and paucity of education regarding appropriate usage remain important driving factors in the evolution of CDI worldwide. The combination of underreporting of true CDI rates, along with continued misuse of antimicrobial agents, poses an alarming threat for regions like Indochina. C. difficile ribotype (RT) 027 has caused outbreaks in North America and European countries, however, C. difficile RT 017 commonly occurs in Asia. Toxin A-negative/toxin B-positive (A-B+) strains of RT 017 have circulated widely and caused outbreaks throughout the world and, in southeast Asia, this strain is endemic.
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Affiliation(s)
- Peng An Khun
- School of Biomedical Sciences, The University of Western Australia, Western Australia, Australia
| | - Thomas V. Riley
- School of Biomedical Sciences, The University of Western Australia, Western Australia, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
- Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, Western Australia, Australia
- Department of Microbiology, PathWest Laboratory Medicine, Nedlands, Western Australia, Australia
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Rousou X, Furuya-Kanamori L, Kostoulas P, Doi SAR. Diagnostic accuracy of multiplex nucleic acid amplification tests for Campylobacter infection: a systematic review and meta-analysis. Pathog Glob Health 2022; 117:259-272. [PMID: 35815907 PMCID: PMC10081061 DOI: 10.1080/20477724.2022.2097830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Abstract
Campylobacter infection is one of the most frequently reported foodborne diseases with approximately 230,000 and 1.5 million cases each year in Europe and the USA, respectively. Culture methods are the reference for the diagnosis of Campylobacter infections; however, these methods are complex and time-consuming. Multiplex nucleic acid amplification test is favored due to its rapidity, automatization in the procedure followed and the quick simultaneous testing of numerous foodborne pathogens. The aim of this meta-analysis was to evaluate the accuracy of these tests for the diagnosis of Campylobacter infection. Scopus, Science Direct, PubMed, Web of Science, and Mendeley were searched for peer-reviewed articles. The split component synthesis method with the use of the inverse variance heterogeneity model was chosen for the quantitative meta-analysis. Sensitivity analysis was performed by age category and index test. The literature search found 34 studies involving 28,105 patients with suspected gastroenteritis. The sensitivity and specificity were 95.3% (92.3; 97.1) and 97.1% (95.1; 98.3), respectively, and AUC (area under the curve) was 0.963 (0.947; 0.974). Pediatric patients had a lower sensitivity (87.4, 48.2; 98.1) and higher specificity (99.2, 91.6; 99.9) estimate compared to all ages category (sensitivity 95.3, 91.3; 97.5, specificity 96.7, 93.7; 98.3). Among the various index tests, Seeplex/Allplex and Amplidiag/Novodiag had the lowest estimate for sensitivity (88.9, 73.8; 95.8) and specificity (95.2, 86; 98.4), respectively. BDMax had the highest (sensitivity 98.1, 96.1; 99 and specificity 98.5, 97; 99.3). Multiplex nucleic acid tests showed excellent accuracy and could play an influential role in diagnosing Campylobacter infections.
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Affiliation(s)
- Xanthoula Rousou
- Laboratory of Epidemiology and Artificial Intelligence, Faculty of Public and One Health, School of Health Sciences, University of Thessaly, Karditsa, Greece
| | - Luis Furuya-Kanamori
- UQ Centre for Clinical Research, Faculty of Medicine, the University of Queensland, Herston, Queensland, Australia
| | - Polychronis Kostoulas
- Laboratory of Epidemiology and Artificial Intelligence, Faculty of Public and One Health, School of Health Sciences, University of Thessaly, Karditsa, Greece
| | - Suhail A R Doi
- Department of Population Medicine, College of Medicine, Qatar University, Doha, Qatar
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Dabbousi AA, Osman M, Dabboussi F, Hamze M. High rates of macrolide and fluoroquinolone resistance in human campylobacteriosis in the Middle East and North Africa. Future Microbiol 2022; 17:957-967. [PMID: 35796073 DOI: 10.2217/fmb-2021-0302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Campylobacter is one of the main causative agents of bacterial gastrointestinal infections. Recently, a rise in the incidence of campylobacteriosis has been reported worldwide. Despite the clinical importance of this zoonotic disease, its microbiological diagnosis is not systematically performed in clinical laboratories in developing countries such as the Middle East and North Africa region. Multidrug-resistant Campylobacter isolates, particularly against erythromycin and ciprofloxacin, have been highly reported. The findings of this study highlight the critical need to urge clinical laboratories in the Middle East and North Africa region to include screening for Campylobacter in the routine stool culture of diarrheal patients. Although there is a paucity of data regarding the epidemiology of human campylobacteriosis, alarming rates of infection prevalence and antimicrobial resistance were found in Egypt, Iran, Qatar and Lebanon.
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Affiliation(s)
| | - Marwan Osman
- Postdoctoral Fellow, Cornell Atkinson Center for Sustainability, Cornell University, Ithaca, NY 14853, USA.,Department of Public & Ecosystem Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Fouad Dabboussi
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences & Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
| | - Monzer Hamze
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences & Technology, Faculty of Public Health, Lebanese University, Tripoli, Lebanon
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Acute Viral Gastrointestinal (GI) Infections in the Tropics—A Role for Cartridge-Based Multiplex PCR Panels? Trop Med Infect Dis 2022; 7:tropicalmed7050080. [PMID: 35622707 PMCID: PMC9143240 DOI: 10.3390/tropicalmed7050080] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 02/04/2023] Open
Abstract
Acute gastroenteritis (AGE) contributes to increased morbidity and mortality worldwide. In particular, children in resource-poor settings suffer from frequent episodes of diarrhea. A variety of pathogens, including bacteria, viruses, fungi, and protozoa, can cause AGE. Common viruses associated with AGE are norovirus, rotavirus, astrovirus, adenovirus, and sapovirus. Due to their similar clinical presentation, AGE pathogens cannot be distinguished on clinical grounds rendering the etiological diagnosis challenging. However, reliable diagnosis is essential for individual and public health reasons, e.g., to limit transmission, for appropriate antibiotic use, prognostic appreciation, and vaccination programs. Therefore, high-quality data derived by accurate diagnostics are important to improve global health. In Western industrialized countries, diagnosis relies on microbiological testing, including culture methods, microscopy, immunochromatography, and single-target molecular methods. Recently, multiplex PCR or syndromic panels have been introduced, which simultaneously analyze for multiple pathogens in a very short time. A further technological advancement is cartridge-based syndromic panels, which allow for near patient/point-of-care testing independently from a laboratory. In resource-poor tropical regions, however, laboratory diagnosis is rarely established, and there are little routine laboratory data on the epidemiology of viral AGE pathogens. Limiting factors for the implementation of syndromic panels are high costs, sophisticated equipment, and the need for trained personnel. In addition, pilot studies have shown a large number of viral (co-)detections among healthy controls, thus further challenging their clinical utilization. Hence, there are little evidence-based data on the impact of multiplex syndromic panels from resource-limited regions. Here, we aim to provide a brief overview of what is known about the use of syndromic panels for virus-associated AGE in tropical regions and to address future challenges.
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Böhrer M, Fitzpatrick E, Hurley K, Xie J, Lee BE, Pang X, Zhuo R, Parsons BD, Berenger BM, Chui L, Tarr PI, Ali S, Vanderkooi OG, Freedman SB, Zemek R, Newton M, Meckler G, Poonai N, Bhatt M, Maki K, McGahern C, Emerton R. Hematochezia in children with acute diarrhea seeking emergency department care - a prospective cohort study. Acad Emerg Med 2022; 29:429-441. [PMID: 34962688 DOI: 10.1111/acem.14434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 12/07/2021] [Accepted: 12/27/2021] [Indexed: 11/27/2022]
Abstract
OBJECTIVES Although the passage of blood in stools in children represents a medical emergency, children seeking emergency department (ED) care remain poorly characterized. Our primary objective was to compare clinical characteristics and etiologic pathogens in children with acute diarrhea with and without caregiver-reported hematochezia. Secondary objectives were to characterize interventions and resource utilization. METHODS We conducted a secondary analysis of the Alberta Provincial Pediatric EnTeric Infection TEam (APPETITE) database. Children <18 years presenting to two pediatric EDs within a 24-hour period and <7 days of symptoms were consecutively recruited. RESULTS Of 1,061 participants, 115 (10.8%) reported hematochezia at the enrollment visit at which time those with hematochezia, compared to those without, had more diarrheal episodes/24-hour period (9 vs. 6; difference: 2; 95% confidence interval [CI]: 2.0, 4.0; p < 0.001), and were less likely to have experienced vomiting (54.8% vs. 80.2%; difference: -25.4; 95% CI: -34.9, -16.0; p < 0.001). They were more likely to receive intravenous fluids (33.0% vs. 17.9%; difference: 15.2; 95% CI: 6.2, 24.1; p < 0.001) and require repeat health care visits (45.5% vs. 34.7%; difference: 10.7; 95% CI: 0.9, 20.6; p = 0.03). A bacterial pathogen was identified in 33.0% of children with hematochezia versus 7.9% without (difference: 25.1; 95% CI: 16.3, 33.9; p < 0.001); viruses were detected in 31.3% of children with hematochezia compared to 72.3% in those without (difference: -41.0%, 95% CI: -49.9, -32.1; p < 0.001). CONCLUSION In children with acute diarrhea, caregiver report of hematochezia, compared to the absence of hematochezia, was associated with more diarrheal but fewer vomiting episodes, and greater resource consumption. The former group of children was also more likely to have bacteria detected in their stool.
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Affiliation(s)
| | | | | | - Jianling Xie
- Department of Pediatrics, Cumming School of Medicine, University of Calgary Calgary Canada
| | - Bonita E. Lee
- Departments of Pediatrics & Emergency Medicine Faculty of Medicine & Dentistry Women and Children's Health Research Institute University of Alberta Edmonton Alberta Canada
| | - Xiao‐Li Pang
- Department of Laboratory Medicine and Pathology University of Alberta Edmonton Canada
| | - Ran Zhuo
- Department of Laboratory Medicine and Pathology University of Alberta Edmonton Canada
| | | | - Byron M. Berenger
- Department of Pathology and Laboratory Medicine University of Calgary Calgary Canada
| | - Linda Chui
- Department of Laboratory Medicine and Pathology University of Alberta Edmonton Canada
| | | | - Samina Ali
- Department of Laboratory Medicine and Pathology University of Alberta Edmonton Canada
| | - Otto G. Vanderkooi
- Section of Pediatric Infectious Diseases. Departments of Pediatrics; Microbiology, Immunology & Infectious Diseases; Pathology and Laboratory Medicine; and Community Health Sciences University of Calgary Alberta Children’s Hospital Research Institute Calgary Canada
| | - Stephen B. Freedman
- Sections of Pediatric Emergency Medicine and Gastroenterology Departments of Pediatrics and Emergency Medicine Alberta Children’s Hospital and the Alberta Children’s Hospital Research Institute Cumming School of Medicine University of Calgary Calgary Canada
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Khun PA, Phi LD, Pham PT, Thu Nguyen HT, Huyen Vu QT, Collins DA, Riley TV. Clostridioides (Clostridium) difficile in children with diarrhoea in Vietnam. Anaerobe 2022; 74:102550. [PMID: 35331913 DOI: 10.1016/j.anaerobe.2022.102550] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/14/2022] [Accepted: 03/17/2022] [Indexed: 01/05/2023]
Abstract
BACKGROUND Clostridioides (Clostridium) difficile commonly causes hospital-acquired infection which can range from mild diarrhoea to life-threatening toxic megacolon and even death. Reports on C. difficile infection (CDI) in Vietnam are limited, so this study was designed to evaluate the prevalence, molecular epidemiology and antimicrobial susceptibility of C. difficile isolated from children with diarrhoea in Vietnam. Infants are often colonised with C. difficile and it was hypothesised that those colonising strains would represent strains of C. difficile circulating in the hospital/region at the time, however, this was not an attempt to determine if C. difficile was the cause of the diarrhoea. METHODS Diarrhoeal stool samples collected at two children's hospitals in northern Vietnam from 1st October 2020 to 28th February 2021 were transported to Perth, Western Australia, for culture of C. difficile and further investigations on isolates; PCR ribotyping, toxin gene profiling and antimicrobial susceptibility testing. RESULTS From these hospitals, 370 diarrhoeal stool samples were collected, most from children aged 1-15 months (71.9%; 266/370). The overall prevalence of C. difficile in stool samples from children aged ≤16 years was 37.8% (140/370) and the highest prevalence was in the 2-12 months age group (52.9%; 74/140). In total, 151 isolates of C. difficile were recovered; the proportion of toxigenic isolates was 16.6% (25/151). Of the 25 toxigenic C. difficile isolates, the toxin gene profiles A+B+CDT- and A-B+CDT- comprised 72% and 28%, respectively. The four most prevalent C. difficile ribotypes (RTs) were QX 011 (25/151), RT 010 (25/151), QX 107 (12/151) and RT 012 (11/151). All isolates were susceptible to vancomycin, metronidazole and fidaxomicin, while there was significant resistance to clindamycin (90.1%), and some to moxifloxacin (6.6%) and rifaximin (3.3%). CONCLUSION The prevalence of C. difficile in children with diarrhoea was high (37.8%) although the proportion of toxigenic strains was comparatively low. The clinical significance of any isolate needs to be determined.
