1
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Gao M, Tan F, Shen Y, Peng Y. Rapid detection method of bacterial pathogens in surface waters and a new risk indicator for water pathogenic pollution. Sci Rep 2024; 14:1614. [PMID: 38238351 PMCID: PMC10796392 DOI: 10.1038/s41598-023-49774-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 12/12/2023] [Indexed: 01/22/2024] Open
Abstract
In this study, a accurate, rapid quantitative PCR method for the simultaneous detection of 4 kinds of pathogenic bacteria in water was established, and the distribution of pathogenic bacteria in surface waters with different levels of pollution (Yulin region, China) was detected. The results showed that the detection accuracy was 94%; the detection limit was 2.7 in bacterial cells. Salmonella enterica subsp. enterica serovar typhimurium and Salmonella dysenteria were always present in water when the universal primer for pathogenic bacteria abundance detection was greater than 104 copies 100 mL-1. When the detection value is lower than 104 copy 100 mL-1, the bacteria in the water are rarely pathogenic bacteria, so the detection value of 104 copy 100 mL-1 can be used as a new indicator of waterborne pathogen pollution.
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Affiliation(s)
- Min Gao
- College of Environmental and Chemical Engineering, Xi'an Key Laboratory of Textile Chemical Engineering Auxiliaries, Xi'an Polytechnic University, Xi'an, 710000, People's Republic of China.
| | - Feiyang Tan
- College of Environmental and Chemical Engineering, Xi'an Key Laboratory of Textile Chemical Engineering Auxiliaries, Xi'an Polytechnic University, Xi'an, 710000, People's Republic of China
| | - Yuan Shen
- College of Environmental and Chemical Engineering, Xi'an Key Laboratory of Textile Chemical Engineering Auxiliaries, Xi'an Polytechnic University, Xi'an, 710000, People's Republic of China
| | - Yao Peng
- College of Environmental and Chemical Engineering, Xi'an Key Laboratory of Textile Chemical Engineering Auxiliaries, Xi'an Polytechnic University, Xi'an, 710000, People's Republic of China
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2
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Kim HJ, Jung Y, Kim MJ, Kim HY. Novel Heptaplex PCR-Based Diagnostics for Enteric Fever Caused by Typhoidal Salmonella Serovars and Its Applicability in Clinical Blood Culture. J Microbiol Biotechnol 2023; 33:1457-1466. [PMID: 37674393 DOI: 10.4014/jmb.2307.07031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/12/2023] [Accepted: 08/14/2023] [Indexed: 09/08/2023]
Abstract
Enteric fever is caused by typhoidal Salmonella serovars (Typhi, Paratyphi A, Paratyphi B, and Paratyphi C). Owing to the importance of Salmonella serovars in clinics and public hygiene, reliable diagnostics for typhoidal serovars are crucial. This study aimed to develop a novel diagnostic tool for typhoidal Salmonella serovars and evaluate the use of human blood for clinically diagnosing enteric fever. Five genes were selected to produce specific PCR results against typhoidal Salmonella serovars based on the genes of Salmonella Typhi. Heptaplex PCR, including genetic markers of generic Salmonella, Salmonella enterica subsp. enterica, and typhoidal Salmonella serovars, was developed. Typhoidal Salmonella heptaplex PCR using genomic DNAs from 200 Salmonella strains (112 serovars) provided specifically amplified PCR products for each typhoidal Salmonella serovar. These results suggest that heptaplex PCR can sufficiently discriminate between typhoidal and nontyphoidal Salmonella serovars. Heptaplex PCR was applied to Salmonella-spiked blood cultures directly and provided diagnostic results after 12- or 13.5-h blood culture. Additionally, it demonstrated diagnostic performance with colonies recovered from a 6-h blood culture. This study provides a reliable DNA-based tool for diagnosing typhoidal Salmonella serovars that may be useful in clinical microbiology and epidemiology.
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Affiliation(s)
- Hyun-Joong Kim
- Department of Food Engineering, Mokpo National University, Muan 58554, Republic of Korea
| | - Younsik Jung
- Institute of Life Sciences and Resources and the Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104 Republic of Korea
| | - Mi-Ju Kim
- Institute of Life Sciences and Resources and the Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104 Republic of Korea
| | - Hae-Yeong Kim
- Institute of Life Sciences and Resources and the Department of Food Science and Biotechnology, Kyung Hee University, Yongin 17104 Republic of Korea
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3
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Guo K, Guo W, Liu D, Zhang W, Yang Y, Zhang Z, Li S, Wang J, Chu X, Wang Y, Hu Z, Wang X. Development and application of a competitive ELISA for the detection of antibodies against Salmonella Abortusequi in equids. J Clin Microbiol 2023; 61:e0027323. [PMID: 37874302 PMCID: PMC10662346 DOI: 10.1128/jcm.00273-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 08/26/2023] [Indexed: 10/25/2023] Open
Abstract
The high abortion rate associated with Salmonella Abortusequi (S. Abortusequi) infection in equids has re-emerged over the past 10 years and has caused serious economic losses to China. Our previous studies showed that the flagellin FljB gene could distinguish S. Abortusequi from most Salmonella serotypes. In this study, the flagellin antigen was used to develop a competitive enzyme-linked immunosorbent assay (cELISA) that could be used to detect both horse and donkey serum samples using a monoclonal antibody (MAb) that was found to bind to FljB. A cELISA was established using the purified MAb coating of the plate and incubation of the mixture of horseradish peroxidase (HRP)-conjugated FljB antigen with the undiluted serum sample. The performance of the cELISA and the tube agglutination test (TAT) assay was compared with respect to sensitivity and specificity, by testing a panel containing 660 S. Abortusequi-positive and 515 S. Abortusequi-negative serum samples, all of which had been characterized by Western blotting. Receiver operator characteristic (ROC) analyses were performed to determine the cutoff value and estimate the detection specificity (Sp) and sensitivity (Se). ROC analysis showed that the area under the ROC curve (AUC) values of cELISA [AUC = 0.9941; 95% confidence interval (CI), 0.9898-0.9984] were higher than those of TAT (AUC = 0.7705; 95% Cl, 0.7437-0.7972). A cutoff value of 39.5% was selected with Sp and Se values of 100 (95% Cl, 99.26-100.00) and 97.58 (95% Cl, 96.10-98.50), respectively. The cELISA has excellent futures compared with TAT, such as shortened detection time, no need for pre-treatment of sera, and easy interpretation of the results, and is more suitable for disease surveillance.
