1
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Yu Y, Yao Y, Song Y, Shan H, Han X. Establishment and application of multiplex PCR for rapid detection of three mink diarrhea-associated viruses. J Virol Methods 2024; 328:114958. [PMID: 38801834 DOI: 10.1016/j.jviromet.2024.114958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 05/07/2024] [Accepted: 05/19/2024] [Indexed: 05/29/2024]
Abstract
In this report, a multiplex PCR method was developed for the detection of three diarrhea-associated viruses in mink, including circovirus (MCV), bocavirus (MBoV), and enteritis virus (MEV). Three compatible sets of primers specific for each virus were designed respectively based on their conserved sequences. After optimization of the crucial factors such as primer concentration and annealing temperature in single and multiple amplification, three specific fragments were simultaneously amplified with the highest sensitivity and specificity in one PCR reaction. The fragments amplified were 259 bp (MCV),455 bp (MBoV) and 671 bp (MEV). The sensibility of this one-step multiplex PCR is about 10 times lower than that of regular singleplex PCR. There were no cross-reactions with some relevant pathogens like mink coronavirus, canine distemper virus, and aleutian mink disease virus. In our study we analyzed viral DNA in mink fecal samples by multiplex PCR assay from China, which revealed the occurrence of MCV, MBoV, and MEV as 3.1 %, 5.7 %, and 9.8 %, respectively. The testing results of multiplex PCR agreed with the singleplex PCR results with a coincidence rate of 100 %. These results indicated that the method could provide technical support for rapid detection of the three diarrhea-associated viruses, and epidemiological investigation of mink viral diarrhea.
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Affiliation(s)
- Yongle Yu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, PR China.
| | - Yanzhu Yao
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao 266109, PR China
| | - Yihang Song
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, PR China
| | - Hu Shan
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, PR China
| | - Xianjie Han
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, PR China.
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2
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Sameer M, Masood A, Almutawea L, Fox G, Loni R, Ahmed A, Ben Turkia H, Abdulsamad M, Mary I. Gastrointestinal Panel Performance for the Diagnosis of Acute Gastroenteritis in Pediatric Patients. Cureus 2024; 16:e61979. [PMID: 38983994 PMCID: PMC11231452 DOI: 10.7759/cureus.61979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2024] [Indexed: 07/11/2024] Open
Abstract
BACKGROUND Various methods are used to identify the causative organisms of acute gastroenteritis (AGE) in children. The gastrointestinal (GI) panel has the potential to detect up to 22 pathogens rapidly through the multiplex real-time PCR test. We studied the impact of the GI panel on clinical management in the pediatric population. METHODS A retrospective study was conducted to collect data on GI panel results and clinical details of inpatient children presenting with AGE at King Hamad University Hospital, Kingdom of Bahrain, over the course of one year. RESULTS One hundred nine samples were collected. The GI panel was positive in 96 samples (88.1%), with the majority detected in the toddler age group. Forty-one (42.7%) samples were positive for at least one organism. Salmonella was the most frequently encountered bacteria as a single isolate, 10/55 (18.2%), while enteropathogenic Escherichia coli was the most common co-infected organism, 16/41 (39%). Norovirus was the most common virus among the viruses. Bacterial detection peaked from July to October, while viral detection plateaued throughout the year. The GI panel and stool culture were positive for the same organism in 17 samples, versus one sample with a different organism. Sixty-two (56.9%) samples had a positive GI panel but negative stool cultures and stool analysis, and half of those detected viruses. The GI panel was positive in 86.2% of severely ill patients; the majority were bacteria. Bacterial detection was associated with a higher CRP compared to viruses. CONCLUSION The GI panel is an informative tool for detecting the causative pathogen of AGE in children. However, it can detect multiple organisms, indicating a possible carrier status, which points toward future studies.
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Affiliation(s)
- Marwa Sameer
- Pediatric and Neonatology Department, King Hamad University Hospital, Muharraq, BHR
| | - Abdulrahman Masood
- Cardiology Department, Mohammed Bin Khalifa Bin Salman Al Khalifa Specialist Cardiac Center, Riffa, BHR
| | - Lateefa Almutawea
- Pediatric and Neonatology Department, King Hamad University Hospital, Muharraq, BHR
| | - Gabriel Fox
- Pediatric and Neonatology Department, King Hamad University Hospital, Muharraq, BHR
| | - Ramaning Loni
- Pediatric and Neonatology Department, King Hamad University Hospital, Muharraq, BHR
| | - Amira Ahmed
- Pathology, Blood Bank, and Laboratory Medicine Department, King Hamad University Hospital, Muharraq, BHR
| | - Hadhami Ben Turkia
- Pediatric and Neonatology Department, King Hamad University Hospital, Muharraq, BHR
| | - Maryam Abdulsamad
- Pathology, Blood Bank, and Laboratory Medicine Department, King Hamad University Hospital, Muharraq, BHR
| | - Imelda Mary
- Pediatric and Neonatology Department, King Hamad University Hospital, Muharraq, BHR
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3
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Fang PH, Chang HC, Cheng HL, Huang CC, Wang S, Teng CH, Chia ZC, Chiang HP, Ruan J, Shih WA, Chou WY. Bacteria Contaminants Detected by Organic Inverter-Based Biosensors. Polymers (Basel) 2024; 16:1462. [PMID: 38891409 PMCID: PMC11174487 DOI: 10.3390/polym16111462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/19/2024] [Accepted: 05/20/2024] [Indexed: 06/21/2024] Open
Abstract
The importance of bacteria detection lies in its role in enabling early intervention, disease prevention, environmental protection, and effective treatment strategies. Advancements in technology continually enhance the speed, accuracy, and sensitivity of detection methods, aiding in addressing these critical issues. This study first reports the fabrication of an inverter constructed using crosslinked-poly(4-vinylphenol) (C-PVP) as the dielectric layer and an organic complementary metal-oxide semiconductor (O-CMOS) based on pentacene and N,N'-ditridecylperylene-3,4,9,10-tetracarboxylic diimide (PTCDI-C13) as a diagnostic biosensor to rapidly detect bacterial concentration. Bacteria including Escherichia coli O157, Staphylococcus aureus ATCC25922, and Enterococcus faecalis SH-1051210 were analysed on the inverters at an ultra-low operating voltage of 2 V. The high density of negative charge on bacteria surfaces strongly modulates the accumulated negative carriers within the inverter channel, resulting in a shift of the switching voltage. The inverter-based bacteria sensor exhibits a linear-like response to bacteria concentrations ranging from 102 to 108 CFU/mL, with a sensitivity above 60%. Compared to other bacterial detectors, the advantage of using an inverter lies in its ability to directly read the switching voltage without requiring an external computing device. This facilitates rapid and accurate bacterial concentration measurement, offering significant ease of use and potential for mass production.
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Affiliation(s)
- Po-Hsiang Fang
- Department of Photonics, National Cheng Kung University, Tainan 70101, Taiwan
| | - Han-Chun Chang
- Department of Photonics, National Cheng Kung University, Tainan 70101, Taiwan
| | - Horng-Long Cheng
- Department of Photonics, National Cheng Kung University, Tainan 70101, Taiwan
| | - Chih-Chia Huang
- Department of Photonics, National Cheng Kung University, Tainan 70101, Taiwan
| | - Shuying Wang
- Department of Microbiology and Immunology, Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
| | - Ching-Hao Teng
- Institute of Molecular Medicine, National Cheng Kung University, Tainan 70101, Taiwan
| | - Zi-Chun Chia
- Department of Photonics, National Cheng Kung University, Tainan 70101, Taiwan
| | - Hai-Pang Chiang
- Department of Optoelectronics and Materials Technology, National Taiwan Ocean University, Keelung 20224, Taiwan
| | - Jrjeng Ruan
- Department of Materials Science and Engineering, National Cheng Kung University, Tainan 70101, Taiwan
| | - Wei-An Shih
- Institute of Molecular Medicine, National Cheng Kung University, Tainan 70101, Taiwan
| | - Wei-Yang Chou
- Department of Photonics, National Cheng Kung University, Tainan 70101, Taiwan
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4
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Mohtar J, Mallah H, Mardirossian JM, El-Bikai R, Jisr TE, Soussi S, Naoufal R, Alam G, Chaar ME. Enhancing enteric pathogen detection: implementation and impact of multiplex PCR for improved diagnosis and surveillance. BMC Infect Dis 2024; 24:171. [PMID: 38326773 PMCID: PMC10848388 DOI: 10.1186/s12879-024-09047-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 01/23/2024] [Indexed: 02/09/2024] Open
Abstract
BACKGROUND Syndromic surveillance of acute gastroenteritis plays a significant role in the diagnosis and management of gastrointestinal infections that are responsible for a substantial number of deaths globally, especially in developing countries. In Lebanon, there is a lack of national surveillance for acute gastroenteritis, and limited data exists regarding the prevalence of pathogens causing diarrhea. The one-year study aims to investigate the epidemiology of common gastrointestinal pathogens and compare our findings with causative agents of diarrhea reported by our study collaborative centers. METHODS A multicenter, cross-sectional study was conducted over a one-year period. A total of 271 samples were obtained from outpatients and inpatients presenting with symptoms of acute gastroenteritis at various healthcare facilities. The samples were then analyzed using Allplex gastrointestinal assay that identifies a panel of enteric pathogens. RESULTS Overall, enteropathogens were detected in 71% of the enrolled cases, 46% of those were identified in patients as single and 54% as mixed infections. Bacteria were observed in 48%, parasites in 12% and viruses in 11%. Bacterial infections were the most prevalent in all age groups. Enteroaggregative E. coli (26.5%), Enterotoxigenic E. coli (23.2%) and Enteropathogenic E. coli (20.3%) were the most frequently identified followed by Blastocystis hominis (15.5%) and Rotavirus (7.7%). Highest hospitalization rate occurred with rotavirus (63%), Enterotoxigenic E. coli (50%), Blastocystis hominis (45%) and Enteropathogenic E. coli (43%). Enteric pathogens were prevalent during summer, fall and winter seasons. CONCLUSIONS The adoption of multiplex real-time PCR assays in the diagnosis of gastrointestinal infections has identified gaps and improved the rates of detection for multiple pathogens. Our findings highlight the importance of conducting comprehensive surveillance to monitor enteric infections. The implementation of a syndromic testing panel can therefore provide healthcare professionals with timely and accurate information for more effective treatment and public health interventions.
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Affiliation(s)
- Jad Mohtar
- Faculty of Health Sciences, University of Balamand, Beirut, Lebanon
| | - Hiba Mallah
- Faculty of Health Sciences, University of Balamand, Beirut, Lebanon
| | - Jean Marc Mardirossian
- Faculty of Health Sciences, University of Balamand, Beirut, Lebanon
- Mayo Clinic Discovery and Translational Polycystic Kidney Disease Center, Florida, USA
| | - Rana El-Bikai
- Faculty of Health Sciences, University of Balamand, Beirut, Lebanon
| | - Tamima El Jisr
- Clinical Laboratory Department, Makassed General Hospital, Beirut, Lebanon
| | - Shatha Soussi
- Clinical Laboratory Department, Makassed General Hospital, Beirut, Lebanon
| | - Rania Naoufal
- Clinical Laboratory Department, Saint Georges Hospital University Medical Center, Beirut, Lebanon
| | - Gabriella Alam
- Clinical Laboratory Department, Saint Georges Hospital University Medical Center, Beirut, Lebanon
| | - Mira El Chaar
- Faculty of Health Sciences, University of Balamand, Beirut, Lebanon.
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5
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Koeffer J, Kolb M, Sorel O, Ulekleiv C, Feenstra JDM, Eigner U. Clinical performance evaluation of TAQPATH Enteric Bacterial Select Panel for the detection of common enteric bacterial pathogens in comparison to routine stool culture and other qPCR-based diagnostic tests. Microbiol Spectr 2024; 12:e0317223. [PMID: 38054723 PMCID: PMC10783074 DOI: 10.1128/spectrum.03172-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 11/01/2023] [Indexed: 12/07/2023] Open
Abstract
IMPORTANCE Enteric bacterial infections caused by Salmonella, Shigella, pathogenic Escherichia coli, and Campylobacter represent one of the most common causes of infectious enteritis worldwide. The timely and accurate diagnosis of pathogens causing gastroenteritis is crucial for patient care, public health, and disease surveillance. While stool culture has long been the standard and highly specific method for detecting enteric pathogens, it is labor-intensive and time-consuming with limited sensitivity. To improve patient outcomes, there is a need to implement new cost-effective approaches for the detection of bacterial enteric pathogens with higher sensitivity and faster time to result. This study shows that multiplex real-time polymerase chain reaction-based tests, such as the TAQPATH Enteric Bacterial Select Panel, are accurate and cost-effective diagnostic alternatives for the detection and differentiation of the most common enteric bacterial pathogens, offering quicker time to result and higher sensitivity compared to routine stool culture.
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Affiliation(s)
- Jasmin Koeffer
- Department of Infectious Diseases, MVZ Labor Dr. Limbach & Kollegen GbR, Heidelberg, Germany
| | - Melissa Kolb
- Department of Infectious Diseases, MVZ Labor Dr. Limbach & Kollegen GbR, Heidelberg, Germany
| | - Oceane Sorel
- Thermo Fisher Scientific, South San Francisco, California, USA
| | | | | | - Ulrich Eigner
- Department of Infectious Diseases, MVZ Labor Dr. Limbach & Kollegen GbR, Heidelberg, Germany
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Besser J, Singer R, Jervis RH, Boxrud D, Smith K, Daly ER. Laboratory Criteria for Exclusion and Readmission of Potentially Infectious Persons in Sensitive Settings in the Age of Culture-Independent Diagnostic Tests: Report of a Multidisciplinary Workgroup. J Food Prot 2023; 86:100173. [PMID: 37797737 DOI: 10.1016/j.jfp.2023.100173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 09/23/2023] [Accepted: 09/27/2023] [Indexed: 10/07/2023]
Abstract
Culture-independent diagnostic tests (CIDTs) are increasingly used for clinical diagnosis of gastrointestinal diseases such as salmonellosis, Shiga toxin-producing E. coli disease, and shigellosis because of their speed, convenience, and generally high-performance characteristics. These tests are also used to screen potentially infectious asymptomatic persons during outbreak investigations in sensitive settings such as childcare, food service, and healthcare. However, only limited performance data are available for CIDTs used on specimens from asymptomatic persons. The Association of Public Health Laboratories (APHL) and Council of State and Territorial Epidemiologists (CSTE) convened a workgroup to examine the available scientific data to inform interim decision-making related to exclusion and readmission criteria for potentially infectious persons in sensitive settings, the risks and benefits of different testing strategies, and to identify knowledge gaps for further research. This is the report on the Workgroup findings.