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Affiliation(s)
- Peng An Khun
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Long Duc Phi
- Thai Binh University of Medicine and Pharmacy, Thai Binh, Viet Nam
| | | | | | | | - Deirdre A Collins
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Thomas V Riley
- School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia; School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia; Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, WA, Australia; PathWest Laboratory Medicine, Department of Microbiology, Nedlands, WA, Australia.
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9
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Dynamic of the human gut microbiome under infectious diarrhea. Curr Opin Microbiol 2022; 66:79-85. [PMID: 35121284 DOI: 10.1016/j.mib.2022.01.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/06/2022] [Accepted: 01/11/2022] [Indexed: 11/20/2022]
Abstract
Despite the widespread implementation of sanitation, immunization and appropriate treatment, infectious diarrheal diseases still inflict a great health burden to children living in low resource settings. Conventional microbiology research in diarrhea have focused on the pathogen's biology and pathogenesis, but initial enteric infections could trigger subsequent perturbations in the gut microbiome, leading to short-term or long-term health effects. Conversely, such pre-existing perturbations could render children more vulnerable to enteropathogen colonization and diarrhea. Recent advances in DNA sequencing and bioinformatic analyses have been integrated in well-designed clinical and epidemiological studies, which allow us to track how the gut microbiome changes from disease onset to recovery. Here, we aim to summarize the current understanding on the diarrheal gut microbiome, stratified into different disease stages. Furthermore, we discuss how such perturbations could have impacts beyond an acute diarrhea episode, specifically on the child's nutritional status and the facilitation of antimicrobial resistance.
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Luka G, Samiei E, Tasnim N, Dalili A, Najjaran H, Hoorfar M. Comprehensive review of conventional and state-of-the-art detection methods of Cryptosporidium. JOURNAL OF HAZARDOUS MATERIALS 2022; 421:126714. [PMID: 34325293 DOI: 10.1016/j.jhazmat.2021.126714] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 07/06/2021] [Accepted: 07/19/2021] [Indexed: 06/13/2023]
Abstract
Cryptosporidium is a critical waterborne protozoan pathogen found in water resources that have been a major cause of death and serious illnesses worldwide, costing millions of dollars annually for its detection and treatment. Over the past several decades, substantial efforts have been made towards developing techniques for the detection of Cryptosporidium. Early diagnostic techniques were established based on the existing tools in laboratories, such as microscopes. Advancements in fluorescence microscopy, immunological, and molecular techniques have led to the development of several kits for the detection of Cryptosporidium spp. However, these methods have several limitations, such as long processing times, large sample volumes, the requirement for bulky and expensive laboratory tools, and the high cost of reagents. There is an urgent need to improve these existing techniques and develop low-cost, portable and rapid detection tools for applications in the water quality industry. In this review, we compare recent advances in nanotechnology, biosensing and microfluidics that have facilitated the development of sophisticated tools for the detection of Cryptosporidium spp.Finally, we highlight the advantages and disadvantages, of these state-of-the-art detection methods compared to current analytical methodologies and discuss the need for future developments to improve such methods for detecting Cryptosporidium in the water supply chain to enable real-time and on-site monitoring in water resources and remote areas.
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Affiliation(s)
- George Luka
- School of Engineering, University of British Columbia, 3333 University Way, Kelowna, BC V1V1V7, Canada.
| | - Ehsan Samiei
- Department of Mechanical & Industrial Engineering, University of Toronto, Toronto, ON M5S 3G8, Canada.
| | - Nishat Tasnim
- School of Engineering, University of British Columbia, 3333 University Way, Kelowna, BC V1V1V7, Canada.
| | - Arash Dalili
- School of Engineering, University of British Columbia, 3333 University Way, Kelowna, BC V1V1V7, Canada.
| | - Homayoun Najjaran
- School of Engineering, University of British Columbia, 3333 University Way, Kelowna, BC V1V1V7, Canada.
| | - Mina Hoorfar
- School of Engineering, University of British Columbia, 3333 University Way, Kelowna, BC V1V1V7, Canada.
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Harrison CJ, Hassan F, Lee B, Boom J, Sahni LC, Johnson C, Dunn J, Payne DC, Wikswo ME, Parashar U, Selvarangan R. Multiplex PCR Pathogen Detection in Acute Gastroenteritis Among Hospitalized US Children Compared With Healthy Controls During 2011-2016 in the Post-Rotavirus Vaccine Era. Open Forum Infect Dis 2021; 8:ofab592. [PMID: 34988246 PMCID: PMC8694200 DOI: 10.1093/ofid/ofab592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 11/18/2021] [Indexed: 12/02/2022] Open
Abstract
Background Despite vaccine-induced decreases in US rotavirus (RV) disease, acute gastroenteritis (AGE) remains relatively common. We evaluated AGE pathogen distribution in hospitalized US children in the post–RV vaccine era. Methods From December 2011 to June 2016, the New Vaccine Surveillance Network (NVSN) conducted prospective, active, population-based surveillance in hospitalized children with AGE. We tested stools from 2 NVSN sites (Kansas City, Houston) with Luminex x-TAG Gastrointestinal Pathogen Panels (Luminex GPP) and analyzed selected signs and symptoms. Results For 660 pediatric AGE inpatients and 624 age-matched healthy controls (HCs), overall organism detection was 51.2% and 20.6%, respectively (P < .001). Among AGE subjects, GPP polymerase chain reaction detected >1 virus in 39% and >1 bacterium in 14% of specimens. Detection frequencies for AGE subjects vs HCs were norovirus (NoV) 18.5% vs 6.6%, RV 16.1% vs 9.8%, adenovirus 7.7% vs 1.4%, Shigella 4.8% vs 1.0%, Salmonella 3.1% vs 0.1%, and Clostridioides difficile in ≥2-year-olds 4.4% vs 2.4%. More co-detections occurred among AGE patients (37/660, 5.6%) than HCs (14/624, 2.2%; P = .0024). Per logistic regression analysis, ill contacts increased risk for NoV, RV, and Shigella (P < .001). More vomiting episodes occurred with NoV and RV, and more diarrheal episodes with Shigella and Salmonella. Modified Vesikari scores were highest for Shigella and lowest for C. difficile. Conclusions NoV detection was most frequent; however, RV remained important in hospitalized AGE in the post–RV vaccine era. Continued active surveillance is important to document ongoing vaccine effects, pathogen emergence, and baseline disease burden for new vaccines.
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Affiliation(s)
- Christopher J Harrison
- Children's Mercy Kansas City and University of Missouri Kansas City-School of Medicine, Missouri, USA
| | - Ferdaus Hassan
- Children's Mercy Kansas City and University of Missouri Kansas City-School of Medicine, Missouri, USA
| | - Brian Lee
- Children's Mercy Kansas City and University of Missouri Kansas City-School of Medicine, Missouri, USA
| | - Julie Boom
- Texas Children's Hospital, Houston, Texas, USA
| | | | | | - James Dunn
- Texas Children's Hospital, Houston, Texas, USA
| | - Daniel C Payne
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Mary E Wikswo
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Umesh Parashar
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Rangaraj Selvarangan
- Department of Pathology and Laboratory Medicine, Children's Mercy Kansas City and University of Missouri-Kansas City, School of Medicine, Kansas City, Missouri, USA
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12
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Schuele L, Cassidy H, Peker N, Rossen JWA, Couto N. Future potential of metagenomics in clinical laboratories. Expert Rev Mol Diagn 2021; 21:1273-1285. [PMID: 34755585 DOI: 10.1080/14737159.2021.2001329] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Rapid and sensitive diagnostic strategies are necessary for patient care and public health. Most of the current conventional microbiological assays detect only a restricted panel of pathogens at a time or require a microbe to be successfully cultured from a sample. Clinical metagenomics next-generation sequencing (mNGS) has the potential to unbiasedly detect all pathogens in a sample, increasing the sensitivity for detection and enabling the discovery of unknown infectious agents. AREAS COVERED High expectations have been built around mNGS; however, this technique is far from widely available. This review highlights the advances and currently available options in terms of costs, turnaround time, sensitivity, specificity, validation, and reproducibility of mNGS as a diagnostic tool in clinical microbiology laboratories. EXPERT OPINION The need for a novel diagnostic tool to increase the sensitivity of microbial diagnostics is clear. mNGS has the potential to revolutionise clinical microbiology. However, its role as a diagnostic tool has yet to be widely established, which is crucial for successfully implementing the technique. A clear definition of diagnostic algorithms that include mNGS is vital to show clinical utility. Similarly to real-time PCR, mNGS will one day become a vital tool in any testing algorithm.
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Affiliation(s)
- Leonard Schuele
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands
| | - Hayley Cassidy
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands
| | - Nilay Peker
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands
| | - John W A Rossen
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands.,Department of Pathology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Natacha Couto
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, the Netherlands.,The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom
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13
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Knee J, Sumner T, Adriano Z, Anderson C, Bush F, Capone D, Casmo V, Holcomb D, Kolsky P, MacDougall A, Molotkova E, Braga JM, Russo C, Schmidt WP, Stewart J, Zambrana W, Zuin V, Nalá R, Cumming O, Brown J. Effects of an urban sanitation intervention on childhood enteric infection and diarrhea in Maputo, Mozambique: A controlled before-and-after trial. eLife 2021; 10:e62278. [PMID: 33835026 PMCID: PMC8121544 DOI: 10.7554/elife.62278] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 04/03/2021] [Indexed: 12/12/2022] Open
Abstract
We conducted a controlled before-and-after trial to evaluate the impact of an onsite urban sanitation intervention on the prevalence of enteric infection, soil transmitted helminth re-infection, and diarrhea among children in Maputo, Mozambique. A non-governmental organization replaced existing poor-quality latrines with pour-flush toilets with septic tanks serving household clusters. We enrolled children aged 1-48 months at baseline and measured outcomes before and 12 and 24 months after the intervention, with concurrent measurement among children in a comparable control arm. Despite nearly exclusive use, we found no evidence that intervention affected the prevalence of any measured outcome after 12 or 24 months of exposure. Among children born into study sites after intervention, we observed a reduced prevalence of Trichuris and Shigella infection relative to the same age group at baseline (<2 years old). Protection from birth may be important to reduce exposure to and infection with enteric pathogens in this setting.
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Affiliation(s)
- Jackie Knee
- London School of Hygiene & Tropical Medicine, Faculty of Infectious Tropical Diseases, Disease Control DepartmentLondonUnited Kingdom
- Georgia Institute of Technology, School of Civil and Environmental EngineeringAtlantaUnited States
| | - Trent Sumner
- Georgia Institute of Technology, School of Civil and Environmental EngineeringAtlantaUnited States
| | | | - Claire Anderson
- Georgia Institute of Technology, School of Civil and Environmental EngineeringAtlantaUnited States
| | - Farran Bush
- Georgia Institute of Technology, School of Chemical and Biomolecular EngineeringAtlantaUnited States
| | - Drew Capone
- Georgia Institute of Technology, School of Civil and Environmental EngineeringAtlantaUnited States
- University of North Carolina at Chapel Hill, Gillings School of Global Public Health, Department of EpidemiologyChapel HillUnited States
| | | | - David Holcomb
- University of North Carolina at Chapel Hill, Gillings School of Global Public Health, Department of EpidemiologyChapel HillUnited States
- University of North Carolina at Chapel Hill, Gillings School of Global Public Health, Department of Environmental Sciences and EngineeringChapel HillUnited States
| | - Pete Kolsky
- University of North Carolina at Chapel Hill, Gillings School of Global Public Health, Department of EpidemiologyChapel HillUnited States
| | - Amy MacDougall
- London School of Hygiene & Tropical Medicine, Faculty of Epidemiology and Population Health, Department of Medical StatisticsLondonUnited Kingdom
| | - Evgeniya Molotkova
- Georgia Institute of Technology, School of Biological SciencesAtlantaUnited States
| | | | - Celina Russo
- Georgia Institute of Technology, School of Civil and Environmental EngineeringAtlantaUnited States
| | - Wolf Peter Schmidt
- London School of Hygiene & Tropical Medicine, Faculty of Infectious Tropical Diseases, Disease Control DepartmentLondonUnited Kingdom
| | - Jill Stewart
- University of North Carolina at Chapel Hill, Gillings School of Global Public Health, Department of EpidemiologyChapel HillUnited States
| | - Winnie Zambrana
- Georgia Institute of Technology, School of Civil and Environmental EngineeringAtlantaUnited States
| | - Valentina Zuin
- Yale-NUS College, Division of Social ScienceSingaporeSingapore
| | | | - Oliver Cumming
- London School of Hygiene & Tropical Medicine, Faculty of Infectious Tropical Diseases, Disease Control DepartmentLondonUnited Kingdom
| | - Joe Brown
- Georgia Institute of Technology, School of Civil and Environmental EngineeringAtlantaUnited States
- University of North Carolina at Chapel Hill, Gillings School of Global Public Health, Department of EpidemiologyChapel HillUnited States
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14
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Chang LJ, Hsiao CJ, Chen B, Liu TY, Ding J, Hsu WT, Su-Ortiz V, Chen ST, Su KY, Wu HP, Lee CC. Accuracy and comparison of two rapid multiplex PCR tests for gastroenteritis pathogens: a systematic review and meta-analysis. BMJ Open Gastroenterol 2021; 8:bmjgast-2020-000553. [PMID: 33648983 PMCID: PMC7925250 DOI: 10.1136/bmjgast-2020-000553] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 01/07/2021] [Accepted: 01/13/2021] [Indexed: 12/19/2022] Open
Abstract
Objectives The primary aim is to provide a summary of evidence for the diagnostic accuracies of multiplex PCR gastrointestinal (GI) panels—BioFire FilmArray and Luminex xTAG on the detection of gastroenteritis pathogens. The secondary aim is to compare the performance of these GI panels head to head. Methods A comprehensive search up to 1 December 2019 was conducted on PubMed, Embase, Ovid Medline and Web of Science for studies that used FilmArray or Luminex xTAG Gastrointestinal Pathogen Panel (GPP) for diagnosis of acute gastroenteritis. A summary of diagnostic accuracies for the 16 pathogens were calculated by comparing the GI panels to the current gold standards (conventional standard microbiology techniques such as culture or PCR for bacteria, PCR or enzyme immunoassay (EIA) for viruses, microscopy or EIA for parasite). Hierarchical summary receiver operating characteristic (HSROC) curve analysis, pretest and post-test probabilities were used for estimating the pathogen detection performance. Results A total of 11 studies with 7085 stool samples were eligible for analysis. Multiplex PCRs demonstrated high diagnostic accuracy, with specificity ≧0.98 and area under the ROC curve (AUROC) ≧0.97 for all the pathogens except for Yersinia enterocolitica (AUROC 0.91). The FilmArray panel demonstrated a higher sensitivity than xTAG GPP for most of the pathogens with the exception of Rotavirus A (xTAG GPP and FilmArray were both 0.93). Conclusions This is the first meta-analysis that is a head-to-head comparison examining the performance of the novel multiplex PCR-based tests Luminex xTAG GPP and FilmArray GI panel in detecting each pathogen. Point estimates calculated from eligible studies showed that both GI panels are highly accurate and may provide important diagnostic information for early identification of gastroenteritis. In addition, although FilmArray has higher sensitivity and post-test probability than xTAG GPP for most of the pathogens, how this will translate to a clinical setting remains unclear.