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Affiliation(s)
- Kui Guo
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Wei Guo
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Diqiu Liu
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Weiguo Zhang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yan Yang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Zenan Zhang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Shuaijie Li
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Jinhui Wang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Xiaoyu Chu
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yaoxin Wang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Zhe Hu
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
| | - Xiaojun Wang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, the Chinese Academy of Agricultural Sciences, Harbin, China
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Chatterjee R, Chowdhury AR, Mukherjee D, Chakravortty D. From Eberthella typhi to Salmonella Typhi: The Fascinating Journey of the Virulence and Pathogenicity of Salmonella Typhi. ACS OMEGA 2023; 8:25674-25697. [PMID: 37521659 PMCID: PMC10373206 DOI: 10.1021/acsomega.3c02386] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 06/30/2023] [Indexed: 08/01/2023]
Abstract
Salmonella Typhi (S. Typhi), the invasive typhoidal serovar of Salmonella enterica that causes typhoid fever in humans, is a severe threat to global health. It is one of the major causes of high morbidity and mortality in developing countries. According to recent WHO estimates, approximately 11-21 million typhoid fever illnesses occur annually worldwide, accounting for 0.12-0.16 million deaths. Salmonella infection can spread to healthy individuals by the consumption of contaminated food and water. Typhoid fever in humans sometimes is accompanied by several other critical extraintestinal complications related to the central nervous system, cardiovascular system, pulmonary system, and hepatobiliary system. Salmonella Pathogenicity Island-1 and Salmonella Pathogenicity Island-2 are the two genomic segments containing genes encoding virulent factors that regulate its invasion and systemic pathogenesis. This Review aims to shed light on a comparative analysis of the virulence and pathogenesis of the typhoidal and nontyphoidal serovars of S. enterica.
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Affiliation(s)
- Ritika Chatterjee
- Department
of Microbiology and Cell Biology, Division of Biological Sciences, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Atish Roy Chowdhury
- Department
of Microbiology and Cell Biology, Division of Biological Sciences, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Debapriya Mukherjee
- Department
of Microbiology and Cell Biology, Division of Biological Sciences, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Dipshikha Chakravortty
- Department
of Microbiology and Cell Biology, Division of Biological Sciences, Indian Institute of Science, Bangalore, Karnataka 560012, India
- Centre
for Biosystems Science and Engineering, Indian Institute of Science, Bangalore, Karnataka 560012, India
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Veronese P, Pappalardo M, Maffini V, Rubini M, Giacometti A, Ruozi MB, Cella S, Dodi I. Severe Typhoid Fever Complicated by Superior Mesenteric and Splenic Vein Thrombosis. Infect Dis Rep 2023; 15:377-385. [PMID: 37489392 PMCID: PMC10366850 DOI: 10.3390/idr15040038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 06/19/2023] [Accepted: 06/29/2023] [Indexed: 07/26/2023] Open
Abstract
Typhoid fever (Typhoid or enteric fever) is still the most common bacterial bloodstream infection worldwide, caused by Salmonella typhi. The transmission route is indirect through passive vehicles such as contaminated water or food. Main clinical findings are a fever lasting more than three days, abdominal symptoms, leukocytosis, and anemia. Typhoid can cause a wide range of multi-organ complications. We report a particularly severe form of this infection complicated by superior mesenteric vein and splenic vein thrombosis, an extremely uncommon manifestation.
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Affiliation(s)
- Piero Veronese
- Pediatric Infectious Disease, Children's Hospital of Parma, 43126 Parma, Italy
| | - Marco Pappalardo
- Pediatric Infectious Disease, Children's Hospital of Parma, 43126 Parma, Italy
| | - Valentina Maffini
- Pediatric Infectious Disease, Children's Hospital of Parma, 43126 Parma, Italy
| | - Monica Rubini
- Pediatric Infectious Disease, Children's Hospital of Parma, 43126 Parma, Italy
| | | | | | - Simone Cella
- Pediatric Radiology, Institute of Radiology, University of Parma, 43126 Parma, Italy
| | - Icilio Dodi
- Pediatric Infectious Disease, Children's Hospital of Parma, 43126 Parma, Italy
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Saha T, Arisoyin AE, Bollu B, Ashok T, Babu A, Issani A, Jhaveri S, Avanthika C. Enteric Fever: Diagnostic Challenges and the Importance of Early Intervention. Cureus 2023; 15:e41831. [PMID: 37575696 PMCID: PMC10423039 DOI: 10.7759/cureus.41831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/12/2023] [Indexed: 08/15/2023] Open
Abstract
Enteric fever is a systemic infection caused by highly virulent Salmonella enterica serovars: Typhi and Paratyphi. Diagnosis of enteric fever is challenging due to a wide variety of clinical features which overlap with other febrile illnesses. The current diagnostic methods are limited because of the suboptimal sensitivity of conventional tests like blood culture in detecting organisms and the invasive nature of bone marrow culture. It emphasizes the need to develop improved and more reliable diagnostic modalities. The rising rates of multidrug-resistant Salmonella strains call for an accurate understanding of the current management of the disease. Proper public health measures and large-scale immunization programs will help reduce the burden of the disease. A comprehensive surveillance system can help detect the chronic carrier state and is crucial in understanding antibiotic susceptibility patterns. We conducted an all-language literature search on Medline, Cochrane, Embase, and Google Scholar till May 2022. The following search words and medical subject headings (MeSH) were used: "enteric fever," "Salmonella Typhi," "multidrug-resistant Salmonella," chronic carrier state," "Salmonella detection, "and "typhoid vaccine." We reviewed the literature on clinical features, pathophysiology, new diagnostic tests, and interventions to prevent the disease. This article explores enteric fever and its various clinical features and addresses the emerging threat of multidrug resistance. It focuses on novel methods for diagnosis and prevention strategies, including vaccines and the use of surveillance systems employed across different parts of the world.
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Affiliation(s)
- Tias Saha
- Internal Medicine, Samorita General Hospital, Faridpur, BGD
- Internal Medicine, Diabetic Association Medical College, Faridpur, BGD
| | | | - Bhaswanth Bollu
- Emergency Medicine, All India Institute of Medical Sciences, New Delhi, IND
| | - Tejaswini Ashok
- Internal Medicine, Jagadguru Sri Shivarathreeshwara Medical College, Mysore, IND
| | - Athira Babu
- Pediatrics, Saudi German Hospital, Dubai, ARE
| | - Ali Issani
- Emergency Medicine, Aga Khan University, Karachi, PAK
| | - Sharan Jhaveri
- Internal Medicine, Nathiba Hargovandas Lakhmichand Municipal Medical College, Ahmedabad, IND
| | - Chaithanya Avanthika
- Pediatrics, Icahn School of Medicine at Mount Sinai, Elmhurst Hospital Center, New York, USA
- Medicine and Surgery, Karnataka Institute of Medical Sciences, Hubli, IND
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7
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Fatima S, Ishaq Z, Irfan M, AlAsmari AF, Achakzai JK, Zaheer T, Ali A, Akbar A. Whole-genome sequencing of multidrug resistance Salmonella Typhi clinical strains isolated from Balochistan, Pakistan. Front Public Health 2023; 11:1151805. [PMID: 37261234 PMCID: PMC10227597 DOI: 10.3389/fpubh.2023.1151805] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/17/2023] [Indexed: 06/02/2023] Open
Abstract
Introduction Salmonella enterica serovar Typhi (S. Typhi) is a major cause of morbidity and mortality in developing countries, contributing significantly to the global disease burden. Methods In this study, S. Typhi strains were isolated from 100 patients exhibiting symptoms of typhoid fever at a tertiary care hospital in Pakistan. Antimicrobial testing of all isolates was performed to determine the sensitivity and resistance pattern. Three MDR strains, namely QS194, QS430, and QS468, were subjected to whole genome sequencing for genomic characterization. Results and Discussion MLST analysis showed that QS194, belonged to ST19, which is commonly associated with Salmonella enterica serovar typhimurium. In contrast, QS430 and QS468, belonged to ST1, a sequence type frequently associated with S. Typhi. PlasmidFinder identified the presence of IncFIB(S) and IncFII(S) plasmids in QS194, while IncQ1 was found in QS468. No plasmid was detected in QS430. CARD-based analysis showed that the strains were largely resistant to a variety of antibiotics and disinfecting agents/antiseptics, including fluoroquinolones, cephalosporins, monobactams, cephamycins, penams, phenicols, tetracyclines, rifamycins, aminoglycosides, etc. The S. Typhi strains possessed various virulence factors, such as Vi antigen, Agf/Csg, Bcf, Fim, Pef, etc. The sequencing data indicated that the strains had antibiotic resistance determinants and shared common virulence factors. Pangenome analysis of the selected S. Typhi strains identified 13,237 genes, with 3,611 being core genes, 2,093 shell genes, and 7,533 cloud genes. Genome-based typing and horizontal gene transfer analysis revealed that the strains had different evolutionary origins and may have adapted to distinct environments or host organisms. These findings provide important insights into the genetic characteristics of S. Typhi strains and their potential association with various ecological niches and host organisms.
