1
|
Wang Y, Liu C, Xia W, Cui Y, Yu L, Zhao D, Guan X, Wang Y, Wang Y, Li Y, Hu J, Liu J. Association of coagulase-negative staphylococci with orthopedic infections detected by in-house multiplex real-time PCR. Front Microbiol 2024; 15:1400096. [PMID: 38912353 PMCID: PMC11193334 DOI: 10.3389/fmicb.2024.1400096] [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: 03/13/2024] [Accepted: 05/10/2024] [Indexed: 06/25/2024] Open
Abstract
Introduction Clinical significance of coagulase-negative staphylococci (CoNS) has been gradually acknowledged in both healthcare and clinical research, but approaches for their precise discrimination at the species level remain scarce. The current study aimed to evaluate the association of CoNS with orthopedic infections, where accurate and prompt identification of etiology is crucial for appropriate diagnosis and treatment decision-making. Methods A 16S rRNA-based quantitative PCR (qPCR) assay was developed for the detection of Staphylococcus genus and two panels of 3-plex qPCR assays for further differentiation of six CoNS species with remarkable clinical significance, including S. epidermidis, S. haemolyticus, S. simulans, S. hominis, S. capitis, and S. caprae. All the assays exhibited excellent analytical performance. ΔCq (quantification cycle) between 16S rRNA and CoNS species-specific targets was established to determine the primary CoNS. These methods were applied to detect CoNS in wound samples from orthopedic patients with and without infection. Results and discussion Overall, CoNS were detected in 17.8% (21/118) of patients with clinically suspected infection and in 9.8% (12/123) of patients without any infection symptom (p < 0.05). Moreover, the association with infection was found to be bacterial quantity dependent. S. epidermidis was identified as the predominant species, followed by S. simulans, S. haemolyticus, and S. hominis. Male sex, open injury, trauma, and lower extremity were determined as risk factors for CoNS infections. CoNS-positive patients had significantly longer hospitalization duration (20 days (15, 33) versus 13 days (7, 22) for Staphylococcus-negative patients, p = 0.003), which could be a considerable burden for healthcare and individual patients. Considering the complex characteristics and devastating consequences of orthopedic infections, further expanding the detection scope for CoNS may be pursued to better understand the etiology of orthopedic infections and to improve therapeutic strategies.
Collapse
Affiliation(s)
- Ying Wang
- School of Public Health, Qingdao University, Qingdao, Shandong, China
| | - Chao Liu
- School of Public Health, Qingdao University, Qingdao, Shandong, China
| | - Wenbo Xia
- Department of Orthopedics, Qingdao Huangdao Traditional Chinese Medicine Hospital, Qingdao, Shandong, China
| | - Yanxiang Cui
- Department of Clinical Laboratory, Qingdao Huangdao Traditional Chinese Medicine Hospital, Qingdao, Shandong, China
| | - Linhong Yu
- Qingdao Medical College, Qingdao University, Qingdao, Shandong, China
| | - Dan Zhao
- School of Public Health, Qingdao University, Qingdao, Shandong, China
| | - Xiaoxuan Guan
- Department of Clinical Laboratory, Qingdao Huangdao Traditional Chinese Medicine Hospital, Qingdao, Shandong, China
| | - Yingdi Wang
- School of Public Health, Qingdao University, Qingdao, Shandong, China
| | - Yani Wang
- School of Public Health, Qingdao University, Qingdao, Shandong, China
| | - Yisong Li
- School of Public Health, Qingdao University, Qingdao, Shandong, China
| | - Jianqiang Hu
- Department of Orthopedics, Qingdao Huangdao Traditional Chinese Medicine Hospital, Qingdao, Shandong, China
| | - Jie Liu
- School of Public Health, Qingdao University, Qingdao, Shandong, China
| |
Collapse
|
2
|
Wongstitwilairoong B, Anothaisintawee T, Ruamsap N, Lertsethtakarn P, Kietsiri P, Oransathid W, Oransathid W, Gonwong S, Silapong S, Suksawad U, Sornsakrin S, Bodhidatta L, Boudreaux DM, Livezey JR. Prevalence of Intestinal Parasitic Infections, Genotypes, and Drug Susceptibility of Giardia lamblia among Preschool and School-Aged Children: A Cross-Sectional Study in Thailand. Trop Med Infect Dis 2023; 8:394. [PMID: 37624332 PMCID: PMC10457730 DOI: 10.3390/tropicalmed8080394] [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: 05/01/2023] [Revised: 07/18/2023] [Accepted: 07/21/2023] [Indexed: 08/26/2023] Open
Abstract
This study aimed to estimate the prevalence of intestinal parasitic infections in children and assess the drug susceptibility and genotypes/assemblages of Giardia lamblia in Thailand. This cross-sectional study was conducted among children aged 3-12 years in Sangkhlaburi District, Kanchanaburi Province, Thailand, between 25 September 2017 and 12 January 2018. Parasites were identified by stool microscopic examination, cultivation of intestinal parasitic protozoa, and enzyme-linked immunosorbent assay (ELISA). Drug susceptibility and genotype of G. lamblia were performed, respectively, by a resazurin assay and Triosephosphate Isomerase A and B genes using modified primers and probes. Among the 661 participants, 445 had an intestinal parasitic infection, resulting in a prevalence of 67.32% (95% CI: 63.60-70.89%). Blastocystis hominis was the most prevalent protozoa infection (49.32%; 95% CI: 45.44-53.22%), while Ascaris lumbricoides was the most prevalent helminth infection (0.91%; 95% CI: 0.33-1.97%). The prevalence of G. lamblia was 17.40%, with genotype B being the most common. According to our study, intestinal parasitic infections were commonly found in Thai children. G. lamblia was the most common pathogenic protozoa infection identified and exhibited less susceptibility to metronidazole compared to furazolidone and mebendazole.
Collapse
Affiliation(s)
| | - Thunyarat Anothaisintawee
- Department of Bacterial and Parasitic Diseases, US Army Medical Directorate of the Armed Forces Research Institute of Medical Sciences, Bangkok 10120, Thailand; (B.W.); (P.L.); (P.K.); (W.O.); (W.O.); (S.G.); (S.S.); (U.S.); (S.S.); (L.B.); (D.M.B.); (J.R.L.)
| | - Nattaya Ruamsap
- Department of Bacterial and Parasitic Diseases, US Army Medical Directorate of the Armed Forces Research Institute of Medical Sciences, Bangkok 10120, Thailand; (B.W.); (P.L.); (P.K.); (W.O.); (W.O.); (S.G.); (S.S.); (U.S.); (S.S.); (L.B.); (D.M.B.); (J.R.L.)
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
3
|
Mbareche H, Dion-Dupont V, Veillette M, Brisebois E, Lavoie J, Duchaine C. Influence of seasons and sites on bioaerosols in indoor wastewater treatment plants and proposal for air quality indicators. JOURNAL OF THE AIR & WASTE MANAGEMENT ASSOCIATION (1995) 2022; 72:1000-1011. [PMID: 35426760 DOI: 10.1080/10962247.2022.2066735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 04/07/2022] [Accepted: 04/07/2022] [Indexed: 06/14/2023]
Abstract
During wastewater treatment, bioaerosols are generated and, can either remain in suspension for several hours or settle on surfaces and workers may be exposed. The presence of pathogens in the air could contribute to an increased frequency of gastrointestinal or respiratory illness amongst workers. Due to harsh winter conditions in Eastern Canada, many of the steps in the wastewater treatment process occur indoors, leading to a greater risk of significant occupational exposure especially if there is inadequate ventilation or a lack of personal protection. This work has used stationary sampling at various indoor wastewater treatment steps both in winter and summer. Bioaerosols were evaluated using both culture and molecular methods along with ventilation characterization. Endotoxins were quantified, as well as total cultivable and gram-negative bacteria and pathogen indicators using qPCR. This study highlights the presence of potential pathogens at all steps in the treatment process, which may represent a potential occupational hazard. Comparisons between summer and winter data suggest that water temperature is an important factor for microbial activity and suggest that increasing the rate of air changes per hour in summer would be beneficial to reduce the concentration of bioaerosols during this time of the year. The screening, grit/FOGs removal and biofiltration were the most bioaerosol-loaded sites. Based on strong correlations, we suggest the reconsideration of exposure limits in WWTPs. Workers should be encouraged to use personal respiratory protection to limit the risk of health problems, especially during long-term work.Implications: The work presented herein showcases significant correlations between concentrations of endotoxins, cultivable bacteria, gram-negative bacteria, and total bacteria by qPCR from air collected in indoor wastewater treatment plants. These correlations lead us to propose new limit of exposure values, revisited to fit the endotoxin exposure limits recommendations. The results can serve as guidelines for future proposals for air quality indicators.
Collapse
Affiliation(s)
- Hamza Mbareche
- Biological Platform, Sunnybrook Research Institute, Toronto, ON Canada
- Laboratory of Medicine and Pathobiology, University of Toronto, Toronto, ON, USA
| | - Vanessa Dion-Dupont
- Pavillon Alexandre Vachon, Université Laval, Québec, QC Canada
- Axe de pneumologie, CRIUCPQ, Québec, QC Canada
| | | | - Evelyne Brisebois
- Pavillon Alexandre Vachon, Université Laval, Québec, QC Canada
- Axe de pneumologie, CRIUCPQ, Québec, QC Canada
| | - Jacques Lavoie
- Prévention des risques chimiques et biologiques, IRSST, Montréal, QC Canada
| | - Caroline Duchaine
- Pavillon Alexandre Vachon, Université Laval, Québec, QC Canada
- Axe de pneumologie, CRIUCPQ, Québec, QC Canada
| |
Collapse
|
4
|
Aziz A, Abbas MA, Siddique N, Shah A, Rahim A, Rafique S, Khan A, Midrarullah, Khan S, Rashid F, Hui Y, Suleman M. Development of multiplex PCR for rapid and simultaneous detection of E. coli (APEC), Salmonella, Mycoplasma gallisepticum and Mycoplasma Synoviae. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
|
5
|
Brum JM, Gibb RD, Ramsey DL, Balan G, Yacyshyn BR. Systematic Review and Meta-Analyses Assessment of the Clinical Efficacy of Bismuth Subsalicylate for Prevention and Treatment of Infectious Diarrhea. Dig Dis Sci 2021; 66:2323-2335. [PMID: 32772204 PMCID: PMC8236042 DOI: 10.1007/s10620-020-06509-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 07/21/2020] [Indexed: 12/09/2022]
Abstract
BACKGROUND A large number of studies have evaluated the pharmacology, safety, and/or efficacy of bismuth subsalicylate for the relief of common gastrointestinal symptoms, diarrhea and vomiting due to acute gastroenteritis. In addition, short-term (48 h) medication with bismuth subsalicylate is known to be effective against infectious gastroenteritis such as travelers' diarrhea. AIMS Previous studies have documented the bacteriostatic/bactericidal effects of bismuth subsalicylate against a variety of pathogenic gastrointestinal bacteria. However, meta-analyses of the clinical efficacy of bismuth subsalicylate for both prevention and treatment of travelers' diarrhea have not yet been published. METHODS A total of 14 clinical studies (from 1970s to 2007) comprised the core data used in this assessment of efficacy of bismuth subsalicylate against infectious (including travelers') diarrhea. These studies allowed for statistical meta-analyses regarding prevention (three travelers' diarrhea studies) and treatment of infectious diarrhea (11 studies [five travelers' diarrhea]). RESULTS The results show that subjects treated with bismuth subsalicylate for up to 21 days have 3.5 times greater odds of preventing travelers' diarrhea compared with placebo (95% CI 2.1, 5.9; p < 0.001). In addition, subjects with infectious diarrhea treated with bismuth subsalicylate had 3.7 times greater odds of diarrhea relief (recorded on diaries as subjective symptomatic improvement) compared to those receiving placebo (95% CI 2.1, 6.3; p < 0.001). CONCLUSIONS This systematic review and meta-analysis suggests that bismuth subsalicylate can be beneficial for those at risk or affected by food and waterborne diarrheal disease such as traveler's (infectious) diarrhea, and may decrease the risk of inappropriate antibiotic utilization.