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Affiliation(s)
- John Besser
- Association of Public Health Laboratories, 284 Vickers DR NE, Atlanta, GA 30307, USA.
| | - Rachael Singer
- Council of State and Territorial Epidemiologists, 2635 Century Parkway NE, Suite 700, Atlanta, GA 30345, USA.
| | - Rachel H Jervis
- Colorado Department of Public Health and Environment, 4300 Cherry Creek Drive South, Denver, CO 80246, USA.
| | - David Boxrud
- Centers for Disease Control and Prevention, 1600 Clifton Road NE. Atlanta GA 30329, USA.
| | - Kirk Smith
- Minnesota Department of Health, 625 Robert St. N. P.O. Box 64975, St. Paul, MN 55164, USA.
| | - Elizabeth R Daly
- Council of State and Territorial Epidemiologists, 2635 Century Parkway NE, Suite 700, Atlanta, GA 30345, USA.
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7
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Lamps LW. Infectious Disease Pathology of the Gastrointestinal Tract: Diagnosing the Challenging Cases. Surg Pathol Clin 2023; 16:779-804. [PMID: 37863566 DOI: 10.1016/j.path.2023.05.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2023]
Abstract
Infectious diseases of the GI tract mimic a variety of other GI diseases, including chronic idiopathic inflammatory bowel disease and ischemia. It can be challenging to identify pathogens in tissue sections as well, as many trainees are not exposed to infectious disease pathology other than in the context of microbiology. Our ability to diagnose infections in formalin fixed, paraffin embedded material has grown exponentially with the advent of new histochemical and immunohistochemical stains, as well as more options for molecular testing. Correlating these diagnostic techniques with morphology has led to increasing understanding of the histologic patterns that are associated with specific pathogens.
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Affiliation(s)
- Laura W Lamps
- Department of Pathology, University of Michigan, NCRC Building 35, 2800 Plymouth Road, Ann Arbor, MI 48109, USA.
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8
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Johansen RL, Schouw CH, Madsen TV, Nielsen XC, Engberg J. Epidemiology of gastrointestinal infections: lessons learned from syndromic testing, Region Zealand, Denmark. Eur J Clin Microbiol Infect Dis 2023; 42:1091-1101. [PMID: 37468662 PMCID: PMC10427544 DOI: 10.1007/s10096-023-04642-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 07/09/2023] [Indexed: 07/21/2023]
Abstract
The aim of this study was to investigate the value of syndromic diagnostic testing for a better understanding of the epidemiology of gastrointestinal infections in Denmark. Here we evaluated the QIAstat-Dx® Gastrointestinal (GI) Panel 1 assay on 18,610 fecal samples requested for analysis for enteric pathogens in Region Zealand, Denmark, in 1 year (October 1, 2021, to September 30, 2022). In total, 6905 (37%) samples were detected positive for one or more diarrhoeal bacteria, viruses, and protozoa. The most common bacterial, viral, and parasitic pathogens detected with the QIAstat-Dx® Gastrointestinal Panel 1 were EPEC (in patients ≥ 2 years of age) (n = 1420 (20.6%)), rotavirus (n = 948 (13.7%)), and Cryptosporidium spp. (n = 196 (2.84%)). We identified a large diversity in infections likely reflecting substantial differences in the epidemiology including origin of infections, mode of transmission, seasonality, age-dependent susceptibility to disease, severity, and travel history. All pathogens were detected as both single and coinfections. Viral infections peaked in March with a positive rate of 31.6%, and bacterial infections peaked in August with a positive rate of 35.3%. ETEC, Shigella/EIEC, EAEC, and P. shigelloides were most related to travel activity, and coinfections were frequent. The distribution of Ct values varied significantly between the pathogens, with the lowest Ct values (median 17-18) observed in astrovirus, adenovirus, and rotavirus. Our results highlight the value of providing extensive diagnostic testing on fecal samples for sufficient detection of relevant diarrhoeal pathogens for optimal clinical care.
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Affiliation(s)
- Rikke Lykke Johansen
- The Regional Department of Clinical Microbiology, Zealand University Hospital, Koege, Ingemannsvej 46, DK-4200, Slagelse, Denmark
| | - Christian Højte Schouw
- The Regional Department of Clinical Microbiology, Zealand University Hospital, Koege, Ingemannsvej 46, DK-4200, Slagelse, Denmark
| | - Tina Vasehus Madsen
- The Regional Department of Clinical Microbiology, Zealand University Hospital, Koege, Ingemannsvej 46, DK-4200, Slagelse, Denmark
| | - Xiaohui Chen Nielsen
- The Regional Department of Clinical Microbiology, Zealand University Hospital, Koege, Ingemannsvej 46, DK-4200, Slagelse, Denmark
| | - Jørgen Engberg
- The Regional Department of Clinical Microbiology, Zealand University Hospital, Koege, Ingemannsvej 46, DK-4200, Slagelse, Denmark.
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Kelly GA, Iordanov R, Franklin A, Ahmed A, Srinivasan K, Hayon J, Lasco T, Amini R, Shay S, Kulkarni PA, Al Mohajer M. Impact of gastrointestinal polymerase chain reaction panels on antibiotic utilization in hospitalized adult patients. ANTIMICROBIAL STEWARDSHIP & HEALTHCARE EPIDEMIOLOGY : ASHE 2023; 3:e135. [PMID: 37592964 PMCID: PMC10428147 DOI: 10.1017/ash.2023.174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/03/2023] [Accepted: 04/05/2023] [Indexed: 08/19/2023]
Abstract
Multiplex stool polymerase chain reaction (PCR) panels offer rapid comprehensive testing for patients with infectious diarrhea. We compared antibiotic utilization among hospitalized patients with suspected infectious diarrhea who underwent diagnostic testing with either a stool culture or stool PCR panel. No significant differences in antibiotic utilization were identified.
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Affiliation(s)
- Gillean A. Kelly
- Baylor College of Medicine, School of Medicine, Houston, Texas
- University of Texas Health Science Center at Houston, School of Public Health, Houston, Texas
| | - Roumen Iordanov
- Baylor College of Medicine, Department of Medicine, Section of Infectious Diseases, Houston, Texas
| | - Alex Franklin
- Baylor College of Medicine, Department of Medicine, Section of Infectious Diseases, Houston, Texas
| | - Amna Ahmed
- Baylor College of Medicine, Department of Medicine, Section of Infectious Diseases, Houston, Texas
| | - Krithika Srinivasan
- Baylor College of Medicine, Department of Medicine, Section of Infectious Diseases, Houston, Texas
| | - Jesica Hayon
- Baylor College of Medicine, Department of Medicine, Section of Infectious Diseases, Houston, Texas
| | - Todd Lasco
- Baylor College of Medicine, Department of Pathology & Immunology, Houston, Texas
| | - Rosie Amini
- Premier Inc., Department of Clinical Intelligence, Charlotte, North Carolina
| | - Sabra Shay
- Premier Inc., Department of Clinical Intelligence, Charlotte, North Carolina
| | - Prathit A. Kulkarni
- Baylor College of Medicine, Department of Medicine, Section of Infectious Diseases, Houston, Texas
- Michael E. DeBakey Veterans Affairs Medical Center, Medical Care Line, Houston, Texas
| | - Mayar Al Mohajer
- Baylor College of Medicine, Department of Medicine, Section of Infectious Diseases, Houston, Texas
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10
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Köffer J, Frontzek A, Eigner U. Development and validation of a bacterial gastrointestinal multiplex RT-PCR assay for use on a fully automated molecular system. J Microbiol Methods 2023; 210:106754. [PMID: 37263528 DOI: 10.1016/j.mimet.2023.106754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 05/26/2023] [Accepted: 05/28/2023] [Indexed: 06/03/2023]
Abstract
PCR-based enteric multiplex panels represent a rapid and reliable alternative to conventional "classical" phenotypic stool diagnostics. The aim of this study was to establish a laboratory-developed non-commercial multiplex Real-Time-PCR panel for the detection of the most important bacterial stool pathogens, Salmonella spp., Shigella spp., Yersinia enterocolitica/ pseudotuberculosis and Campylobacter jejuni/coli. on the "open" cobas omni Utility Channel (UC) of the cobas 6800 system (Roche). The aim was to replace the laborious phenotypical stool diagnostics with a high throughput Real-Time PCR method. The respective primers and probes were designed to cover conserved genomic regions of the pathogens and validated using Ultramer oligonucleotides, positive stool material and reference strains. To further validate the multiplex PCR-assay, the following parameters were evaluated: analytical-sensitivity and -specificity, cross-reactivity, linearity and inter- and intra-assay variance as well as limit of detection (LOD). In addition a retrospective analysis of culture positive and negative samples from daily routine was performed using 745 native stool samples. The Gastro assay was linear over a 5-log-unit and within the expected dynamic range with amplification efficiencies ranging from 94.6% to 120%. In addition, all targets showed excellent coefficients of repeatability (≤ 1.11%), intermediate precision (≤ 1.02%) and total variance (≤ 1.39%). In terms of analytical sensitivity the assay demonstrated detection limits ranging from 7.83 copies per reaction to 14.4 copies per reaction. The assay showed excellent agreement with culture methods (>95%) and a 100% sensitivity and specificity after resolution of discrepant results. The multiplex-PCR assay provides a comprehensive, rapid and sensitive alternative to conventional methods for the detection of the major bacterial stool pathogens in diagnostic laboratories.
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Affiliation(s)
| | - André Frontzek
- Roche Diagnostics (formerly, during study: Labor Stein, Mönchengladbach, Germany), Mannheim, Germany
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11
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Li Y, Zhao L, Wang J, Qi P, Yang Z, Zou X, Peng F, Li S. A new application of multiplex PCR combined with membrane biochip assay for rapid detection of 9 common pathogens in sepsis. PeerJ 2023; 11:e15325. [PMID: 37197582 PMCID: PMC10184654 DOI: 10.7717/peerj.15325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 04/10/2023] [Indexed: 05/19/2023] Open
Abstract
Rapid and accurate identification of specific sepsis pathogens is critical for patient treatment and disease control. This study aimed to establish a new application for the rapid identification of common pathogens in patients with suspected sepsis and evaluate its role in clinical application. A multiplex PCR assay was designed to simultaneously amplify specific conserved regions of nine common pathogenic microorganisms in sepsis, including Acinetobacter baumannii, Escherichia coli, Klebsiella pneumonia, Pseudomonas aeruginosa, Enterococcus faecalis, Staphylococcus aureus, Staphylococcus epidermidis, Streptococcus pneumonia, and Candida albicans. The PCR products were analyzed by a membrane biochip. The analytical sensitivity of the assay was determined at a range of 5-100 copies/reaction for each standard strain, and the detection range was 20-200 cfu/reaction in a series dilution of simulated clinical samples at different concentrations. Out of the 179 clinical samples, the positive rate for pathogens detected by the membrane biochip assay and blood culture method was 20.11% (36/179) and 18.44% (33/179), respectively. However, by comparing the positive rate of the nine common pathogens we detected, the membrane biochip assay tended to be more sensitive than the blood culture method (20.11% vs 15.64%). The clinical sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of the membrane biochip assay were 92.9%, 93.2%, 72.2% and 98.6%, respectively. Generally, this multiplex PCR combined membrane biochip assay can be used to detect major sepsis pathogens, and is useful for early initiation of effective antimicrobial treatment, and is feasible for sepsis pathogens identification in routine clinical practice.
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Affiliation(s)
- Yun Li
- School of Basic Medical Sciences, Weifang Medical University, Weifang, China
| | - LuJie Zhao
- School of Basic Medical Sciences, Weifang Medical University, Weifang, China
| | - Jingye Wang
- Department of Pathology, Weifang Maternal and Child Health Care Hospital, Weifang, China
| | - Peipei Qi
- The Third Department of Neurology Weifang People’s Hospital, Weifang, China
| | - Zhongfa Yang
- School of Basic Medical Sciences, Weifang Medical University, Weifang, China
| | - Xiangyu Zou
- School of Basic Medical Sciences, Weifang Medical University, Weifang, China
| | - Fujun Peng
- School of Basic Medical Sciences, Weifang Medical University, Weifang, China
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12
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Schmitz JE, Stratton CW, Persing DH, Tang YW. Forty Years of Molecular Diagnostics for Infectious Diseases. J Clin Microbiol 2022; 60:e0244621. [PMID: 35852340 PMCID: PMC9580468 DOI: 10.1128/jcm.02446-21] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Nearly 40 years have elapsed since the invention of the PCR, with its extremely sensitive and specific ability to detect nucleic acids via in vitro enzyme-mediated amplification. In turn, more than 2 years have passed since the onset of the coronavirus disease 2019 (COVID-19) pandemic, during which time molecular diagnostics for infectious diseases have assumed a larger global role than ever before. In this context, we review broadly the progression of molecular techniques in clinical microbiology, to their current prominence. Notably, these methods now entail both the detection and quantification of microbial nucleic acids, along with their sequence-based characterization. Overall, we seek to provide a combined perspective on the techniques themselves, as well as how they have come to shape health care at the intersection of technologic innovation, pathophysiologic knowledge, clinical/laboratory logistics, and even financial/regulatory factors.
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Affiliation(s)
- Jonathan E. Schmitz
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Urology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Charles W. Stratton
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - David H. Persing
- Medical and Scientific Affairs, Cepheid, Sunnyvale, California, USA
| | - Yi-Wei Tang
- Medical Affairs, Danaher Diagnostic Platform/Cepheid, Shanghai, China
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13
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DiDiodato G, Allen A, Bradbury N, Brown J, Cruise K, Jedrzejko C, MacDonald V, Pigeon J, Sturgeon A, Yellenik D. The Efficacy of the BioFire FilmArray Gastrointestinal Panel to Reduce Hospital Costs Associated With Contact Isolation: A Pragmatic Randomized Controlled Trial. Cureus 2022; 14:e27931. [PMID: 36120274 PMCID: PMC9464456 DOI: 10.7759/cureus.27931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/12/2022] [Indexed: 11/05/2022] Open
Abstract
Background: Molecular syndromic panels can rapidly detect common pathogens responsible for acute gastroenteritis in hospitalized patients. Their impact on both patient and healthcare system outcomes is uncertain compared to conventional stool testing. This randomized trial evaluates the impact of molecular testing on in-hospital resource utilization compared to conventional stool testing. Methods: Hospitalized patients with acute diarrheal illness were randomized 1:1 to either conventional or molecular stool testing with the BioFire FilmArray gastrointestinal panel (FGP). The primary outcome was the duration of contact isolation, and secondary outcomes included other in-hospital resource utilization such as diagnostic imaging and antimicrobial use. Results: A total of 156 patients were randomized. Randomization resulted in a balanced allocation of patients across all three age strata (<18, 18-69, ≥70 years old). The proportion of positive stools was 20.5% vs 29.5% in the control and FGP groups, respectively (p=0.196). The median duration of contact isolation was 51 hours (interquartile range [iqr] 66) and 69 hours (iqr 81) in the conventional and FGP groups, respectively (p=0.0513). There were no significant differences in other in-hospital resource utilization between groups. Conclusions: There were no differences in in-hospital resource utilization observed between the FGP and conventional stool testing groups.