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Affiliation(s)
- Sareen Fatima
- Department of Microbiology, University of Balochistan, Quetta, Balochistan, Pakistan
| | - Zaara Ishaq
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology, (NUST), Islamabad, Pakistan
| | - Muhammad Irfan
- Jamil-ur-Rahman Center for Genome Research, International Center for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, Pakistan
| | - Abdullah F. AlAsmari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Jahangir Khan Achakzai
- Disipline of Biochemistry, Department of Natural and Basic Sciences, University of Turbat Kech, Balochistan, Pakistan
| | - Tahreem Zaheer
- Department of Biology, Indiana University Bloomington, Bloomington, IN, United States
| | - Amjad Ali
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology, (NUST), Islamabad, Pakistan
| | - Ali Akbar
- Department of Microbiology, University of Balochistan, Quetta, Balochistan, Pakistan
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Igiri BE, Okoduwa SIR, Munirat SA, Otu-Bassey IB, Bashir A, Onyiyioza OM, Enang IA, Okoduwa UJ. Diversity in Enteric Fever Diagnostic Protocols and Recommendation for Composite Reference Standard. IRANIAN JOURNAL OF MEDICAL MICROBIOLOGY 2023; 17:22-38. [DOI: 10.30699/ijmm.17.1.22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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Ain Q, Tahir M, Sadaqat A, Ayub A, Awan AB, Wajid M, Ali A, Iqbal M, Haque A, Sarwar Y. First Detection of Extensively Drug-Resistant Salmonella Typhi Isolates Harboring VIM and GES Genes for Carbapenem Resistance from Faisalabad, Pakistan. Microb Drug Resist 2022; 28:1087-1098. [DOI: 10.1089/mdr.2022.0094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Quratul Ain
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Mahnoor Tahir
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Amna Sadaqat
- Pediatric Medicine Unit, Allied Hospital, Faisalabad, Pakistan
| | - Ambreen Ayub
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Asad Bashir Awan
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Muhammad Wajid
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Aamir Ali
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Mazhar Iqbal
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
| | - Abdul Haque
- Akhuwat Faisalabad Institute for Research in Science and Technology, Faisalabad, Pakistan
| | - Yasra Sarwar
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, Pakistan
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Multiplex PCR assay to detect high risk lineages of Salmonella Typhi and Paratyphi A. PLoS One 2022; 17:e0267805. [PMID: 35867662 PMCID: PMC9307194 DOI: 10.1371/journal.pone.0267805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 04/14/2022] [Indexed: 11/19/2022] Open
Abstract
Enteric fever infections remain a significant public health issue, with up to 20 million infections per year. Increasing rates of antibiotic resistant strains have rendered many first-line antibiotics potentially ineffective. Genotype 4.3.1 (H58) is the main circulating lineage of S. Typhi in many South Asian countries and is associated with high levels of antibiotic resistance. The emergence and spread of extensively drug resistant (XDR) typhoid strains has increased the need for a rapid molecular test to identify and track these high-risk lineages for surveillance and vaccine prioritisation. Current methods require samples to be cultured for several days, followed by DNA extraction and sequencing to determine the specific lineage. We designed and evaluated the performance of a new multiplex PCR assay, targeting S. Paratyphi A as well as the H58 and XDR lineages of S. Typhi on a collection of bacterial strains. Our assay was 100% specific for the identification of lineage specific S. Typhi and S. Paratyphi A, when tested with a mix of non-Typhi Salmonella and non-Salmonella strains. With additional testing on clinical and environmental samples, this assay will allow rapid lineage level detection of typhoid of clinical significance, at a significantly lower cost to whole-genome sequencing. To our knowledge, this is the first report of a SNP-based multiplex PCR assay for the detection of lineage specific serovars of Salmonella Typhi.
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Salman HA, Abdulmohsen AM, Falih MN, Romi ZM. Detection of multidrug-resistant Salmonella enterica subsp. enterica serovar Typhi isolated from Iraqi subjects. Vet World 2021; 14:1922-1928. [PMID: 34475718 PMCID: PMC8404135 DOI: 10.14202/vetworld.2021.1922-1928] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 06/18/2021] [Indexed: 11/16/2022] Open
Abstract
Background and Aim Enteric fever initiated by Salmonella enterica subsp. enterica serovar Typhi (S. Typhi) is among the most consistent disease worldwide, particularly in developing countries. The present study aimed to isolate and identify S. Typhi from typhoid suspected patients and determine their antibacterial susceptibility testing. Materials and Methods Thirty blood samples were collected from typhoid suspected patients in Baghdad, Iraq. The samples were cultured on SS agar and XLD agar for screening of S. Typhi. The suspected colonies were picked up and subjected to Vitek 2 compact for biochemical identification and antibacterial susceptibility testing of the organisms. Molecular identification of the isolates was performed by real-time polymerase chain reaction (RT-PCR). Results Black colonies were observed on cultured plates. Out of 30 samples, 27 and 29 isolates were identified as S. Typhi using Vitek 2 compact and RT-PCR, respectively. The data of the present study revealed that the strains of S. Typhi were showing multidrug resistance. All S. Typhi strains exhibited resistance to penicillins (ticarcillin and piperacillin), cephalosporins 4th G (cefepime), and monobactam (aztreonam). However, all the strains showed susceptibility against carbapenems (imipenem and meropenem) and tetracycline (minocycline). Conclusion RT-PCR and Vitek 2 compact showed a high level of accuracy in the detection of S. Typhi. Multidrug resistance was observed, which is an alert for the reduction of antibiotic consumption.