Collapse
Affiliation(s)
- Jose M Brum
- Procter and Gamble Global Clinical Sciences, Health Care and Quantitative Sciences, 8700 Mason Montgomery Road, Mason, OH, 45040, USA
| | - Roger D Gibb
- Procter and Gamble Global Clinical Sciences, Health Care and Quantitative Sciences, 8700 Mason Montgomery Road, Mason, OH, 45040, USA
| | - David L Ramsey
- Procter and Gamble Global Clinical Sciences, Health Care and Quantitative Sciences, 8700 Mason Montgomery Road, Mason, OH, 45040, USA
| | - Guhan Balan
- Procter and Gamble Global Clinical Sciences, Health Care and Quantitative Sciences, 8700 Mason Montgomery Road, Mason, OH, 45040, USA
| | - Bruce R Yacyshyn
- Division of Gastroenterology, Hepatology and Nutrition, University of Louisville School of Medicine, Louisville, KY, 40292, USA.
| |
Collapse
|
6
|
An XL, Wang JY, Pu Q, Li H, Pan T, Li HQ, Pan FX, Su JQ. High-throughput diagnosis of human pathogens and fecal contamination in marine recreational water. ENVIRONMENTAL RESEARCH 2020; 190:109982. [PMID: 32745749 DOI: 10.1016/j.envres.2020.109982] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 07/17/2020] [Accepted: 07/18/2020] [Indexed: 06/11/2023]
Abstract
Waterborne pathogens and their associated diseases are major threats to public health, and surveillance of pathogens and identification of the sources of pollution are imperative for preventing infections. However, simultaneously quantitative detection of multiple pathogens and pollution sources in water environments is the major challenge. In this study, we developed and validated a highly sensitive (mostly >80%) and highly specific (>99%) high-throughput quantitative PCR (HT-qPCR) approach, which could simultaneously quantify 68 marker genes of 33 human pathogens and 23 fecal markers of 10 hosts. The HT-qPCR approach was then successfully used to investigate pathogens and fecal pollution in marine recreational water samples of Xiamen, China. Totally, seven pathogenic marker genes were found in 13 beach bathing waters, which targeted Acanthamoeba spp., Clostridium perfringens, enteropathogenic Escherichia coli, Klebsiella pneumoniae, Vibrio cholera/V. parahaemolyticus and Legionella spp.. Fecal markers from human and dog were the most frequently detected, indicating human and dog feces were the main contamination in the recreational waters. Nanopore sequencing of full-length 16S rRNA gene revealed that 28 potential human pathogens were detected and electrical conductivity, salinity, oxidation-reduction potential and dissolved oxygen were significantly correlated with the variation in bacterial community. Our results demonstrated that HT-qPCR approach had the potential rapid quantification of microbial contamination, providing useful data for assessment of microbial pathogen associated health risk and development of management practices to protect human health.
Collapse
Affiliation(s)
- Xin-Li An
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Jia-Ying Wang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiang Pu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hu Li
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Ting Pan
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huan-Qin Li
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; College of the Environmental & Ecology, Xiamen University, 361102, China
| | - Fu-Xia Pan
- Jinan Environmental Research Institute, Jinan, 250100, China
| | - Jian-Qiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China.
| |
Collapse
|
7
|
Zhang X, Das S, Dunbar S, Tang YW. Molecular and non-molecular approaches to etiologic diagnosis of gastroenteritis. Adv Clin Chem 2020; 99:49-85. [PMID: 32951639 DOI: 10.1016/bs.acc.2020.02.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Gastroenteritis is a major cause of mortality and morbidity globally and rapid identification of the causative pathogen is important for appropriate treatment and patient management, implementation of effective infection control measures, reducing hospital length of stay, and reducing overall medical costs. Although stool culture and microscopic examination of diarrheal stool has been the primary method for laboratory diagnosis, culture-independent proteomic and genomic tests are receiving increased attention. Antigen tests for stool pathogens are routinely implemented as rapid and simple analytics whereas molecular tests are now available in various formats from high complexity to waived point-of-care tests. In addition, metagenomic next-generation sequencing stands poised for use as a method for both diagnosis and routine characterization of the gut microbiome in the very near future. Analysis of host biomarkers as indicators of infection status and pathogenesis may also become important for prediction, diagnosis, and monitoring of gastrointestinal infection. Here we review current methods and emerging technologies for the etiologic diagnosis of gastroenteritis in the clinical laboratory. Benefits and limitations of these evolving methods are highlighted.
Collapse
Affiliation(s)
- Xin Zhang
- Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China; Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | | | | | - Yi-Wei Tang
- Memorial Sloan Kettering Cancer Center, New York, NY, United States; Weill Medical College of Cornell University, New York, NY, United States; Cepheid, Danaher Diagnostic Platform, Shanghai, China.
| |
Collapse
|
8
|
The application research of xTAG GPP multiplex PCR in the diagnosis of persistent and chronic diarrhea in children. BMC Pediatr 2020; 20:309. [PMID: 32590971 PMCID: PMC7318512 DOI: 10.1186/s12887-020-02206-6] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 06/15/2020] [Indexed: 12/22/2022] Open
Abstract
Background Persistent and chronic diarrhea is difficult to treat, and infection is still the main cause. In this study, we investigate the application value of xTAG gastrointestinal pathogen panel (xTAG GPP) multiplex PCR in the early diagnosis of persistent and chronic diarrhea in children and to understand the epidemiology of intestinal diarrhea pathogens. Methods One hundred ninety-nine specimens were collected from Nanjing Children’s Hospital Affiliated to Nanjing Medical University (Nanjing, China). We compared the xTAG GPP multiplex PCR assay with traditional methods (culture, rapid enzyme immunoassay chromatography, and microscopic examination) and performed a statistical analysis. Results The positive rate of the xTAG GPP multiplex PCR assay of diarrhea specimens from 199 patients was 72.86% (145/199). The virus detection rate was 48.7%, and rotavirus A was the most common organism detected (34.67%), concentrated in winter, and was common in children. The second most common organism detected was norovirus GI/GII (20.6%). The positive rate of this bacteria was 40.2%, and Campylobacter (22.11%, 44/199) was most frequently detected. C. difficile toxins A/B and Salmonella was detected in 44 and 17 samples, respectively. Infections with Shigella occurred 4 times, and E. coli O157 was only detected once. Three samples were parasitic (1.51%), two samples were positive for Entamoeba histolytica, and one was positive for Cryptosporidium. Adenovirus 40/41, STEC, ETEC, Giardia, Yersinia enterocolitica and Vibrio cholerae were not detected. In total, 86 (43.2%) infected specimens with a single pathogen were detected. There were 59 coinfections (29.65% of the samples) of viruses and/or bacteria and/or parasites. Coinfections involved 49 double infections (24.62%), 9 triple infections (4.52%) and 1 quadruple infections (0.5%). Norovirus GI/GII was found to have the highest involvement, with 32 coinfections (16.08%). Conclusion The xTAG GPP multiplex PCR assay is simple, sensitive, and specific and can be used as a quick way to diagnose persistent and chronic diarrhea in children.
Collapse
|
9
|
Siciliano V, Nista EC, Rosà T, Brigida M, Franceschi F. Clinical Management of Infectious Diarrhea. Rev Recent Clin Trials 2020; 15:298-308. [PMID: 32598272 DOI: 10.2174/1574887115666200628144128] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 05/05/2020] [Accepted: 05/11/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Infectious diarrhea is the most common cause of diarrhea worldwide and is responsible for more deaths than other gastrointestinal tract diseases such as gastrointestinal cancers, peptic ulcer disease or inflammatory bowel disease. Diarrheal disease still represents the 8th leading cause of death worldwide, with more than 1,6 million attributed fatalities in 2016 alone. The majority of cases can be divided into three principal clinical presentations: acute watery diarrhea lasting 5-10 days and normally self-limiting, bloody diarrhea (dysentery), and persistent diarrhea with or without intestinal malabsorption. METHODS We performed an electronic search on PUBMED of the scientific literature concerning infectious diarrhea and its clinical management. AIM In this review article, we analyze the most important causes of infectious diarrhea and their constellation of signs and symptoms, providing an update on the diagnostic tools available in today's practice and on the different treatment options. CONCLUSION Even though the majority of intestinal infections are self-limiting in immunocompetent individuals, specific diagnosis and identification of the causative agent remain crucial from public health and epidemiological perspectives. Specific diagnostic investigation can be reserved for patients with severe dehydration, more severe illness, persistent fever, bloody stools, immunosuppression, and for cases of suspected nosocomial infection or outbreak and it includes complete blood count, creatinine and electrolytes evaluation, determination of leukocytes and lactoferrin presence in the stools, stool culture, together with C. difficile testing, PCR, ova and parasites' search, endoscopy and abdominal imaging. Since acute diarrhea is most often self-limited and caused by viruses, routine antibiotic use is not recommended for most adults with mild, watery diarrhea. However, when used appropriately, antibiotics are effective against shigellosis, campylobacteriosis, C. difficile colitis, traveler's diarrhea, and protozoal infections. Furthermore, antibiotics use should be considered in patients who are older than 65 years, immunocompromised, severely ill, or septic.
Collapse
Affiliation(s)
| | | | - Tommaso Rosà
- Universita Cattolica del Sacro Cuore - Rome, Italy
| | | | | |
Collapse
|
10
|
de Castro Carvalho SV, Rogovski P, Cadamuro RD, Viancelli A, Michelon W, Dos Reis DA, Santana das Chagas IA, Assenço R, da Silva Lanna MC, Treichel H, Fongaro G. Co-contamination of food products from family farms in an environmental disaster area in Southeast Brazil with pathogenic bacteria and enteric viruses. Arch Virol 2019; 165:715-718. [PMID: 31873766 DOI: 10.1007/s00705-019-04501-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 11/12/2019] [Indexed: 12/25/2022]
Abstract
In the present study, we evaluated the degree of contamination of fresh vegetables, cheeses and jellies from disaster area in Brazil with bacteria and enteric viruses. Food samples (n = 350) were tested for Escherichia coli, Salmonella spp., Listeria monocytogenes, Staphylococcus spp., and enteric viruses (rotavirus A (RVA), human adenovirus (HAdV), hepatitis A virus (HAV), and human norovirus (HNoV). E. coli was present in 56% of the samples, Salmonella spp. was present in 14% of the samples, L. monocytogenes and Staphylococcus spp. (coagulase-positive) were present in 36% of the samples. The enteric viruses RVA and HAdV were detected in cheeses and vegetables.
Collapse
Affiliation(s)
| | - Paula Rogovski
- Applied Virology Laboratory, Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Rafael Dorighello Cadamuro
- Applied Virology Laboratory, Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil
| | - Aline Viancelli
- University of Contestado, PMPECSA-UnC, Concórdia, Santa Catarina, Brazil
| | - William Michelon
- University of Contestado, PMPECSA-UnC, Concórdia, Santa Catarina, Brazil
| | | | | | - Regiana Assenço
- Federal University of Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| | | | - Helen Treichel
- Federal University of Fronteira Sul, Erechim, Rio Grande do Sul, Brazil
| | - Gislaine Fongaro
- Applied Virology Laboratory, Federal University of Santa Catarina, Florianópolis, Santa Catarina, Brazil.
| |
Collapse
|
11
|
Abstract
The clinical presentation of brucellosis in humans is variable and unspecific, and thus, laboratory corroboration of the diagnosis is essential for the patient's proper treatment. The diagnosis of brucellar infections can be made by culture, serological tests, and nucleic acid amplification assays. Modern automated blood culture systems enable detection of acute cases of brucellosis within the routine 5- to 7-day incubation protocol employed in clinical microbiology laboratories, although a longer incubation and performance of blind subcultures may be needed for protracted cases. Serological tests, though they lack specificity and provide results that may be difficult to interpret in individuals repeatedly exposed to Brucella organisms, nevertheless remain a diagnostic cornerstone in resource-poor countries. Nucleic acid amplification assays combine exquisite sensitivity, specificity, and safety and enable rapid diagnosis of the disease. However, long-term persistence of positive molecular test results in patients that have apparently fully recovered is common and has unclear clinical significance and therapeutic implications. Therefore, as long as there are no sufficiently validated commercial tests or studies that demonstrate an adequate interlaboratory reproducibility of the different homemade PCR assays, cultures and serological methods will remain the primary tools for the diagnosis and posttherapeutic follow-up of human brucellosis.