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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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Yu SJ, Heo JH, Choi EJ, Kim JH, Lee HS, Kim SY, Lim JH. Role of multidetector computed tomography in patients with acute infectious colitis. World J Clin Cases 2022; 10:3686-3697. [PMID: 35647171 PMCID: PMC9100710 DOI: 10.12998/wjcc.v10.i12.3686] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 09/14/2021] [Accepted: 03/06/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The role of multidetector computed tomography (MDCT) in patients with acute infectious colitis is still unclear.
AIM To examine the usefulness of MDCT in distinguishing the etiology of acute infectious colitis.
METHODS Overall, 244 patients who met the criteria for acute infectious colitis and visited the Hospital from February 2015 to 2018 were retrospectively enrolled and divided into two groups (bacterial: 204, viral: 40) according to causes of acute colitis, based on stool PCR. Eleven MDCT parameters, including wall thickening, submucosal edema, mucosal enhancement, serosa involvement, empty colon sign, small bowel involvement, comb sign, continuous distribution, accordion sign, mucosal thickening, and lymph node enlargement, were constructed in a blinded fashion.
RESULTS MDCT parameters of wall thickening (OR: 13.60; 95%CI: 5.80–31.88; P < 0.001), submucosal edema (OR: 36.08; 95%CI: 13.54–96.13; P < 0.001), mucosal enhancement (OR: 22.55; 95%CI: 9.28–54.81; P < 0.001), serosal involvement (OR: 14.50; 95%CI: 3.33–63.23; P < 0.001), empty colon sign (OR: 6.68; 95%CI: 2.44–18.32; P < 0.001), continuous distribution (OR: 24.09; 95%CI: 9.38–61.90; P < 0.001), accordion sign (OR: 9.02; 95%CI: 1.12–72.35; P = 0.038), mucosal thickening (OR: 46.41; 95%CI: 10.38–207.51; P < 0.001), and lymph node enlargement (OR: 4.39; 95%CI: 1.22–15.72; P = 0.023) were significantly associated with bacterial colitis. At least one positive finding in four CT outcomes (submucosal edema, mucosal enhancement, continuous distribution, mucosal thickening) in summer showed a high probability of bacterial colitis (sensitivity, 41.67; specificity, 92.50; OR: 24.95).
CONCLUSION MDCT provides many clues that can be useful in suggesting a specific etiology of acute infectious colitis.
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Affiliation(s)
- Seung Jung Yu
- Department of Internal Medicine, Inje University Busan Paik Hospital, Busan 47392, South Korea
| | - Jae Hyuk Heo
- Department of Internal Medicine, Inje University Busan Paik Hospital, Busan 47392, South Korea
| | - Eun Jeong Choi
- Department of Internal Medicine, Inje University Busan Paik Hospital, Busan 47392, South Korea
| | - Jong Hyuk Kim
- Department of Radiology, Myongji Hospital, Hanyang University College of Medicine, Goyang 10475, South Korea
| | - Hong Sub Lee
- Department of Internal Medicine, Inje University Busan Paik Hospital, Busan 47392, South Korea
| | - Sun Young Kim
- Department of Cancer Control and Population Health, National Cancer Center, Goyang 10408, South Korea
| | - Jae Hoon Lim
- Department of Radiology, Myongji Hospital, Hanyang University College of Medicine, Goyang 10475, South Korea
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Tabata A, Shirai R, Miki H, Nishikawa Y, Kashima T, Aoyama T, Murakami S, Azuma M, Tomoyasu T, Nagamune H. Hapten-labeled fusion-polymerase chain reaction of multiple marker genes for the application of immunochromatographic test. J Biosci Bioeng 2022; 134:70-76. [PMID: 35450786 DOI: 10.1016/j.jbiosc.2022.03.006] [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: 09/30/2021] [Revised: 03/15/2022] [Accepted: 03/22/2022] [Indexed: 10/18/2022]
Abstract
A variety of methods have been reported using polymerase chain reaction (PCR)-based nucleic acid testing (NAT) because of its potential to be used in highly sensitive inspection systems. Among these NATs, fusion-PCR (also called as overlap-extension-PCR) has been focused on this study and adopted to generate the fused amplicon composed of plural marker gene fragments for detection. Generally, conventional agarose gel electrophoresis followed by gel staining is employed to check the PCR results. However, these are time-consuming processes that use specific equipment. To overcome these disadvantages, the immunochromatographic test (ICT) for the detection of PCR amplicons with hapten-labels that were generated by PCR using hapten-labeled primers was also adopted in this study. Based on these concepts, we constructed the systems of hapten-labeled fusion-PCR (HL-FuPCR) followed by ICT (HL-FuPCR-ICT) for the two and three marker genes derived from pathogenic microbe. As a result, we successfully developed a two marker genes system for the pathogenic influenza A virus and a three marker genes system for the penicillin-resistant Streptococcus pneumoniae. These detection systems of HL-FuPCR-ICT are characterized by simple handling and rapid detection within few minutes, and also showed the results as clear lines. Thus, the HL-FuPCR-ICT system introduced in this study has potential for use as a user-friendly inspection tool with the advantages especially in the detection of specific strains or groups expressing the characteristic phenotype(s) such as antibiotic resistance and/or high pathogenicity even in the same species.
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Affiliation(s)
- Atsushi Tabata
- Department of Bioscience and Bioindustry, Graduate School of Technology, Industrial and Social Sciences, Tokushima University, 2-1 Minamijousanjima-cho, Tokushima, Tokushima 770-8513, Japan; Department of Bioscience and Bioindustry, Faculty of Bioscience and Bioindustry, Tokushima University, 2-1 Minamijousanjima-cho, Tokushima, Tokushima 770-8513, Japan; Department of Biological Science and Technology, Faculty of Engineering, Tokushima University, 2-1 Minamijousanjima-cho, Tokushima, Tokushima 770-8506, Japan
| | - Rina Shirai
- Department of Bioscience and Bioindustry, Faculty of Bioscience and Bioindustry, Tokushima University, 2-1 Minamijousanjima-cho, Tokushima, Tokushima 770-8513, Japan
| | - Haruka Miki
- Department of Bioscience and Bioindustry, Faculty of Bioscience and Bioindustry, Tokushima University, 2-1 Minamijousanjima-cho, Tokushima, Tokushima 770-8513, Japan
| | - Yukihiro Nishikawa
- Department of Biological Science and Technology, Faculty of Engineering, Tokushima University, 2-1 Minamijousanjima-cho, Tokushima, Tokushima 770-8506, Japan
| | - Tatsuya Kashima
- Department of Biological Science and Technology, Faculty of Engineering, Tokushima University, 2-1 Minamijousanjima-cho, Tokushima, Tokushima 770-8506, Japan
| | - Tomomi Aoyama
- Department of Biological Science and Technology, Faculty of Engineering, Tokushima University, 2-1 Minamijousanjima-cho, Tokushima, Tokushima 770-8506, Japan
| | - Shu Murakami
- Department of Biological Science and Technology, Faculty of Engineering, Tokushima University, 2-1 Minamijousanjima-cho, Tokushima, Tokushima 770-8506, Japan
| | - Momoyo Azuma
- Department of Respiratory Medicine and Rheumatology, Graduate School of Biomedical Sciences, Tokushima University, 3-18-15 Kuramoto-cho, Tokushima, Tokushima 770-8503, Japan
| | - Toshifumi Tomoyasu
- Department of Bioscience and Bioindustry, Graduate School of Technology, Industrial and Social Sciences, Tokushima University, 2-1 Minamijousanjima-cho, Tokushima, Tokushima 770-8513, Japan; Department of Bioscience and Bioindustry, Faculty of Bioscience and Bioindustry, Tokushima University, 2-1 Minamijousanjima-cho, Tokushima, Tokushima 770-8513, Japan; Department of Biological Science and Technology, Faculty of Engineering, Tokushima University, 2-1 Minamijousanjima-cho, Tokushima, Tokushima 770-8506, Japan
| | - Hideaki Nagamune
- Department of Bioscience and Bioindustry, Graduate School of Technology, Industrial and Social Sciences, Tokushima University, 2-1 Minamijousanjima-cho, Tokushima, Tokushima 770-8513, Japan; Department of Bioscience and Bioindustry, Faculty of Bioscience and Bioindustry, Tokushima University, 2-1 Minamijousanjima-cho, Tokushima, Tokushima 770-8513, Japan; Department of Biological Science and Technology, Faculty of Engineering, Tokushima University, 2-1 Minamijousanjima-cho, Tokushima, Tokushima 770-8506, Japan.
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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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18
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Wang Z, Wang M, Xu Q, Liu S, Gao Y, Chang H, Sui Z. Rapid and Multiplexed Detection of Single Cells of Salmonella, Escherichia coli O157, and Shigella flexneri in Ground Beef by Flow Cytometry. Foodborne Pathog Dis 2022; 19:272-280. [PMID: 35263171 DOI: 10.1089/fpd.2021.0088] [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: 11/12/2022] Open
Abstract
Salmonella, Escherichia coli O157, and Shigella flexneri are typical foodborne pathogens in ground beef, which can cause severe infection even when present as a single cell. Flow cytometry (FCM) methods are widely applied in the rapid detection of pathogens in food products. In this study, we report an FCM-based method for detecting single cells of Salmonella, E. coli O157, and S. flexneri in 25 g ground beef samples. We fluorescently labeled specific antibodies that could effectively identify bacterial cells, prepared single-cell samples by serial dilution, and optimized the pre-enrichment time. The results showed that 7 h of pre-enrichment is appropriate for sensitive single-cell detection by FCM. Finally, we evaluated this method in artificially contaminated and retail beef samples. This study outlines a novel highly sensitive FCM-based method to detect Salmonella, E. coli O157, and S. flexneri in beef samples within 8 h that can be applied to the rapid and multiplexed detection of foodborne pathogens.
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Affiliation(s)
- Ziquan Wang
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Meng Wang
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Qian Xu
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China.,College of Life Sciences, Hunan Normal University, Changsha, China
| | - Siyuan Liu
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Ying Gao
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
| | - Haiyan Chang
- College of Life Sciences, Hunan Normal University, Changsha, China
| | - Zhiwei Sui
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing, China
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19
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Argy N, Nourrisson C, Aboubacar A, Poirier P, Valot S, Laude A, Desoubeaux G, Pomares C, Machouart M, Le Govic Y, Dalle F, Botterel F, Bourgeois N, Cateau E, Leterrier M, Le Pape P, Morio F, Houze S. Selecting a multiplex PCR panel for accurate molecular diagnosis of intestinal protists: a comparative study of Allplex ® (Seegene ®), G-DiaParaTrio (Diagenode ®), and RIDA ®GENE (R-Biopharm ®) assays and microscopic examination. Parasite 2022; 29:5. [PMID: 35138245 PMCID: PMC8826582 DOI: 10.1051/parasite/2022003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 01/14/2022] [Indexed: 12/17/2022] Open
Abstract
Commercial multiplex PCR assay panels were developed to overcome the limitations of microscopic examination for parasitological diagnosis on stool samples. However, given the increased supply of this diagnostic approach, these assays must be evaluated to position them in a diagnostic algorithm. Analytical performances of the multiplex PCR assay G-DiaParaTrio, Allplex® GI parasite and RIDA®GENE parasitic stool panel for detecting Blastocystis sp., Entamoeba histolytica, Giardia duodenalis, Cryptosporidium spp., Dientamoeba fragilis, and Cyclospora cayetanensis, were assessed through a retrospective comparative study on 184 stool samples initially sent for parasitological investigation. The composite reference method for parasitological diagnosis was microscopic observation and Entamoeba histolytica-specific adhesion detection when necessary. Multiplex PCR assays were performed on extracted DNA from each stool, following the manufacturer's recommendations. Discrepant results with the composite reference method were investigated with species-specific PCR to approach a final parasitological diagnosis. Overall sensitivity/specificity for the multiplex PCR assays was 93.2%/100% for G-DiaParaTrio, 96.5%/98.3% for Allplex® GI parasite and 89.6%/98.3% for RIDA®GENE, whereas the composite reference method presented an overall sensitivity/specificity of 59.6%/99.8%. These results confirmed the added diagnostic value of the multiplex PCR approach for gastrointestinal protists. Nevertheless, the PCR procedure and the analytical performance for each protist of interest, variable depending on the multiplex PCR assay, must be considered when implementing a PCR-based diagnostic approach.