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Affiliation(s)
- Hamzah Abdulrahman Salman
- Department of Medical Laboratory Techniques, College of Medical Sciences Techniques, The University of Mashreq, Baghdad, Iraq
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12
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Chmel M, Bartoš O, Beran O, Pajer P, Dresler J, Čurdová M, Holub M. Salmonella Paratyphi Infection: Use of Nanopore Sequencing as a Vivid Alternative for the Identification of Invading Bacteria. Prague Med Rep 2021; 122:96-105. [PMID: 34137685 DOI: 10.14712/23362936.2021.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
In our study we present an overview of the use of Oxford Nanopore Technologies (ONT) sequencing technology on the background of Enteric fever. Unlike traditional methods (e.g., qPCR, serological tests), the nanopore sequencing technology enables virtually real-time data generation and highly accurate pathogen identification and characterization. Blood cultures were obtained from a 48-year-old female patient suffering from a high fever, headache and diarrhea. Nevertheless, both the initial serological tests and stool culture appeared to be negative. Therefore, the bacterial isolate from blood culture was used for nanopore sequencing (ONT). This technique in combination with subsequent bioinformatic analyses allowed for prompt identification of the disease-causative agent as Salmonella enterica subsp. enterica serovar Paratyphi A. The National Reference Laboratory for Salmonella (NIPH) independently reported this isolate also as serovar Paratyphi A on the basis of results of biochemical and agglutination tests. Therefore, our results are in concordance with certified standards. Furthermore, the data enabled us to assess some basic questions concerning the comparative genomics, i.e., to describe whether the isolated strain differs from the formerly published ones or not. Quite surprisingly, these results indicate that we have detected a novel and so far, unknown variety of this bacteria.
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Affiliation(s)
- Martin Chmel
- Department of Infectious Diseases, First Faculty of Medicine, Charles University and Military University Hospital Prague, Prague, Czech Republic. .,Military Health Institute, Military Medical Agency, Prague, Czech Republic.
| | - Oldřich Bartoš
- Institute of Animal Physiology and Genetics, Laboratory of Fish Genetics, The Czech Academy of Sciences, Liběchov, Czech Republic.,Military Health Institute, Military Medical Agency, Prague, Czech Republic
| | - Ondřej Beran
- Department of Infectious Diseases, First Faculty of Medicine, Charles University and Military University Hospital Prague, Prague, Czech Republic
| | - Petr Pajer
- Military Health Institute, Military Medical Agency, Prague, Czech Republic
| | - Jiří Dresler
- Military Health Institute, Military Medical Agency, Prague, Czech Republic
| | - Martina Čurdová
- Department of Clinical Microbiology, Military University Hospital Prague, Prague, Czech Republic
| | - Michal Holub
- Department of Infectious Diseases, First Faculty of Medicine, Charles University and Military University Hospital Prague, Prague, Czech Republic
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Kim JH, Kim S, Hwang SH, Yoon TH, Park JS, Lee ES, Woo J, Park KS. Three-Way Junction-Induced Isothermal Amplification with High Signal-to-Background Ratio for Detection of Pathogenic Bacteria. SENSORS 2021; 21:s21124132. [PMID: 34208674 PMCID: PMC8235052 DOI: 10.3390/s21124132] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/10/2021] [Accepted: 06/12/2021] [Indexed: 11/30/2022]
Abstract
The consumption of water and food contaminated by pathogens is a major cause of numerous diseases and deaths globally. To control pathogen contamination and reduce the risk of illness, a system is required that can quickly detect and monitor target pathogens. We developed a simple and reproducible strategy, termed three-way junction (3WJ)-induced transcription amplification, to detect target nucleic acids by rationally combining 3WJ-induced isothermal amplification with a light-up RNA aptamer. In principle, the presence of the target nucleic acid generates a large number of light-up RNA aptamers (Spinach aptamers) through strand displacement and transcription amplification for 2 h at 37 °C. The resulting Spinach RNA aptamers specifically bind to fluorogens such as 3,5-difluoro-4-hydroxybenzylidene imidazolinone and emit a highly enhanced fluorescence signal, which is clearly distinguished from the signal emitted in the absence of the target nucleic acid. With the proposed strategy, concentrations of target nucleic acids selected from the genome of Salmonellaenterica serovar Typhi (S. Typhi) were quantitatively determined with high selectivity. In addition, the practical applicability of the method was demonstrated by performing spike-and-recovery experiments with S. Typhi in human serum.
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14
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Nucleic Acid-Based Lateral Flow Biosensor for Salmonella Typhi and Salmonella Paratyphi: A Detection in Stool Samples of Suspected Carriers. Diagnostics (Basel) 2021; 11:diagnostics11040700. [PMID: 33919817 PMCID: PMC8070779 DOI: 10.3390/diagnostics11040700] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/11/2021] [Accepted: 04/11/2021] [Indexed: 11/17/2022] Open
Abstract
A multiplex rapid detection system, based on a PCR-lateral flow biosensor (mPCR-LFB) was developed to identify Salmonella Typhi and Salmonella Paratyphi A from suspected carriers. The lower detection limit for S. Typhi and S. Paratyphi A was 0.16 and 0.08 ng DNA equivalent to 10 and 102 CFU/mL, respectively. Lateral flow biosensor was used for visual detection of mPCR amplicons (stgA, SPAint, ompC, internal amplification control) by labeling forward primers with fluorescein-isothiocyanate (FITC), Texas Red, dinitrophenol (DNP) and digoxigenin (DIG) and reverse primers with biotin. Binding of streptavidin-colloidal gold conjugate with the amplicons resulted in formation of a red color dots on the strip after 15-20 min of sample exposure. The nucleic acid lateral flow analysis of the mPCR-LFB was better in sensitivity and more rapid than the conventional agarose gel electrophoresis. Moreover, the mPCR-LFB showed 100% sensitivity and specificity when evaluated with stools spiked with 100 isolates of Salmonella genus and other bacteria. A prospective cohort study on stool samples of 1176 food handlers in outbreak areas (suspected carriers) resulted in 23 (2%) positive for S. Typhi. The developed assay has potential to be used for rapid detection of typhoid carriers in surveillance program.
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15
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Enteric Fever Diagnosis: Current Challenges and Future Directions. Pathogens 2021; 10:pathogens10040410. [PMID: 33915749 PMCID: PMC8065732 DOI: 10.3390/pathogens10040410] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 03/23/2021] [Accepted: 03/27/2021] [Indexed: 12/21/2022] Open
Abstract
Enteric fever is a life-threatening systemic febrile disease caused by Salmonella enterica serovars Typhi and Paratyphi (S. Typhi and S. Paratyphi). Unfortunately, the burden of the disease remains high primarily due to the global spread of various drug-resistant Salmonella strains despite continuous advancement in the field. An accurate diagnosis is critical for effective control of the disease. However, enteric fever diagnosis based on clinical presentations is challenging due to overlapping symptoms with other febrile illnesses that are also prevalent in endemic areas. Current laboratory tests display suboptimal sensitivity and specificity, and no diagnostic methods are available for identifying asymptomatic carriers. Several research programs have employed systemic approaches to identify more specific biomarkers for early detection and asymptomatic carrier detection. This review discusses the pros and cons of currently available diagnostic tests for enteric fever, the advancement of research toward improved diagnostic tests, and the challenges of discovering new ideal biomarkers and tests.