Collapse
Affiliation(s)
- Pablo Yagupsky
- Clinical Microbiology Laboratory, Soroka University Medical Center, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Pilar Morata
- Biochemistry and Molecular Biology Department, Faculty of Medicine, University of Málaga, Málaga, Spain
- IBIMA, Málaga, Spain
| | - Juan D Colmenero
- Infectious Diseases Service, University Regional Hospital, Málaga, Spain
- IBIMA, Málaga, Spain
| |
Collapse
|
12
|
Charlermroj R, Makornwattana M, Phuengwas S, Meerak J, Pichpol D, Karoonuthaisiri N. DNA-based bead array technology for simultaneous identification of eleven foodborne pathogens in chicken meat. Food Control 2019. [DOI: 10.1016/j.foodcont.2019.02.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
|
13
|
Kumar SS, Ghosh AR. Assessment of bacterial viability: a comprehensive review on recent advances and challenges. Microbiology (Reading) 2019; 165:593-610. [DOI: 10.1099/mic.0.000786] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Shravanthi S. Kumar
- Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore-632014, Tamil Nadu, India
| | - Asit Ranjan Ghosh
- Department of Integrative Biology, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore-632014, Tamil Nadu, India
| |
Collapse
|
14
|
Maruoka H, Hinenoya A, Yasuda N, Takeda A, Inoue S, Sumi T, Koitabashi K, Yasue H, Kogou K, Yamasaki S. Evaluation of the GeneFields® EHEC/SS PCR dipstick DNA chromatography kit for the detection of enteric bacterial pathogens in stool specimens of healthy humans. J Microbiol Methods 2019; 161:111-117. [PMID: 31054865 DOI: 10.1016/j.mimet.2019.04.016] [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: 03/05/2019] [Revised: 04/21/2019] [Accepted: 04/22/2019] [Indexed: 11/29/2022]
Abstract
We developed a new GeneFields® EHEC/SS PCR dipstick DNA chromatography kit for the simultaneously detection of invA, ipaH, and stx genes in Salmonella enterica (56 strains), Shigella spp. (44), and enterohemorrhagic Escherichia coli (EHEC) (28), respectively, and evaluated the sensitivity and specificity with other bacteria (57) by this kit. The sensitivity and specificity were 100%, respectively. The detection limit of various methods was determined using 5% (w/v) stool suspensions spiked with each bacterium. The detection limit of the GeneFields® EHEC/SS kit ranged from approximately 102-103 CFU/g. Additionally, the relative sensitivities and specificities of the GeneFields® EHEC/SS kit vs two commercially available real-time PCR kits were >85.0% and >90.0%, respectively. These results indicate that the GeneFields® EHEC/SS kit can be used for genetic screening of S. enterica, Shigella spp., and EHEC in human stool specimens with sensitivities and specificities similar to those of the commercially available real-time PCR kits.
Collapse
Affiliation(s)
- Hiroki Maruoka
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano-shi, Osaka, Japan; Technical Research Laboratory, KURABO INDUSTRIES LTD., Neyagawa, Osaka, Japan
| | - Atsushi Hinenoya
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano-shi, Osaka, Japan
| | - Noritomo Yasuda
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano-shi, Osaka, Japan
| | - Atsuyoshi Takeda
- TOHO Biological Laboratories Co., Ltd., Osaka, Naniwa-ku, Osaka, Japan
| | - Shin Inoue
- TOHO Biological Laboratories Co., Ltd., Osaka, Naniwa-ku, Osaka, Japan
| | - Tomoko Sumi
- Japan Institute of Foods Ecology, Inc., Kobe, Hyogo, Japan
| | | | - Hiroshi Yasue
- Tsukuba GeneTechnology Laboratories Inc., Tsuchiura, Ibaraki, Japan
| | - Kazuhiko Kogou
- Bio-Medical Department, Advanced Technology Division, KURABO INDUSTRIES LTD., Neyagawa, Osaka, Japan
| | - Shinji Yamasaki
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano-shi, Osaka, Japan.
| |
Collapse
|
15
|
Zhao C, Wang X, Zhang C, Liu B, Jing H, Ming L, Jiang H, Zheng Y, Liu P, Liu G, Jiang Y. Development of a TaqMan Array card to target 21 purulent meningitis-related pathogens. BMC Infect Dis 2019; 19:289. [PMID: 30922257 PMCID: PMC6438039 DOI: 10.1186/s12879-019-3856-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 02/27/2019] [Indexed: 02/08/2023] Open
Abstract
Background Purulent meningitis (PM) is a serious life-threatening infection of the central nervous system (CNS) by bacteria or fungi and associated with high mortality and high incidence of CNS sequelae in children. However, the conventional cerebrospinal fluid (CSF) culture method is time-consuming and has a low sensitivity. Methods Our study developed a real-time PCR-based purulent meningitis-TaqMan array card (PM-TAC) that targeted 21 PM-related pathogens and could produce results within 3 h. Primers and probes were adapted from published sources possibly. The performance of them were evaluated and optimized and then they were spotted on TAC. Results The PM-TAC showed a sensitivity and specificity of 95 and 96%, respectively. For all of the 21 targeted pathogens, the PM-TAC assay had a LOD ranging from 5 copies/reaction to 100 copies/reaction, an intra-assay variation of 0.07–4.45%, and an inter-assay variation of 0.11–6.81%. Of the 15 CSF samples collected from patients with PM after empiric antibiotic therapies, the positive rate was 53.3% (8/15) for our PM-TAC assay but was only 13.3% (2/15) for the CSF culture method. Of the 17 CSF samples showing negative CSF culture, the PM-TAC assay identified a case of Neisseria meningitidis infection. Furthermore, all of the 10 CSF samples from patients without CNS infection showed negative for the PM-TAC assay. Conclusions Our PM-TAC assay also demonstrated that the pathogen loads in the CSF samples correlated with the severity of PM. Thus, the PM-TAC may be helpful to improve the prognosis of PM and clinical outcomes from antibiotic therapies. Electronic supplementary material The online version of this article (10.1186/s12879-019-3856-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Chengna Zhao
- Anhui Medical University, Hefei, China.,State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xi Wang
- Department of Infectious Medicine, Beijing Children's Hospital, Capital Medical University, National Center for Chidren's Health, Beijing, China
| | - Chao Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Bing Liu
- Department of Infectious Medicine, Beijing Children's Hospital, Capital Medical University, National Center for Chidren's Health, Beijing, China
| | - Hongbo Jing
- Shunyi District Center for Disease Control and Prevention, Beijing, China
| | - Lihua Ming
- Chest Hospital of Xinjiang, Urumqi, China
| | - Hua Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Yuling Zheng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Peng Liu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.
| | - Gang Liu
- Department of Infectious Medicine, Beijing Children's Hospital, Capital Medical University, National Center for Chidren's Health, Beijing, China.
| | - Yongqiang Jiang
- Anhui Medical University, Hefei, China. .,State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.
| |
Collapse
|
16
|
Virulence-Related Genes and Coenteropathogens Associated with Clinical Outcomes of Enteropathogenic Escherichia coli Infections in Children from the Brazilian Semiarid Region: a Case-Control Study of Diarrhea. J Clin Microbiol 2019; 57:JCM.01777-18. [PMID: 30728193 DOI: 10.1128/jcm.01777-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 01/26/2019] [Indexed: 12/26/2022] Open
Abstract
Enteropathogenic Escherichia coli (EPEC) is a major cause of diarrhea in children from developing countries and presents high genetic variability. We aimed to characterize the EPEC virulence-related gene (VRG) distribution and copathogens associated with diarrhea and nutrition-related outcomes in children from the low-income Brazilian semiarid region. A cross-sectional case-control study of diarrhea was conducted in 1,191 children aged 2 to 36 months from the northeast region of Brazil. Stool samples were collected and clinical, epidemiological, and anthropometric data were identified from each child. A broad molecular evaluation of enteropathogens was performed, and EPEC-positive samples were further investigated for 18 VRGs using five multiplex PCRs. EPEC was detected in 28.2% of the study population, with similar proportions among cases and controls. Typical EPEC (tEPEC) infections were more often associated with diarrhea than atypical EPEC (aEPEC) infections, while aEPEC infections presented a higher prevalence. The VRG ler, a negative regulator of the locus of enterocyte effacement, was associated with the absence of diarrhea in aEPEC-positive children; espB, a major component of the type 3 secretion system, was associated with diarrhea in tEPEC-positive children; the presence of procolonization VRGs-the combination of cesT positivity, espP negativity, and the presence of the map gene-was associated with undernutrition; and Campylobacter spp., norovirus, and enteroaggregative E. coli (EAEC) coinfections were associated with increased clinical severity in EPEC-infected children. These data identified tEPEC strains associated with diarrhea and specific VRGs of EPEC (ler, espB, cesT, and map genes) and Campylobacter spp., norovirus, and EAEC to be major contributors to diarrhea and undernutrition in children from a low-income Brazilian region.
Collapse
|
17
|
Genetic Diversity of Norovirus Infections, Coinfections, and Undernutrition in Children From Brazilian Semiarid Region. J Pediatr Gastroenterol Nutr 2018; 67:e117-e122. [PMID: 29985875 DOI: 10.1097/mpg.0000000000002085] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
BACKGROUND AND OBJECTIVE Norovirus (NoV) infections are known to have high-morbidity and mortality rates and are a major health problem globally. The impact of NoV on child development is, however, poorly understood. We evaluated the distribution of NoV genotypes in children from a low-income Brazilian semiarid region, in relation with their clinical symptoms, nutritional status, and co-pathogens. METHODS The test population included children aged 2 to 36 months from 6 cities of the Brazilian semiarid region. Fecal samples were collected from each child, along with the information regarding their socioeconomic/clinical conditions using a standardized questionnaire. Detection and quantification of NoV were performed by reverse-transcription quantitative polymerase chain reaction, followed by molecular and phylogenetic analyses. RESULTS The NoV detection rate was 45.2%. Presence of NoV was associated with lower z scores for weight-for-age (P = 0.03), weight-for-height (P = 0.03), and body mass index-for-age (P = 0.03). NoV infection was associated with more frequent respiratory illnesses (P < 0.01). GII.P7 (polymerase) and GII.3 (capsid) were the most frequent NoV genotypes. Analysis of the open reading frame (ORF)1-2 junction identified recombinant NoV strains in 80% of the sequenced samples. Enteroaggregative Escherichia coli coinfection was the major predictor for diarrhea in NoV-positive samples (P < 0.02). Moreover, Shigella spp was also associated with NoV-positive diagnosis (P = 0.02). CONCLUSIONS This study highlights the genetic variability of NoV and, associated co-infections and undernutrition in infants from low-income Brazilian semiarid region.