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Affiliation(s)
- Nicolas Argy
- Parasitology-Mycology Laboratory, Bichat-Claude Bernard hospital, APHP, 75018 Paris, France - IRD MERIT UMR 261, Pharmacy Faculty, Paris University, 75006 Paris, France
| | - Céline Nourrisson
- Parasitology-Mycology Laboratory, CHU de Clermont-Ferrand, 3IHP, INSERM, 63000 Clermont-Ferrand, France
| | - Ahmed Aboubacar
- Parasitology-Mycology Laboratory, CHU de Strasbourg, 67000 Strasbourg, France
| | - Philippe Poirier
- Parasitology-Mycology Laboratory, CHU de Clermont-Ferrand, 3IHP, INSERM, 63000 Clermont-Ferrand, France
| | - Stéphane Valot
- Parasitology-Mycology Laboratory, CHU de Dijon, 21000 Dijon, France
| | - Adrien Laude
- Parasitology-Mycology Laboratory, Institut de Biologie, CHU de Nantes, 44093 Nantes, France
| | - Guillaume Desoubeaux
- Parasitology-Mycology-Tropical Diseases Department, CHU de Tours, 37000 Tours, France
| | | | - Marie Machouart
- Parasitology-Mycology Laboratory, CHU de Nancy, 54511 Vandoeuvre-les-Nancy, France
| | - Yohann Le Govic
- Parasitology-Mycology Laboratory, CHU d'Angers, 49100 Angers, France
| | - Frédéric Dalle
- Parasitology-Mycology Laboratory, CHU de Dijon, 21000 Dijon, France
| | - Françoise Botterel
- Parasitology-Mycology Laboratory, CHU Henri Mondor, APHP, 94000 Créteil, France
| | - Nathalie Bourgeois
- Parasitology-Mycology Laboratory, CHU de Montpellier, 34295 Montpellier, France
| | - Estelle Cateau
- Parasitology-Mycology Laboratory, CHU de Poitiers, 86021 Poitiers, France
| | - Marion Leterrier
- Microbiology Laboratory, CHD de la Roche-Sur-Yon, 85000 la Roche-Sur-Yon, France
| | - Patrice Le Pape
- Parasitology-Mycology Laboratory, Institut de Biologie, CHU de Nantes, 44093 Nantes, France
| | - Florent Morio
- Parasitology-Mycology Laboratory, Institut de Biologie, CHU de Nantes, 44093 Nantes, France
| | - Sandrine Houze
- Parasitology-Mycology Laboratory, Bichat-Claude Bernard hospital, APHP, 75018 Paris, France - IRD MERIT UMR 261, Pharmacy Faculty, Paris University, 75006 Paris, France
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Hasan H, Nasirudeen NA, Ruzlan MAF, Mohd Jamil MA, Ismail NAS, Wahab AA, Ali A. Acute Infectious Gastroenteritis: The Causative Agents, Omics-Based Detection of Antigens and Novel Biomarkers. CHILDREN (BASEL, SWITZERLAND) 2021; 8:1112. [PMID: 34943308 PMCID: PMC8700514 DOI: 10.3390/children8121112] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/19/2021] [Accepted: 11/22/2021] [Indexed: 12/25/2022]
Abstract
Acute infectious gastroenteritis (AGE) is among the leading causes of mortality in children less than 5 years of age worldwide. There are many causative agents that lead to this infection, with rotavirus being the commonest pathogen in the past decade. However, this trend is now being progressively replaced by another agent, which is the norovirus. Apart from the viruses, bacteria such as Salmonella and Escherichia coli and parasites such as Entamoeba histolytica also contribute to AGE. These agents can be recognised by their respective biological markers, which are mainly the specific antigens or genes to determine the causative pathogen. In conjunction to that, omics technologies are currently providing crucial insights into the diagnosis of acute infectious gastroenteritis at the molecular level. Recent advancement in omics technologies could be an important tool to further elucidate the potential causative agents for AGE. This review will explore the current available biomarkers and antigens available for the diagnosis and management of the different causative agents of AGE. Despite the high-priced multi-omics approaches, the idea for utilization of these technologies is to allow more robust discovery of novel antigens and biomarkers related to management AGE, which eventually can be developed using easier and cheaper detection methods for future clinical setting. Thus, prediction of prognosis, virulence and drug susceptibility for active infections can be obtained. Case management, risk prediction for hospital-acquired infections, outbreak detection, and antimicrobial accountability are aimed for further improvement by integrating these capabilities into a new clinical workflow.
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Affiliation(s)
- Haziqah Hasan
- Department of Pediatric, Faculty of Medicine, Universiti Kebangsaan Malaysia, Jalan Yaacob Latif, Kuala Lumpur 56000, Malaysia; (H.H.); (N.A.N.); (M.A.F.R.); (M.A.M.J.)
| | - Nor Ashika Nasirudeen
- Department of Pediatric, Faculty of Medicine, Universiti Kebangsaan Malaysia, Jalan Yaacob Latif, Kuala Lumpur 56000, Malaysia; (H.H.); (N.A.N.); (M.A.F.R.); (M.A.M.J.)
| | - Muhammad Alif Farhan Ruzlan
- Department of Pediatric, Faculty of Medicine, Universiti Kebangsaan Malaysia, Jalan Yaacob Latif, Kuala Lumpur 56000, Malaysia; (H.H.); (N.A.N.); (M.A.F.R.); (M.A.M.J.)
| | - Muhammad Aiman Mohd Jamil
- Department of Pediatric, Faculty of Medicine, Universiti Kebangsaan Malaysia, Jalan Yaacob Latif, Kuala Lumpur 56000, Malaysia; (H.H.); (N.A.N.); (M.A.F.R.); (M.A.M.J.)
| | - Noor Akmal Shareela Ismail
- Department of Biochemistry, Faculty of Medicine, Universiti Kebangsaan Malaysia, Jalan Yaacob Latif, Kuala Lumpur 56000, Malaysia;
| | - Asrul Abdul Wahab
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Jalan Yaacob Latif, Kuala Lumpur 56000, Malaysia;
| | - Adli Ali
- Department of Pediatric, Faculty of Medicine, Universiti Kebangsaan Malaysia, Jalan Yaacob Latif, Kuala Lumpur 56000, Malaysia; (H.H.); (N.A.N.); (M.A.F.R.); (M.A.M.J.)
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21
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Oliva A, Miele MC, Al Ismail D, Di Timoteo F, De Angelis M, Rosa L, Cutone A, Venditti M, Mascellino MT, Valenti P, Mastroianni CM. Challenges in the Microbiological Diagnosis of Implant-Associated Infections: A Summary of the Current Knowledge. Front Microbiol 2021; 12:750460. [PMID: 34777301 PMCID: PMC8586543 DOI: 10.3389/fmicb.2021.750460] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 10/04/2021] [Indexed: 12/14/2022] Open
Abstract
Implant-associated infections are characterized by microbial biofilm formation on implant surface, which renders the microbiological diagnosis challenging and requires, in the majority of cases, a complete device removal along with a prolonged antimicrobial therapy. Traditional cultures have shown unsatisfactory sensitivity and a significant advance in the field has been represented by both the application of the sonication technique for the detachment of live bacteria from biofilm and the implementation of metabolic and molecular assays. However, despite the recent progresses in the microbiological diagnosis have considerably reduced the rate of culture-negative infections, still their reported incidence is not negligible. Overall, several culture- and non-culture based methods have been developed for diagnosis optimization, which mostly relies on pre-operative and intra-operative (i.e., removed implants and surrounding tissues) samples. This review outlines the principal culture- and non-culture based methods for the diagnosis of the causative agents of implant-associated infections and gives an overview on their application in the clinical practice. Furthermore, advantages and disadvantages of each method are described.
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Affiliation(s)
- Alessandra Oliva
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Maria Claudia Miele
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Dania Al Ismail
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Federica Di Timoteo
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Massimiliano De Angelis
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Luigi Rosa
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Antimo Cutone
- Department of Biosciences and Territory, University of Molise, Pesche, Italy
| | - Mario Venditti
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Maria Teresa Mascellino
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Piera Valenti
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
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22
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Hong S, Zaki TA, Main M, Hine AM, Chang S, Hudesman D, Axelrad JE. Comparative Evaluation of Conventional Stool Testing and Multiplex Molecular Panel in Outpatients With Relapse of Inflammatory Bowel Disease. Inflamm Bowel Dis 2021; 27:1634-1640. [PMID: 33386740 PMCID: PMC9115373 DOI: 10.1093/ibd/izaa336] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Indexed: 12/15/2022]
Abstract
BACKGROUND Differentiating between enteric infection and relapse of inflammatory bowel disease (IBD) is a common clinical challenge. Few studies have evaluated the impact of multiplex gastrointestinal polymerase chain reaction (GI PCR) pathogen panels on clinical practice compared to stool culture. Our aim was to compare the impact of PCR stool testing to conventional stool testing in outpatients presenting with relapse of IBD. METHODS In a retrospective cohort study of outpatients with IBD presenting to NYU Langone Health with flare from September 2015 to April 2019, we compared patients who underwent stool testing with GI PCR to age-, sex-, and IBD-subtype-matched patients who underwent culture and ova and parasite exam (conventional testing). The primary outcome was IBD therapy escalation after testing. Secondary outcomes included rates of posttesting endoscopy, abdominal radiography, antibiotics, and IBD-related emergency department visits, hospitalizations, and abdominal surgeries. RESULTS We identified 134 patients who underwent GI PCR matched to 134 patients who underwent conventional testing. Pathogens were more frequently identified on GI PCR (26 vs 5%; P < 0.01). We found that GI PCR was associated with less escalation in IBD therapy (16 vs 29%; P < 0.01) and fewer posttest endoscopies (10% vs 18%; P = 0.04), with no differences in IBD outcomes. On multivariate analysis, testing with GI PCR was associated with an odds ratio of 0.26 (95% confidence interval, 0.08-0.84; P = 0.02) for escalation of IBD therapies. CONCLUSIONS Testing with GI PCR was associated with higher rates of pathogen detection and lower rates of IBD therapy escalation and endoscopy in the outpatient setting. These changes in management were not associated with a difference in IBD outcomes.
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Affiliation(s)
- Soonwook Hong
- Department of Medicine, NYU Langone Health, New York, New York, New York, USA
- Address correspondence to: Soonwook Hong, MD, Department of Medicine, NYU Langone Health, 555 First Ave., New York, NY 10016, USA ()
| | - Timothy A Zaki
- Department of Medicine, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Michael Main
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Ashley M Hine
- Department of Medicine, University of Connecticut School of Medicine, Farmington, Connecticut, USA
| | - Shannon Chang
- Department of Gastroenterology, NYU Langone Health , New York, New York, USA
| | - David Hudesman
- Department of Gastroenterology, NYU Langone Health , New York, New York, USA
| | - Jordan E Axelrad
- Department of Gastroenterology, NYU Langone Health , New York, New York, USA
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23
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Luo Y, Yan X, Xiao Q, Long Y, Pu J, Li Q, Cai Y, Chen Y, Zhang H, Chen C, Ou S. Application of Sigma metrics in the quality control strategies of immunology and protein analytes. J Clin Lab Anal 2021; 35:e24041. [PMID: 34606652 PMCID: PMC8605144 DOI: 10.1002/jcla.24041] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/22/2021] [Accepted: 09/23/2021] [Indexed: 12/19/2022] Open
Abstract
Background Six Sigma (6σ) is an efficient laboratory management method. We aimed to analyze the performance of immunology and protein analytes in terms of Six Sigma. Methods Assays were evaluated for these 10 immunology and protein analytes: Immunoglobulin G (IgG), Immunoglobulin A (IgA), Immunoglobulin M (IgM), Complement 3 (C3), Complement 4 (C4), Prealbumin (PA), Rheumatoid factor (RF), Anti streptolysin O (ASO), C‐reactive protein (CRP), and Cystatin C (Cys C). The Sigma values were evaluated based on bias, four different allowable total error (TEa) and coefficient of variation (CV) at QC materials levels 1 and 2 in 2020. Sigma Method Decision Charts were established. Improvement measures of analytes with poor performance were recommended according to the quality goal index (QGI), and appropriate quality control rules were given according to the Sigma values. Results While using the TEaNCCL, 90% analytes had a world‐class performance with σ>6, Cys C showed marginal performance with σ<4. While using minimum, desirable, and optimal biological variation of TEa, only three (IgG, IgM, and CRP), one (CRP), and one (CRP) analytes reached 6σ level, respectively. Based on σNCCL that is calculated from TEaNCCL, Sigma Method Decision Charts were constructed. For Cys C, five multi‐rules (13s/22s/R4s/41s/6X, N = 6, R = 1, Batch length: 45) were adopted for QC management. The remaining analytes required only one QC rule (13s, N = 2, R = 1, Batch length: 1000). Cys C need to improve precision (QGI = 0.12). Conclusions The laboratories should choose appropriate TEa goals and make judicious use of Sigma metrics as a quality improvement tool.
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Affiliation(s)
- Yanfen Luo
- Department of Medicine Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Medicine Laboratory, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Xingxing Yan
- Department of Medicine Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Medicine Laboratory, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Qian Xiao
- Department of Medicine Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Medicine Laboratory, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Yifei Long
- Department of Medicine Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Medicine Laboratory, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Jieying Pu
- Department of Medicine Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Medicine Laboratory, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Qiwei Li
- Department of Medicine Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Medicine Laboratory, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Yimei Cai
- Department of Medicine Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Medicine Laboratory, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Yushun Chen
- Department of Medicine Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Medicine Laboratory, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Hongyuan Zhang
- Department of Medicine Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Medicine Laboratory, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Cha Chen
- Department of Medicine Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China.,Department of Medicine Laboratory, Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China
| | - Songbang Ou
- Reproductive center, Department of Obstetrics and Gynecology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
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24
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Engberg J, Vejrum LK, Madsen TV, Nielsen XC. Verification of analytical bacterial spectrum of QIAstat-Dx® GI V2 and Novodiag® Bacterial GE+ V2-0 diagnostic panels. J Antimicrob Chemother 2021; 76:iii50-iii57. [PMID: 34555154 PMCID: PMC8460093 DOI: 10.1093/jac/dkab242] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Background Implementing multiplex PCR or syndromic panel-based testing platforms to detect microbial species that cause acute diarrhoea may guide patient management more effectively and efficiently. Objectives To assess and compare the performance of two syndromic panel-based testing systems, QIAstat-Dx® Gastrointestinal Panel V2 (QGI) and the Novodiag® Bacterial GE+ V2-0 (NGE). Methods The QGI and NGE panels include 16 and 14 bacterial gastrointestinal pathogens, respectively. The performance of the panels was tested retrospectively using 141 positive clinical stool specimens, External Quality Assessment (EQA) panels and spiked faecal specimens. Results For Campylobacter jejuni and coli (n = 20), Salmonella (n = 24), Shigella (n = 13), Yersinia enterocolitica (non-1A biotypes) (n = 8), Clostridioides difficile (n = 24) and Vibrio parahaemolyticus (n = 2), QGI correctly verified 19/20, 20/24, 13/13, 8/8, 23/24 and 2/2, whereas NGE correctly verified 20/20, 17/24, 13/13, 8/8, 14/24 and 1/2. Among diarrhoeagenic Escherichia coli (n = 29), QGI reported one Shiga toxin-producing E. coli (STEC) stx1a O26:H11 as STEC serotype O157:H7 and NGE failed on one enteropathogenic E. coli, one enteroaggregative E. coli and one STEC (stx2e). Y. enterocolitica biotype 1A (non-pathogenic) (n = 6) were all positive in QGI, but negative in NGE. Conclusions Both QGI and NGE testing panels can improve laboratory workflow and patient management by providing user-friendly platforms that can rapidly detect a number of targets with one specimen. QGI was significantly more sensitive in identifying C. difficile. Both methods had suboptimal detection of Salmonella and this needs to be examined further. The short hands-on time and turnaround time are of value for on-demand testing and use in a high-throughput setting.