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Affiliation(s)
- Li-Jun Chang
- Department of Medical Education, National Taiwan University Hospital, Taipei, Taiwan
| | - Chun-Jen Hsiao
- Department of Medical Education, National Taiwan University Hospital, Taipei, Taiwan
| | - Bing Chen
- Department of Medicine, Mount Sinai Morningside Hospital, New York, New York, USA
| | - Tzu-Yu Liu
- Department of Medicine, Brown University Warren Alpert Medical School, Providence, Rhode Island, USA
| | - Julia Ding
- Internal Medicine, Brown University Division of Biology and Medicine, Providence, Rhode Island, USA
| | - Wan-Ting Hsu
- Department of Epidemiology, Harvard University T H Chan School of Public Health, Boston, Massachusetts, USA.,Medical Wizdom, LLC, Brooklinw, MA, USA
| | - Victor Su-Ortiz
- Department of Medical Engineering, College of Engineering, Cornell University, Ithaca, New York, USA.,Department of Computer Science, College of Engineering, Cornell University, Ithaca, NY, USA
| | - Szu-Ta Chen
- Department of Epidemiology, Harvard University T H Chan School of Public Health, Boston, Massachusetts, USA
| | - Ke-Ying Su
- Department of Emergency Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Han-Ping Wu
- Department of Pediatric Emergency Medicine and Medical Research, China Medical University Children's Hospital, Taichung, Taiwan.,Department of Medicine, School of Medicine, China Medical University, Taichung, Taiwan
| | - Chien-Chang Lee
- Department of Emergency Medicine, National Taiwan University Hospital, Taipei, Taiwan .,Center of Intelligent Healthcare, National Taiwan University Hospital, Taipei, Taiwan.,Byers Center for Biodesign, Stanford University, Stanford, CA, USA
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15
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de Alwis R, My Phuc T, Yu Hang Bai B, Le Thi Quynh N, Thi Thanh Tam P, Thi Ngoc Dung T, Thi Thanh Nhan N, Vinh C, Van Hien H, Thanh Hoang Nhat L, Thi Thu Hong N, Thi Mong Tuyen N, Thi Thuy Trang H, Phuong Thao L, Thi Ngoc Diep V, Thi Hai Chau P, Quan Thinh L, Thi Ngoc Thu H, Nguyet Hang N, Cong Danh M, Doan Hao T, Anh Dao T, Dai L, Thi Huyen Diu V, Thi En N, Thi Tuyet Hanh N, Thi Hanh L, Pham Thu Hien H, Thi Thuy Linh N, Darton TC, Thwaites GE, Kestelyn E, Lan Vi L, Thi Thuy Tien B, Thi Diem Tuyet H, Anderson C, Baker S. The influence of human genetic variation on early transcriptional responses and protective immunity following immunization with Rotarix vaccine in infants in Ho Chi Minh City in Vietnam: A study protocol for an open single-arm interventional trial. Wellcome Open Res 2020. [DOI: 10.12688/wellcomeopenres.16090.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background: Rotavirus (RoV) remains the leading cause of acute gastroenteritis in infants and children aged under five years in both high- and low-middle-income countries (LMICs). In LMICs, RoV infections are associated with substantial mortality. Two RoV vaccines (Rotarix and Rotateq) are widely available for use in infants, both of which have been shown to be highly efficacious in Europe and North America. However, for unknown reasons, these RoV vaccines have markedly lower efficacy in LMICs. We hypothesize that poor RoV vaccine efficacy across in certain regions may be associated with genetic heritability or gene expression in the human host. Methods/design: We designed an open-label single-arm interventional trial with the Rotarix RoV vaccine to identify genetic and transcriptomic markers associated with generating a protective immune response against RoV. Overall, 1,000 infants will be recruited prior to Expanded Program on Immunization (EPI) vaccinations at two months of age and vaccinated with oral Rotarix vaccine at two and three months, after which the infants will be followed-up for diarrheal disease until 18 months of age. Blood sampling for genetics, transcriptomics, and immunological analysis will be conducted before each Rotarix vaccination, 2-3 days post-vaccination, and at each follow-up visit (i.e. 6, 12 and 18 months of age). Stool samples will be collected during each diarrheal episode to identify RoV infection. The primary outcome will be Rotarix vaccine failure events (i.e. symptomatic RoV infection despite vaccination), secondary outcomes will be antibody responses and genotypic characterization of the infection virus in Rotarix failure events. Discussion: This study will be the largest and best powered study of its kind to be conducted to date in infants, and will be critical for our understanding of RoV immunity, human genetics in the Vietnam population, and mechanisms determining RoV vaccine-mediated protection. Registration: ClinicalTrials.gov, ID: NCT03587389. Registered on 16 July 2018.
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16
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Zhang X, Das S, Dunbar S, Tang YW. Molecular and non-molecular approaches to etiologic diagnosis of gastroenteritis. Adv Clin Chem 2020; 99:49-85. [PMID: 32951639 DOI: 10.1016/bs.acc.2020.02.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Gastroenteritis is a major cause of mortality and morbidity globally and rapid identification of the causative pathogen is important for appropriate treatment and patient management, implementation of effective infection control measures, reducing hospital length of stay, and reducing overall medical costs. Although stool culture and microscopic examination of diarrheal stool has been the primary method for laboratory diagnosis, culture-independent proteomic and genomic tests are receiving increased attention. Antigen tests for stool pathogens are routinely implemented as rapid and simple analytics whereas molecular tests are now available in various formats from high complexity to waived point-of-care tests. In addition, metagenomic next-generation sequencing stands poised for use as a method for both diagnosis and routine characterization of the gut microbiome in the very near future. Analysis of host biomarkers as indicators of infection status and pathogenesis may also become important for prediction, diagnosis, and monitoring of gastrointestinal infection. Here we review current methods and emerging technologies for the etiologic diagnosis of gastroenteritis in the clinical laboratory. Benefits and limitations of these evolving methods are highlighted.
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Affiliation(s)
- Xin Zhang
- Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China; Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | | | | | - Yi-Wei Tang
- Memorial Sloan Kettering Cancer Center, New York, NY, United States; Weill Medical College of Cornell University, New York, NY, United States; Cepheid, Danaher Diagnostic Platform, Shanghai, China.
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17
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Zhan Z, Guo J, Xiao Y, He Z, Xia X, Huang Z, Guan H, Ling X, Li J, Diao B, Zhao H, Kan B, Zhang J. Comparison of BioFire FilmArray gastrointestinal panel versus Luminex xTAG Gastrointestinal Pathogen Panel (xTAG GPP) for diarrheal pathogen detection in China. Int J Infect Dis 2020; 99:414-420. [PMID: 32800862 DOI: 10.1016/j.ijid.2020.08.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 08/06/2020] [Accepted: 08/07/2020] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVES To compare the performance of two syndromic panels: Luminex xTAG Gastrointestinal Pathogen Panel (GPP) and FilmArray Gastrointestinal (GI) panel. METHODS A total of 243 diarrhea specimens were detected by two panels in parallel, and the inconsistent results were analyzed by real-time PCR or reverse transcription PCR (RT-PCR). The target concentration in specimens was examined by comparing the crossing point values of FilmArray, the median fluorescence intensity of xTAG and the cycle threshold values in any discrepancies. RESULTS For pathogens detected by both panels, the positive rates of FilmArray GI and xTAG GPP were 65.0% and 48.6%, respectively. The two panels showed high consistency (kappa ≥0.74) in detecting norovirus, rotavirus and Campylobacter, while there was low consistency (kappa ≤0.40) in detecting Cryptosporidium, Salmonella, Shiga toxin-producing Escherichia coli (STEC) and enterotoxigenic Escherichia coli (ETEC). Samples with low concentration targets were more often detected by FilmArray than with xTAG GPP. The xTAG GPP was more likely to be affected by amplification inhibitors. Several defects of xTAG GPP were found in detecting ETEC. CONCLUSIONS FilmArray was more sensitive. For specimens with low target concentrations or containing ETEC heat stable enterotoxin, the false negatives of xTAG GPP need to be considered.
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Affiliation(s)
- Zhifei Zhan
- Hunan Provincial Center for Disease Control and Prevention, Changsha City, China
| | - Jiayin Guo
- Shanghai Changning District Center for Disease Control and Prevention, Shanghai, China
| | - Yong Xiao
- Wuxi Center for Disease Control and Prevention, Jiangsu, China
| | - Zixiang He
- Hunan Provincial Center for Disease Control and Prevention, Changsha City, China
| | - Xin Xia
- Hunan Provincial Center for Disease Control and Prevention, Changsha City, China
| | - Zheng Huang
- Shanghai Changning District Center for Disease Control and Prevention, Shanghai, China
| | - Hongxia Guan
- Wuxi Center for Disease Control and Prevention, Jiangsu, China
| | - Xia Ling
- Wuxi Center for Disease Control and Prevention, Jiangsu, China
| | - Jie Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Baowei Diao
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hongqun Zhao
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Biao Kan
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| | - Jingyun Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
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18
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19
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Berendes D, Knee J, Sumner T, Capone D, Lai A, Wood A, Patel S, Nalá R, Cumming O, Brown J. Gut carriage of antimicrobial resistance genes among young children in urban Maputo, Mozambique: Associations with enteric pathogen carriage and environmental risk factors. PLoS One 2019; 14:e0225464. [PMID: 31756196 PMCID: PMC6874316 DOI: 10.1371/journal.pone.0225464] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 11/05/2019] [Indexed: 12/31/2022] Open
Abstract
Because poor sanitation is hypothesized as a major direct and indirect pathway of exposure to antimicrobial resistance genes (ARGs), we sought to determine a) the prevalence of and b) environmental risk factors for gut carriage of key ARGs in a pediatric cohort at high risk of enteric infections due to poor water, sanitation, and hygiene (WASH) conditions. We investigated ARGs in stool from young children in crowded, low-income settlements of Maputo, Mozambique, and explored potential associations with concurrent enteric pathogen carriage, diarrhea, and environmental risk factors, including WASH. We collected stool from 120 children <14 months old and tested specimens via quantal, multiplex molecular assays for common bacterial, viral, and protozoan enteric pathogens and 84 ARGs encoding potential resistance to 7 antibiotic classes. We estimated associations between ARG detection (number and diversity detected) and concurrently-measured enteric pathogen carriage, recently-reported diarrhea, and risk factors in the child’s living environment. The most commonly-detected ARGs encoded resistance to macrolides, lincosamides, and streptogramins (100% of children); tetracyclines (98%); β-lactams (94%), aminoglycosides (84%); fluoroquinolones (48%); and vancomycin (38%). Neither concurrent diarrhea nor measured environmental (including WASH) conditions were associated with ARG detection in adjusted models. Enteric pathogen carriage and ARG detection were associated: on average, 18% more ARGs were detected in stool from children carrying bacterial pathogens than those without (adjusted risk ratio (RR): 1.18, 95% confidence interval (CI): 1.02, 1.37), with 16% fewer ARGs detected in children carrying parasitic pathogens (protozoans, adjusted RR: 0.84, 95% CI: 0.71, 0.99). We observed gut ARGs conferring potential resistance to a range of antibiotics in this at-risk cohort that had high rates of enteric infection, even among children <14 months-old. Gut ARGs did not appear closely correlated with WASH, though environmental conditions were generally poor. ARG carriage may be associated with concurrent carriage of bacterial enteric pathogens, suggesting indirect linkages to WASH that merit further investigation.