Collapse
|
18
|
Zhang Q, Ishii S. Improved simultaneous quantification of multiple waterborne pathogens and fecal indicator bacteria with the use of a sample process control. WATER RESEARCH 2018; 137:193-200. [PMID: 29550722 DOI: 10.1016/j.watres.2018.03.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 02/26/2018] [Accepted: 03/09/2018] [Indexed: 05/23/2023]
Abstract
Quantitative polymerase chain reaction (qPCR) is now commonly used to detect fecal indicator bacteria (FIB) as well as pathogens in water samples. However, DNA loss during sample processing can cause underestimation of target genes. In this study, we created a sample process control strain (SPC) by genetically engineering a non-pathogenic, Gram-negative bacterium Pseudogulbenkiania sp. strain NH8B. The SPC strain, named NH8B-1D2, has a kanamycin-resistance gene inserted to one of the 23S rRNA genes. To specifically quantify the SPC strain, a new TaqMan qPCR assay was developed. To obtain the relationship between the DNA recovery efficiencies of various pathogens and those of the SPC strain, known amount of E. coli O157:H7, Salmonella Typhimurium, Campylobacter jejuni, or Listeria monocytogenes cells were co-spiked with the SPC strain to environmental water samples. The DNA recovery efficiencies were calculated by comparing the quantity of bacterial cells inoculated to water samples prior to filtration and DNA extraction, and those measured by qPCR. We then obtained the ratios in the recovery efficiencies between pathogens and SPC strain (RRPATH/SPC). The RRPATH/SPC values obtained using Oono pond water collected in Japan were used as a pathogen-specific constant to estimate the accurate concentrations of pathogens in water samples collected from Mississippi River in Minnesota. Estimated pathogen concentrations were not significantly different from the inoculated pathogen concentration, suggesting our normalization approach is useful to estimate the accurate concentrations of pathogens in environmental water samples. The qPCR assay targeting the SPC strains and FIB were incorporated into the microfluidic qPCR chip format (PBQ chip ver. 2); therefore, we can simultaneously quantify multiple pathogens, FIB, and the SPC strain in high throughput from many water samples. This new tool can be useful for water quality monitoring and risk assessment.
Collapse
Affiliation(s)
- Qian Zhang
- BioTechnology Institute, University of Minnesota, St. Paul, MN, United States
| | - Satoshi Ishii
- BioTechnology Institute, University of Minnesota, St. Paul, MN, United States; Department of Soil, Water, and Climate, University of Minnesota, St. Paul, MN, United States; Division of Environmental Engineering, Hokkaido University, Sapporo, Hokkaido, Japan.
| |
Collapse
|
19
|
Aydin M, Carter-Conger J, Gao N, Gilmore DF, Ricke SC, Ahn S. Molecular identification of common Salmonella serovars using multiplex DNA sensor-based suspension array. Anal Bioanal Chem 2018; 410:2637-2646. [DOI: 10.1007/s00216-018-0938-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 01/25/2018] [Accepted: 02/02/2018] [Indexed: 12/15/2022]
|
20
|
Lee K, Kim DS, Chong MS. Multiplex PCR Based Epidemiological Study for the Causes of Acute Diarrheal Disease in Adults Living in Jeju Island. ANNALS OF CLINICAL MICROBIOLOGY 2018. [DOI: 10.5145/acm.2018.21.1.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Kyutaeg Lee
- Department of Laboratory Medicine, Cheju Halla General Hospital, Jeju, Korea
| | - Dae Soon Kim
- Infection Control Service Team, Cheju Halla General Hospital, Jeju, Korea
| | - Moo Sang Chong
- Department of Clinical Pathology, Cheju Halla University, Jeju, Korea
| |
Collapse
|
21
|
A diagnostic and epidemiologic investigation of acute febrile illness (AFI) in Kilombero, Tanzania. PLoS One 2017; 12:e0189712. [PMID: 29287070 PMCID: PMC5747442 DOI: 10.1371/journal.pone.0189712] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 11/30/2017] [Indexed: 12/20/2022] Open
Abstract
Introduction In low-resource settings, empiric case management of febrile illness is routine as a result of limited access to laboratory diagnostics. The use of comprehensive fever syndromic surveillance, with enhanced clinical microbiology, advanced diagnostics and more robust epidemiologic investigation, could enable healthcare providers to offer a differential diagnosis of fever syndrome and more appropriate care and treatment. Methods We conducted a year-long exploratory study of fever syndrome among patients ≥ 1 year if age, presenting to clinical settings with an axillary temperature of ≥37.5°C and symptomatic onset of ≤5 days. Blood and naso-pharyngeal/oral-pharyngeal (NP/OP) specimens were collected and analyzed, respectively, using AFI and respiratory TaqMan Array Cards (TAC) for multi-pathogen detection of 57 potential causative agents. Furthermore, we examined numerous epidemiologic correlates of febrile illness, and conducted demographic, clinical, and behavioral domain-specific multivariate regression to statistically establish associations with agent detection. Results From 15 September 2014–13 September 2015, 1007 febrile patients were enrolled, and 997 contributed an epidemiologic survey, including: 14% (n = 139) 1<5yrs, 19% (n = 186) 5-14yrs, and 67% (n = 672) ≥15yrs. AFI TAC and respiratory TAC were performed on 842 whole blood specimens and 385 NP/OP specimens, respectively. Of the 57 agents surveyed, Plasmodium was the most common agent detected. AFI TAC detected nucleic acid for one or more of seven microbial agents in 49% of AFI blood samples, including: Plasmodium (47%), Leptospira (3%), Bartonella (1%), Salmonella enterica (1%), Coxiella burnetii (1%), Rickettsia (1%), and West Nile virus (1%). Respiratory TAC detected nucleic acid for 24 different microbial agents, including 12 viruses and 12 bacteria. The most common agents detected among our surveyed population were: Haemophilus influenzae (67%), Streptococcus pneumoniae (55%), Moraxella catarrhalis (39%), Staphylococcus aureus (37%), Pseudomonas aeruginosa (36%), Human Rhinovirus (25%), influenza A (24%), Klebsiella pneumoniae (14%), Enterovirus (15%) and group A Streptococcus (12%). Our epidemiologic investigation demonstrated both age and symptomatic presentation to be associated with a number of detected agents, including, but not limited to, influenza A and Plasmodium. Linear regression of fully-adjusted mean cycle threshold (Ct) values for Plasmodium also identified statistically significant lower mean Ct values for older children (20.8), patients presenting with severe fever (21.1) and headache (21.5), as well as patients admitted for in-patient care and treatment (22.4). Conclusions This study is the first to employ two syndromic TaqMan Array Cards for the simultaneous survey of 57 different organisms to better characterize the type and prevalence of detected agents among febrile patients. Additionally, we provide an analysis of the association between adjusted mean Ct values for Plasmodium and key clinical and demographic variables, which may further inform clinical decision-making based upon intensity of infection, as observed across endemic settings of sub-Saharan Africa.
Collapse
|
22
|
Hosangadi D, Smith PG, Giersing BK. Considerations for using ETEC and Shigella disease burden estimates to guide vaccine development strategy. Vaccine 2017; 37:7372-7380. [PMID: 29031690 PMCID: PMC6892262 DOI: 10.1016/j.vaccine.2017.09.083] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 09/26/2017] [Indexed: 01/09/2023]
Abstract
Enterotoxigenic E. coli (ETEC) and Shigella are enteropathogens causing significant global morbidity and mortality, particularly in low-income countries. No licensed vaccine exists for either pathogen, but candidates are in development, with the most advanced candidates potentially approaching pivotal efficacy testing within the next few years. A positive policy recommendation for introduction of any vaccine, following licensure, depends on evidence of vaccine cost-effectiveness and impact on morbidity and mortality. The mortality estimates for these two pathogens have fluctuated over recent years, which has led to uncertainty in the assessment of their relative public health importance for use in low and middle-income countries. This paper summarizes the various ETEC and Shigella disease burden estimates, based on a review of current literature and informal consultations with leading stakeholders in enteric disease modelling. We discuss the factors that underpin the variability, including differences in the modelling methodology; diagnostic tools used to ascertain diarrheal etiology; epidemiological setting; the data that are available to incorporate; and absolute changes in the total number of diarrheal deaths over time. We consider the further work that will strengthen the evidence needed to support future decision making with respect to recommendations on the relative utility of these vaccines.
Collapse
Affiliation(s)
- Divya Hosangadi
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Peter G Smith
- MRC Tropical Epidemiology Group, London School of Hygiene & Tropical Medicine, London, UK
| | - Birgitte K Giersing
- Initiative for Vaccine Research, World Health Organization, CH-1211 Geneva 27, Switzerland.
| |
Collapse
|
23
|
Shang Y, Xu W, Wang Y, Xu Y, Huang K. Novel multiplex qualitative detection using universal primer-multiplex-PCR combined with pyrosequencing. Food Chem 2017; 237:773-778. [PMID: 28764066 DOI: 10.1016/j.foodchem.2017.05.068] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Revised: 05/04/2017] [Accepted: 05/14/2017] [Indexed: 11/19/2022]
Abstract
This study described a novel multiplex qualitative detection method using pyrosequencing. Based on the principle of the universal primer-multiplex-PCR, only one sequencing primer was employed to realize the detection of the multiple targets. Samples containing three genetically modified (GM) crops in different proportions were used to validate the method. The dNTP dispensing order was designed based on the product sequences. Only 12 rounds (ATCTGATCGACT) of dNTPs addition and, often, as few as three rounds (CAT) under ideal conditions, were required to detect the GM events qualitatively, and sensitivity was as low as 1% of a mixture. However, when considering a mixture, calculating signal values allowed the proportion of each GM to be estimated. Based on these results, we concluded that our novel method not only realized detection but also allowed semi-quantitative detection of individual events.
Collapse
Affiliation(s)
- Ying Shang
- Yunnan Institute of Food Safety, Kunming University of Science and Technology, Kunming, Yunnan 650500, China; Laboratory of Food Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Wentao Xu
- Laboratory of Food Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; The Supervision, Inspection and Testing Center of Genetically Modified Organisms, Ministry of Agriculture, Beijing 100083, China
| | - Yong Wang
- Tianjing Institute of Agricultural Quality Standard and Testing Technology, Tianjing Academy of Agricultural Sciences, Tianjin, 300192, China
| | - Yuancong Xu
- Laboratory of Food Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Kunlun Huang
- Laboratory of Food Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; The Supervision, Inspection and Testing Center of Genetically Modified Organisms, Ministry of Agriculture, Beijing 100083, China.
| |
Collapse
|
24
|
Evaluating next-generation sequencing for direct clinical diagnostics in diarrhoeal disease. Eur J Clin Microbiol Infect Dis 2017; 36:1325-1338. [PMID: 28285331 PMCID: PMC5495851 DOI: 10.1007/s10096-017-2947-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 02/21/2017] [Indexed: 02/07/2023]
Abstract
The accurate microbiological diagnosis of diarrhoea involves numerous laboratory tests and, often, the pathogen is not identified in time to guide clinical management. With next-generation sequencing (NGS) becoming cheaper, it has huge potential in routine diagnostics. The aim of this study was to evaluate the potential of NGS-based diagnostics through direct sequencing of faecal samples. Fifty-eight clinical faecal samples were obtained from patients with diarrhoea as part of the routine diagnostics at Hvidovre University Hospital, Denmark. Ten samples from healthy individuals were also included. DNA was extracted from faecal samples and sequenced on the Illumina MiSeq system. Species distribution was determined with MGmapper and NGS-based diagnostic prediction was performed based on the relative abundance of pathogenic bacteria and Giardia and detection of pathogen-specific virulence genes. NGS-based diagnostic results were compared to conventional findings for 55 of the diarrhoeal samples; 38 conventionally positive for bacterial pathogens, two positive for Giardia, four positive for virus and 11 conventionally negative. The NGS-based approach enabled detection of the same bacterial pathogens as the classical approach in 34 of the 38 conventionally positive bacterial samples and predicted the responsible pathogens in five of the 11 conventionally negative samples. Overall, the NGS-based approach enabled pathogen detection comparable to conventional diagnostics and the approach has potential to be extended for the detection of all pathogens. At present, however, this approach is too expensive and time-consuming for routine diagnostics.
Collapse
|
25
|
Reslova N, Michna V, Kasny M, Mikel P, Kralik P. xMAP Technology: Applications in Detection of Pathogens. Front Microbiol 2017; 8:55. [PMID: 28179899 PMCID: PMC5263158 DOI: 10.3389/fmicb.2017.00055] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 01/09/2017] [Indexed: 12/14/2022] Open
Abstract
xMAP technology is applicable for high-throughput, multiplex and simultaneous detection of different analytes within a single complex sample. xMAP multiplex assays are currently available in various nucleic acid and immunoassay formats, enabling simultaneous detection and typing of pathogenic viruses, bacteria, parasites and fungi and also antigen or antibody interception. As an open architecture platform, the xMAP technology is beneficial to end users and therefore it is used in various pharmaceutical, clinical and research laboratories. The main aim of this review is to summarize the latest findings and applications in the field of pathogen detection using microsphere-based multiplex assays.