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Affiliation(s)
- Jørgen Engberg
- Department of Clinical Microbiology, Zealand University Hospital, Koege, Ingemannsvej 46, DK-4200 Slagelse, Denmark
| | - Laus Krems Vejrum
- Department of Clinical Microbiology, Zealand University Hospital, Koege, Ingemannsvej 46, DK-4200 Slagelse, Denmark
| | - Tina Vasehus Madsen
- Department of Clinical Microbiology, Zealand University Hospital, Koege, Ingemannsvej 46, DK-4200 Slagelse, Denmark
| | - Xiaohui Chen Nielsen
- Department of Clinical Microbiology, Zealand University Hospital, Koege, Ingemannsvej 46, DK-4200 Slagelse, Denmark
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25
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O'Leary JK, Sleator RD, Lucey B. Cryptosporidium spp. diagnosis and research in the 21 st century. Food Waterborne Parasitol 2021; 24:e00131. [PMID: 34471706 PMCID: PMC8390533 DOI: 10.1016/j.fawpar.2021.e00131] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/06/2021] [Accepted: 08/17/2021] [Indexed: 01/01/2023] Open
Abstract
The protozoan parasite Cryptosporidium has emerged as a leading cause of diarrhoeal illness worldwide, posing a significant threat to young children and immunocompromised patients. While endemic in the vast majority of developing countries, Cryptosporidium also has the potential to cause waterborne epidemics and large scale outbreaks in both developing and developed nations. Anthroponontic and zoonotic transmission routes are well defined, with the ingestion of faecally contaminated food and water supplies a common source of infection. Microscopy, the current diagnostic mainstay, is considered by many to be suboptimal. This has prompted a shift towards alternative diagnostic techniques in the advent of the molecular era. Molecular methods, particularly PCR, are gaining traction in a diagnostic capacity over microscopy in the diagnosis of cryptosporidiosis, given the laborious and often tedious nature of the latter. Until now, developments in the field of Cryptosporidium detection and research have been somewhat hampered by the intractable nature of this parasite. However, recent advances in the field have taken the tentative first steps towards bringing Cryptosporidium research into the 21st century. Herein, we provide a review of these advances.
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Affiliation(s)
- Jennifer K. O'Leary
- Department of Biological Sciences, Munster Technological University, Bishopstown Campus, Cork, Ireland
| | - Roy D. Sleator
- Department of Biological Sciences, Munster Technological University, Bishopstown Campus, Cork, Ireland
| | - Brigid Lucey
- Department of Biological Sciences, Munster Technological University, Bishopstown Campus, Cork, Ireland
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26
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Zhao H, Yang Y, Lyu J, Ren X, Cheng W. Development and application of a method to detect 27 respiratory pathogens using multiplex RT-PCR combined with MassARRAY technology. BMC Infect Dis 2021; 21:870. [PMID: 34433411 PMCID: PMC8385475 DOI: 10.1186/s12879-021-06404-0] [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: 02/04/2021] [Accepted: 07/18/2021] [Indexed: 12/28/2022] Open
Abstract
Background Respiratory tract infections are the most common infections that lead to morbidity and mortality worldwide. Early recognition and precise diagnosis of microbial etiology is important to treat LRTIs promptly, specifically and effectively. Objectives To establish a method based on multiplex reverse transcription (MRT)-PCR and MassARRAY technology for the simultaneous detection of 27 respiratory pathogens and explore its clinical application value. Methods Analytical sensitivity and specificity of the MRT-PCR-MassARRAY system were validated using inactivated bacterial and viral strains. Also we analyzed samples from 207 patients by MassARRAY methods and compared the results with consensus PCR/reverse transcription (RT)-PCR. Results The minimum detection limit of our MRT-PCR-MassARRAY method for pathogens was 10–100 copies/μl, with high specificity. Comparison test with consensus PCR/RT-PCR on 207 clinical samples, the positive, negative, and total correlation rates were 100, 98.68, and 99.03%, respectively. There was a high degree of agreement between the test results of the two methods (P < 0.01 by McNemar’s test). Conclusion Our detection system of 27 respiratory pathogens based on MassARRAY technology has high sensitivity and specificity, high throughput, and is simple to operate. It provides diagnostic value for the clinical diagnosis of respiratory pathogens and is of great significance in the screening of respiratory pathogens.
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Affiliation(s)
- Huan Zhao
- Department of Respiratory Medicine, The Sixth People's Hospital of Nantong, Nantong, Jiangsu, China
| | - Yichao Yang
- Research and Development Centre, Hangzhou DiAn Medical Laboratory, Hangzhou, Zhejiang, China
| | - Jiangfeng Lyu
- Research and Development Centre, Hangzhou DiAn Medical Laboratory, Hangzhou, Zhejiang, China
| | - Xuyi Ren
- Research and Development Centre, Hangzhou DiAn Medical Laboratory, Hangzhou, Zhejiang, China.
| | - Wei Cheng
- Department of Respiratory Diseases, Nantong Tongzhou People's Hospital, Nantong, Jiangsu, China.
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27
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Diez Valcarce M, Kambhampati AK, Calderwood LE, Hall AJ, Mirza SA, Vinjé J. Global distribution of sporadic sapovirus infections: A systematic review and meta-analysis. PLoS One 2021; 16:e0255436. [PMID: 34411109 PMCID: PMC8376006 DOI: 10.1371/journal.pone.0255436] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 07/15/2021] [Indexed: 02/04/2023] Open
Abstract
Acute gastroenteritis (AGE), characterized by diarrhea and vomiting, is an important cause of global mortality, accounting for 9% of all deaths in children under five years of age. Since the reduction of rotavirus in countries that have included rotavirus vaccines in their national immunization programs, other viruses such as norovirus and sapovirus have emerged as more common causes of AGE. Due to widespread use of real-time RT-PCR testing, sapovirus has been increasingly reported as the etiologic agent in both AGE outbreaks and sporadic AGE cases. We aimed to assess the role of sapovirus as a cause of endemic AGE worldwide by conducting a systematic review of published studies that used molecular diagnostics to assess the prevalence of sapovirus among individuals with AGE symptoms. Of 106 articles included, the pooled sapovirus prevalence was 3.4%, with highest prevalence among children <5 years of age (4.4%) and among individuals in community settings (7.1%). Compared to studies that used conventional RT-PCR, RT-qPCR assays had a higher pooled prevalence (5.6%). Among individuals without AGE symptoms, the pooled sapovirus prevalence was 2.7%. These results highlight the relative contribution of sapovirus to cases of AGE, especially in community settings and among children <5 years of age.
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Affiliation(s)
- Marta Diez Valcarce
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
- Emory University Rollins School of Public Health, Atlanta, GA, United States of America
| | - Anita K. Kambhampati
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Laura E. Calderwood
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
- Cherokee Nation Assurance, Arlington, VA, United States of America
| | - Aron J. Hall
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Sara A. Mirza
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Jan Vinjé
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, United States of America
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Abstract
Giardia duodenalis captured the attention of Leeuwenhoek in 1681 while he was examining his own diarrheal stool, but, ironically, it did not really gain attention as a human pathogen until the 1960s, when outbreaks were reported. Key technological advances, including in vitro cultivation, genomic and proteomic databases, and advances in microscopic and molecular approaches, have led to an understanding that this is a eukaryotic organism with a reduced genome rather than a truly premitochondriate eukaryote. This has included the discovery of mitosomes (vestiges of mitochondria), a transport system with many of the features of the Golgi apparatus, and even evidence for a sexual or parasexual cycle. Cell biology approaches have led to a better understanding of how Giardia survives with two nuclei and how it goes through its life cycle as a noninvasive organism in the hostile environment of the lumen of the host intestine. Studies of its immunology and pathogenesis have moved past the general understanding of the importance of the antibody response in controlling infection to determining the key role of the Th17 response. This work has led to understanding of the requirement for a balanced host immune response that avoids the extremes of an excessive response with collateral damage or one that is unable to clear the organism. This understanding is especially important in view of the remarkable ranges of early manifestations, which range from asymptomatic to persistent diarrhea and weight loss, and longer-term sequelae that include growth stunting in children who had no obvious symptoms and a high frequency of postinfectious irritable bowel syndrome (IBS).
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29
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Maldonado-Garza HJ, Garza-González E, Bocanegra-Ibarias P, Flores-Treviño S. Diagnostic syndromic multiplex approaches for gastrointestinal infections. Expert Rev Gastroenterol Hepatol 2021; 15:743-757. [PMID: 33682566 DOI: 10.1080/17474124.2021.1899807] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Introduction: Gastrointestinal diseases due to infectious pathogens currently represent an important global health concern, especially in children and developing countries. Early and accurate detection of gastrointestinal pathogens is important to initiate the appropriate type of therapy. Multiplex molecular gastrointestinal panels rapidly detect several gastrointestinal pathogens at once with high sensitivity.Areas covered: We assess the scope and limitations of several multiplex gastrointestinal panels approved by the Food and Drug Administration or marked by Conformité Européenne-in vitro diagnostic. We compare 10 syndromic gastrointestinal panels, 14 bacteria-specific multiplex panels, seven parasite-specific multiplex panels, and eight virus-specific multiplex panels.Expert opinion: Thanks to the advances made in the diagnostic approaches for gastrointestinal infections, there are various panels to choose. The choice of a specific syndromic gastrointestinal multiplex panel should be made to improve patient care. Diagnostic syndromic multiplex approaches for gastrointestinal infections should be customized; each hospital should develop its diagnostic algorithm for gastrointestinal infections tailored to its setting, study population, and geographical site. Current multiplex gastrointestinal panels could be improved by including the detection of antimicrobial resistance, toxigenic Clostridioides difficile, and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, the virus responsible for the COVID-19 pandemic).
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Affiliation(s)
- Héctor Jesús Maldonado-Garza
- Departamento de Medicina Interna, Universidad Autónoma De Nuevo León, Hospital Universitario Dr. José Eleuterio González Y Facultad De Medicina, Servicio De Gastroenterología, Monterrey, Nuevo León, Mexico
| | - Elvira Garza-González
- Departamento de Medicina Interna, Universidad Autónoma De Nuevo León, Hospital Universitario Dr. José Eleuterio González Y Facultad De Medicina, Servicio De Gastroenterología, Monterrey, Nuevo León, Mexico
| | - Paola Bocanegra-Ibarias
- Departamento de Medicina Interna, Universidad Autónoma De Nuevo León, Hospital Universitario Dr. José Eleuterio González Y Facultad De Medicina, Servicio De Gastroenterología, Monterrey, Nuevo León, Mexico
| | - Samantha Flores-Treviño
- Departamento de Medicina Interna, Universidad Autónoma De Nuevo León, Hospital Universitario Dr. José Eleuterio González Y Facultad De Medicina, Servicio De Gastroenterología, Monterrey, Nuevo León, Mexico
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30
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Bonura F, Mascarella C, Filizzolo C, Bonura C, Ferraro D, Di Bernardo F, Collura A, Martella V, Giammanco GM, De Grazia S. Evaluation of the diagnostic performances of two commercially available assays for the detection of enteric adenovirus antigens. Diagn Microbiol Infect Dis 2021; 101:115459. [PMID: 34280672 DOI: 10.1016/j.diagmicrobio.2021.115459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/01/2021] [Accepted: 06/15/2021] [Indexed: 12/21/2022]
Abstract
The performance of 2 antigenic commercial assays for enteric adenovirus (AdV) infection, bioNexia Rota-Adeno ImmunoChromatographic Tests (ICT) and LIAISON® Adenovirus ChemiLuminescence Immuno Assays (CLIA), was evaluated on 321 stools from children hospitalized for acute gastroenteritis in Palermo, Italy, using a Real time-PCR (Rt-PCR) as reference method. The CLIA showed higher sensitivity (77% vs 60%), accuracy (94.4 vs 90.9) and concordance (k: 0.81 vs 0.67) with respect to ICT, despite equivalent specificity (98.8%). Using the Ct values of the Rt-PCR as a proxy of the fecal viral load, similar Ct values (mean 9.32 vs 9.89) were observed among the true positive samples, whilst a significant difference (P < 0.05) was observed in false negative samples of CLIA (mean Ct 25.68) and ICT (mean Ct 19.87). Cross-reactivity with other enteric viruses was not observed. These results indicate that both the assays tested are suitable for diagnosis of AdV gastroenteritis.
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Affiliation(s)
- Floriana Bonura
- Dipartimento di Scienze per la Promozione della Salute e Materno Infantile "G. D'Alessandro", Palermo, Italy
| | - Chiara Mascarella
- Dipartimento di Scienze per la Promozione della Salute e Materno Infantile "G. D'Alessandro", Palermo, Italy
| | - Chiara Filizzolo
- Dipartimento di Scienze per la Promozione della Salute e Materno Infantile "G. D'Alessandro", Palermo, Italy
| | - Celestino Bonura
- Dipartimento di Scienze per la Promozione della Salute e Materno Infantile "G. D'Alessandro", Palermo, Italy
| | - Donatella Ferraro
- Dipartimento di Scienze per la Promozione della Salute e Materno Infantile "G. D'Alessandro", Palermo, Italy
| | - Francesca Di Bernardo
- Unità Operativa di Microbiologia e Virologia, Ospedale Civico e Di Cristina, ARNAS, Palermo, Italy
| | - Antonella Collura
- Unità Operativa di Microbiologia e Virologia, Ospedale Civico e Di Cristina, ARNAS, Palermo, Italy
| | - Vito Martella
- Dipartimento di Medicina Veterinaria, Università Aldo Moro di Bari, Valenzano, Italy
| | - Giovanni M Giammanco
- Dipartimento di Scienze per la Promozione della Salute e Materno Infantile "G. D'Alessandro", Palermo, Italy
| | - Simona De Grazia
- Dipartimento di Scienze per la Promozione della Salute e Materno Infantile "G. D'Alessandro", Palermo, Italy.