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Affiliation(s)
- David Berendes
- Division of Foodborne, Waterborne, and Environmental Diseases, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- * E-mail:
| | - Jackie Knee
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Trent Sumner
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Drew Capone
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Amanda Lai
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Anna Wood
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia
| | - Siddhartha Patel
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Rassul Nalá
- National Institute of Health, Maputo, Mozambique
| | - Oliver Cumming
- Department of Disease Control, London School of Tropical Medicine and Hygiene, London, United Kingdom
| | - Joe Brown
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America
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20
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Chung The H, Boinett C, Pham Thanh D, Jenkins C, Weill FX, Howden BP, Valcanis M, De Lappe N, Cormican M, Wangchuk S, Bodhidatta L, Mason CJ, Nguyen TNT, Ha Thanh T, Voong VP, Duong VT, Nguyen PHL, Turner P, Wick R, Ceyssens PJ, Thwaites G, Holt KE, Thomson NR, Rabaa MA, Baker S. Dissecting the molecular evolution of fluoroquinolone-resistant Shigella sonnei. Nat Commun 2019; 10:4828. [PMID: 31645551 PMCID: PMC6811581 DOI: 10.1038/s41467-019-12823-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 09/25/2019] [Indexed: 02/08/2023] Open
Abstract
Shigella sonnei increasingly dominates the international epidemiological landscape of shigellosis. Treatment options for S. sonnei are dwindling due to resistance to several key antimicrobials, including the fluoroquinolones. Here we analyse nearly 400 S. sonnei whole genome sequences from both endemic and non-endemic regions to delineate the evolutionary history of the recently emergent fluoroquinolone-resistant S. sonnei. We reaffirm that extant resistant organisms belong to a single clonal expansion event. Our results indicate that sequential accumulation of defining mutations (gyrA-S83L, parC-S80I, and gyrA-D87G) led to the emergence of the fluoroquinolone-resistant S. sonnei population around 2007 in South Asia. This clone was then transmitted globally, resulting in establishments in Southeast Asia and Europe. Mutation analysis suggests that the clone became dominant through enhanced adaptation to oxidative stress. Experimental evolution reveals that under fluoroquinolone exposure in vitro, resistant S. sonnei develops further intolerance to the antimicrobial while the susceptible counterpart fails to attain complete resistance. Shigella sonnei is one of the main species causing shigellosis worldwide. Here the authors analyse nearly 400 S. sonnei genome sequences and carry out experimental evolution experiments to shed light into the evolutionary processes underlying the recent emergence of fluoroquinolone resistance in this pathogen.
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Affiliation(s)
- Hao Chung The
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Christine Boinett
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Oxford University, Oxford, UK
| | - Duy Pham Thanh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Claire Jenkins
- Gastrointestinal Bacterial Reference Unit, National Infection Service, Public Health England, London, UK
| | | | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia
| | - Niall De Lappe
- National Salmonella, Shigella, and Listeria monocytogenes Reference Laboratory, University Hospital Galway, Galway, Ireland
| | - Martin Cormican
- School of Medicine, National University of Ireland Galway, Galway, Ireland
| | - Sonam Wangchuk
- Public Health Laboratory, Department of Public Health, Ministry of Health, Royal Government of Bhutan, Thimphu, Bhutan
| | - Ladaporn Bodhidatta
- Department of Enteric Diseases, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Carl J Mason
- Department of Enteric Diseases, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - To Nguyen Thi Nguyen
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Tuyen Ha Thanh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Vinh Phat Voong
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Vu Thuy Duong
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Phu Huong Lan Nguyen
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Paul Turner
- Centre for Tropical Medicine and Global Health, Oxford University, Oxford, UK.,Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Ryan Wick
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
| | | | - Guy Thwaites
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Oxford University, Oxford, UK
| | - Kathryn E Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia.,London School of Hygiene and Tropical Medicine, London, UK
| | - Nicholas R Thomson
- London School of Hygiene and Tropical Medicine, London, UK.,The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Maia A Rabaa
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam. .,Centre for Tropical Medicine and Global Health, Oxford University, Oxford, UK.
| | - Stephen Baker
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Oxford University, Oxford, UK.,Cambridge Institute of Therapeutic Immunology and Infectious Disease, The Department of Medicine, University of Cambridge, Cambridge, UK
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21
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Yang Y, Rajendran V, Jayaraman V, Wang T, Bei K, Krishna K, Rajasekaran K, Rajasekaran JJ, Krishnamurthy H. Evaluation of the Vibrant DNA microarray for the high-throughput multiplex detection of enteric pathogens in clinical samples. Gut Pathog 2019; 11:51. [PMID: 31636718 PMCID: PMC6798489 DOI: 10.1186/s13099-019-0329-2] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 09/27/2019] [Indexed: 01/30/2023] Open
Abstract
Background Rapid detection of a wide range of etiologic agents is essential for appropriate treatment and control of gastrointestinal (GI) infections. A variety of microbial species including bacteria, viruses, parasites, and fungi have been recognized as diarrheagenic enteric pathogens. However, multiplex testing of various targets in a single reaction needs further improvement because of its limitation in species and throughput. Results This study aims at developing and evaluating a DNA microarray-based qualitative multiplexed polymerase chain reaction (PCR) assay, Vibrant GI pathogen panel (GPP), for simultaneous detection of 27 enteric GI pathogenic targets (16 bacteria, 5 viruses, 4 parasites, and 2 fungi) directly from stool specimens. Limits of detection ranged from 102 to 104 cells/mL for bacteria, 102 to 103 cells/mL for parasites, 102 to 103 RNA copies/mL for viruses, and 102 to 103 cells/mL for fungi. Performance characteristics were determined using 27 Quantitative Genomic DNAs, 212 spiked stool specimens, 1067 clinical and archived stool specimens. Overall sensitivity was 95.9% (95% CI 92.4–98.1) and specificity was 100% (95% CI 99.9–100). Polymicrobial detections contained either two or three organisms was 20.2% (35/173) of positive clinical specimens and 3.3% (35/1055) of all clinical specimens. Conclusion The Vibrant GPP is a comprehensive, high-throughput, and rapid DNA microarray to provide etiologic diagnosis of GI infections in the laboratory setting.
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Affiliation(s)
| | | | | | | | - Kang Bei
- Vibrant Sciences LLC, San Carlos, CA USA
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22
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Clinical interpretation of enteric molecular diagnostic tests. Clin Microbiol Infect 2019; 25:1454-1456. [PMID: 31491461 DOI: 10.1016/j.cmi.2019.08.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 08/20/2019] [Accepted: 08/22/2019] [Indexed: 11/22/2022]
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23
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Comparative Evaluation of Enteric Bacterial Culture and a Molecular Multiplex Syndromic Panel in Children with Acute Gastroenteritis. J Clin Microbiol 2019; 57:JCM.00205-19. [PMID: 30971465 DOI: 10.1128/jcm.00205-19] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 04/01/2019] [Indexed: 12/31/2022] Open
Abstract
Although enteric multianalyte syndromic panels are increasingly employed, direct comparisons with traditional methods and the inclusion of host phenotype correlations are limited. Luminex xTAG gastrointestinal pathogen panel (GPP) and culture results are highly concordant. However, phenotypic and microbiological confirmatory testing raises concerns regarding the accuracy of the GPP, especially for Salmonella spp. A total of 3,089 children with gastroenteritis submitted stool specimens, rectal swab specimens, and clinical data. The primary outcome was bacterial pathogen detection agreement for shared targets between culture and the Luminex xTAG GPP. Secondary analyses included phenotype assessment, additional testing of GPP-negative/culture-positive isolate suspensions with the GPP, and in-house and commercial confirmatory nucleic acid testing of GPP-positive/culture-negative extracts. The overall percent agreement between technologies was >99% for each pathogen. Salmonella spp. were detected in specimens from 64 participants: 12 (19%) by culture only, 9 (14%) by GPP only, and 43 (67%) by both techniques. Positive percent agreement for Salmonella spp. was 78.2% (95% confidence interval [CI], 64.6%, 87.8%). Isolate suspensions from the 12 participants with specimens GPP negative/culture positive for Salmonella tested positive by GPP. Specimens GPP positive/culture negative for Salmonella originated in younger children with less diarrhea and more vomiting. GPP-positive/culture-negative specimen extracts tested positive using additional assays for 0/2 Campylobacter-positive specimens, 0/4 Escherichia coli O157-positive specimens, 0/9 Salmonella-positive specimens, and 2/3 Shigella-positive specimens. For both rectal swab and stool samples, the median cycle threshold (CT ) values, determined using quantitative PCR, were higher for GPP-negative/culture-positive samples than for GPP-positive/culture-positive samples (for rectal swabs, 36.9 [interquartile range {IQR}, 33.7, 37.1] versus 30.0 [IQR, 26.2, 33.2], respectively [P = 0.002]; for stool samples, 36.9 [IQR, 33.7, 37.1] versus 29.0 [IQR, 24.8, 30.8], respectively [P = 0.001]). GPP and culture have excellent overall agreement; however, for specific pathogens, GPP is less sensitive than culture and, notably, identifies samples false positive for Salmonella spp.
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24
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Tarr GAM, Lin CY, Lorenzetti D, Chui L, Tarr PI, Hartling L, Vandermeer B, Freedman SB. Performance of commercial tests for molecular detection of Shiga toxin-producing Escherichia coli (STEC): a systematic review and meta-analysis protocol. BMJ Open 2019; 9:e025950. [PMID: 30850413 PMCID: PMC6430022 DOI: 10.1136/bmjopen-2018-025950] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 12/22/2018] [Accepted: 01/04/2019] [Indexed: 12/30/2022] Open
Abstract
INTRODUCTION Rapid detection of Shiga toxin-producing Escherichia coli (STEC) enables appropriate treatment. Numerous commercially available molecular tests exist, but they vary in clinical performance. This systematic review aims to synthesise available evidence to compare the clinical performance of enzyme immunoassay (EIA) and nucleic acid amplification tests (NAATs) for the detection of STEC. METHODS AND ANALYSIS The following databases will be searched employing a standardised search strategy: Medline, Embase, Cochrane CENTRAL Register of Controlled Trials, Cochrane Database of Systematic Reviews, PubMed, Scopus and Web of Science. Grey literature will be searched under advice from a medical librarian. Independent reviewers will screen titles, abstracts and full texts of retrieved studies for relevant studies. Data will be extracted independently by two reviewers, using a piloted template. Quality Assessment of Diagnostic Accuracy Studies-2 will be employed to assess the risk of bias of individual studies, and the quality of evidence will be assessed with the Grading of Recommendations Assessment, Development and Evaluation approach. A bivariate random-effects model will be used to meta-analyse the sensitivity and specificity of commercial STEC diagnostic tests, and a hierarchical summary receiver operator characteristic curve will be constructed. Studies of single test accuracy of EIA and NAATs and studies of comparative accuracy will be analysed separately. ETHICS AND DISSEMINATION Ethics approval was not required for this systematic review and meta-analysis. Findings will be disseminated in conferences, through a peer-reviewed journal and via personal interactions with relevant stakeholders. PROSPERO REGISTRATION NUMBER CRD42018099119.