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16
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Pouzol S, Tanmoy AM, Ahmed D, Khanam F, Brooks WA, Bhuyan GS, Fabre L, Bryant JE, Gustin MP, Vanhems P, Carman B, Weill FX, Qadri F, Saha S, Endtz H. Clinical Evaluation of a Multiplex PCR for the Detection of Salmonella enterica Serovars Typhi and Paratyphi A from Blood Specimens in a High-Endemic Setting. Am J Trop Med Hyg 2020; 101:513-520. [PMID: 31287048 PMCID: PMC6726943 DOI: 10.4269/ajtmh.18-0992] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Enteric fever is a major public health concern in endemic areas, particularly in infrastructure-limited countries where Salmonella Paratyphi A has emerged in increasing proportion of cases. We aimed to evaluate a method to detect Salmonella Typhi (S. Typhi) and Salmonella Paratyphi A (S. Paratyphi A) in febrile patients in Bangladesh. We conducted a prospective study enrolling patients with fever > 38°C admitted to two large urban hospitals and two outpatient clinics located in Dhaka, Bangladesh. We developed and evaluated a method combining short culture with a new molecular assay to simultaneously detect and differentiate S. Typhi and S. Paratyphi A from other Salmonella directly from 2 to 4 mL of whole blood in febrile patients (n = 680). A total of 680 cases were enrolled from the four participating sites. An increase in the detection rate (+38.8%) in S. Typhi and S. Paratyphi A was observed with a multiplex polymerase chain reaction (PCR) assay, and absence of non-typhoidal Salmonella detection was reported. All 45 healthy controls were culture and PCR negative, generating an estimated 92.9% of specificity on clinical samples. When clinical performance was assessed in the absence of blood volume prioritization for testing, a latent class model estimates clinical performance ≥ 95% in sensitivity and specificity with likelihood ratio (LR) LR+ > 10 and LR− < 0.1 for the multiplex PCR assay. The alternative method to blood culture we developed may be useful alone or in combination with culture or serological tests for epidemiological studies in high disease burden settings and should be considered as secondary endpoint test for future vaccine trials.
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Affiliation(s)
- Stephane Pouzol
- Laboratoire des Pathogènes Emergents, Fondation Mérieux, Centre International de Recherche en Infectiologie (CIRI), Lyon, France
| | - Arif Mohammad Tanmoy
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC, Rotterdam, The Netherlands.,Child Health Research Foundation (CHRF), Dhaka, Bangladesh
| | - Dilruba Ahmed
- International Centre for Diarrhoeal Disease Research (icddr,b), Dhaka, Bangladesh
| | - Farhana Khanam
- International Centre for Diarrhoeal Disease Research (icddr,b), Dhaka, Bangladesh
| | - W Abdullah Brooks
- Department of International Health, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland
| | - Golam Sarower Bhuyan
- Institute for Developing Science and Health Initiatives (ideSHi), Dhaka, Bangladesh
| | - Laetitia Fabre
- Unité des Bactéries Pathogènes Entériques, Institut Pasteur, Paris, France
| | - Juliet E Bryant
- Laboratoire des Pathogènes Emergents, Fondation Mérieux, Centre International de Recherche en Infectiologie (CIRI), Lyon, France
| | - Marie-Paule Gustin
- Department of Public Health, Institute of Pharmacy, University of Lyon 1, Lyon, France.,Laboratoire des Pathogènes Emergents, Fondation Mérieux, Centre International de Recherche en Infectiologie (CIRI), Lyon, France
| | - Philippe Vanhems
- Service d'Hygiène, Epidémiologie et Prévention, Hôpital Edouard Herriot, Hospices Civils de Lyon, Lyon, France.,Laboratoire des Pathogènes Emergents, Fondation Mérieux, Centre International de Recherche en Infectiologie (CIRI), Lyon, France
| | - Bill Carman
- Fast Track Diagnostics, Esch sur alzette, Esch-sur-Alzette, Luxembourg
| | | | - Firdausi Qadri
- International Centre for Diarrhoeal Disease Research (icddr,b), Dhaka, Bangladesh
| | - Samir Saha
- Child Health Research Foundation (CHRF), Dhaka, Bangladesh
| | - Hubert Endtz
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC, Rotterdam, The Netherlands.,Laboratoire des Pathogènes Emergents, Fondation Mérieux, Centre International de Recherche en Infectiologie (CIRI), Lyon, France
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17
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Paramasivam OR, Trivedi S, Sangith N, Sankaran K. Active sulfite oxidase domain of Salmonella enterica pathogenic protein small intestine invasive factor E (SiiE): a potential diagnostic target. Appl Microbiol Biotechnol 2019; 103:5679-5688. [PMID: 31104097 DOI: 10.1007/s00253-019-09894-w] [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: 03/05/2019] [Revised: 04/23/2019] [Accepted: 04/29/2019] [Indexed: 10/26/2022]
Abstract
Serovars of Salmonella enterica are common food-borne bacterial pathogens. Salmonella typhi, which causes typhoid, is the most dangerous of them. Though detailed molecular pathogenesis studies reveal many virulence factors, inability to identify their biochemical functions hampers the development of diagnostic methods and therapeutic leads. Lack of quicker diagnosis is an impediment in starting early antibiotic treatment to reduce the severe morbidity and mortality in typhoid. In this study, employing bioinformatic prediction, biochemical analysis, and recombinantly cloning the active region, we show that extracellularly secreted virulence-associated protein, small intestinal invasion factor E (SiiE), possesses a sulfite oxidase (SO) domain that catalyzes the conversion of sodium sulfite to sodium sulfate using tungsten as the cofactor. This activity common to Salmonella enterica serovars seems to be specific to them from bioinformatic analysis of available bacterial genomes. Along with the ability of this large non-fimbrial adhesin of 600 kDa binding to sialic acid on the host cells, this activity could aid in subverting the host defense mechanism by destroying sulfites released by the immune cells and colonize the host gastrointestinal epithelium. Being an extracellular enzyme, it could be an ideal candidate for developing diagnostics of S. enterica, particularly S. typhi.
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Affiliation(s)
| | - Swati Trivedi
- Centre for Biotechnology, Anna University, Chennai, 600020, India
| | - Nikhil Sangith
- Centre for Biotechnology, Anna University, Chennai, 600020, India.
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18
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SAMAD ABDUL, ABBAS FERHAT, TANVEER ZUNERA, AHMAD ZAFAR, AHMAD IRSHAD, PATCHING SIMONG, NAWAZ NIGHAT, ASMAT MUHAMMADTAUSEEF, RAZIQ ABDUL, LAH ASADUL, SHEIKH IRFANSHAHZAD, NAEEM MUHAMMAD, POKRYSHKO OLENA, MUSTAFA MOHAMMADZAHID. Prevalence of Salmonella spp. in chicken meat from Quetta retail outlets and typing through multiplex PCR. ROMANIAN BIOTECHNOLOGICAL LETTERS 2019. [DOI: 10.25083/rbl/24.2/271.279] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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19
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Gal-Mor O. Persistent Infection and Long-Term Carriage of Typhoidal and Nontyphoidal Salmonellae. Clin Microbiol Rev 2019; 32:e00088-18. [PMID: 30487167 PMCID: PMC6302356 DOI: 10.1128/cmr.00088-18] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The ability of pathogenic bacteria to affect higher organisms and cause disease is one of the most dramatic properties of microorganisms. Some pathogens can establish transient colonization only, but others are capable of infecting their host for many years or even for a lifetime. Long-term infection is called persistence, and this phenotype is fundamental for the biology of important human pathogens, including Helicobacter pylori, Mycobacterium tuberculosis, and Salmonella enterica Both typhoidal and nontyphoidal serovars of the species Salmonella enterica can cause persistent infection in humans; however, as these two Salmonella groups cause clinically distinct diseases, the characteristics of their persistent infections in humans differ significantly. Here, following a general summary of Salmonella pathogenicity, host specificity, epidemiology, and laboratory diagnosis, I review the current knowledge about Salmonella persistence and discuss the relevant epidemiology of persistence (including carrier rate, duration of shedding, and host and pathogen risk factors), the host response to Salmonella persistence, Salmonella genes involved in this lifestyle, as well as genetic and phenotypic changes acquired during prolonged infection within the host. Additionally, I highlight differences between the persistence of typhoidal and nontyphoidal Salmonella strains in humans and summarize the current gaps and limitations in our understanding, diagnosis, and curing of persistent Salmonella infections.