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31
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Kondapi DS, Ramani S, Estes MK, Atmar RL, Okhuysen PC. Norovirus in Cancer Patients: A Review. Open Forum Infect Dis 2021; 8:ofab126. [PMID: 34189156 PMCID: PMC8232388 DOI: 10.1093/ofid/ofab126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 03/10/2021] [Indexed: 12/15/2022] Open
Abstract
Norovirus (NoV) is the leading cause of viral-related diarrhea in cancer patients, in whom it can be chronic, contributing to decreased quality of life, interruption of cancer care, malnutrition, and altered mucosal barrier function. Immunosuppressed cancer patients shed NoV for longer periods of time than immunocompetent hosts, favoring quasispecies development and emergence of novel NoV variants. While nucleic acid amplification tests (NAATs) for NoV diagnosis have revolutionized our understanding of NoV burden of disease, not all NAATs provide information on viral load or infecting genotype. There is currently no effective antiviral or vaccine for chronic NoV infections. Screening for inhibitors of NoV replication in intestinal organoid culture models and creation of NoV-specific adoptive T cells are promising new strategies to develop treatments for chronic NoV in immunosuppressed patients. Herein we summarize data on the epidemiology, clinical manifestations, diagnostic challenges, and treatment of NoV infection in patients with cancer.
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Affiliation(s)
- Divya Samantha Kondapi
- Department of Infectious Diseases, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Section of Infectious Diseases, Baylor College of Medicine, Houston, Texas, USA
| | - Sasirekha Ramani
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Mary K Estes
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Robert L Atmar
- Section of Infectious Diseases, Baylor College of Medicine, Houston, Texas, USA
| | - Pablo C Okhuysen
- Infection Control and Employee Health, Division of Internal Medicine, Department of Infectious Diseases, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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Aggarwal S, Hassan E, Baldridge MT. Experimental Methods to Study the Pathogenesis of Human Enteric RNA Viruses. Viruses 2021; 13:975. [PMID: 34070283 PMCID: PMC8225081 DOI: 10.3390/v13060975] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/18/2021] [Accepted: 05/20/2021] [Indexed: 12/16/2022] Open
Abstract
Every year, millions of children are infected with viruses that target the gastrointestinal tract, causing acute gastroenteritis and diarrheal illness. Indeed, approximately 700 million episodes of diarrhea occur in children under five annually, with RNA viruses norovirus, rotavirus, and astrovirus serving as major causative pathogens. Numerous methodological advancements in recent years, including the establishment of novel cultivation systems using enteroids as well as the development of murine and other animal models of infection, have helped provide insight into many features of viral pathogenesis. However, many aspects of enteric viral infections remain elusive, demanding further study. Here, we describe the different in vitro and in vivo tools available to explore different pathophysiological attributes of human enteric RNA viruses, highlighting their advantages and limitations depending upon the question being explored. In addition, we discuss key areas and opportunities that would benefit from further methodological progress.
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Affiliation(s)
- Somya Aggarwal
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; (S.A.); (E.H.)
| | - Ebrahim Hassan
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; (S.A.); (E.H.)
| | - Megan T. Baldridge
- Division of Infectious Diseases, Department of Medicine, Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA; (S.A.); (E.H.)
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110, USA
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Ahmad-Nejad P, Ashavaid T, Vacaflores Salinas A, Huggett J, Harris K, Linder MW, Baluchova K, Steimer W, Payne DA. Current and future challenges in quality assurance in molecular diagnostics. Clin Chim Acta 2021; 519:239-246. [PMID: 33971158 DOI: 10.1016/j.cca.2021.05.004] [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] [Received: 10/30/2020] [Revised: 05/04/2021] [Accepted: 05/05/2021] [Indexed: 02/08/2023]
Abstract
The development and performance of molecular genetic assays has required increasingly complex quality assurance in recent years and continues to pose new challenges. Quality management officers, as well as academic and technical personnel are confronted with new molecular genetic parameters, methods, changing regulatory environments, questions regarding appropriate validation, and quality control for these innovative assays that are increasingly applying quantification and/or multiplex formats. Yet, quality assurance and quality control guidelines are still not widely available or in some circumstances have become outdated. For these reasons, the need for solutions to provide test confidence continues to grow. In order to integrate new test procedures into existing quality assurance measures, the ISO 15189 guideline can serve as an orientation. The ISO 15189 guideline describes requirements for medical laboratories and thus includes those performing molecular diagnostics. This article gives an overview of the possibilities and challenges in quality assurance of molecular parameters and shows possible solutions.
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Affiliation(s)
- Parviz Ahmad-Nejad
- Institute for Medicine Laboratory Diagnostics, Centre for Clinical and Translational Research (CCTR), HELIOS University Hospital, Wuppertal, Witten/Herdecke University, Germany.
| | - Tester Ashavaid
- Department of Laboratory Medicine, P.D. Hinduja National Hospital and Medical Research Center, Mumbai, India
| | | | - Jim Huggett
- National Measurement Laboratory (NML) at LGC, Queens Rd, Teddington, TW11 0LY, United Kingdom; School of Biosciences & Medicine, Faculty of Health & Medical Science, University of Surrey, Guildford GU2 7XH, United Kingdom
| | - Kathryn Harris
- Microbiology Department, Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Mark W Linder
- Department of Pathology and Laboratory Medicine, University of Louisville School of Medicine, Louisville, KY, USA
| | - Katarina Baluchova
- OncoLab Diagnostics GmbH Technologie- und Forschungszentrum, Viktor-Kaplan-Straße 2, 2700 Wiener Neustadt, Austria
| | - Werner Steimer
- Institute for Clinical Chemistry and Pathobiochemistry, Munich University of Technology, Klinikum rechts der Isar, D-81675 Munich, Germany
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Castany-Feixas M, Simo S, Garcia-Garcia S, Fernandez de Sevilla M, Launes C, Kalkgruber M, Gene A, Muñoz-Almagro C, Brotons P. Rapid molecular syndromic testing for aetiological diagnosis of gastrointestinal infections and targeted antimicrobial prescription: experience from a reference paediatric hospital in Spain. Eur J Clin Microbiol Infect Dis 2021; 40:2153-2160. [PMID: 33963926 PMCID: PMC8449766 DOI: 10.1007/s10096-021-04266-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 04/28/2021] [Indexed: 11/30/2022]
Abstract
Aetiological diagnosis of gastrointestinal infections is challenging since a wide range of bacteria, parasites and viruses can be causal agents and derived clinical manifestations appear quite similar. Our aim was to evaluate contribution of the novel QIAstat-DxGastrointestinal Panel (GIP) to aetiological diagnosis of gastrointestinal infections and rational antimicrobial prescription in a reference paediatric hospital. Evaluation included comparison of diagnostic yield and agreement of results of QIAstat-Dx GIP and conventional microbiological methods. Parallel testing was performed on stool samples collected prospectively from children admitted to Sant Joan de Deu Barcelona Hospital (Spain) during the period February-March 2019. Influence of the panel test use on antimicrobial prescription was assessed using a pre-post study design. Eighty-six (68.8%) out of 125 specimens were positive by QIAstat-Dx GIP versus 44 (35.2%) positive by a composite of conventional methods (p<0.001). Global agreement of panel test results with rotavirus-adenovirus antigen detection (92.8%) and a two-step antigen/toxin and PCR-based algorithm for toxigenic Clostridioides difficile detection (87.5%) was greater than that with bacterial culture (76.0%) and parasite microscopic identification (64.3%). Panel test results orientated antimicrobial prescription changes in 18 (14.4%) patients, including antimicrobial start in 11 cases initially untreated, targeted antimicrobial prescription in 5 and discontinuation in 2 cases empirically treated. Results showed that QIAstat-Dx GIP significantly expanded aetiological diagnosis of gastrointestinal infections compared to conventional microbiological methods while orientating a more judicious use of antimicrobial drugs in hospitalised children.
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Affiliation(s)
| | - Silvia Simo
- Institut de Recerca Sant Joan de Deu, Barcelona, Spain.,CIBER de Epidemiología y Salud Pública CIBERESP, Madrid, Spain
| | - Selene Garcia-Garcia
- Institut de Recerca Sant Joan de Deu, Barcelona, Spain.,Universitat Internacional de Catalunya, Barcelona, Spain
| | - Mariona Fernandez de Sevilla
- Institut de Recerca Sant Joan de Deu, Barcelona, Spain.,CIBER de Epidemiología y Salud Pública CIBERESP, Madrid, Spain.,University Hospital Sant Joan de Deu, P° Sant Joan de Déu, n° 2 08950 Esplugues, Barcelona, Spain.,Universitat de Barcelona, Barcelona, Spain
| | - Cristian Launes
- Institut de Recerca Sant Joan de Deu, Barcelona, Spain.,CIBER de Epidemiología y Salud Pública CIBERESP, Madrid, Spain.,University Hospital Sant Joan de Deu, P° Sant Joan de Déu, n° 2 08950 Esplugues, Barcelona, Spain.,Universitat de Barcelona, Barcelona, Spain
| | | | - Amadeu Gene
- University Hospital Sant Joan de Deu, P° Sant Joan de Déu, n° 2 08950 Esplugues, Barcelona, Spain
| | - Carmen Muñoz-Almagro
- Institut de Recerca Sant Joan de Deu, Barcelona, Spain. .,CIBER de Epidemiología y Salud Pública CIBERESP, Madrid, Spain. .,Universitat Internacional de Catalunya, Barcelona, Spain. .,University Hospital Sant Joan de Deu, P° Sant Joan de Déu, n° 2 08950 Esplugues, Barcelona, Spain.
| | - Pedro Brotons
- Institut de Recerca Sant Joan de Deu, Barcelona, Spain.,CIBER de Epidemiología y Salud Pública CIBERESP, Madrid, Spain.,Universitat Internacional de Catalunya, Barcelona, Spain
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Aleem A, Firak G, Slenker AK. Multiplex Molecular Stool Testing Rarely Impacts Antimicrobial Treatment Decisions More Than Three Days After Admission. Cureus 2021; 13:e14784. [PMID: 34084686 PMCID: PMC8165332 DOI: 10.7759/cureus.14784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Background Acute diarrheal illness in the United States is a significant cause of healthcare utilization and hospitalizations. For patients who develop diarrhea while hospitalized, testing for pathogens other than Clostridium difficile (C. difficile) using conventional stool testing is low yield. Newer testing modalities for infectious diarrhea such as the multiplex molecular stool testing provide an improved detection rate and a faster turn-around time compared to conventional stool testing. Methods We retrospectively examined the use of a multiplex molecular stool test at our institution for all hospital encounters over a two-year period to determine which organisms were identified ≤ 3 days and > 3 days after admission. Results A total of 2032 patients underwent multiplex molecular stool testing during the study period, with 1698 (83.6%) performed ≤ 3 days and 334 (16.3%) > 3 days after admission. An enteric non-C. difficile pathogen was identified more frequently when patients were tested ≤ 3 days after admission (350, 20.6%) as compared to > 3 days after admission (38, 11.4%, p<0.0001). Excluding coinfections, C. difficile was identified more frequently when patients were tested > 3 days after admission (64, 20.3%) versus another organism (30, 9.0%) (p<0.0001). Of those patients with a non-C. difficile pathogen identified > 3 days after admission, a bacterial pathogen amenable to treatment was only identified in 6% (21) of patients. Conclusion Multiplex molecular stool testing for patients tested > 3 days after admission is a low yield of information that could guide antimicrobial treatment decisions, and C. difficile testing is more useful in this clinical situation.
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Affiliation(s)
- Abdul Aleem
- Gastroenterology and Hepatology, Lehigh Valley Health Network, Allentown, USA
| | - Gabriela Firak
- Internal Medicine, Tower Health-Reading Hospital, Reading, USA
| | - Amy K Slenker
- Infectious Diseases, Lehigh Valley Health Network, Allentown, USA
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Peng S, Zhang J, Zhou W, Mao W, Han Z. Practical application of Westgard Sigma rules with run size in analytical biochemistry processes in clinical settings. J Clin Lab Anal 2021; 35:e23665. [PMID: 33270940 PMCID: PMC7957980 DOI: 10.1002/jcla.23665] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 11/07/2020] [Accepted: 11/10/2020] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND The performance of 18 routine chemical detection methods was evaluated by the sigma (σ) metric, and Westgard Sigma rules with run size were used to establish internal quality control (IQC) standards to reduce patient risks. MATERIALS AND METHODS External quality assessment (EQA) and internal quality control data from 18 assays in a biochemical laboratory were collected from January to June 2020. The sigma values of each assay were calculated, based on the bias, total error allowable, and coefficient of variation, appropriate quality control rules were selected. According to the quality goal index, the main causes of poor performance were determined to guide quality improvement. RESULTS At IQC material level 1, seven of the 18 assays achieved five sigma (excellent), and five assays (UA, Crea, AMY, TC and Na) showed world-class performance. At IQC material level 2, 14 of the 18 assays achieved 5 sigma (excellent), and thirteen assays (UA, ALT, CK, Crea, AMY, K, AST, ALP, Na, LDH, Mg, TC and GGT) showed world-class performance. The quality goal index (QGI) was calculated for items with analysis performance <5 sigma, and the main causes of poor performance were determined to guide quality improvement. CONCLUSIONS Westgard sigma rules with run size are an effective tool for evaluating the performance of biochemical assays. These rules can be used to more simply and intuitively select the quality control strategy of related items and reduce the risk to patients.
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Affiliation(s)
- SongQing Peng
- Department of Clinical LaboratoryShengzhou People's HospitalShengzhou Branch of the First Affiliated Hospital of Zhejiang UniversityShengzhouChina
| | - JinFei Zhang
- Department of Clinical LaboratoryShengzhou People's HospitalShengzhou Branch of the First Affiliated Hospital of Zhejiang UniversityShengzhouChina
| | - WuQiong Zhou
- Department of Clinical LaboratoryShengzhou People's HospitalShengzhou Branch of the First Affiliated Hospital of Zhejiang UniversityShengzhouChina
| | - WeiLin Mao
- Department of Clinical LaboratoryShengzhou People's HospitalShengzhou Branch of the First Affiliated Hospital of Zhejiang UniversityShengzhouChina
- Key laboratory of digestive system diseases of ShengzhouShengzhou People’s HospitalShengzhouChina
| | - Zhong Han
- Department of Clinical LaboratoryShengzhou People's HospitalShengzhou Branch of the First Affiliated Hospital of Zhejiang UniversityShengzhouChina
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Liu Q, Chen X, Han J, Chen Y, Wang M, Zhao J, Liang W, Yang F. Application of a six sigma model to the evaluation of the analytical performance of serum enzyme assays and the design of a quality control strategy for these assays: A multicentre study. Clin Biochem 2021; 91:52-58. [PMID: 33617847 DOI: 10.1016/j.clinbiochem.2021.02.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 01/29/2021] [Accepted: 02/10/2021] [Indexed: 02/04/2023]
Abstract
BACKGROUND Six medical testing laboratories at six different sites in China participated in this study. We applied a six sigma model for (a) the evaluation of the analytical performance of serum enzyme assays at each of the laboratories, (b) the design of individualized quality control programs and (c) the development of improvement measures for each of the assays, as appropriate. METHODS Internal quality control (IQC) and external quality assessment (EQA) data for selected serum enzyme assays were collected from each of the laboratories. Sigma values for these assays were calculated using coefficients of variation, bias, and total allowable error (TEa). Normalized sigma method decision charts were generated using these parameters. IQC design and improvement measures were defined using the Westgard sigma rules. The quality goal index (QGI) was used to assist with identification of deficiencies (bias problems, precision problems, or their combination) affecting the analytical performance of assays with sigma values <6. RESULTS Sigma values for the selected serum enzyme assays were significantly different at different levels of enzyme activity. Differences in assay quality in different laboratories were also seen, despite the use of identical testing instruments and reagents. Based on the six sigma data, individualized quality control programs were outlined for each assay with sigma <6 at each laboratory. CONCLUSIONS In multi-location laboratory systems, a six sigma model can evaluate the quality of the assays being performed, allowing management to design individualized IQC programs and strategies for continuous improvement as appropriate for each laboratory. This will improve patient care, especially for patients transferred between sites within multi-hospital systems.