Collapse
Affiliation(s)
- Nikol Reslova
- Department of Food and Feed Safety, Veterinary Research InstituteBrno, Czechia; Department of Botany and Zoology, Faculty of Science, Masaryk UniversityBrno, Czechia
| | - Veronika Michna
- Department of Food and Feed Safety, Veterinary Research InstituteBrno, Czechia; Department of Experimental Biology, Faculty of Science, Masaryk UniversityBrno, Czechia
| | - Martin Kasny
- Department of Botany and Zoology, Faculty of Science, Masaryk University Brno, Czechia
| | - Pavel Mikel
- Department of Food and Feed Safety, Veterinary Research InstituteBrno, Czechia; Department of Experimental Biology, Faculty of Science, Masaryk UniversityBrno, Czechia
| | - Petr Kralik
- Department of Food and Feed Safety, Veterinary Research Institute Brno, Czechia
| |
Collapse
|
26
|
Taniuchi M, Platts-Mills JA, Begum S, Uddin MJ, Sobuz SU, Liu J, Kirkpatrick BD, Colgate ER, Carmolli MP, Dickson DM, Nayak U, Haque R, Petri WA, Houpt ER. Impact of enterovirus and other enteric pathogens on oral polio and rotavirus vaccine performance in Bangladeshi infants. Vaccine 2016; 34:3068-3075. [PMID: 27154394 PMCID: PMC4912219 DOI: 10.1016/j.vaccine.2016.04.080] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Revised: 04/21/2016] [Accepted: 04/26/2016] [Indexed: 01/19/2023]
Abstract
BACKGROUND Oral polio vaccine (OPV) and rotavirus vaccine (RV) exhibit poorer performance in low-income settings compared to high-income settings. Prior studies have suggested an inhibitory effect of concurrent non-polio enterovirus (NPEV) infection, but the impact of other enteric infections has not been comprehensively evaluated. METHODS In urban Bangladesh, we tested stools for a broad range of enteric viruses, bacteria, parasites, and fungi by quantitative PCR from infants at weeks 6 and 10 of life, coincident with the first OPV and RV administration respectively, and examined the association between enteropathogen quantity and subsequent OPV serum neutralizing titers, serum rotavirus IgA, and rotavirus diarrhea. RESULTS Campylobacter and enterovirus (EV) quantity at the time of administration of the first dose of OPV was associated with lower OPV1-2 serum neutralizing titers, while enterovirus quantity was also associated with diminished rotavirus IgA (-0.08 change in log titer per tenfold increase in quantity; P=0.037), failure to seroconvert (OR 0.78, 95% CI: 0.64-0.96; P=0.022), and breakthrough rotavirus diarrhea (OR 1.34, 95% CI: 1.05-1.71; P=0.020) after adjusting for potential confounders. These associations were not observed for Sabin strain poliovirus quantity. CONCLUSION In this broad survey of enteropathogens and oral vaccine performance we find a particular association between EV carriage, particularly NPEV, and OPV immunogenicity and RV protection. Strategies to reduce EV infections may improve oral vaccine responses. ClinicalTrials.gov Identifier: NCT01375647.
Collapse
Affiliation(s)
- Mami Taniuchi
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville 22908, USA.
| | - James A Platts-Mills
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville 22908, USA
| | - Sharmin Begum
- Center for Vaccine Science and Parasitology Lab, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka 1212, Bangladesh
| | - Md Jashim Uddin
- Center for Vaccine Science and Parasitology Lab, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka 1212, Bangladesh
| | - Shihab U Sobuz
- Center for Vaccine Science and Parasitology Lab, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka 1212, Bangladesh
| | - Jie Liu
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville 22908, USA
| | - Beth D Kirkpatrick
- Vaccine Testing Center and Unit of Infectious Diseases, Department of Medicine, University of Vermont College of Medicine, Burlington, VT 05405, USA
| | - E Ross Colgate
- Vaccine Testing Center and Unit of Infectious Diseases, Department of Medicine, University of Vermont College of Medicine, Burlington, VT 05405, USA
| | - Marya P Carmolli
- Vaccine Testing Center and Unit of Infectious Diseases, Department of Medicine, University of Vermont College of Medicine, Burlington, VT 05405, USA
| | - Dorothy M Dickson
- Vaccine Testing Center and Unit of Infectious Diseases, Department of Medicine, University of Vermont College of Medicine, Burlington, VT 05405, USA
| | - Uma Nayak
- Center for Public Health Genomics, University of Virginia, Charlottesville 22908, USA
| | - Rashidul Haque
- Center for Vaccine Science and Parasitology Lab, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka 1212, Bangladesh
| | - William A Petri
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville 22908, USA
| | - Eric R Houpt
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville 22908, USA
| |
Collapse
|
27
|
Evaluation of the Luminex xTAG ®-GPP (Gastrointestinal Pathogen Panel) in the diagnosis of diseases with acute diarrhoea. Enferm Infecc Microbiol Clin 2016; 35:574-577. [PMID: 27059749 DOI: 10.1016/j.eimc.2016.02.022] [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: 10/23/2015] [Revised: 02/22/2016] [Accepted: 02/23/2016] [Indexed: 11/23/2022]
Abstract
INTRODUCTION Most Microbiology laboratories use different techniques for the diagnosis of gastrointestinal infections. Some of which require at least 72 hours to obtain final results. MATERIAL AND METHODS The gastrointestinal panel Luminex (xTAG-GPP, Luminex Molecular Diagnostics, Toronto, Canada) is a qualitative multiplex fast and sensitive assay able to detect and to identify the 15 most common pathogens causing gastrointestinal infection simultaneously. We evaluated this multiplex panel comparing it with conventional methods used in our laboratory. RESULTS We analyzed 225 samples of feces. Through the conventional methods were positive 74 samples (32.9%). Through the Luminex method were positive 137 samples (60.9%). CONCLUSIONS The use of the xTAG® GPP system in Clinical Microbiology can improve the diagnosis of gastrointestinal infectious because it provides results in less than 8 hours. Some pathogens should be applied with caution and should be interpreted based on the patient́s clinical data.
Collapse
|
28
|
Zhang C, Niu P, Hong Y, Wang J, Zhang J, Ma X. A probe-free four-tube real-time PCR assay for simultaneous detection of twelve enteric viruses and bacteria. J Microbiol Methods 2015; 118:93-8. [PMID: 26342434 DOI: 10.1016/j.mimet.2015.08.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 08/27/2015] [Accepted: 08/27/2015] [Indexed: 12/30/2022]
Abstract
OBJECTIVES We aim to develop a multiplex real-time PCR assay to detect the most common pathogens causing community outbreaks of diarrhea. METHODS Four reaction systems of fluorescence dye-based real-time PCR assay were performed to amplify genes of norovirus, sapovirus, rotavirus, astrovirus, adenovirus, Campylobacter jejuni, Yersinia enterocolitica, Vibrio parahaemolyticus, Salmonella spp., Escherichia coli, and Shigella spp. PCR products of each pathogen were identified by characteristic peaks in melting curves. RESULTS The assay was able to achieve detection limit of 50 copies/reaction for each individual virus target, and 140-500CFU/mL for each individual bacterium target. A total of 122 clinical specimens from hospitalized children with acute diarrhea were used to evaluate the assay. The clinical sensitivity was very similar to that of reference methods. Norovirus genogroup II revealed the highest detectable rate (45/122, 36.9%). Coinfection was found in 28 out of 122 (23%) clinical specimens. CONCLUSION This assay proved to be a cost-effective, sensitive and reliable method for simultaneous detection of enteric viruses and bacteria.
Collapse
Affiliation(s)
- Chen Zhang
- Key Laboratory for Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Peihua Niu
- Key Laboratory for Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yanying Hong
- Beijing Traditional Chinese Medicine Hospital, Capital Medical University Medical Laboratory, Beijing, China
| | - Ji Wang
- Key Laboratory for Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Jingyun Zhang
- National Institute for Infectious Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Xuejun Ma
- Key Laboratory for Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
| |
Collapse
|
29
|
Kawase J, Etoh Y, Ikeda T, Yamaguchi K, Watahiki M, Shima T, Kameyama M, Horikawa K, Fukushima H, Goto R, Shirabe K. An Improved Multiplex Real-Time SYBR Green PCR Assay for Analysis of 24 Target Genes from 16 Bacterial Species in Fecal DNA Samples from Patients with Foodborne Illnesses. Jpn J Infect Dis 2015; 69:191-201. [PMID: 26166499 DOI: 10.7883/yoken.jjid.2015.027] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Here, we developed a new version of our original screening system (Rapid Foodborne Bacterial Screening 24; RFBS24), which can simultaneously detect 24 genes of foodborne pathogens in fecal DNA samples. This new version (RFBS24 ver. 5) detected all known stx2 subtypes, enterotoxigenic Escherichia coli (STh genotype), and Vibrio parahaemolyticus (trh2), which were not detected by the original RFBS24 assay. The detection limits of RFBS24 ver. 5 were approximately 5.6 × 10(-2)-5.6 × 10(-5) (ng DNA)/reaction, significantly lower (10- to 100-fold) than those of the original RFBS24 for the 22 target genes analyzed here. We also tested the new assay on fecal DNA samples from patients infected with Salmonella, Campylobacter, or enterohemorrhagic E. coli. The number of bacterial target genes detected by RFBS24 ver. 5 was greater than that detected by RFBS24. RFBS24 ver. 5 combined with an Ultra Clean Fecal DNA Isolation Kit showed adequate performance (sensitivity and specificity 89% and 100%, respectively, for Salmonella spp. and 100% and 83%, respectively, for Campylobacter jejuni) in terms of rapid detection of a causative pathogen during foodborne-illness outbreaks. Thus, RFBS24 ver. 5 is more useful than the previous assay system for detection of foodborne pathogens and offers quick simultaneous analysis of many targets and thus facilitates rapid dissemination of information to public health officials.
Collapse
Affiliation(s)
- Jun Kawase
- Shimane Prefectural Institute of Public Health and Environmental Science
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
30
|
The contribution of PCR testing to influenza and pertussis notifications in Australia. Epidemiol Infect 2015; 144:306-14. [DOI: 10.1017/s0950268815001004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
SUMMARYInfluenza and pertussis are the two most common vaccine-preventable infections notified in Australia. We assessed the role of polymerase chain reaction (PCR) diagnosis in influenza and pertussis cases notified to the Australian National Notifiable Diseases Surveillance System (NNDSS). There were a total of 2 10 786 notified influenza cases (2001–2013) and 2 55 866 notified pertussis cases (1991–2013). After 1 January 2007, the majority of influenza and pertussis notifications were PCR-based (80·5% and 59·6%, respectively). Before 31 December 2006, PCR-based notifications were limited (29·1% and 11·7%, respectively). By 2013, PCR-based notifications had largely replaced all other diagnostic methods, with the exception of serology-based notifications in pertussis cases in adults aged ⩾25 years.
Collapse
|
31
|
Lalani T, Tisdale MD, Maguire JD, Wongsrichanalai C, Riddle MS, Tribble DR. Detection of enteropathogens associated with travelers' diarrhea using a multiplex Luminex-based assay performed on stool samples smeared on Whatman FTA Elute cards. Diagn Microbiol Infect Dis 2015; 83:18-20. [PMID: 26072151 DOI: 10.1016/j.diagmicrobio.2015.05.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 04/27/2015] [Accepted: 05/19/2015] [Indexed: 01/03/2023]
Abstract
We evaluated the limits of detection (LoD) for an 11-plex PCR-Luminex assay performed on Whatman(™) FTA Elute cards smeared with stool containing pathogens associated with travelers' diarrhea. LoDs ranged from 10(2) to 10(5)CFU, PFU, or cysts/g for most pathogens except Cryptosporidium. Campylobacter and norovirus LoDs increased with prolonged storage of cards.