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Affiliation(s)
- Gillian A M Tarr
- Department of Pediatrics, University of Calgary, Calgary, Alberta, Canada
| | - Chu Yang Lin
- Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada
| | - Diane Lorenzetti
- Department of Community Health Sciences, University of Calgary, Calgary, Alberta, Canada
- Health Sciences Library, University of Calgary, Calgary, Alberta, Canada
| | - Linda Chui
- Microbiology Section, Provincial Laboratory for Public Health-Alberta Public Laboratories, Edmonton, Alberta, Canada
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Phillip I Tarr
- Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Lisa Hartling
- Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada
| | - Ben Vandermeer
- Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada
| | - Stephen B Freedman
- Sections of Pediatric Emergency Medicine and Gastroenterology, Department of Pediatrics, Alberta Children's Hospital and Alberta Children's Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
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25
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Yoo J, Park J, Lee HK, Yu JK, Lee GD, Park KG, Oak HC, Park YJ. Comparative Evaluation of Seegene Allplex Gastrointestinal, Luminex xTAG Gastrointestinal Pathogen Panel, and BD MAX Enteric Assays for Detection of Gastrointestinal Pathogens in Clinical Stool Specimens. Arch Pathol Lab Med 2019; 143:999-1005. [PMID: 30763118 DOI: 10.5858/arpa.2018-0002-oa] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT.— Infectious gastroenteritis is caused by various pathogens, including bacteria, viruses, and parasites. OBJECTIVE.— To compare the performance of Seegene Allplex Gastrointestinal (24 targets: 13 bacteria, 5 viruses, and 6 parasites in 4 panels), Luminex xTAG Gastrointestinal Pathogen Panel (15 targets: 9 bacteria, 3 viruses, and 3 parasites), and BD MAX Enteric panel (5 bacteria and 3 parasites). We estimated the agreement among 3 molecular assays. DESIGN.— A total of 858 stool samples (554 bacterial/parasite and 304 viral pathogens) were included. A consensus positive/negative was defined as concordant results from at least 2 tests. To evaluate the agreement among the assays, κ value was calculated. RESULTS.— The overall positive percentage agreements of Seegene, Luminex, and BD MAX were 94% (258 of 275), 92% (254 of 275), and 78% (46 of 59), respectfully. For Salmonella, Luminex showed low negative percentage agreement because of frequent false positives (n = 31) showing low median fluorescent intensity. For viruses, positive/negative percentage agreements of Seegene and Luminex were 99%/96% and 93%/99%, respectively. Compared with routine microbiology testing, Seegene, Luminex, and BD MAX additionally identified 39, 40, and 12 pathogens, respectively. Sixty-one cases (16 cases with Seegene, 51 cases with Luminex, and 1 case with BD MAX) showed positive results for multiple pathogens, but only 3 were consensus positive. CONCLUSIONS.— These multiplex molecular assays appear to be promising tools for the detection and identification of multiple gastrointestinal pathogens simultaneously. However, careful interpretation of positive results for multiple pathogens is required.
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Affiliation(s)
- Jaeeun Yoo
- From the Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea (Drs Yoo, J. Park, H. K. Lee, and Y.-J. Park); the Department of Laboratory Medicine, Seoul St Mary's Hospital, The Catholic University of Korea, Seoul, Korea (Mss Yu and K. G. Park and Mr G. D. Lee); and the Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge (Ms Oak)
| | - Joonhong Park
- From the Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea (Drs Yoo, J. Park, H. K. Lee, and Y.-J. Park); the Department of Laboratory Medicine, Seoul St Mary's Hospital, The Catholic University of Korea, Seoul, Korea (Mss Yu and K. G. Park and Mr G. D. Lee); and the Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge (Ms Oak)
| | - Hae Kyung Lee
- From the Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea (Drs Yoo, J. Park, H. K. Lee, and Y.-J. Park); the Department of Laboratory Medicine, Seoul St Mary's Hospital, The Catholic University of Korea, Seoul, Korea (Mss Yu and K. G. Park and Mr G. D. Lee); and the Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge (Ms Oak)
| | - Jin Kyung Yu
- From the Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea (Drs Yoo, J. Park, H. K. Lee, and Y.-J. Park); the Department of Laboratory Medicine, Seoul St Mary's Hospital, The Catholic University of Korea, Seoul, Korea (Mss Yu and K. G. Park and Mr G. D. Lee); and the Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge (Ms Oak)
| | - Gun Dong Lee
- From the Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea (Drs Yoo, J. Park, H. K. Lee, and Y.-J. Park); the Department of Laboratory Medicine, Seoul St Mary's Hospital, The Catholic University of Korea, Seoul, Korea (Mss Yu and K. G. Park and Mr G. D. Lee); and the Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge (Ms Oak)
| | - Kang Gyun Park
- From the Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea (Drs Yoo, J. Park, H. K. Lee, and Y.-J. Park); the Department of Laboratory Medicine, Seoul St Mary's Hospital, The Catholic University of Korea, Seoul, Korea (Mss Yu and K. G. Park and Mr G. D. Lee); and the Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge (Ms Oak)
| | - Hayeon Caitlyn Oak
- From the Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea (Drs Yoo, J. Park, H. K. Lee, and Y.-J. Park); the Department of Laboratory Medicine, Seoul St Mary's Hospital, The Catholic University of Korea, Seoul, Korea (Mss Yu and K. G. Park and Mr G. D. Lee); and the Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge (Ms Oak)
| | - Yeon-Joon Park
- From the Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea (Drs Yoo, J. Park, H. K. Lee, and Y.-J. Park); the Department of Laboratory Medicine, Seoul St Mary's Hospital, The Catholic University of Korea, Seoul, Korea (Mss Yu and K. G. Park and Mr G. D. Lee); and the Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge (Ms Oak)
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26
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Heyworth MF. Molecular diagnosis of human microsporidian infections. Trans R Soc Trop Med Hyg 2019; 111:382-383. [PMID: 29244189 DOI: 10.1093/trstmh/trx070] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 10/31/2017] [Indexed: 11/13/2022] Open
Abstract
With the transformation of HIV infection from an acutely life-threatening disease into a chronic condition (as a consequence of the development of effective antiretroviral medication), the perceived clinical importance of diagnosing and treating microsporidian infections diminished, at least in industrialized countries. In locales where effective antiretroviral therapy is not available, as well as in patients with immunodeficiency for reasons other than HIV infection (e.g., following organ transplantation), and in individuals with suspected ocular microsporidiosis, diagnosing microsporidian infections remains a clinical priority. Molecular techniques can readily distinguish different species of microsporidia. At least one molecular diagnostic platform that can detect the intestinal parasites Encephalitozoon intestinalis and Enterocytozoon bieneusi is commercially available.
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Affiliation(s)
- Martin F Heyworth
- Research Service (151), Corporal Michael J. Crescenz Department of Veterans Affairs (VA) Medical Center, University and Woodland Avenues, Philadelphia, PA 19104, USA.,Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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27
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Knee J, Sumner T, Adriano Z, Berendes D, de Bruijn E, Schmidt WP, Nalá R, Cumming O, Brown J. Risk factors for childhood enteric infection in urban Maputo, Mozambique: A cross-sectional study. PLoS Negl Trop Dis 2018; 12:e0006956. [PMID: 30419034 PMCID: PMC6258421 DOI: 10.1371/journal.pntd.0006956] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 11/26/2018] [Accepted: 10/29/2018] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Enteric infections are common where public health infrastructure is lacking. This study assesses risk factors for a range of enteric infections among children living in low-income, unplanned communities of urban Maputo, Mozambique. METHODS & FINDINGS We conducted a cross-sectional survey in 17 neighborhoods of Maputo to assess the prevalence of reported diarrheal illness and laboratory-confirmed enteric infections in children. We collected stool from children aged 1-48 months, independent of reported symptoms, for molecular detection of 15 common enteric pathogens by multiplex RT-PCR. We also collected survey and observational data related to water, sanitation, and hygiene (WASH) characteristics; other environmental factors; and social, economic, and demographic covariates. We analyzed stool from 759 children living in 425 household clusters (compounds) representing a range of environmental conditions. We detected ≥1 enteric pathogens in stool from most children (86%, 95% confidence interval (CI): 84-89%) though diarrheal symptoms were only reported for 16% (95% CI: 13-19%) of children with enteric infections and 13% (95% CI: 11-15%) of all children. Prevalence of any enteric infection was positively associated with age and ranged from 71% (95% CI: 64-77%) in children 1-11 months to 96% (95% CI: 93-98%) in children 24-48 months. We found poor sanitary conditions, such as presence of feces or soiled diapers around the compound, to be associated with higher risk of protozoan infections. Certain latrine features, including drop-hole covers and latrine walls, and presence of a water tap on the compound grounds were associated with a lower risk of bacterial and protozoan infections. Any breastfeeding was also associated with reduced risk of infection. CONCLUSIONS We found a high prevalence of enteric infections, primarily among children without diarrhea, and weak associations between bacterial and protozoan infections and environmental risk factors including WASH. Findings suggest that environmental health interventions to limit infections would need to be transformative given the high prevalence of enteric pathogen shedding and poor sanitary conditions observed. TRIAL REGISTRATION ClinicalTrials.gov NCT02362932.
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Affiliation(s)
- Jackie Knee
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Trent Sumner
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Zaida Adriano
- We Consult, Maputo, Mozambique
- Departamento de Geografia, Universidade Eduardo Mondlane, Maputo, Mozambique
| | - David Berendes
- Waterborne Disease Prevention Branch, Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging Zoonotic and Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | | | - Wolf-Peter Schmidt
- Department of Disease Control, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Rassul Nalá
- Ministério da Saúde, Instituto Nacional de Saúde Maputo, Maputo, Republic of Mozambique
| | - Oliver Cumming
- Department of Disease Control, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Joe Brown
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- * E-mail:
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28
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Senescau A, Kempowsky T, Bernard E, Messier S, Besse P, Fabre R, François JM. Innovative DendrisChips ® Technology for a Syndromic Approach of In Vitro Diagnosis: Application to the Respiratory Infectious Diseases. Diagnostics (Basel) 2018; 8:E77. [PMID: 30423863 PMCID: PMC6316573 DOI: 10.3390/diagnostics8040077] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 10/31/2018] [Accepted: 11/08/2018] [Indexed: 02/03/2023] Open
Abstract
Clinical microbiology is experiencing the emergence of the syndromic approach of diagnosis. This paradigm shift will require innovative technologies to detect rapidly, and in a single sample, multiple pathogens associated with an infectious disease. Here, we report on a multiplex technology based on DNA-microarray that allows detecting and discriminating 11 bacteria implicated in respiratory tract infection. The process requires a PCR amplification of bacterial 16S rDNA, a 30 min hybridization step on species-specific oligoprobes covalently linked on dendrimers coated glass slides (DendriChips®) and a reading of the slides by a dedicated laser scanner. A diagnostic result is delivered in about 4 h as a predictive value of presence/absence of pathogens using a decision algorithm based on machine-learning method, which was constructed from hybridization profiles of known bacterial and clinical isolated samples and which can be regularly enriched with hybridization profiles from clinical samples. We demonstrated that our technology converged in more than 95% of cases with the microbiological culture for bacteria detection and identification.
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Affiliation(s)
| | | | | | | | - Philippe Besse
- Département Génie Mathématiques et Modélisation, Fédérale Université of Toulouse, F-31077 Toulouse, France.
| | | | - Jean Marie François
- LISBP, Fédérale Université de Toulouse, CNRS, INRA, INSA, F-31077 Toulouse, France.
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29
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Wu M, Cong F, Zhu Y, Lian Y, Chen M, Huang R, Guo P. Multiplex Detection of Five Canine Viral Pathogens for Dogs as Laboratory Animals by the Luminex xTAG Assay. Front Microbiol 2018; 9:1783. [PMID: 30174654 PMCID: PMC6107692 DOI: 10.3389/fmicb.2018.01783] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 07/16/2018] [Indexed: 01/07/2023] Open
Abstract
More and more dogs have been used as a disease model for medical research and drug safety evaluation. Therefore, it is important to make sure that the dogs and their living houses are special pathogen free. In this study, the development and evaluation of a Luminex xTAG assay for simultaneous detection of five canine viruses was carried out, including canine distemper virus, canine parvovirus, canine parainfluenza virus, canine adenovirus, and rabies virus. Assay specificity was accomplished by targeting conserved genomic regions for each virus. Hybridization between multiplexed PCR products and the labeled fluorescence microspheres was detected in a high throughput format using a Luminex fluorescence reader. The Luminex xTAG assay showed high sensitivity with limits of detection for the five viruses was 100 copies/μL. Specificity of the xTAG assay showed no amplification of canine coronavirus, pseudorabies virus and canine influenza virus indicating that the xTAG assay was specific. Seventy-five clinical samples were tested to evaluate the xTAG assay. The results showed 100% coincidence with the conventional PCR method. This is the first report of a specific and sensitive multiplex Luminex xTAG assay for simultaneous detection of five major canine viral pathogens. This assay will be a useful tool for quality control and environmental monitoring for dogs used as laboratory animals, may even be applied in laboratory epidemiological investigations.