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Affiliation(s)
- Ohad Gal-Mor
- Infectious Diseases Research Laboratory, Sheba Medical Center, Tel-Hashomer, Israel
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
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20
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Ajibola O, Mshelia MB, Gulumbe BH, Eze AA. Typhoid Fever Diagnosis in Endemic Countries: A Clog in the Wheel of Progress? MEDICINA (KAUNAS, LITHUANIA) 2018; 54:E23. [PMID: 30344254 PMCID: PMC6037256 DOI: 10.3390/medicina54020023] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 04/17/2018] [Accepted: 04/19/2018] [Indexed: 12/27/2022]
Abstract
Typhoid fever causes significant morbidity and mortality in developing countries, with inaccurate estimates in some countries affected, especially those situated in Sub-Saharan Africa. Disease burden assessment is limited by lack of a high degree of sensitivity and specificity by many current rapid diagnostic tests. Some of the new technologies, such as PCR and proteomics, may also be useful but are difficult for low-resource settings to apply as point-of-care diagnostics. Weak laboratory surveillance systems may also contribute to the spread of multidrug resistant Salmonella serovar Typhi across endemic areas. In addition, most typhoid-endemic countries employ serological tests that have low sensitivity and specificity making diagnosis unreliable. Here we review currently available typhoid fever diagnostics, and advances in serodiagnosis of S. Typhi.
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Affiliation(s)
- Olumide Ajibola
- Department of Microbiology, Faculty of Science, Federal University Birnin Kebbi, P.M.B. 1157 Kalgo, Kebbi State, Nigeria.
| | - Mari B Mshelia
- Department of Microbiology, Faculty of Science, Federal University Birnin Kebbi, P.M.B. 1157 Kalgo, Kebbi State, Nigeria.
| | - Bashar H Gulumbe
- Department of Microbiology, Faculty of Science, Federal University Birnin Kebbi, P.M.B. 1157 Kalgo, Kebbi State, Nigeria.
| | - Anthonius A Eze
- Department of Medical Biochemistry, University of Nigeria, Enugu Campus, Enugu 400241, Nigeria.
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21
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Straub J, Paula H, Mayr M, Kasper D, Assadian O, Berger A, Rittenschober-Böhm J. Diagnostic accuracy of the ROCHE Septifast PCR system for the rapid detection of blood pathogens in neonatal sepsis-A prospective clinical trial. PLoS One 2017; 12:e0187688. [PMID: 29117261 PMCID: PMC5678863 DOI: 10.1371/journal.pone.0187688] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 10/24/2017] [Indexed: 12/03/2022] Open
Abstract
Introduction Diagnosis of neonatal sepsis remains a major challenge in neonatology. Most molecular-based methods are not customized for neonatal requirements. The aim of the present study was to assess the diagnostic accuracy of a modified multiplex PCR protocol for the detection of neonatal sepsis using small blood volumes. Methods 212 episodes of suspected neonatal late onset sepsis were analyzed prospectively using the Roche SeptiFast® MGRADE PCR with a modified DNA extraction protocol and software-handling tool. Results were compared to blood culture, laboratory biomarkers and clinical signs of sepsis. Results Of 212 episodes, 85 (40.1%) were categorized as “not infected”. Among these episodes, 1 was false positive by blood culture (1.2%) and 23 were false positive by PCR (27.1%). Of 51 (24.1%) episodes diagnosed as “culture proven sepsis”, the same pathogen was detected by blood culture and PCR in 39 episodes (76.5%). In 8 episodes, more pathogens were detected by PCR compared to blood culture, and in 4 episodes the pathogen detected by blood culture was not found by PCR. One of these episodes was caused by Bacillus cereus, a pathogen not included in the PCR panel. In 76/212 (35.8%) episodes, clinical sepsis was diagnosed. Among these, PCR yielded positive results in 39.5% of episodes (30/76 episodes). For culture-positive sepsis, PCR showed a sensitivity of 90.2% (95%CI 86.2–94.2%) and a specificity of 72.9% (95%CI 67.0–79.0%). Conclusion The Roche SeptiFast® MGRADE PCR using a modified DNA extraction protocol showed acceptable results for rapid detection of neonatal sepsis in addition to conventional blood culture. The benefit of rapid pathogen detection has to be balanced against the considerable risk of contamination, loss of information on antibiotic sensitivity pattern and increased costs.
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Affiliation(s)
- Julia Straub
- Department of Pediatrics and Adolescent Medicine, Division of Neonatology, Pediatric Intensive Care and Neuropediatrics, Medical University Vienna, Vienna, Austria
| | - Helga Paula
- Department of Hospital Epidemiology and Infection Control, Medical University Vienna, Vienna, Austria
| | - Michaela Mayr
- Department of Pediatrics and Adolescent Medicine, Division of Neonatology, Pediatric Intensive Care and Neuropediatrics, Medical University Vienna, Vienna, Austria
| | - David Kasper
- Department of Pediatrics and Adolescent Medicine, Research Core Unit of Pediatric Biochemistry and Analytics, Medical University Vienna, Vienna, Austria
| | - Ojan Assadian
- Department of Hospital Epidemiology and Infection Control, Medical University Vienna, Vienna, Austria
| | - Angelika Berger
- Department of Pediatrics and Adolescent Medicine, Division of Neonatology, Pediatric Intensive Care and Neuropediatrics, Medical University Vienna, Vienna, Austria
| | - Judith Rittenschober-Böhm
- Department of Pediatrics and Adolescent Medicine, Division of Neonatology, Pediatric Intensive Care and Neuropediatrics, Medical University Vienna, Vienna, Austria
- * E-mail:
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22
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Tung HY, Chen WC, Ou BR, Yeh JY, Cheng YH, Tsng PH, Hsu MH, Tsai MS, Liang YC. Simultaneous detection of multiple pathogens by multiplex PCR coupled with DNA biochip hybridization. Lab Anim 2017; 52:186-195. [PMID: 28691600 DOI: 10.1177/0023677217718864] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Traditional serological enzyme-linked immunosorbent assay (ELISA) is routinely used to monitor pathogens during quarantine in most animal facilities to prevent possible infection. However, the ELISA platform is a single-target assay, and screening all targeted pathogens is time-consuming and laborious. In this study, to increase sensitivity and to reduce diagnosis time for high-throughput processes, multiplex PCR and DNA biochip techniques were combined to develop a multi-pathogen diagnostic method for use instead of routine ELISA. Eight primer sets were designed for multiplex PCR to detect genes from seven targeted bacterial and viral pathogens. DNA-DNA hybridization was conducted on a biochip following the multiple PCR analysis. Using this method, a total of 24 clinical samples were tested, and the result showed that not only single infection but also co-infection by multi-pathogens can be detected. In conclusion, multiplex PCR coupled with a DNA biochip is an efficient method for detecting multi-pathogens in a reaction. This platform is a useful tool for quarantine services and disease prevention in animal facilities.