Collapse
Affiliation(s)
- Tahaniyat Lalani
- Infectious Disease Clinic, Naval Medical Center, Portsmouth, VA, USA; Infectious Disease Clinical Research Program, Uniformed Services University, Bethesda, MD, USA; Henry M Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA.
| | - Michele D Tisdale
- Infectious Disease Clinic, Naval Medical Center, Portsmouth, VA, USA; Infectious Disease Clinical Research Program, Uniformed Services University, Bethesda, MD, USA; Henry M Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Jason D Maguire
- Infectious Disease Clinic, Naval Medical Center, Portsmouth, VA, USA
| | | | - Mark S Riddle
- Enteric Diseases Department, Naval Medical Research Center, Silver Spring, MD, USA
| | - David R Tribble
- Infectious Disease Clinical Research Program, Uniformed Services University, Bethesda, MD, USA
| |
Collapse
|
32
|
Pankhurst L, Macfarlane-Smith L, Buchanan J, Anson L, Davies K, O'Connor L, Ashwin H, Pike G, Dingle KE, Peto TE, Wordsworth S, Walker AS, Wilcox MH, Crook DW. Can rapid integrated polymerase chain reaction-based diagnostics for gastrointestinal pathogens improve routine hospital infection control practice? A diagnostic study. Health Technol Assess 2015; 18:1-167. [PMID: 25146932 DOI: 10.3310/hta18530] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Every year approximately 5000-9000 patients are admitted to a hospital with diarrhoea, which in up to 90% of cases has a non-infectious cause. As a result, single rooms are 'blocked' by patients with non-infectious diarrhoea, while patients with infectious diarrhoea are still in open bays because of a lack of free side rooms. A rapid test for differentiating infectious from non-infectious diarrhoea could be very beneficial for patients. OBJECTIVE To evaluate MassCode multiplex polymerase chain reaction (PCR) for the simultaneous diagnosis of multiple enteropathogens directly from stool, in terms of sensitivity/specificity to detect four common important enteropathogens: Clostridium difficile, Campylobacter spp., Salmonella spp. and norovirus. DESIGN A retrospective study of fixed numbers of samples positive for C. difficile (n = 200), Campylobacter spp. (n = 200), Salmonella spp. (n = 100) and norovirus (n = 200) plus samples negative for all these pathogens (n = 300). Samples were sourced from NHS microbiology laboratories in Oxford and Leeds where initial diagnostic testing was performed according to Public Health England methodology. Researchers carrying out MassCode assays were blind to this information. A questionnaire survey, examining current practice for infection control teams and microbiology laboratories managing infectious diarrhoea, was also carried out. SETTING MassCode assays were carried out at Oxford University Hospitals NHS Trust. Further multiplex assays, carried out using Luminex, were run on the same set of samples at Leeds Teaching Hospitals NHS Trust. The questionnaire was completed by various NHS trusts. MAIN OUTCOME MEASURES Sensitivity and specificity to detect C. difficile, Campylobacter spp., Salmonella spp., and norovirus. RESULTS Nucleic acids were extracted from 948 clinical samples using an optimised protocol (200 Campylobacter spp., 199 C. difficile, 60 S. enterica, 199 norovirus and 295 negative samples; some samples contained more than one pathogen). Using the MassCode assay, sensitivities for each organism compared with standard microbiological testing ranged from 43% to 94% and specificities from 95% to 98%, with particularly poor performance for S. enterica. Relatively large numbers of unexpected positives not confirmed with quantitative PCR were also observed, particularly for S. enterica, Giardia lamblia and Cryptosporidium spp. As the results indicated that S. enterica detection might provide generic challenges to other multiplex assays for gastrointestinal pathogens, the Luminex xTag(®) gastrointestinal assay was also run blinded on the same extracts (937/948 remaining) and on re-extracted samples (839/948 with sufficient material). For Campylobacter spp., C. difficile and norovirus, high sensitivities (> 92%) and specificities (> 96%) were observed. For S. enterica, on the original MassCode/Oxford extracts, Luminex sensitivity compared with standard microbiological testing was 84% [95% confidence interval (CI) 73% to 93%], but this dropped to 46% on a fresh extract, very similar to MassCode, with a corresponding increase in specificity from 92% to 99%. Overall agreement on the per-sample diagnosis compared with combined microbiology plus PCR for the main four/all pathogens was 85.6%/64.7%, 87.0%/82.9% and 89.8%/86.8% for the MassCode assay, Luminex assay/MassCode extract and Luminex assay/fresh extract, respectively. Luminex assay results from fresh extracts implied that 5% of samples did not represent infectious diarrhoea, even though enteropathogens were genuinely present. Managing infectious diarrhoea was a significant burden for infection control teams (taking 21% of their time) and better diagnostics were identified as having major potential benefits for patients. CONCLUSIONS Overall, the Luminex xTag gastrointestinal panel showed similar or superior sensitivity and specificity to the MassCode assay. However, on fresh extracts, this test had low sensitivity to detect a key enteric pathogen, S. enterica; making it an unrealistic option for most microbiology laboratories. Extraction efficiency appears to be a major obstacle for nucleic acid-based tests for this organism, and possibly the whole Enterobacteriaceae family. To improve workflows in service microbiology laboratories, to reduce workload for infection control practitioners, and to improve outcomes for NHS patients, further research on deoxyribonucleic acid-based multiplex gastrointestinal diagnostics is urgently needed. FUNDING The Health Technology Assessment programme of the National Institute for Health Research.
Collapse
Affiliation(s)
- Louise Pankhurst
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | | | - James Buchanan
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Luke Anson
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Kerrie Davies
- Leeds Teaching Hospitals NHS Trust, Leeds General Infirmary, Leeds, UK
| | - Lily O'Connor
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Helen Ashwin
- University of Leeds, Microbiology, Leeds General Infirmary Old Medical School, Leeds, UK
| | - Graham Pike
- Oxford University Hospitals NHS Trust, Oxford, UK
| | - Kate E Dingle
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Timothy Ea Peto
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Sarah Wordsworth
- Health Economics Research Centre, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - A Sarah Walker
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Mark H Wilcox
- Leeds Teaching Hospitals NHS Trust, Leeds General Infirmary, Leeds, UK
| | - Derrick W Crook
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| |
Collapse
|
33
|
Vocale C, Rimoldi SG, Pagani C, Grande R, Pedna F, Arghittu M, Lunghi G, Maraschini A, Gismondo MR, Landini MP, Torresani E, Topin F, Sambri V. Comparative evaluation of the new xTAG GPP multiplex assay in the laboratory diagnosis of acute gastroenteritis. Clinical assessment and potential application from a multicentre Italian study. Int J Infect Dis 2015; 34:33-7. [PMID: 25749649 DOI: 10.1016/j.ijid.2015.02.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 02/16/2015] [Accepted: 02/17/2015] [Indexed: 01/08/2023] Open
Abstract
OBJECTIVE Gastroenteritis caused by a single pathogen or multiple pathogens remains a major diagnostic challenge for the laboratory. The treatment of diarrhoea is based on microbiological results. Diagnosis is achieved using different laboratory techniques that have variable sensitivity and specificity. xTAG GPP is a new multiplex PCR assay that simultaneously detects 15 different pathogens responsible for diarrhoea. The results of the first multicentre study in Italy to evaluate the potential clinical application of the GPP assay in the laboratory diagnosis of diarrhoea are reported here. METHODS Faeces specimens (N=664) from hospitalized patients were tested with the GPP assay using a Luminex 200 instrument. All specimens were run using comparator methods following a routine algorithm: culture for bacteria, enzyme immunoassay and PCR for viruses, and microscopy for parasites. RESULTS Of the samples tested with the GPP, 53.61% (356/664) gave positive results, as compared to 45.33% by routine testing. Of the positive specimens, 34.55% showed the presence of genomic DNA from multiple pathogens. The Luminex method showed an increase in the percentage of positivity of 8.28%. CONCLUSIONS The GPP assay can be considered a helpful tool for the detection of gastrointestinal pathogens, with a hands-on time of 5h; it provides accurate data for the clinical management of hospitalized patients and for epidemiological surveillance.
Collapse
Affiliation(s)
- C Vocale
- Unit of Clinical Microbiology, Regional Reference Centre for Microbiological Emergencies, St. Orsola Malpighi University Hospital, Via Massarenti 9, 40138 Bologna, Italy.
| | - S G Rimoldi
- Laboratory of Clinical Microbiology, Virology and Bioemergency, "L. Sacco" University Hospital, Milan, Italy
| | - C Pagani
- Laboratory of Clinical Microbiology, Virology and Bioemergency, "L. Sacco" University Hospital, Milan, Italy
| | - R Grande
- Laboratory of Clinical Microbiology, Virology and Bioemergency, "L. Sacco" University Hospital, Milan, Italy
| | - F Pedna
- Unit of Clinical Microbiology, The Hub Laboratory of the Greater Romagna Area, Pievesestina, Cesena, Italy
| | - M Arghittu
- Department of Clinical Chemistry and Microbiology, Bacteriology and Virology Units, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - G Lunghi
- Department of Clinical Chemistry and Microbiology, Bacteriology and Virology Units, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - A Maraschini
- Department of Clinical Chemistry and Microbiology, Bacteriology and Virology Units, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - M R Gismondo
- Laboratory of Clinical Microbiology, Virology and Bioemergency, "L. Sacco" University Hospital, Milan, Italy
| | - M P Landini
- Unit of Clinical Microbiology, Regional Reference Centre for Microbiological Emergencies, St. Orsola Malpighi University Hospital, Via Massarenti 9, 40138 Bologna, Italy; DIMES, University of Bologna, Bologna, Italy
| | - E Torresani
- Department of Clinical Chemistry and Microbiology, Bacteriology and Virology Units, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - F Topin
- Luminex Corporation, Oosterhout NB, Netherlands
| | - V Sambri
- Unit of Clinical Microbiology, The Hub Laboratory of the Greater Romagna Area, Pievesestina, Cesena, Italy; DIMES, University of Bologna, Bologna, Italy
| |
Collapse
|
34
|
Dunbar SA, Ritchie VB, Hoffmeyer MR, Rana GS, Zhang H. Luminex(®) multiplex bead suspension arrays for the detection and serotyping of Salmonella spp. Methods Mol Biol 2015; 1225:1-27. [PMID: 25253245 DOI: 10.1007/978-1-4939-1625-2_1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
In this chapter we describe two commercially available bead-based molecular assays for detection, identification and serotyping of Salmonella. The xTAG(®) Gastrointestinal Pathogen Panel (GPP) is a qualitative multiplex test for the simultaneous detection of nucleic acids from Salmonella plus 14 other gastroenteritis-causing bacteria, viruses, and parasites from stool specimens. xTAG GPP uses the Luminex(®) xTAG universal array technology for the identification of specific target sequences combined with the xMAP(®) bead multiplexing platform for detection of the targets that were present in the starting sample. The xMAP Salmonella Serotyping Assay (SSA) is a multiplex nucleic acid-based direct hybridization assay for molecular identification of the serotype of Salmonella isolates. In xMAP SSA, target sequences amplified from cultured Salmonella isolates are captured by hybridization to sequence-specific capture probes which have been coupled to the multiplexed bead sets. Herein we provide detailed protocols for each of these assays and present data which describe their performance characteristics for detection and serotyping Salmonella.