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Affiliation(s)
- Miaoli Wu
- Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou, China.,Guangdong Laboratory Animals Monitoring Institute, Guangzhou, China
| | - Feng Cong
- Guangdong Laboratory Animals Monitoring Institute, Guangzhou, China
| | - Yujun Zhu
- Guangdong Laboratory Animals Monitoring Institute, Guangzhou, China
| | - Yuexiao Lian
- Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou, China
| | - Meili Chen
- Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou, China
| | - Ren Huang
- Guangdong Laboratory Animals Monitoring Institute, Guangzhou, China
| | - Pengju Guo
- Guangdong Provincial Key Laboratory of Laboratory Animals, Guangzhou, China
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30
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López-Medina E, Parra B, Dávalos DM, López P, Villamarín E, Pelaez M. Acute gastroenteritis in a pediatric population from Cali, Colombia in the post rotavirus vaccine era. Int J Infect Dis 2018; 73:52-59. [PMID: 29908961 DOI: 10.1016/j.ijid.2018.06.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 06/05/2018] [Accepted: 06/08/2018] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Epidemiological data from Latin America on acute gastroenteritis (AGE) in the post rotavirus vaccine era obtained using highly sensitive molecular techniques are scarce. METHODS This prospective surveillance study was performed between March 15, 2015 and March 19, 2016 in two municipal health networks (MHNs) in Cali, Colombia to detect AGE in children <5 years of age. Consecutive sampling was performed simultaneously in all health facilities belonging to both MHNs until completion of the required sample size. Stool samples from AGE patients were tested with a nucleic acid assay for 16 pathogens. Detection frequency and incidence rates were obtained for specific pathogens according to age-group in children with AGE leading to hospitalization or outpatient care. RESULTS Overall incidence rates of AGE-related hospitalization and outpatient care were 20 and 237 per 1000 children <5 years of age, respectively. Despite almost complete rotavirus vaccine uptake, rotavirus was the most common etiology overall, including hospitalization and outpatient treatment of 0-23-month-olds, with incidence rates of 12 and 108 per 1000 children, respectively. Norovirus incidence rates were similar to rotavirus rates in this age group and associated with high Vesikari scores. Shigella predominated in 24-59-month-olds. CONCLUSIONS AGE remains an important cause of morbidity in children under 5 years of age, especially in those under 2 years. Rotavirus remains the leading AGE-associated pathogen, followed closely by norovirus in younger children. Preventive measures, including novel vaccination strategies, are necessary in this population to further reduce AGE-related morbidity.
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Affiliation(s)
- Eduardo López-Medina
- Department of Pediatrics, Universidad del Valle, Cali, Colombia; Centro de Estudios en Infectología Pediátrica, Cali, Colombia; Centro Médico Imbanaco, Cali, Colombia.
| | - Beatriz Parra
- Department of Microbiology, Universidad del Valle, Cali, Colombia
| | - Diana M Dávalos
- Department of Public Health, Universidad Icesi, Cali, Colombia.
| | - Pio López
- Department of Pediatrics, Universidad del Valle, Cali, Colombia; Centro de Estudios en Infectología Pediátrica, Cali, Colombia
| | - Eder Villamarín
- Department of Pediatrics, Universidad del Valle, Cali, Colombia
| | - Melissa Pelaez
- Department of Microbiology, Universidad del Valle, Cali, Colombia
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31
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Learoyd TP, Gaut RM. Cholera: under diagnosis and differentiation from other diarrhoeal diseases. J Travel Med 2018; 25:S46-S51. [PMID: 29718439 DOI: 10.1093/jtm/tay017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 02/08/2018] [Indexed: 02/06/2023]
Abstract
BACKGROUND Globally 1.4 billion people are at risk from cholera in countries where the disease is endemic, with an estimated 2.8 million cases annually. The disease is significantly under reported due to economic, social and political disincentives as well as poor laboratory resources and epidemiological surveillance in those regions. In addition, identification of cholera from other diarrhoeal causes is often difficult due to shared pathology and symptoms with few reported cases in travellers from Northern Europe. METHODS A search of PubMed and Ovid Medline for publications on cholera diagnosis from 2010 through 2017 was conducted. Search terms included were cholera, Rapid Diagnostic Test (RDT), multiplex PCR and diagnosis of diarrhoea. Studies were included if they are published in English, French or Spanish. RESULTS An increase of RDT study publications for diarrhoeal disease and attempted test validations were seen over the publication period. RDTs were noted as having varied selectivity and specificity, as well as associated costs and local resource requirements that can prohibit their use. CONCLUSIONS Despite opportunities to employ RDTs with high selectivity and specificity in epidemic areas, or in remote locations without access to health services, such tests are limited to surveillance use. This may represent a missed opportunity to discover the true global presence of Vibrio cholerae and its role in all cause diarrhoeal disease in underdeveloped countries and in travellers to those areas. The wider applicability of RDTs may also represent an opportunity in the wider management of traveller's diarrhoea.
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Affiliation(s)
- Tristan P Learoyd
- Valneva UK, Centaur House, Ancells Business Park, Ancells Road, Fleet, Hampshire GU51 2UJ, UK
| | - Rupert M Gaut
- Xnomics Ltd, Yarm Road, Eaglescliffe, Stockton-on-Tees TS16 9BJ, UK
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Ko DH, Kim HS, Hyun J, Kim HS, Kim JS, Park KU, Song W. Comparison of the Luminex xTAG Respiratory Viral Panel Fast v2 Assay With Anyplex II RV16 Detection Kit and AdvanSure RV Real-Time RT-PCR Assay for the Detection of Respiratory Viruses. Ann Lab Med 2018. [PMID: 28643489 PMCID: PMC5500739 DOI: 10.3343/alm.2017.37.5.408] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Background The accurate and rapid identification of the causative viruses is important for the timely diagnosis and management of respiratory infections. Multiplex molecular diagnostic techniques have been widely adopted to detect respiratory viruses. We compared the results of a newly upgraded, multiplex, molecular bead-based respiratory viral panel (RVP) assay with the results of Anyplex II RV16 detection kit and AdvanSure RV real-time RT-PCR assay. Methods We tested 254 respiratory specimens and cultured viral strains using the Luminex xTAG RVP Fast v2 assay (Luminex Molecular Diagnostics, Canada) and Anyplex II RV16 detection kit and compared the results. Specimens showing discordant results between the two assays were tested with a AdvanSure RV real-time RT-PCR assay. Results Of the 254 respiratory specimens, there was total agreement in the results between the xTAG RVP Fast v2 assay and the other real-time PCR assay in 94.1–100% of the specimens. The agreement levels were relatively low (94.1–97.6%) for specimens of adenovirus, coronavirus NL63, and parainfluenza type 3. In comparison to the other assay, the xTAG RVP Fast v2 assay detected a higher number of parainfluenza type 3 (4 cases) and metapneumovirus (9 cases). Conclusions The xTAG RVP Fast v2 assay showed comparable capabilities compared with the other assays; it will be useful for identifying respiratory viral infections in patients with respiratory symptoms. Clinicians should be aware of the characteristics of the assays they use, since different assays show different detectability for each virus.
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Affiliation(s)
- Dae Hyun Ko
- Department of Laboratory Medicine, Hallym University College of Medicine, Hwaseong, Korea
| | - Hyun Soo Kim
- Department of Laboratory Medicine, Hallym University College of Medicine, Hwaseong, Korea.
| | - Jungwon Hyun
- Department of Laboratory Medicine, Hallym University College of Medicine, Hwaseong, Korea
| | - Han Sung Kim
- Department of Laboratory Medicine, Hallym University College of Medicine, Hwaseong, Korea
| | - Jae Seok Kim
- Department of Laboratory Medicine, Hallym University College of Medicine, Hwaseong, Korea
| | - Kyoung Un Park
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Wonkeun Song
- Department of Laboratory Medicine, Hallym University College of Medicine, Hwaseong, Korea
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Freeman K, Mistry H, Tsertsvadze A, Royle P, McCarthy N, Taylor-Phillips S, Manuel R, Mason J. Multiplex tests to identify gastrointestinal bacteria, viruses and parasites in people with suspected infectious gastroenteritis: a systematic review and economic analysis. Health Technol Assess 2018; 21:1-188. [PMID: 28619124 DOI: 10.3310/hta21230] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Gastroenteritis is a common, transient disorder usually caused by infection and characterised by the acute onset of diarrhoea. Multiplex gastrointestinal pathogen panel (GPP) tests simultaneously identify common bacterial, viral and parasitic pathogens using molecular testing. By providing test results more rapidly than conventional testing methods, GPP tests might positively influence the treatment and management of patients presenting in hospital or in the community. OBJECTIVE To systematically review the evidence for GPP tests [xTAG® (Luminex, Toronto, ON, Canada), FilmArray (BioFire Diagnostics, Salt Lake City, UT, USA) and Faecal Pathogens B (AusDiagnostics, Beaconsfield, NSW, Australia)] and to develop a de novo economic model to compare the cost-effectiveness of GPP tests with conventional testing in England and Wales. DATA SOURCES Multiple electronic databases including MEDLINE, EMBASE, Web of Science and the Cochrane Database were searched from inception to January 2016 (with supplementary searches of other online resources). REVIEW METHODS Eligible studies included patients with acute diarrhoea; comparing GPP tests with standard microbiology techniques; and patient, management, test accuracy or cost-effectiveness outcomes. Quality assessment of eligible studies used tailored Quality Assessment of Diagnostic Accuracy Studies-2, Consolidated Health Economic Evaluation Reporting Standards and Philips checklists. The meta-analysis included positive and negative agreement estimated for each pathogen. A de novo decision tree model compared patients managed with GPP testing or comparable coverage with patients managed using conventional tests, within the Public Health England pathway. Economic models included hospital and community management of patients with suspected gastroenteritis. The model estimated costs (in 2014/15 prices) and quality-adjusted life-year losses from a NHS and Personal Social Services perspective. RESULTS Twenty-three studies informed the review of clinical evidence (17 xTAG, four FilmArray, two xTAG and FilmArray, 0 Faecal Pathogens B). No study provided an adequate reference standard with which to compare the test accuracy of GPP with conventional tests. A meta-analysis (of 10 studies) found considerable heterogeneity; however, GPP testing produces a greater number of pathogen-positive findings than conventional testing. It is unclear whether or not these additional 'positives' are clinically important. The review identified no robust evidence to inform consequent clinical management of patients. There is considerable uncertainty about the cost-effectiveness of GPP panels used to test for suspected infectious gastroenteritis in hospital and community settings. Uncertainties in the model include length of stay, assumptions about false-positive findings and the costs of tests. Although there is potential for cost-effectiveness in both settings, key modelling assumptions need to be verified and model findings remain tentative. LIMITATIONS No test-treat trials were retrieved. The economic model reflects one pattern of care, which will vary across the NHS. CONCLUSIONS The systematic review and cost-effectiveness model identify uncertainties about the adoption of GPP tests within the NHS. GPP testing will generally correctly identify pathogens identified by conventional testing; however, these tests also generate considerable additional positive results of uncertain clinical importance. FUTURE WORK An independent reference standard may not exist to evaluate alternative approaches to testing. A test-treat trial might ascertain whether or not additional GPP 'positives' are clinically important or result in overdiagnoses, whether or not earlier diagnosis leads to earlier discharge in patients and what the health consequences of earlier intervention are. Future work might also consider the public health impact of different testing treatments, as test results form the basis for public health surveillance. STUDY REGISTRATION This study is registered as PROSPERO CRD2016033320. FUNDING The National Institute for Health Research Health Technology Assessment programme.
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Affiliation(s)
- Karoline Freeman
- Division of Health Sciences, Warwick Medical School, University of Warwick, Coventry, UK
| | - Hema Mistry
- Division of Health Sciences, Warwick Medical School, University of Warwick, Coventry, UK
| | - Alexander Tsertsvadze
- Division of Health Sciences, Warwick Medical School, University of Warwick, Coventry, UK
| | - Pam Royle
- Division of Health Sciences, Warwick Medical School, University of Warwick, Coventry, UK
| | - Noel McCarthy
- Division of Health Sciences, Warwick Medical School, University of Warwick, Coventry, UK
| | - Sian Taylor-Phillips
- Division of Health Sciences, Warwick Medical School, University of Warwick, Coventry, UK
| | | | - James Mason
- Division of Health Sciences, Warwick Medical School, University of Warwick, Coventry, UK
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Direct Detection of Shigella in Stool Specimens by Use of a Metagenomic Approach. J Clin Microbiol 2018; 56:JCM.01374-17. [PMID: 29118177 PMCID: PMC5786726 DOI: 10.1128/jcm.01374-17] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 11/02/2017] [Indexed: 02/04/2023] Open
Abstract
The underestimation of Shigella species as a cause of childhood diarrhea disease has become increasingly apparent with quantitative PCR (qPCR)-based diagnostic methods versus culture. We sought to confirm qPCR-based detection of Shigella via a metagenomics approach. Three groups of samples were selected from diarrheal cases from the Global Enteric Multicenter Study: nine Shigella culture-positive and qPCR-positive (culture+ qPCR+) samples, nine culture-negative but qPCR-positive (culture− qPCR+) samples, and nine culture-negative and qPCR-negative (culture− qPCR−) samples. Fecal DNA was sequenced using paired-end Illumina HiSeq, whereby 3.26 × 108 ± 5.6 × 107 high-quality reads were generated for each sample. We used Kraken software to compare the read counts specific to “Shigella” among the three groups. The proportions of Shigella-specific nonhuman sequence reads between culture+ qPCR+ (0.65 ± 0.42%) and culture− qPCR+ (0.55 ± 0.31%) samples were similar (Mann-Whitney U test, P = 0.627) and distinct from the culture− qPCR− group (0.17 ± 0.15%, P < 0.05). The read counts of sequences previously targeted by Shigella/enteroinvasive Escherichia coli (EIEC) qPCR assays, namely, ipaH, virA, virG, ial, ShET2, and ipaH3, were also similar between the culture+ qPCR+ and culture− qPCR+ groups and distinct from the culture− qPCR− groups (P < 0.001). Kraken performed well versus other methods: its precision and recall of Shigella were excellent at the genus level but variable at the species level. In summary, metagenomic sequencing indicates that Shigella/EIEC qPCR-positive samples are similar to those of Shigella culture-positive samples in Shigella sequence composition, thus supporting qPCR as an accurate method for detecting Shigella.