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Affiliation(s)
- Qian Liu
- Department of Laboratory Medicine, The Second People's Hospital of Lianyungang, Lianyungang, PR China
| | - Xinkuan Chen
- Department of Laboratory Medicine, Xuzhou Medical University Affiliated Hospital of Lianyungang, Lianyungang, PR China
| | - Jingjing Han
- Department of Laboratory Medicine, Wuxi Branch of Ruijin Hospital, Wuxi, PR China
| | - Ying Chen
- Department of Laboratory Medicine, Nantong Hospital of Traditional Chinese Medicine, Nantong, PR China
| | - Menglin Wang
- Department of Laboratory Medicine, Suqian First Hospital, Suqian, PR China
| | - Jun Zhao
- Department of Laboratory Medicine, Wuxi Maternal and Child Health Hospital, Wuxi, PR China
| | - Wei Liang
- Department of Laboratory Medicine, The Second People's Hospital of Lianyungang, Lianyungang, PR China
| | - Fumeng Yang
- Department of Laboratory Medicine, The Second People's Hospital of Lianyungang, Lianyungang, PR China.
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Halasa N, Piya B, Stewart LS, Rahman H, Payne DC, Woron A, Thomas L, Constantine-Renna L, Garman K, McHenry R, Chappell J, Spieker AJ, Fonnesbeck C, Batarseh E, Hamdan L, Wikswo ME, Parashar U, Bowen MD, Vinjé J, Hall AJ, Dunn JR. The Changing Landscape of Pediatric Viral Enteropathogens in the Post-Rotavirus Vaccine Era. Clin Infect Dis 2021; 72:576-585. [PMID: 32009161 PMCID: PMC7884803 DOI: 10.1093/cid/ciaa100] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 01/31/2020] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Acute gastroenteritis (AGE) is a common reason for children to receive medical care. However, the viral etiology of AGE illness is not well described in the post-rotavirus vaccine era, particularly in the outpatient (OP) setting. METHODS Between 2012 and 2015, children 15 days through 17 years old presenting to Vanderbilt Children's Hospital, Nashville, Tennessee, with AGE were enrolled prospectively from the inpatient, emergency department, and OP settings, and stool specimens were collected. Healthy controls (HCs) were enrolled and frequency matched for period, age group, race, and ethnicity. Stool specimens were tested by means of reverse-transcription real-time quantitative polymerase chain reaction for norovirus, sapovirus, and astrovirus RNA and by Rotaclone enzyme immunoassay for rotavirus antigen, followed by polymerase chain reaction verification of antigen detection. RESULTS A total of 3705 AGE case patients and 1563 HCs were enrolled, among whom 2885 case patients (78%) and 1110 HCs (71%) provided stool specimens that were tested. All 4 viruses were more frequently detected in AGE case patients than in HCs (norovirus, 22% vs 8%, respectively; rotavirus, 10% vs 1%; sapovirus, 10% vs 5%; and astrovirus, 5% vs 2%; P < .001 for each virus). In the OP setting, rates of AGE due to norovirus were higher than rate for the other 3 viruses. Children <5 years old had higher OP AGE rates than older children for all viruses. CONCLUSIONS Norovirus remains the most common virus detected in all settings, occurring nearly twice as frequently as the next most common pathogens, sapovirus and rotavirus. Combined, norovirus, sapovirus, rotavirus, and astrovirus were associated with almost half of all AGE visits and therefore are an important reason for children to receive medical care.
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Affiliation(s)
- Natasha Halasa
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Bhinnata Piya
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Laura S Stewart
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Herdi Rahman
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Daniel C Payne
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Amy Woron
- Communicable and Environmental Diseases and Emergency Preparedness, Tennessee Department of Health, Nashville, Tennessee, USA
| | - Linda Thomas
- Communicable and Environmental Diseases and Emergency Preparedness, Tennessee Department of Health, Nashville, Tennessee, USA
| | - Lisha Constantine-Renna
- Communicable and Environmental Diseases and Emergency Preparedness, Tennessee Department of Health, Nashville, Tennessee, USA
| | - Katie Garman
- Communicable and Environmental Diseases and Emergency Preparedness, Tennessee Department of Health, Nashville, Tennessee, USA
| | - Rendie McHenry
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - James Chappell
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Andrew J Spieker
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Christopher Fonnesbeck
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Einas Batarseh
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Lubna Hamdan
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Mary E Wikswo
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Umesh Parashar
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Michael D Bowen
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jan Vinjé
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Aron J Hall
- Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - John R Dunn
- Communicable and Environmental Diseases and Emergency Preparedness, Tennessee Department of Health, Nashville, Tennessee, USA
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Liu Q, Zhu W, Bian G, Liang W, Zhao C, Yang F. Application of the sigma metrics to evaluate the analytical performance of cystatin C and design a quality control strategy. Ann Clin Biochem 2021; 58:203-210. [PMID: 33393354 DOI: 10.1177/0004563220988032] [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: 02/04/2023]
Abstract
BACKGROUND Sigma metrics are commonly used to evaluate laboratory management. In this study, we aimed to evaluate the analytical performance of cystatin C using sigma metrics and to develop an individualized quality control scheme for cystatin C concentrations. METHODS Bias was calculated based on the samples used for the external quality assessment. The coefficient of variation was calculated using six months of internal quality control measurements at two levels, and desirable specification derived from biological variation was used as the quality goal. The sigma value for cystatin C was calculated using the above data. The internal quality control scheme and improvement measures were formulated according to the Westgard sigma standards for batch size and quality goal index. RESULTS The sigma values for cystatin C, for quality control levels 1 and 2, were 3.04 and 4.95, respectively. The 13s/22s/R4s/41s/6x multirules (n = 6, R = 1), with a batch size of 45 patient samples, were selected as the internal quality control schemes for cystatin C. With different concentrations of cystatin C, the power function graph showed a probability for error detection of 94% and 100% and a probability for false rejection of 4% and 2%, respectively. According to the quality goal index of cystatin C, its precision needs to be improved. CONCLUSIONS With a 'desirable' biological variation of 6.50%, the Westgard rule 13s/22s/R4s/41s/6x (n = 6, R = 1, batch size of 45) with high efficacy for determining the detection error is recommended for individualized quality control schemes of cystatin C.
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Affiliation(s)
- Qian Liu
- Department of Laboratory Medicine, The Second People's Hospital of Lianyungang, Lianyungang, PR China
| | - Wenjun Zhu
- Department of Laboratory Medicine, The Second People's Hospital of Lianyungang, Lianyungang, PR China
| | - Guangrong Bian
- Department of Laboratory Medicine, The Second People's Hospital of Lianyungang, Lianyungang, PR China
| | - Wei Liang
- Department of Laboratory Medicine, The Second People's Hospital of Lianyungang, Lianyungang, PR China
| | - Changxin Zhao
- Department of Laboratory Medicine, The Second People's Hospital of Lianyungang, Lianyungang, PR China
| | - Fumeng Yang
- Department of Laboratory Medicine, The Second People's Hospital of Lianyungang, Lianyungang, PR China
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Alsuwaidi AR, Al Dhaheri K, Al Hamad S, George J, Ibrahim J, Ghatasheh G, Issa M, Al-Hammadi S, Narchi H. Etiology of diarrhea by multiplex polymerase chain reaction among young children in the United Arab Emirates: a case-control study. BMC Infect Dis 2021; 21:7. [PMID: 33407198 PMCID: PMC7788778 DOI: 10.1186/s12879-020-05693-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 12/08/2020] [Indexed: 12/15/2022] Open
Abstract
Background Little is known about the etiology of childhood diarrhea in the United Arab Emirates (UAE) especially after the introduction of rotavirus vaccines. This study aimed to identify gastrointestinal pathogens in children with diarrhea (cases) and the carriage rate of these pathogens in asymptomatic children (controls). Methods Stool samples were collected from 203 cases and 73 controls who presented to two major hospitals in Al Ain city, UAE. Samples were analyzed with Allplex™ Gastrointestinal Full Panel Assay for common entero-pathogens. The association between diarrhea and the isolated pathogens was calculated in a multivariate logistic regression model. The adjusted attributable fractions (aAFs) were calculated for all pathogens significantly associated with cases. Results At least one pathogen was identified in 87 samples (42.8%) from cases and 17 (23.3%) from controls (P < 0.001). Rotavirus, norovirus GII and adenovirus were significantly more prevalent in cases. Their aAFs with 95% ci are 0.95 (0.64, 1.00) for rotavirus, 0.86 (0.38, 0.97) for norovirus GII and 0.84 (0.29, 0.96) for adenovirus. None of the 13 bacteria tested for were more commonly found in the cases than in controls. Cryptosporidium spp. were more significantly detected in cases than in controls. Co-infections occurred in 27.9% of the children. Viruses and parasites were significantly more likely to occur together only in the cases. Conclusions Multiplex PCR revealed high positivity rates in both cases and controls which demand a cautious interpretation. Rotavirus remains the main childhood diarrhea pathogen in UAE. Effective strategies are needed to better control rotavirus and other causative pathogens. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-020-05693-1.
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Affiliation(s)
- Ahmed R Alsuwaidi
- Department of Pediatrics, College of Medicine and Health Sciences, United Arab Emirates University, P. O. Box 17666, Al Ain, UAE.
| | - Klaithem Al Dhaheri
- Institute of Child Health, Al Ain Hospital, Abu Dhabi Health Services Company (SEHA), Al Ain, UAE
| | - Sania Al Hamad
- Department of Pediatrics, College of Medicine and Health Sciences, United Arab Emirates University, P. O. Box 17666, Al Ain, UAE
| | - Junu George
- Department of Pediatrics, College of Medicine and Health Sciences, United Arab Emirates University, P. O. Box 17666, Al Ain, UAE
| | - Judy Ibrahim
- Department of Pediatrics, Tawam Hospital, Abu Dhabi Health Services Company (SEHA), Al Ain, UAE
| | - Ghassan Ghatasheh
- Department of Pediatrics, Tawam Hospital, Abu Dhabi Health Services Company (SEHA), Al Ain, UAE
| | - Mohammed Issa
- Department of Emergency Medicine, Tawam Hospital, Abu Dhabi Health Services Company (SEHA), Al Ain, UAE
| | - Suleiman Al-Hammadi
- Department of Pediatrics, College of Medicine and Health Sciences, United Arab Emirates University, P. O. Box 17666, Al Ain, UAE
| | - Hassib Narchi
- Department of Pediatrics, College of Medicine and Health Sciences, United Arab Emirates University, P. O. Box 17666, Al Ain, UAE
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Hartzler ML, Castle L, Lewis C, Zakaria L. A functional approach to the chronic disease epidemic. Am J Health Syst Pharm 2020; 77:668-672. [PMID: 32236457 DOI: 10.1093/ajhp/zxaa032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Melody L Hartzler
- Department of Pharmacy Practice, Cedarville University School of Pharmacy, Cedarville, OH, and Western Medicine Family, Physicians, Fairborn, OH
| | - Lauren Castle
- Functional Medicine Pharmacists Alliance, Miamisburg, OH
| | - Christine Lewis
- Potter's House Apothecary, Midwestern University College of Pharmacy-Glendale, Glendale, AZ
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Chamseddine S, Chmaisse A, Akel I, Zein ZE, Khalil S, Raad SA, Khati A, Ghandour H, Khafaja S, Haj M, Abboud M, Mahfouz R, Araj G, Zaraket H, Hanna-Wakim R, Muwakkit S, Dbaibo G. Epidemiology and clinical characteristics of viral infections in hospitalized children and adolescents with cancer in Lebanon. PLoS One 2020; 15:e0239258. [PMID: 32961548 PMCID: PMC7508634 DOI: 10.1371/journal.pone.0239258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 09/02/2020] [Indexed: 11/30/2022] Open
Abstract
Background Viral infections in children and adolescents with malignancy are commonly encountered and have a significant impact on morbidity and mortality. Studies and epidemiological data regarding viral infections in children with cancer in developing countries are lacking. This retrospective cohort study aims to assess the burden of viral infections in children and adolescents with cancer, by assessing prevalence, risk factors, as well as morbidity and mortality of common viruses over a period of 8 years. Methods and findings Medical records of cancer patients treated at the Children Cancer Center of Lebanon were reviewed and 155 participants under the age of 21 were identified with at least one documented viral infection during the period from July 2009 to November 2017. This subset included 136 participants with active malignancy and 19 participants with a history of cancer who underwent hematopoietic stem cell transplantation [HSCT] and were in remission; the latter group was analyzed separately. Information regarding participant characteristics, hospital course, and complications were obtained. Associations between viral infections and certain factors were assessed. In the cohort, 64% were male, 81% were Lebanese. In participants with active malignancy, 90% received chemotherapy in the 6 months preceding the viral infection episode, 11% received radiotherapy. 51% of participants were neutropenic at the time of viral detection, and 77% were lymphopenic. 17% experienced a bacterial co-infection, and 3 experienced a viral co-infection. Among 162 viral infection episodes, clinically diagnosed skin infections, mainly herpes simplex virus type 1 and varicella-zoster virus, were the most common [44% of cases]. These were followed by laboratory-proven systemic herpes infections: cytomegalovirus [14%] and Epstein-Barr virus [6%]. Respiratory viruses: influenza and respiratory syncytial virus, accounted for 9% and 4%, respectively, whereas rotavirus represented 11% and BK virus represented 3% of cases. Acute lymphocytic leukemia was the most prevalent neoplasia [57%]. Fever was the most common presenting symptom [55%] and febrile neutropenia was the reason for admission in 24% of cases. The mean length of stay was significantly longer in participants with cytomegalovirus infections and significantly lower in rotavirus infection. Admission to the ICU occurred in 9%, complications in 8%, and mortality in 5%. Participants with viral infections post-HSCT were noted to have a significantly longer length of hospital stay compared to non-HSCT participants, with no other significant differences in clinical course and outcome. The study was limited by its retrospective nature and by the late introduction and underuse of multiplex PCR panels, which may have led to underdiagnosis of viral infections. Conclusions Viral infections were prevalent in our sample of cancer patients and may have contributed to morbidity and mortality. Newly available viral diagnostics are likely to vastly increase the number and scope of detectable viral infections in this population. Prospective studies using multiplex PCR technology with systematic testing of patients will be more helpful in defining the burden of viral infections. Furthermore, efforts at antimicrobial stewardship would benefit from the identification of viral causes of infection and limit the unnecessary use of antibiotics in the pediatric cancer population.