Collapse
Affiliation(s)
- Sherry A Dunbar
- Luminex Corporation, 12212 Technology Boulevard, Austin, TX, 78727, USA,
| | | | | | | | | |
Collapse
|
35
|
Gomez A, Miller N, Smolina I. Visual detection of bacterial pathogens via PNA-based padlock probe assembly and isothermal amplification of DNAzymes. Anal Chem 2014; 86:11992-8. [PMID: 25415469 PMCID: PMC4270401 DOI: 10.1021/ac5018748] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 11/21/2014] [Indexed: 12/12/2022]
Abstract
We have developed a self-reporting isothermal system for visual bacterial pathogen detection with single base resolution. The new DNA diagnostic is based on combination of peptide nucleic acid (PNA) technology, rolling circle amplification (RCA) and DNAzymes. PNAs are used as exceedingly selective chemical tools that bind genomic DNA at a predetermined sequence under nondenaturing conditions. After assembly of the PNA-DNA construct a padlock probe is circularized on the free strand. The probe incorporates a G-quadruplex structure flanked by nicking enzyme recognition sites. The assembled circle serves as a template for a novel hybrid RCA strategy that allows for exponential amplification and production of short single-stranded DNA pieces. These DNA fragments fold into G-quadruplex structures and when complexed with hemin become functional DNAzymes. The catalytic activity of each DNAzyme unit leads to colorimetric detection and provides the second amplification step. The combination of PNA, RCA, and DNAzymes allows for sequence-specific and highly sensitive detection of bacteria with a colorimetric output observed with the naked eye. Herein, we apply this method for the discrimination of Escherichia coli, Salmonella typhimurium, and Clostridium difficile genomes.
Collapse
Affiliation(s)
- Anastasia Gomez
- Department
of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts 02215, United States
| | - Nancy
S. Miller
- Department
of Pathology and Laboratory Medicine, Boston
Medical Center and Boston University School of Medicine, 670 Albany Street, Boston, Massachusetts 02118, United States
| | - Irina Smolina
- Department
of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts 02215, United States
| |
Collapse
|
36
|
Sjöling Å, Sadeghipoorjahromi L, Novak D, Tobias J. Detection of major diarrheagenic bacterial pathogens by multiplex PCR panels. Microbiol Res 2014; 172:34-40. [PMID: 25542594 DOI: 10.1016/j.micres.2014.12.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 12/03/2014] [Accepted: 12/07/2014] [Indexed: 02/07/2023]
Abstract
Diarrheal diseases remain a major threat to the youngest population in low- and middle-income countries. The main bacterial pathogens causing diarrhea are diarrheagenic Escherichia coli (DEC) that consists of enteroaggregative (EAEC), enteropathogenic (EPEC), enterotoxigenic (ETEC), enterohemorrhagic EHEC and enteroinvasive E. coli (EIEC), Salmonella, Shigella spp. (S. dysenteria, S. sonnei, S. flexneri) Campylobacter (C. coli, C. jejuni), Vibrio (V. vulnificus, V. parahaemolyticusm, V. cholerae), Yersinia enterocolitica and Aeromonas hydrophila. The aim of this study was to set up rapid multiplex PCR (mPCR) panels to identify these diarrheagenic pathogens based on their specific virulence genes. Primers against specific target genes were combined into three mPCR panels: one for diarrheal E. coli, one for pathogens causing mainly bloody diarrhea, and the third for the remaining pathogens. The panels were tested against a set of stool samples from Swedish children with diarrhea and controls and the analysis identified bacterial pathogens in 14/54 (26%) of the samples. These results show that our three developed mPCR panels can detect main bacterial diarrheagenic pathogens in clinical samples.
Collapse
Affiliation(s)
- Åsa Sjöling
- University of Gothenburg Vaccine Research Institute (GUVAX), Department of Microbiology and Immunology, Institute of Biomedicine, The Sahlgrenska Academy of University of Gothenburg, Gothenburg, Sweden; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Leila Sadeghipoorjahromi
- University of Gothenburg Vaccine Research Institute (GUVAX), Department of Microbiology and Immunology, Institute of Biomedicine, The Sahlgrenska Academy of University of Gothenburg, Gothenburg, Sweden
| | - Daniel Novak
- Department of Pediatrics, Queen Silvia Children's Hospital Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Joshua Tobias
- University of Gothenburg Vaccine Research Institute (GUVAX), Department of Microbiology and Immunology, Institute of Biomedicine, The Sahlgrenska Academy of University of Gothenburg, Gothenburg, Sweden.
| |
Collapse
|
37
|
Verkerke HP, Sobuz SU, Petri WA. Molecular diagnosis of infectious diarrhea: focus on enteric protozoa. Expert Rev Mol Diagn 2014; 14:935-46. [PMID: 25139776 DOI: 10.1586/14737159.2014.951035] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Robust detection of enteric protozoa is a critical step toward determining the etiology of diarrhea. Widespread use of conventional microscopy, culturing and antigen detection in both industrial and developing countries is limited by relatively low sensitivity and specificity. Refinements of these conventional approaches that reduce turnaround time and instrumentation have yielded strong alternatives for clinical and research use. However, advances in molecular diagnostics for protozoal, bacterial, viral and helminth infections offer significant advantages in studies seeking to understand pathogenesis, transmission and long-term consequences of infectious diarrhea. Quantitation of enteropathogen burden and highly multiplexed platforms for molecular detection dramatically improve predictive power in emerging models of diarrheal etiology, while eliminating the expense of multiple tests.
Collapse
Affiliation(s)
- Hans P Verkerke
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, 22901, USA
| | | | | |
Collapse
|
38
|
Hamza IA, Jurzik L, Wilhelm M. Development of a Luminex assay for the simultaneous detection of human enteric viruses in sewage and river water. J Virol Methods 2014; 204:65-72. [DOI: 10.1016/j.jviromet.2014.04.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 03/06/2014] [Accepted: 04/04/2014] [Indexed: 12/28/2022]
|
39
|
Pentaplex PCR assay for detection of hemorrhagic bacteria from stool samples. J Clin Microbiol 2014; 52:3244-9. [PMID: 24958797 DOI: 10.1128/jcm.00891-14] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Diarrheal diseases cause illness and death among children younger than 10 years in developing countries. Conventional testing for the detection of hemorrhagic bacteria takes 2 to 5 days to yield complete information on the organism and its antibiotic sensitivity pattern. Hence, in the present study, we developed a molecular-based diagnostic assay that identifies common hemorrhagic bacteria in stool samples. A set of specific primers were designed for the detection of Salmonella spp., Shigella spp., enterohemorrhagic Escherichia coli (EHEC), and Campylobacter spp., suitable for use in a one-tube PCR assay. The assay in the present study simultaneously detected five genes, namely, ompC for the Salmonella genus, virA for the Shigella genus, eaeA for EHEC, 16S rRNA for the Campylobacter genus, and hemA for an internal control. Specific primer pairs were successfully designed and simultaneously amplified the targeted genes. Validation with 20 Gram-negative and 17 Gram-positive strains yielded 100% specificity. The limit of detection of the multiplex PCR assay was 1 × 10(3) CFU at the bacterial cell level and 100 pg at the genomic DNA level. Further evaluation of the multiplex PCR with 223 bacterium-spiked stool specimens revealed 100% sensitivity and specificity. We conclude that the developed multiplex PCR assay was rapid, giving results within 4 h, which is essential for the identification of hemorrhagic bacteria, and it might be useful as an additional diagnostic tool whenever time is important in the diagnosis of hemorrhagic bacteria that cause diarrhea. In addition, the presence of an internal control in the multiplex PCR assay is important for excluding false-negative cases.
Collapse
|
40
|
Affiliation(s)
- Herbert L DuPont
- From the University of Texas School of Public Health and Medical School, Baylor St. Luke's Medical Center, Baylor College of Medicine, and the Kelsey Research Foundation - all in Houston
| |
Collapse
|
41
|
Zboromyrska Y, Hurtado JC, Salvador P, Alvarez-Martínez MJ, Valls ME, Mas J, Marcos MA, Gascón J, Vila J. Aetiology of traveller's diarrhoea: evaluation of a multiplex PCR tool to detect different enteropathogens. Clin Microbiol Infect 2014; 20:O753-9. [PMID: 24621195 DOI: 10.1111/1469-0691.12621] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Revised: 03/07/2014] [Accepted: 03/10/2014] [Indexed: 12/13/2022]
Abstract
Traveller's diarrhoea (TD) is the most common illness reported in international travellers. TD is caused by a wide range of pathogens, including bacteria, viruses and parasites. Multiplex PCR assays can be especially useful for studying the aetiology of TD. The first objective of this study was to evaluate the utility of the commercially available multiplex PCR (xTAG(®) Gastrointestinal Pathogen Panel (GPP)) for the diagnosis of TD. A total of 185 stool specimens obtained from 174 patients were processed using the GPP assay. This test detected 86 pathogens in 67 stool samples (67/185, 36.2%). Sixteen pathogens out of 86 were also detected by routine testing. The remaining pathogens (n = 70) required further confirmation by alternative techniques. Finally, 60 out of 70 pathogens were confirmed. The second objective of this study was to analyse the aetiology of TD based on the results obtained by the GPP test and routine methods. The primary pathogens causing TD were Shigella (24.2%) followed by enterotoxigenic Escherichia coli (ETEC) (23.2%), enteroaggregative E. coli (14.7%) and Giardia (13.7%). Significant regional differences were observed for ETEC with 19.4% of TD cases acquired in Africa, 11.3% in Asia and none in South Central (SC) America (p 0.01), Giardia was found in 1.5% of cases among those who had travelled to Africa, 14.1% of those who had travelled to Asia and 3% of those who had travelled to SC America (p 0.01). In conclusion, the GPP test improved the detection of enteropathogens and allowed better assessment of the aetiology of TD.
Collapse
Affiliation(s)
- Y Zboromyrska
- Department of Clinical Microbiology, Hospital Clínic, School of Medicine, University of Barcelona, Barcelona, Spain
| | | | | | | | | | | | | | | | | |
Collapse
|
42
|
Abstract
Gastroenteritis persists as a worldwide problem, responsible for approximately 2 million deaths annually. Traditional diagnostic methods used in the clinical microbiology laboratory include a myriad of tests, such as culture, microscopy, and immunodiagnostics, which can be labor intensive and suffer from long turnaround times and, in some cases, poor sensitivity. [corrected]. This article reviews recent advances in genomic and proteomic technologies that have been applied to the detection and identification of gastrointestinal pathogens. These methods simplify and speed up the detection of pathogenic microorganisms, and their implementation in the clinical microbiology laboratory has potential to revolutionize the diagnosis of gastroenteritis.
Collapse
|
43
|
Rundell MS, Pingle M, Das S, Hussain A, Ocheretina O, Charles M, Larone DH, Spitzer ED, Golightly L, Barany F. A multiplex PCR/LDR assay for simultaneous detection and identification of the NIAID category B bacterial food and water-borne pathogens. Diagn Microbiol Infect Dis 2014; 79:135-40. [PMID: 24709368 DOI: 10.1016/j.diagmicrobio.2014.02.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 02/17/2014] [Accepted: 02/26/2014] [Indexed: 01/06/2023]
Abstract
Enteric pathogens that cause gastroenteritis remain a major global health concern. The goal of this study was to develop a multiplex PCR/ligation detection reaction (LDR) assay for the detection of all NIAID category B bacterial food and water-borne pathogens directly from stool specimens. To validate the PCR/LDR assay, clinical isolates of Campylobacter spp., Vibrio spp., Shigella spp., Salmonella spp., Listeria monocytogenes, Yersinia enterocolitica, and diarrheagenic Escherichia coli were tested. The sensitivity and specificity of the assay were assessed using a large number of seeded culture-negative stool specimens and a smaller set of clinical specimens from Haiti. The overall sensitivity ranged from 91% to 100% (median 100%) depending on the species. For the majority of organisms, the sensitivity was 100%. The overall specificity based on initial testing ranged from 98% to 100% depending on the species. After additional testing of discordant samples, the lowest specificity was 99.4%. PCR/LDR detected additional category B agents (particularly diarrheagenic E. coli) in 11/40 specimens from Haiti that were culture-positive for V. cholerae and in approximately 1% of routine culture-negative stool specimens from a hospital in New York. This study demonstrated the ability of the PCR/LDR assay to detect a large comprehensive panel of category B enteric bacterial pathogens as well as mixed infections. This type of assay has the potential to provide earlier warnings of possible public health threats and more accurate surveillance of food and water-borne pathogens.