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Affiliation(s)
- Hsiang-Yun Tung
- 1 College of Biotechnology and Bioresources, Dayeh University, Changhua, Taiwan
| | - Wei-Chen Chen
- 2 Agricultural Biotechnology Research Center, Academia Sinica, Nankang, Taipei, Taiwan
| | - Bor-Rung Ou
- 3 Department of Animal Science and Biotechnology, Tunghai University, Taichung, Taiwan
| | - Jan-Ying Yeh
- 4 Department of Post-Baccalaureate Veterinary Medicine, Asia University, Wufeng Taichung, Taiwan.,5 Food Safety and Inspection Center, Asia University, Wufeng Taichung, Taiwan
| | - Yeong-Hsiang Cheng
- 6 Department of Biotechnology and Animal Science, National I-Lan University, I-Lan, Taiwan
| | - Ping-Hua Tsng
- 7 GeneReach Biotechnology Corporation, Taichung, Taiwan
| | - Ming-Hua Hsu
- 8 Nuclear Science and Technology Development Center, National Tsing Hua University, Hsinchu, Taiwan
| | - Ming-Shiun Tsai
- 1 College of Biotechnology and Bioresources, Dayeh University, Changhua, Taiwan
| | - Yu-Chuan Liang
- 2 Agricultural Biotechnology Research Center, Academia Sinica, Nankang, Taipei, Taiwan
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23
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Prabagaran SR, Kalaiselvi V, Chandramouleeswaran N, Deepthi KNG, Brahmadathan KN, Mani M. Molecular diagnosis of Salmonella typhi and its virulence in suspected typhoid blood samples through nested multiplex PCR. J Microbiol Methods 2017; 139:150-154. [PMID: 28545919 DOI: 10.1016/j.mimet.2017.05.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 05/19/2017] [Accepted: 05/22/2017] [Indexed: 10/19/2022]
Abstract
A nested multiplex polymerase chain reaction (PCR) based diagnosis was developed for the detection of virulent Salmonella typhi in the blood specimens from patients suspected for typhoid fever. After the Widal test, two pairs of primers were used for the detection of flagellin gene (fliC) of S. typhi. Among them, those positive for fliC alone were subjected to identification of genes in Via B operon of Salmonella Pathogenesity Island (SPI-7) where four primer pairs were used to detect tviA and tviB genes. Among 250 blood samples tested, 115 were positive by fliC PCR; 22 of these were negative for tviA and tviB. Hence, the method described here can be used to diagnose the incidence of Vi-negative serovar typhi especially in endemic regions where the Vi vaccine is administered.
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Affiliation(s)
| | - Vellingiri Kalaiselvi
- Department of Biotechnology, Bharathiar University, Coimbatore, Tamilnadu 641 046, India
| | | | | | | | - Mariappa Mani
- Microbiological Laboratory, Cowley Brown Road (East), R. S. Puram, Coimbatore- 641 002, India
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24
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Darton TC, Zhou L, Blohmke CJ, Jones C, Waddington CS, Baker S, Pollard AJ. Blood culture-PCR to optimise typhoid fever diagnosis after controlled human infection identifies frequent asymptomatic cases and evidence of primary bacteraemia. J Infect 2017; 74:358-366. [PMID: 28130144 PMCID: PMC5345565 DOI: 10.1016/j.jinf.2017.01.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 01/11/2017] [Accepted: 01/14/2017] [Indexed: 01/09/2023]
Abstract
Background Improved diagnostics for typhoid are needed; a typhoid controlled human infection model may accelerate their development and translation. Here, we evaluated a blood culture-PCR assay for detecting infection after controlled human infection with S. Typhi and compared test performance with optimally performed blood cultures. Methodology/Principal findings Culture-PCR amplification of blood samples was performed alongside daily blood culture in 41 participants undergoing typhoid challenge. Study endpoints for typhoid diagnosis (TD) were fever and/or bacteraemia. Overall, 24/41 (59%) participants reached TD, of whom 21/24 (86%) had ≥1 positive blood culture (53/674, 7.9% of all cultures) or 18/24 (75%) had ≥1 positive culture-PCR assay result (57/684, 8.3%). A further five non-bacteraemic participants produced culture-PCR amplicons indicating infection; overall sensitivity/specificity of the assay compared to the study endpoints were 70%/65%. We found no significant difference between blood culture and culture-PCR methods in ability to identify cases (12 mismatching pairs, p = 0.77, binomial test). Clinical and stool culture metadata demonstrated that additional culture-PCR amplification positive individuals likely represented true cases missed by blood culture, suggesting the overall attack rate may be 30/41 (73%) rather than 24/41 (59%). Several participants had positive culture-PCR results soon after ingesting challenge providing new evidence for occurrence of an early primary bacteraemia. Conclusions/Significance Overall the culture-PCR assay performed well, identifying extra typhoid cases compared with routine blood culture alone. Despite limitations to widespread field-use, the benefits of increased diagnostic yield, reduced blood volume and faster turn-around-time, suggest that this assay could enhance laboratory typhoid diagnostics in research applications and high-incidence settings. Culture in ox-bile/tryptone soy broth selectively enriches for bile-tolerant Salmonella Typhi while lysing human cells. PCR sensitivity for detecting typhoid in clinical blood is limited by very low level bacteraemia during clinical illness. PCR amplification of S. Typhi fliC-d in pre-cultured blood can accurately identify typhoid infection in challenge study participants. Daily culture-PCR of blood collected from challenge study participants suggests primary bacteraemia occurs 12–36 h after S. Typhi ingestion. Additional use of culture-PCR demonstrates the true attack rate after typhoid challenge is markedly higher (75%) than previously assumed (60%).
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Affiliation(s)
- Thomas C Darton
- Oxford Vaccine Group, Department of Paediatrics and the NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom; The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam.
| | - Liqing Zhou
- Oxford Vaccine Group, Department of Paediatrics and the NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Christoph J Blohmke
- Oxford Vaccine Group, Department of Paediatrics and the NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Claire Jones
- Oxford Vaccine Group, Department of Paediatrics and the NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Claire S Waddington
- Oxford Vaccine Group, Department of Paediatrics and the NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
| | - Stephen Baker
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam; Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, United Kingdom
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics and the NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, United Kingdom
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25
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Identification of Five Novel Salmonella Typhi-Specific Genes as Markers for Diagnosis of Typhoid Fever Using Single-Gene Target PCR Assays. BIOMED RESEARCH INTERNATIONAL 2016; 2016:8905675. [PMID: 27975062 PMCID: PMC5126401 DOI: 10.1155/2016/8905675] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 09/27/2016] [Accepted: 10/18/2016] [Indexed: 12/21/2022]
Abstract
Salmonella Typhi (S. Typhi) causes typhoid fever which is a disease characterised by high mortality and morbidity worldwide. In order to curtail the transmission of this highly infectious disease, identification of new markers that can detect the pathogen is needed for development of sensitive and specific diagnostic tests. In this study, genomic comparison of S. Typhi with other enteric pathogens was performed, and 6 S. Typhi genes, that is, STY0201, STY0307, STY0322, STY0326, STY2020, and STY2021, were found to be specific in silico. Six PCR assays each targeting a unique gene were developed to test the specificity of these genes in vitro. The diagnostic sensitivities and specificities of each assay were determined using 39 S. Typhi, 62 non-Typhi Salmonella, and 10 non-Salmonella clinical isolates. The results showed that 5 of these genes, that is, STY0307, STY0322, STY0326, STY2020, and STY2021, demonstrated 100% sensitivity (39/39) and 100% specificity (0/72). The detection limit of the 5 PCR assays was 32 pg for STY0322, 6.4 pg for STY0326, STY2020, and STY2021, and 1.28 pg for STY0307. In conclusion, 5 PCR assays using STY0307, STY0322, STY0326, STY2020, and STY2021 were developed and found to be highly specific at single-gene target resolution for diagnosis of typhoid fever.