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Affiliation(s)
- Sarah Chamseddine
- Center for Infectious Diseases Research, American University of Beirut, Beirut, Lebanon
| | - Ahmad Chmaisse
- Center for Infectious Diseases Research, American University of Beirut, Beirut, Lebanon
| | - Imad Akel
- Center for Infectious Diseases Research, American University of Beirut, Beirut, Lebanon
| | - Zeinab El Zein
- Center for Infectious Diseases Research, American University of Beirut, Beirut, Lebanon
- Department of Pediatrics and Adolescent Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Suzan Khalil
- Center for Infectious Diseases Research, American University of Beirut, Beirut, Lebanon
| | - Sarah Abi Raad
- Center for Infectious Diseases Research, American University of Beirut, Beirut, Lebanon
| | - Antoine Khati
- Center for Infectious Diseases Research, American University of Beirut, Beirut, Lebanon
| | - Hiba Ghandour
- Center for Infectious Diseases Research, American University of Beirut, Beirut, Lebanon
| | - Sarah Khafaja
- Center for Infectious Diseases Research, American University of Beirut, Beirut, Lebanon
- Department of Pediatrics and Adolescent Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Magda Haj
- Center for Infectious Diseases Research, American University of Beirut, Beirut, Lebanon
| | - Miguel Abboud
- Department of Pediatrics and Adolescent Medicine, American University of Beirut Medical Center, Beirut, Lebanon
- Department of Pediatrics and Adolescent Medicine, Children’s Cancer Center of Lebanon, American University of Beirut Medical Center, Beirut, Lebanon
| | - Rami Mahfouz
- Center for Infectious Diseases Research, American University of Beirut, Beirut, Lebanon
- Department of Pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - George Araj
- Center for Infectious Diseases Research, American University of Beirut, Beirut, Lebanon
- Department of Pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Hassan Zaraket
- Center for Infectious Diseases Research, American University of Beirut, Beirut, Lebanon
- Department of Experimental Pathology, Immunology and Microbiology, Faculty of Medicine, Beirut, Lebanon
| | - Rima Hanna-Wakim
- Center for Infectious Diseases Research, American University of Beirut, Beirut, Lebanon
- Department of Pediatrics and Adolescent Medicine, American University of Beirut Medical Center, Beirut, Lebanon
- Division of Pediatric Infectious Diseases, Department of Pediatrics and Adolescent Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Samar Muwakkit
- Department of Pediatrics and Adolescent Medicine, American University of Beirut Medical Center, Beirut, Lebanon
- Department of Pediatrics and Adolescent Medicine, Children’s Cancer Center of Lebanon, American University of Beirut Medical Center, Beirut, Lebanon
| | - Ghassan Dbaibo
- Center for Infectious Diseases Research, American University of Beirut, Beirut, Lebanon
- Department of Pediatrics and Adolescent Medicine, American University of Beirut Medical Center, Beirut, Lebanon
- Division of Pediatric Infectious Diseases, Department of Pediatrics and Adolescent Medicine, American University of Beirut Medical Center, Beirut, Lebanon
- * E-mail:
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Diagnostic tools for bacterial infections in travellers: Current and future options. Travel Med Infect Dis 2020; 37:101856. [PMID: 32841728 DOI: 10.1016/j.tmaid.2020.101856] [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: 04/03/2019] [Revised: 04/30/2020] [Accepted: 08/19/2020] [Indexed: 11/22/2022]
Abstract
International travel has increased dramatically over the past 50 years, and travel destinations have diversified. Although physicians are more familiar with the panel of aetiological agents responsible for illnesses of returning travellers, thanks to regular epidemiological studies, the spectrum of pathogens potentially encountered in various travel destinations is nevertheless increasing. In addition, the wide array of approaches currently available and addressed in this paper could render the procedures for microbiological analyses increasingly complex. As the time to result is crucial to adequately manage patients, modern approaches have been developed to shorten diagnosis delays. The syndromic approach, which consists of simultaneously testing a wide panel of microorganisms, substantially increases the diagnostic yield with significant time savings, particularly when coupled with point-of-care laboratories. The tools commonly used for this purpose are immunochromatographic tests, mainly targeting bacterial antigens, and multiplex real-time PCR. The emergence of next-generation sequencing technologies, which enable random amplification of genetic material of any microbe present in a clinical specimen, provides further exciting perspectives in the diagnosis of infectious diseases.
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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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Torres-Miranda D, Akselrod H, Karsner R, Secco A, Silva-Cantillo D, Siegel MO, Roberts AD, Simon GL. Use of BioFire FilmArray gastrointestinal PCR panel associated with reductions in antibiotic use, time to optimal antibiotics, and length of stay. BMC Gastroenterol 2020; 20:246. [PMID: 32727381 PMCID: PMC7392718 DOI: 10.1186/s12876-020-01394-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 07/22/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Rapid and accurate diagnostic tools are needed for appropriate management of infectious diarrhea. METHODS We evaluated the impact of the introduction of rapid multiplex PCR testing using the FilmArray gastrointestinal (GI) panel (BioFire Diagnostics, LLC, Salt Lake City, UT) at our institution, and compared the results to those of standard stool cultures. RESULTS The most common pathogens detected by the FilmArray GI panel were Clostridium difficile (55.0%), Campylobacter species (20.9%), Salmonella species (12.4%), and Shigella/EIEC species (12.4%). Rates of reproducibility in stool culture for these pathogens ranged from 56.3 to 77.8%. Co-detection of two or more organisms was common (24.2%), most commonly involving EPEC, EAEC, ETEC, and STEC. The time from arrival in the Emergency Department to discharge or admission to the hospital was unchanged after the introduction of FilmArray GI panel, but length of hospital stay was shorter (3 vs. 7.5 days, p = 0.0002) for the FilmArray group. The time to empiric antibiotics did not differ significantly, but optimal antibiotics were started earlier after introduction of the FilmArray GI panel (hospital day 1 vs. 2, p < 0.0001). More patients were discharged without antibiotics after introduction of the FilmArray GI panel (14.0% vs. 4.5%; p < 0.001). CONCLUSION Our results demonstrate that the FilmArray GI panel is an important tool for improving both patient care and antibiotic stewardship, despite the tendency for positive results with multiple pathogens.
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Affiliation(s)
- Daisy Torres-Miranda
- Division of Infectious Diseases, George Washington University School of Medicine and Health Sciences, 2150 Pennsylvania Avenue NW, Washington, DC, 20037, USA
| | - Hana Akselrod
- Division of Infectious Diseases, George Washington University School of Medicine and Health Sciences, 2150 Pennsylvania Avenue NW, Washington, DC, 20037, USA.
| | - Ryan Karsner
- Division of Infectious Diseases, George Washington University School of Medicine and Health Sciences, 2150 Pennsylvania Avenue NW, Washington, DC, 20037, USA
| | - Alessandra Secco
- Division of Infectious Diseases, George Washington University School of Medicine and Health Sciences, 2150 Pennsylvania Avenue NW, Washington, DC, 20037, USA
| | - Diana Silva-Cantillo
- Division of Infectious Diseases, George Washington University School of Medicine and Health Sciences, 2150 Pennsylvania Avenue NW, Washington, DC, 20037, USA
| | - Marc O Siegel
- Division of Infectious Diseases, George Washington University School of Medicine and Health Sciences, 2150 Pennsylvania Avenue NW, Washington, DC, 20037, USA
| | - Afsoon D Roberts
- Division of Infectious Diseases, George Washington University School of Medicine and Health Sciences, 2150 Pennsylvania Avenue NW, Washington, DC, 20037, USA
| | - Gary L Simon
- Division of Infectious Diseases, George Washington University School of Medicine and Health Sciences, 2150 Pennsylvania Avenue NW, Washington, DC, 20037, USA
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De Grazia S, Bonura F, Bonura C, Mangiaracina L, Filizzolo C, Martella V, Giammanco GM. Assessing the burden of viral co-infections in acute gastroenteritis in children: An eleven-year-long investigation. J Clin Virol 2020; 129:104513. [PMID: 32575023 DOI: 10.1016/j.jcv.2020.104513] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/05/2020] [Accepted: 06/14/2020] [Indexed: 12/18/2022]
Abstract
BACKGROUND Acute gastroenteritis is an important cause of childhood morbidity and mortality worldwide. A number of pathogens are responsible for human acute gastroenteritis. The recent introduction of syndromic assays for the diagnosis of enteric infections, including a wide panel of enteric pathogens, has unveiled the frequency of mixed infections. This study was carried out to assess the burden of viral co-infections and the genetic diversity of the viruses detected in children hospitalized with acute gastroenteritis in Italy. METHODS A total of 4161 stool samples collected from diarrheic children over 11 years, from January 2008 to December 2018, were investigated for the presence of four enteric viruses, i.e. group A rotavirus, norovirus, astrovirus and adenovirus. The samples were initially screened by either molecular or immunochromatographic assays and subsequently confirmed by Real-time PCR and sequence analyses. RESULTS At least one viral agent was detected in 48.6 %of specimens. Rotavirus was the most prevalent virus (24.7 %) followed by norovirus (19.6 %), adenovirus (5.3 %) and astrovirus (3%). Co-infections were detected in 8.3 % of virus-positive patients, with common viral combination being rotavirus with norovirus (70.6 % of co-infections) or with astrovirus (9.6 %). A variety of viral genotypes was detected in co-infections and in single infections. Using Real-time PCR cycle thresholds as a proxy measure of fecal viral load, rotavirus was generally detected at higher levels in co-infected patients. CONCLUSIONS Combining and deciphering measurable indicators of viral load and epidemiological information could be useful for an accurate interpretation of viral co-infections.
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Affiliation(s)
- Simona De Grazia
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", Università di Palermo, Palermo, Italy.
| | - Floriana Bonura
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", Università di Palermo, Palermo, Italy
| | - Celestino Bonura
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", Università di Palermo, Palermo, Italy
| | - Leonardo Mangiaracina
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", Università di Palermo, Palermo, Italy
| | - Chiara Filizzolo
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", Università di Palermo, Palermo, Italy
| | - Vito Martella
- Dipartimento di Medicina Veterinaria, Università Aldo Moro di Bari, Valenzano, Italy
| | - Giovanni M Giammanco
- Dipartimento di Promozione della Salute, Materno-Infantile, di Medicina Interna e Specialistica di Eccellenza "G. D'Alessandro", Università di Palermo, Palermo, Italy
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Abstract
Microbial contaminations and infections are hazardous and pose crucial concerns for humans. They result in severe morbidity and mortality around the globe. Even though dish-culturing, polymerase chain reaction (PCR), an enzyme-linked immunosorbent assay (ELISA) exhibits accurate and reliable detection of bacteria but these methods are time-consuming, laborious, and expensive. This warrants early detection and quantification of bacteria for timely diagnosis and treatment. Bacteria imprinting ensures a solution for selective and early detection of bacteria by snagging them inside their imprinted cavities. This review provides an insight into MIPs based bacterial detection strategies, challenges, and future perspectives.
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Affiliation(s)
- Shabi Abbas Zaidi
- Department of Chemistry and Earth Sciences, College of Arts and Sciences, Qatar University, Doha 2713, Qatar
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Mitra S, Nayak MK, Majumdar A, Sinha A, Chatterjee S, Deb A, Chawla-Sarkar M, Dutta S. Development and evaluation of a multiplex conventional reverse-transcription polymerase chain reaction assay for detection of common viral pathogens causing acute gastroenteritis. Diagn Microbiol Infect Dis 2020; 97:115061. [PMID: 32585545 DOI: 10.1016/j.diagmicrobio.2020.115061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/27/2020] [Accepted: 04/12/2020] [Indexed: 12/11/2022]
Abstract
Timely identification of etiological agents of enteric infections is necessary to reduce the burden of infantile diarrheal mortality. Nucleic acid amplification-based detection methods offer a quick, reliable way for diagnosis of microbes in clinical specimens. This study was undertaken to evaluate an easy-to-use, cost-effective multiplex conventional reverse-transcription polymerase chain reaction (RT-PCR) assay developed at the Indian Council of Medical Research-National Institute of Cholera and Enteric Diseases virology laboratory to identify 4 common enteric viruses (rotavirus, norovirus, adenovirus, astrovirus) in stool samples from patients who were being evaluated for acute diarrhea. On comparison with a commercially available real-time PCR method, significant agreement in sensitivity and specificity was observed. Though the turnaround time for RT-PCR was 6-8 h compared to 5-6 h for real-time PCR, the real-time PCR has high test cost (approximately 28 USD/2000 INR) for Fast-Track Diagnostics kit-based quantitative RT-PCR versus 6 USD or 400 INR for conventional multiplex RT-PCR/sample. Thus, the conventional RT-PCR method is expected to be adaptable at local hospitals and health cares in resource-poor settings.
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Affiliation(s)
- Suvrotoa Mitra
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, WB, India
| | | | - Agniva Majumdar
- Regional Virus Research and Diagnostic Lab (VRDL), ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, WB, India
| | - Avisek Sinha
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, WB, India
| | - Soumyadipta Chatterjee
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, WB, India
| | - Alok Deb
- Division of Epidemiology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, WB, India
| | - Mamta Chawla-Sarkar
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, WB, India.
| | - Shanta Dutta
- Regional Virus Research and Diagnostic Lab (VRDL), ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, WB, India
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Arbefeville S, Ferrieri P. Role of Multiplex Molecular Diagnosis for Acute Gastroenteritis. Curr Infect Dis Rep 2020. [DOI: 10.1007/s11908-020-0718-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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