Collapse
Affiliation(s)
- Mark S Rundell
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, Box 62, New York, NY 10021
| | - Maneesh Pingle
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, Box 62, New York, NY 10021
| | - Sanchita Das
- Department of Medicine, Division of International Medicine and Infectious Diseases, Weill Medical College of Cornell University, Box 62, New York, NY 10021
| | - Aashiq Hussain
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, Box 62, New York, NY 10021
| | - Oksana Ocheretina
- Department of Medicine, Division of International Medicine and Infectious Diseases, Weill Medical College of Cornell University, Box 62, New York, NY 10021; Groupe Haitien d'Étude du Sarcome de Kaposi et des Infections Opportunistes, Port-Au-Prince, Haiti
| | - Macarthur Charles
- Department of Medicine, Division of International Medicine and Infectious Diseases, Weill Medical College of Cornell University, Box 62, New York, NY 10021; Groupe Haitien d'Étude du Sarcome de Kaposi et des Infections Opportunistes, Port-Au-Prince, Haiti
| | - Davise H Larone
- Department of Pathology and Laboratory Medicine, Weill Medical College of Cornell University, Box 62, New York, NY 10021
| | - Eric D Spitzer
- Department of Pathology, Stony Brook University Medical Center, Stony Brook, NY 11794
| | - Linnie Golightly
- Department of Medicine, Division of International Medicine and Infectious Diseases, Weill Medical College of Cornell University, Box 62, New York, NY 10021
| | - Francis Barany
- Department of Microbiology and Immunology, Weill Medical College of Cornell University, Box 62, New York, NY 10021.
| |
Collapse
|
44
|
Onori M, Coltella L, Mancinelli L, Argentieri M, Menichella D, Villani A, Grandin A, Valentini D, Raponi M, Russo C. Evaluation of a multiplex PCR assay for simultaneous detection of bacterial and viral enteropathogens in stool samples of paediatric patients. Diagn Microbiol Infect Dis 2014; 79:149-54. [PMID: 24656922 DOI: 10.1016/j.diagmicrobio.2014.02.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 02/04/2014] [Accepted: 02/05/2014] [Indexed: 12/17/2022]
Abstract
We evaluated a multiplex PCR assay, the Seeplex Diarrhoea ACE detection, that simultaneously detects 15 enteric pathogens, including Salmonella spp., Shigella spp., Vibrio spp., toxin B producer Clostridium difficile, Campylobacter spp., Clostridium perfringens, Yersinia enterocolitica, Aeromonas spp., Escherichia coli O157:H7, verocytotoxin-producing Escherichia coli, adenovirus, Group A rotavirus, norovirus GI and GII, and astrovirus. We compared this assay with clinical methods routinely used in our laboratory, for detecting enteropathogens in stool samples collected from 245 paediatric patients with suspected infectious gastroenteritis. We recovered 61 bacterial pathogens and 121 enteric viruses with our laboratory assays, while we detected 78 bacteria and 167 viruses with the molecular assay. We calculated specificity and sensitivity for both methods after analysis of discordant results and demonstrated greater sensitivity for multiplex PCR than for our routine methods, with the exception of Salmonella spp. and toxigenic C. difficile detection. The multiplex PCR assay proved to be a reliable tool to directly detect the most common enteropathogens in stool samples but with some limitations.
Collapse
Affiliation(s)
- Manuela Onori
- Department of Laboratory Medicine, Virology Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy.
| | - Luana Coltella
- Department of Laboratory Medicine, Virology Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Livia Mancinelli
- Department of Laboratory Medicine, Virology Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Marta Argentieri
- Department of Laboratory Medicine, Bacteriology Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Donato Menichella
- Medical Direction, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Alberto Villani
- Paediatric and Infectious Disease Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Annalisa Grandin
- Paediatric and Infectious Disease Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Diletta Valentini
- Paediatric and Infectious Disease Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | | | - Cristina Russo
- Department of Laboratory Medicine, Virology Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| |
Collapse
|
45
|
Comparison of the BD MAX enteric bacterial panel to routine culture methods for detection of Campylobacter, enterohemorrhagic Escherichia coli (O157), Salmonella, and Shigella isolates in preserved stool specimens. J Clin Microbiol 2014; 52:1222-4. [PMID: 24430460 DOI: 10.1128/jcm.03099-13] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
We compared the BD MAX enteric bacterial panel (EBP) to culture for the detection of Salmonella, Shigella, Campylobacter, and Shiga toxin-producing enterohemorrhagic Escherichia coli (EHEC) O157 in seeded stool samples. The EBP panel demonstrated superior sensitivity and reliably detected Salmonella, EHEC O157, Shigella, and Campylobacter at concentrations 1- to 2-log10 lower than those needed for culture detection.
Collapse
|
46
|
Christopher-Hennings J, Araujo KPC, Souza CJH, Fang Y, Lawson S, Nelson EA, Clement T, Dunn M, Lunney JK. Opportunities for bead-based multiplex assays in veterinary diagnostic laboratories. J Vet Diagn Invest 2013; 25:671-91. [DOI: 10.1177/1040638713507256] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Bead-based multiplex assays (BBMAs) are applicable for high throughput, simultaneous detection of multiple analytes in solution (from several to 50–500 analytes within a single, small sample volume). Currently, few assays are commercially available for veterinary applications, but they are available to identify and measure various cytokines, growth factors and their receptors, inflammatory proteins, kinases and inhibitors, neurobiology proteins, and pathogens and antibodies in human beings, nonhuman primates, and rodent species. In veterinary medicine, various nucleic acid and protein-coupled beads can be used in, or for the development of, antigen and antibody BBMAs, with the advantage that more data can be collected using approximately the same amount of labor as used for other antigen and antibody assays. Veterinary-related BBMAs could be used for detection of pathogens, genotyping, measurement of hormone levels, and in disease surveillance and vaccine assessment. It will be important to evaluate whether BBMAs are “fit for purpose,” how costs and efficiencies compare between assays, which assays are published or commercially available for specific veterinary applications, and what procedures are involved in the development of the assays. It is expected that many veterinary-related BBMAs will be published and/or become commercially available in the next few years. The current review summarizes the BBMA technology and some of the currently available BBMAs developed for veterinary settings. Some of the human diagnostic BBMAs are also described, providing an example of possible templates for future development of new veterinary-related BBMAs.
Collapse
Affiliation(s)
- Jane Christopher-Hennings
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Karla P. C. Araujo
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Carlos J. H. Souza
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Ying Fang
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Steven Lawson
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Eric A. Nelson
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Travis Clement
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Michael Dunn
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| | - Joan K. Lunney
- Veterinary and Biomedical Sciences Department, South Dakota State University, Brookings, SD (Christopher-Hennings, Fang, Lawson, Nelson, Clement, Dunn)
- Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD (Araujo, Souza, Lunney)
- Brazilian Agricultural Research Corp. (EMBRAPA), Pecuaria Sul, Bage, Rio Grande do Sul, Brazil (Souza)
| |
Collapse
|
47
|
Taniuchi M, Sobuz SU, Begum S, Platts-Mills JA, Liu J, Yang Z, Wang XQ, Petri WA, Haque R, Houpt ER. Etiology of diarrhea in Bangladeshi infants in the first year of life analyzed using molecular methods. J Infect Dis 2013; 208:1794-802. [PMID: 24041797 DOI: 10.1093/infdis/jit507] [Citation(s) in RCA: 147] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Diarrhea causes enormous morbidity and mortality in developing countries, yet the relative importance of multiple potential enteropathogens has been difficult to ascertain. METHODS We performed a longitudinal cohort study from birth to 1 year of age in 147 infants in Dhaka, Bangladesh. Using multiplex polymerase chain reaction, we analyzed 420 episodes of diarrhea and 1385 monthly surveillance stool specimens for 32 enteropathogen gene targets. For each infant we examined enteropathogen quantities over time to ascribe each positive target as a probable or less-likely contributor to diarrhea. RESULTS Multiple enteropathogens were detected by the first month of life. Diarrhea was associated with a state of overall pathogen excess (mean number of enteropathogen gene targets (± SE), 5.6 ± 0.1 vs 4.3 ± 0.1 in surveillance stool specimens; P < .05). After a longitudinal, quantitative approach was applied to filter out less-likely contributors, each diarrheal episode still had an average of 3.3 probable or dominant targets. Enteroaggregative Escherichia coli, Campylobacter, enteropathogenic E. coli, rotavirus, and Entamoeba histolytica were the most frequent probable contributors to diarrhea. Rotavirus was enriched in moderate to severe diarrheal episodes. CONCLUSIONS In this community-based study diarrhea seemed to be a multipathogen event and a state of enteropathogen excess above a high carriage baseline.
Collapse
Affiliation(s)
- Mami Taniuchi
- Division of Infectious Diseases and International Health, Department of Medicine
| | | | | | | | | | | | | | | | | | | |
Collapse
|
48
|
New concepts in diagnostics for infectious diarrhea. Mucosal Immunol 2013; 6:876-85. [PMID: 23881355 DOI: 10.1038/mi.2013.50] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2013] [Accepted: 06/11/2013] [Indexed: 02/04/2023]
Abstract
Conventional approaches to the diagnosis of infectious diarrhea must include several modalities to detect an array of potential viruses, bacteria, and parasites. We will provide a general overview of the wide range of diagnostic modalities available for enteropathogens, briefly discuss some of the limitations of conventional methods, and then focus on new molecular methods, including real-time PCR and next-generation sequencing. In particular, we will discuss quantitation of pathogen load with these techniques. We will then describe examples whereby novel diagnostics may help illuminate the etiology of infectious diarrhea, where they may not, and how they may benefit studies of immunity to enteric infections.
Collapse
|
49
|
Kaminski RW, Clarkson K, Kordis AA, Oaks EV. Multiplexed immunoassay to assess Shigella-specific antibody responses. J Immunol Methods 2013; 393:18-29. [DOI: 10.1016/j.jim.2013.04.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 03/05/2013] [Accepted: 04/03/2013] [Indexed: 10/27/2022]
|
50
|
Improved detection of bacterial pathogens in patients presenting with gastroenteritis by use of the EntericBio real-time Gastro Panel I assay. J Clin Microbiol 2013; 51:2679-85. [PMID: 23761157 DOI: 10.1128/jcm.00809-13] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this study, we evaluated the use of EntericBio real-time Gastro Panel I (Serosep, Limerick, Ireland) for routine use in a clinical microbiology laboratory for simultaneous detection of Campylobacter jejuni, coli, and lari, Shiga toxin-producing Escherichia coli (STEC), Salmonella spp., and Shigella spp. in feces. This system differs from its predecessor (the EntericBio Panel II system, Serosep) in that it allows real-time detection of pathogens directly from feces, without pre-enrichment. It also specifically detects Campylobacter jejuni, coli, and lari rather than all Campylobacter species, as is the case with the previous system. A total of 528 samples from patients presenting with acute gastroenteritis were screened prospectively with this assay, and results were compared with those of the current method, which combines screening the samples with a molecular assay (the EntericBio Panel II assay) and retrospective culture of the specimens in which the target was detected. Discrepancy analysis was conducted using culture and molecular methods. The real-time assay produced 84 positive results, specifically, Campylobacter spp. (n=44); Stx1 and/or Stx2 (n=35); Shigella spp. (n=3); and Salmonella spp. (n=6). Of these, 4 samples represented coinfections with Campylobacter spp. and STEC. The real-time assay showed an increased detection rate for pathogens, apart from Salmonella spp. Four Campylobacter-positive and 6 Stx-positive results remained unconfirmed by any other method used. The isolation rates for PCR-positive samples were as follows: Campylobacter spp., 80%; STEC, 45.7%; Salmonella spp., 100%; and Shigella spp., 66.7%. The sensitivity, specificity, positive predictive value, negative predictive value, and efficiency were 100%, 97.8%, 88.1%, 100%, and 98.1%, respectively.
Collapse
|