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The HC, Florez de Sessions P, Jie S, Pham Thanh D, Thompson CN, Nguyen Ngoc Minh C, Chu CW, Tran TA, Thomson NR, Thwaites GE, Rabaa MA, Hibberd M, Baker S. Assessing gut microbiota perturbations during the early phase of infectious diarrhea in Vietnamese children. Gut Microbes 2018; 9:38-54. [PMID: 28767339 PMCID: PMC5914913 DOI: 10.1080/19490976.2017.1361093] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 07/24/2017] [Accepted: 07/24/2017] [Indexed: 02/06/2023] Open
Abstract
Diarrheal diseases remain the second most common cause of mortality in young children in developing countries. Efforts have been made to explore the impact of diarrhea on bacterial communities in the human gut, but a thorough understanding has been impeded by inadequate resolution in bacterial identification and the examination of only few etiological agents. Here, by profiling an extended region of the 16S rRNA gene in the fecal microbiome, we aimed to elucidate the nature of gut microbiome perturbations during the early phase of infectious diarrhea caused by various etiological agents in Vietnamese children. Fecal samples from 145 diarrheal cases with a confirmed infectious etiology before antimicrobial therapy and 54 control subjects were analyzed. We found that the diarrheal fecal microbiota could be robustly categorized into 4 microbial configurations that either generally resembled or were highly divergent from a healthy state. Factors such as age, nutritional status, breastfeeding, and the etiology of the infection were significantly associated with these microbial community structures. We observed a consistent elevation of Fusobacterium mortiferum, Escherichia, and oral microorganisms in all diarrheal fecal microbiome configurations, proposing similar mechanistic interactions, even in the absence of global dysbiosis. We additionally found that Bifidobacterium pseudocatenulatum was significantly depleted during dysenteric diarrhea regardless of the etiological agent, suggesting that further investigations into the use of this species as a dysentery-orientated probiotic therapy are warranted. Our findings contribute to the understanding of the complex influence of infectious diarrhea on gut microbiome and identify new opportunities for therapeutic interventions.
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Affiliation(s)
- Hao Chung The
- Department of Enteric Infections, The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Song Jie
- The Genome Institute of Singapore, GIS Efficient Rapid Microbial Sequencing (GERMS), Singapore
| | - Duy Pham Thanh
- Department of Enteric Infections, The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Corinne N. Thompson
- Department of Enteric Infections, The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Oxford University, Oxford, United Kingdom
- The London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Chau Nguyen Ngoc Minh
- Department of Enteric Infections, The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Collins Wenhan Chu
- The Genome Institute of Singapore, GIS Efficient Rapid Microbial Sequencing (GERMS), Singapore
| | - Tuan-Anh Tran
- Department of Enteric Infections, The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nicholas R. Thomson
- The London School of Hygiene and Tropical Medicine, London, United Kingdom
- Infection Genomics, The Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Guy E. Thwaites
- Department of Enteric Infections, The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Oxford University, Oxford, United Kingdom
| | - Maia A. Rabaa
- Department of Enteric Infections, The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Oxford University, Oxford, United Kingdom
| | - Martin Hibberd
- The Genome Institute of Singapore, GIS Efficient Rapid Microbial Sequencing (GERMS), Singapore
- The London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Stephen Baker
- Department of Enteric Infections, The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Oxford University, Oxford, United Kingdom
- The Department of Medicine, The University of Cambridge, Cambridge, United Kingdom
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Chau TTH, Chau NNM, Le NTH, The HC, Vinh PV, To NTN, Ngoc NM, Tuan HM, Ngoc TLC, Kolader ME, Farrar JJ, Wolbers M, Thwaites GE, Baker S. A Double-blind, Randomized, Placebo-controlled Trial of Lactobacillus acidophilus for the Treatment of Acute Watery Diarrhea in Vietnamese Children. Pediatr Infect Dis J 2018; 37:35-42. [PMID: 28787388 PMCID: PMC5681247 DOI: 10.1097/inf.0000000000001712] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
BACKGROUND Probiotics are the most frequently prescribed treatment for children hospitalized with diarrhea in Vietnam. We were uncertain of the benefits of probiotics for the treatment of acute watery diarrhea in Vietnamese children. METHODS We conducted a double-blind, placebo-controlled, randomized trial of children hospitalized with acute watery diarrhea in Vietnam. Children meeting the inclusion criteria (acute watery diarrhea) were randomized to receive either 2 daily oral doses of 2 × 10 CFUs of a local probiotic containing Lactobacillus acidophilus or placebo for 5 days as an adjunct to standard of care. The primary end point was time from the first dose of study medication to the start of the first 24-hour period without diarrhea. Secondary outcomes included the total duration of diarrhea and hospitalization, daily stool frequency, treatment failure, daily fecal concentrations of rotavirus and norovirus, and Lactobacillus colonization. RESULTS One hundred and fifty children were randomized into each study group. The median time from the first dose of study medication to the start of the first 24-hour diarrhea-free period was 43 hours (interquartile range, 15-66 hours) in the placebo group and 35 hours (interquartile range, 20-68 hours) in the probiotic group (acceleration factor 1.09 [95% confidence interval, 0.78-1.51]; P = 0.62). There was also no evidence that probiotic treatment was efficacious in any of the predefined subgroups nor significantly associated with any secondary end point. CONCLUSIONS This was a large double-blind, placebo-controlled trial in which the probiotic underwent longitudinal quality control. We found under these conditions that L. acidophilus was not beneficial in treating children with acute watery diarrhea.
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Affiliation(s)
- Tran Thi Hong Chau
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nguyen Ngoc Minh Chau
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nhat Thanh Hoang Le
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Hao Chung The
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Phat Voong Vinh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nguyen Thi Nguyen To
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Ha Manh Tuan
- Children’s Hospital 2 (CH2), Ho Chi Minh City, Vietnam
| | | | | | - Jeremy J. Farrar
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam,Centre for Tropical Medicine, Oxford University, Oxford, United Kingdom
| | - Marcel Wolbers
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam,Centre for Tropical Medicine, Oxford University, Oxford, United Kingdom
| | - Guy E. Thwaites
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam,Centre for Tropical Medicine, Oxford University, Oxford, United Kingdom
| | - Stephen Baker
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam,Centre for Tropical Medicine, Oxford University, Oxford, United Kingdom,The Department of Medicine, The University of Cambridge, Cambridge, United Kingdom,Corresponding Author: Professor Stephen Baker, the Hospital for Tropical Diseases, 764 Vo Van Kiet, Quan 5, Ho Chi Minh City, Vietnam. Tel: +84 89241761; Fax: +84 89238904;
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Nguyen NH, Nguyen TNM, Hotzel H, El Adawy H, Nguyen AQ, Tran HT, Le MTH, Tomaso H, Neubauer H, Hafez HM. Thermophilic Campylobacter - Neglected Foodborne Pathogens in Cambodia, Laos and Vietnam. GASTROENTEROLOGY & HEPATOLOGY (BARTLESVILLE, OKLA.) 2017; 8:00279. [PMID: 31544148 PMCID: PMC6754824 DOI: 10.15406/ghoa.2017.08.00279] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Thermophilic Campylobacter are the most common bacterial cause of gastroenteritis in humans worldwide. Poultry and poultry products are the main sources for human infections. Epidemiological data concerning campylobacteriosis in Asia are limited. Overall, it is difficult to accurately assess the burden of Campylobacter infections. South-East Asia including Cambodia, Laos and Vietnam is known as a hotspot for emerging diseases. Campylobacteriosis is a problem of public health concern in these countries, hence. Epidemiological data are scarce. This is influenced by the limited number of laboratory facilities and lack of equipment and awareness in physicians and veterinarians resulting in the lack of surveys. This review lists articles and reports on Campylobacter and campylobacteriosis in these developing third world countries. Subjects are prevalence of thermophilic Campylobacter in humans, animals and food and their resistance to several antibiotics.
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Affiliation(s)
| | - Tuan Ngoc Minh Nguyen
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Bacterial Infections and Zoonoses, Germany
- Hung Vuong University, Vietnam
- Institute for Poultry Diseases, Free University Berlin, Germany
| | - Helmut Hotzel
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Bacterial Infections and Zoonoses, Germany
| | - Hosny El Adawy
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Bacterial Infections and Zoonoses, Germany
- Department of Poultry Disease, Faculty of Veterinary Medicine, Kafrelsheikh University, Egypt
| | | | - Hanh Thi Tran
- Biodiversity Conversation and Tropical Disease Research Institute (BioD), Vietnam
| | - Minh Thi Hong Le
- Biodiversity Conversation and Tropical Disease Research Institute (BioD), Vietnam
- Institute of Marine Biochemistry, Vietnam Academy of Science and Technology, Vietnam
| | - Herbert Tomaso
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Bacterial Infections and Zoonoses, Germany
| | - Heinrich Neubauer
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Bacterial Infections and Zoonoses, Germany
| | - Hafez M Hafez
- Institute for Poultry Diseases, Free University Berlin, Germany
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Abstract
PURPOSE OF REVIEW The review examines the changing causes and the investigation of infectious and noninfectious diarrhoea in individuals with HIV. RECENT FINDINGS Despite the excellent prognosis conferred by combination antiretroviral therapy, diarrhoea is still common in HIV-positive individuals and is associated with reduced quality of life and survival. There is increasing interest in the importance of Th17 and Th22 T cells in the maintenance of mucosal immunity within the gut, and in the role of the gut microbiome in gut homeostasis. Bacterial causes of HIV-associated diarrhoea continue to be important in resource-poor settings. In other settings, sexually transmitted enteric infections such as lymphogranuloma venereum and shigellosis are increasingly reported in men who have sex with men. HIV increases the risk of such infections and the presence of antimicrobial resistance. Parasitic causes of diarrhoea are more common in individuals with uncontrolled HIV and low CD4 counts. Noninfectious causes of diarrhoea include all classes of antiretroviral therapy, which is under-recognised as a cause of poor treatment adherence. Pancreatic dysfunction is remediable and the diagnostic workup of HIV-related diarrhoea should include faecal elastase measurements. New antimotility agents such as crofelemer may be useful in managing secretory diarrhoea symptoms. SUMMARY Clinicians looking after patients with HIV should ask about diarrhoeal symptoms, which are under-reported and may have a remediable infectious or noninfectious cause.
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Cheong E, Roberts T, Rattanavong S, Riley TV, Newton PN, Dance DAB. Clostridium difficile infection in the Lao People's Democratic Republic: first isolation and review of the literature. BMC Infect Dis 2017; 17:635. [PMID: 28934954 PMCID: PMC5609038 DOI: 10.1186/s12879-017-2737-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 09/14/2017] [Indexed: 11/25/2022] Open
Abstract
Background Current knowledge of the epidemiology of Clostridium difficile infection in Asia, and in particular the Greater Mekong Subregion, is very limited. Only a few studies from Thailand and Vietnam have been reported from the region with variable testing methods and results, and no studies from Lao People’s Democratic Republic (PDR). Therefore we investigated the presence of C. difficile in a single centre in the Lao PDR and determined the ribotypes present. Method Seventy unformed stool samples from hospital inpatients at Mahosot Hospital, Vientiane, were tested for the presence of C. difficile using selective differential agar and confirmed by latex agglutination. C. difficile isolates were further characterised by ribotyping and toxin gene detection. Results C. difficile was isolated from five of the 70 patients, and five different ribotypes were identified (014, 017, 020, QX 107 and QX 574). Conclusion This is the first isolation of C. difficile from human stool samples in the Lao PDR. These results will add to the limited amount of data on C. difficile in the region. In addition, we hope this information will alert clinicians to the presence of C. difficile in the country and will help inform future investigations into the epidemiology and diagnosis of C. difficile in Lao PDR.
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Affiliation(s)
- Elaine Cheong
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic. .,Department of Microbiology, Concord Repatriation General Hospital, Sydney, Concord, Australia.
| | - Tamalee Roberts
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Sayaphet Rattanavong
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic
| | - Thomas V Riley
- PathWest Laboratory Medicine (WA), Edith Cowan University and Murdoch University, Queen Elizabeth II Medical Centre, Nedlands, Australia
| | - Paul N Newton
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic.,Centre for Tropical Medicine & Global Health, University of Oxford, Oxford, UK
| | - David A B Dance
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao People's Democratic Republic.,Centre for Tropical Medicine & Global Health, University of Oxford, Oxford, UK.,Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
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Abbott AN, Fang FC. Clinical Impact of Multiplex Syndromic Panels in the Diagnosis of Bloodstream, Gastrointestinal, Respiratory, and Central Nervous System Infections. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.clinmicnews.2017.08.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Ryan U, Paparini A, Oskam C. New Technologies for Detection of Enteric Parasites. Trends Parasitol 2017; 33:532-546. [DOI: 10.1016/j.pt.2017.03.005] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 03/13/2017] [Accepted: 03/13/2017] [Indexed: 12/21/2022]
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Epidemiology, clinical features, and microbiology of patients with diarrhea in community clinics in Taiwan. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2017; 51:527-534. [PMID: 28688828 DOI: 10.1016/j.jmii.2017.05.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 05/16/2017] [Accepted: 05/24/2017] [Indexed: 02/05/2023]
Abstract
OBJECTIVE To investigate the clinical features and microbiology of patients with diarrheal diseases in Taiwan. METHODS From March 2014 to October 2014, patients with diarrheal diseases referred from the community clinics were enrolled into our prospective study. Demographics and clinical features of the participants were acquired. Stool samples were examined by the Luminex Gastrointestinal Pathogen Panel assay. Data were analyzed by SAS version 9.4. RESULTS A total of 545 patients were enrolled into this study. Male and adults accounted for 52.3% and 82.6% of patients, respectively. The median age was 36 years. Enteropathogen(s) was identified in 43.3% of patients and 8.5% of them had more than one agent in their stool samples. Viruses, especially norovirus GI/GII, were the predominant agents of gastroenteritis. Moreover, Campylobacter species was the most common bacterial agent. Bloody stool was frequently reported in patients with bacterial diarrhea (P = 0.002); contrarily, watery stool was significantly associated with viral diarrhea (P < 0.0001). Regional variation and seasonality of microbiological distribution were also observed. CONCLUSION In Taiwan, viruses were the predominant pathogens among patients with diarrheal diseases who visited community clinics. The therapeutic strategies for diarrheal patients should be based on the epidemiological and clinical characteristics.
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Abstract
Eleven published studies of the etiology of travellers' diarrhea (TD) were reviewed define the etiology of TD and to exam newly developed technology such as Real-Time multiplex polymerase chain reaction (PCR) to identify multiple pathogens in one assay to define the cause of TD. Using PCR methods bacterial pathogens were found in 72% of patients acquiring diarrhea in Latin America and in 80% in travellers with illness acquired in Southeast Asia). In these studies, enterotoxigenic Escherichia coli as the predominant pathogen (42% in Latin America and 28% in Southeast Asia). Ciprofloxacin-resistant Campylobacter was commonly associated with TD in Southeast Asia. Multiplex PCR has improved the detection of enteropathogens and allowed better assessment returning travellers hospitalized with TD and those with persistent diarrhea.
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Affiliation(s)
- Z D Jiang
- School of Medicine, University of Texas, Houston, TX, USA
| | - H L DuPont
- Houston School of Public Health, The University of Texas, and Medical School, Center for Infectious Diseases, Houston, TX, USA
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Freeman K, Tsertsvadze A, Taylor-Phillips S, McCarthy N, Mistry H, Manuel R, Mason J. Agreement between gastrointestinal panel testing and standard microbiology methods for detecting pathogens in suspected infectious gastroenteritis: Test evaluation and meta-analysis in the absence of a reference standard. PLoS One 2017; 12:e0173196. [PMID: 28253337 PMCID: PMC5333893 DOI: 10.1371/journal.pone.0173196] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 02/16/2017] [Indexed: 01/26/2023] Open
Abstract
Objective Multiplex gastrointestinal pathogen panel (GPP) tests simultaneously identify bacterial, viral and parasitic pathogens from the stool samples of patients with suspected infectious gastroenteritis presenting in hospital or the community. We undertook a systematic review to compare the accuracy of GPP tests with standard microbiology techniques. Review methods Searches in Medline, Embase, Web of Science and the Cochrane library were undertaken from inception to January 2016. Eligible studies compared GPP tests with standard microbiology techniques in patients with suspected gastroenteritis. Quality assessment of included studies used tailored QUADAS-2. In the absence of a reference standard we analysed test performance taking GPP tests and standard microbiology techniques in turn as the benchmark test, using random effects meta-analysis of proportions. Results No study provided an adequate reference standard with which to compare the test accuracy of GPP and conventional tests. Ten studies informed a meta-analysis of positive and negative agreement. Positive agreement across all pathogens was 0.93 (95% CI 0.90 to 0.96) when conventional methods were the benchmark and 0.68 (95% CI: 0.58 to 0.77) when GPP provided the benchmark. Negative agreement was high in both instances due to the high proportion of negative cases. GPP testing produced a greater number of pathogen-positive findings than conventional testing. It is unclear whether these additional ‘positives’ are clinically important. Conclusions GPP testing has the potential to simplify testing and accelerate reporting when compared to conventional microbiology methods. However the impact of GPP testing upon the management, treatment and outcome of patients is poorly understood and further studies are needed to evaluate the health economic impact of GPP testing compared with standard methods. The review protocol is registered with PROSPERO as CRD42016033320.
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Affiliation(s)
- Karoline Freeman
- Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | | | | | - Noel McCarthy
- Warwick Medical School, University of Warwick, Coventry, United Kingdom
- NIHR Health Protection Research Unit in Gastrointestinal Infections, Oxford, United Kingdom
| | - Hema Mistry
- Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Rohini Manuel
- NIHR Health Protection Research Unit in Gastrointestinal Infections, London, United Kingdom
| | - James Mason
- Warwick Medical School, University of Warwick, Coventry, United Kingdom
- * E-mail:
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Liu J, Platts-Mills JA, Juma J, Kabir F, Nkeze J, Okoi C, Operario DJ, Uddin J, Ahmed S, Alonso PL, Antonio M, Becker SM, Blackwelder WC, Breiman RF, Faruque ASG, Fields B, Gratz J, Haque R, Hossain A, Hossain MJ, Jarju S, Qamar F, Iqbal NT, Kwambana B, Mandomando I, McMurry TL, Ochieng C, Ochieng JB, Ochieng M, Onyango C, Panchalingam S, Kalam A, Aziz F, Qureshi S, Ramamurthy T, Roberts JH, Saha D, Sow SO, Stroup SE, Sur D, Tamboura B, Taniuchi M, Tennant SM, Toema D, Wu Y, Zaidi A, Nataro JP, Kotloff KL, Levine MM, Houpt ER. Use of quantitative molecular diagnostic methods to identify causes of diarrhoea in children: a reanalysis of the GEMS case-control study. Lancet 2016; 388:1291-301. [PMID: 27673470 PMCID: PMC5471845 DOI: 10.1016/s0140-6736(16)31529-x] [Citation(s) in RCA: 543] [Impact Index Per Article: 67.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 07/18/2016] [Accepted: 07/19/2016] [Indexed: 12/13/2022]
Abstract
BACKGROUND Diarrhoea is the second leading cause of mortality in children worldwide, but establishing the cause can be complicated by diverse diagnostic approaches and varying test characteristics. We used quantitative molecular diagnostic methods to reassess causes of diarrhoea in the Global Enteric Multicenter Study (GEMS). METHODS GEMS was a study of moderate to severe diarrhoea in children younger than 5 years in Africa and Asia. We used quantitative real-time PCR (qPCR) to test for 32 enteropathogens in stool samples from cases and matched asymptomatic controls from GEMS, and compared pathogen-specific attributable incidences with those found with the original GEMS microbiological methods, including culture, EIA, and reverse-transcriptase PCR. We calculated revised pathogen-specific burdens of disease and assessed causes in individual children. FINDINGS We analysed 5304 sample pairs. For most pathogens, incidence was greater with qPCR than with the original methods, particularly for adenovirus 40/41 (around five times), Shigella spp or enteroinvasive Escherichia coli (EIEC) and Campylobactor jejuni o C coli (around two times), and heat-stable enterotoxin-producing E coli ([ST-ETEC] around 1·5 times). The six most attributable pathogens became, in descending order, Shigella spp, rotavirus, adenovirus 40/41, ST-ETEC, Cryptosporidium spp, and Campylobacter spp. Pathogen-attributable diarrhoeal burden was 89·3% (95% CI 83·2-96·0) at the population level, compared with 51·5% (48·0-55·0) in the original GEMS analysis. The top six pathogens accounted for 77·8% (74·6-80·9) of all attributable diarrhoea. With use of model-derived quantitative cutoffs to assess individual diarrhoeal cases, 2254 (42·5%) of 5304 cases had one diarrhoea-associated pathogen detected and 2063 (38·9%) had two or more, with Shigella spp and rotavirus being the pathogens most strongly associated with diarrhoea in children with mixed infections. INTERPRETATION A quantitative molecular diagnostic approach improved population-level and case-level characterisation of the causes of diarrhoea and indicated a high burden of disease associated with six pathogens, for which targeted treatment should be prioritised. FUNDING Bill & Melinda Gates Foundation.
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Affiliation(s)
- Jie Liu
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - James A Platts-Mills
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - Jane Juma
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Furqan Kabir
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Joseph Nkeze
- Center for Vaccine Development and Institute of Global Health, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | | | - Darwin J Operario
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - Jashim Uddin
- International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR, B), Dhaka, Bangladesh
| | - Shahnawaz Ahmed
- International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR, B), Dhaka, Bangladesh
| | - Pedro L Alonso
- Centro de Investigação em Saúde da Manhiça, Maputo, Mozambique; Barcelona Centre for International Health Research (CRESIB, Hospital Clinic-Universitat de Barcelona), Barcelona, Spain
| | | | - Stephen M Becker
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - William C Blackwelder
- Center for Vaccine Development and Institute of Global Health, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Robert F Breiman
- Global Disease Detection Division, Kenya Office of the US Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Abu S G Faruque
- International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR, B), Dhaka, Bangladesh
| | - Barry Fields
- Global Disease Detection Division, Kenya Office of the US Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Jean Gratz
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - Rashidul Haque
- International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR, B), Dhaka, Bangladesh
| | - Anowar Hossain
- International Centre for Diarrhoeal Disease Research, Bangladesh (ICDDR, B), Dhaka, Bangladesh
| | | | - Sheikh Jarju
- Medical Research Council Unit, Banjul, The Gambia
| | - Farah Qamar
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Najeeha Talat Iqbal
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | | | | | - Timothy L McMurry
- Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Caroline Ochieng
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - John B Ochieng
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Melvin Ochieng
- Center for Global Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Clayton Onyango
- Global Disease Detection Division, Kenya Office of the US Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Sandra Panchalingam
- Center for Vaccine Development and Institute of Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Adil Kalam
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Fatima Aziz
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Shahida Qureshi
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | | | - James H Roberts
- Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | | | - Samba O Sow
- Centre pour le Développement des Vaccins, Bamako, Mali
| | - Suzanne E Stroup
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - Dipika Sur
- National Institute of Cholera and Enteric Diseases, Kolkata, India
| | | | - Mami Taniuchi
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA
| | - Sharon M Tennant
- Center for Vaccine Development and Institute of Global Health, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Deanna Toema
- Center for Vaccine Development and Institute of Global Health, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Yukun Wu
- Center for Vaccine Development and Institute of Global Health, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Anita Zaidi
- Department of Paediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - James P Nataro
- Department of Pediatrics, University of Virginia, Charlottesville, VA, USA
| | - Karen L Kotloff
- Center for Vaccine Development and Institute of Global Health, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Myron M Levine
- Center for Vaccine Development and Institute of Global Health, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Pediatrics, University of Maryland School of Medicine, Baltimore, MD, USA; Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Eric R Houpt
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, USA.
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Diagnostic performance of the Luminex xTAG gastrointestinal pathogens panel to detect rotavirus in Ghanaian children with and without diarrhoea. Virol J 2016; 13:132. [PMID: 27473598 PMCID: PMC4966796 DOI: 10.1186/s12985-016-0588-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 07/24/2016] [Indexed: 02/04/2023] Open
Abstract
Background Rotavirus is one of the leading causes of childhood diarrhoea worldwide. The highest disease burden is seen in resource-constrained settings of sub-Saharan Africa. Recently, commercial multiplex PCR panels proved their accuracy to diagnose infectious gastroenteritis in Europe and the USA. However, data on their performance using samples from tropical regions in general and to detect rotavirus in particular remains scant. We aimed to analyse the diagnostic performance of the Luminex xTAG gastrointestinal pathogens panel, a multiplex PCR, to detect rotavirus in stool samples from Ghanaian children. Methods A total of 682 stool samples were collected in the Ashanti region of Ghana between 2007 and 2008. Of these, 341 were from cases (children with diarrhoea), and another 341 from controls (children without diarrhoea). All samples were analysed using the Luminex xTAG assay and compared to a rotavirus quantitative reverse-transcription PCR (reference assay). Rotavirus reference assay positive samples were P and G genotyped by sequencing the rotavirus VP4 and VP7 genes. Results Overall agreement between the Luminex xTAG and the reference assay was excellent (kappa 0.93). The sensitivity and specificity was 88.2 % (95 % confidence interval [CI] 78.2–94.1) and 100 % (95 % CI 99.2–100), respectively. Of 76 rotavirus reference assay positive samples, 64 were successfully genotyped and the Luminex xTAG assay was able to detect all rotavirus genotypes present in the study. Conclusion The Luminex xTAG assay proved a sensitive and highly specific tool to detect rotavirus and may aid clinicians and public health authorities in the diagnosis and surveillance of rotavirus.
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