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Tröger B, Härtel C, Buer J, Dördelmann M, Felderhoff-Müser U, Höhn T, Hepping N, Hillebrand G, Kribs A, Marissen J, Olbertz D, Rath PM, Schmidtke S, Siegel J, Herting E, Göpel W, Steinmann J, Stein A. Clinical Relevance of Pathogens Detected by Multiplex PCR in Blood of Very-Low-Birth Weight Infants with Suspected Sepsis - Multicentre Study of the German Neonatal Network. PLoS One 2016; 11:e0159821. [PMID: 27472282 PMCID: PMC4966931 DOI: 10.1371/journal.pone.0159821] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 07/09/2016] [Indexed: 11/18/2022] Open
Abstract
Introduction In the German Neonatal Network (GNN) 10% of very-low-birth weight infants (VLBWI) suffer from blood-culture confirmed sepsis, while 30% of VLBWI develop clinical sepsis. Diagnosis of sepsis is a difficult task leading to potential over-treatment with antibiotics. This study aims to investigate whether the results of blood multiplex-PCR (SeptiFast®) for common sepsis pathogens are relevant for clinical decision making when sepsis is suspected in VLBWI. Methods We performed a prospective, multi-centre study within the GNN including 133 VLBWI with 214 episodes of suspected late onset sepsis (LOS). In patients with suspected sepsis a multiplex-PCR (LightCycler SeptiFast MGRADE-test®) was performed from 100 μl EDTA blood in addition to center-specific laboratory biomarkers. The attending neonatologist documented whether the PCR-result, which was available after 24 to 48 hrs, had an impact on the choice of antibiotic drugs and duration of therapy. Results PCR was positive in 110/214 episodes (51%) and blood culture (BC) was positive in 55 episodes (26%). Both methods yielded predominantly coagulase-negative staphylococci (CoNS) followed by Escherichia coli and Staphylococcus aureus. In 214 BC—PCR paired samples concordant results were documented in 126 episodes (59%; n = 32 were concordant pathogen positive results, n = 94 were negative in both methods). In 65 episodes (30%) we found positive PCR results but negative BCs, with CoNS being identified in 43 (66%) of these samples. Multiplex-PCR results influenced clinical decision making in 30% of episodes, specifically in 18% for the choice of antimicrobial therapy and in 22% for the duration of antimicrobial therapy. Conclusions Multiplex-PCR results had a moderate impact on clinical management in about one third of LOS-episodes. The main advantage of multiplex-PCR was the rapid detection of pathogens from micro-volume blood samples. In VLBWI limitations include risk of contamination, lack of resistance testing and high costs. The high rate of positive PCR results in episodes of negative BC might lead to overtreatment of infants which is associated with risk of mortality, antibiotic resistance, fungal sepsis and NEC.
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Affiliation(s)
- Birte Tröger
- Department of Pediatrics at the University of Lübeck, Lübeck, Germany
- * E-mail:
| | - Christoph Härtel
- Department of Pediatrics at the University of Lübeck, Lübeck, Germany
| | - Jan Buer
- Institute of Medical Microbiology, University of Duisburg-Essen, Essen, Germany
| | - Michael Dördelmann
- Department of Pediatrics at Diakonissen Hospital Flensburg, Flensburg, Germany
| | - Ursula Felderhoff-Müser
- Department of Pediatrics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Thomas Höhn
- Department of Pediatrics at the University of Düsseldorf, Düsseldorf, Germany
| | - Nico Hepping
- Department of Pediatrics at St. Marien Hospital Bonn, Bonn, Germany
| | - Georg Hillebrand
- Department of Pediatrics at Hospital of Itzehoe, Itzehoe, Germany
| | - Angela Kribs
- Department of Pediatrics at the University of Cologne, Cologne, Germany
| | - Janina Marissen
- Department of Pediatrics at the University of Lübeck, Lübeck, Germany
| | - Dirk Olbertz
- Neonatology Unit at Südstadt Hospital Rostock, Rostock, Germany
| | - Peter-Michael Rath
- Institute of Medical Microbiology, University of Duisburg-Essen, Essen, Germany
| | - Susanne Schmidtke
- Neonatology Unit at Asclepios Hospital Hamburg-Barmbek, Hamburg, Germany
| | - Jens Siegel
- Neonatology Unit at the Children´s Hospital Hannover Auf der Bult, Hannover, Germany
| | - Egbert Herting
- Department of Pediatrics at the University of Lübeck, Lübeck, Germany
| | - Wolfgang Göpel
- Department of Pediatrics at the University of Lübeck, Lübeck, Germany
| | - Joerg Steinmann
- Institute of Medical Microbiology, University of Duisburg-Essen, Essen, Germany
| | - Anja Stein
- Department of Pediatrics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
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Das S, Ray U, Akhter I, Chattopadhyay A, Paul DK, Dutta S. Evaluation of fliC-d based direct blood PCR assays for typhoid diagnosis. BMC Microbiol 2016; 16:108. [PMID: 27296619 PMCID: PMC4906692 DOI: 10.1186/s12866-016-0723-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 06/01/2016] [Indexed: 12/18/2022] Open
Abstract
Background Typhoid cases need to be diagnosed accurately for early antibiotic therapy and reducing mortality. Identification of Salmonella Typhi (S. Typhi) in blood culture is conclusive, but has poor sensitivity. Detection of S. Typhi by PCR from blood sample has shown promise. Real-time quantitative PCR (Q-PCR) has been widely used in diagnostics for its rapidity and reliability. In the present study, the performance of molecular methods like conventional PCR (C-PCR), nested PCR (N-PCR) and Q-PCR were investigated and compared by targeting S. Typhi specific flagellar fliC-d gene directly in blood samples for typhoid diagnosis. Results Analytical sensitivities and specificities of the PCR assays were determined under laboratory condition followed by diagnostic performances were demonstrated in 110 clinically diagnosed typhoid fever (CDTF) cases included as study subjects. The DNA detection limit of C-PCR was observed 3 × 104 copies/reaction; those of N-PCR and Q-PCR (cutoff Ct value, ≤37) were 3 copies/reaction. The C-PCR was not further evaluated since it showed negative results with all clinical samples due to low sensitivity. Low isolation rate (21.8 %, 24/110) of S. Typhi by blood culture did not reflect the true burden of typhoid fever among the study subjects. Hence diagnostic performances of N-PCR and Q-PCR were determined considering CDTF cases positive by any of the diagnostic assay methods (n = 81) as true positives. Laboratory confirmed non-typhoidal cases (n = 29) were included as true negatives. On comparison, although both the assays were 100 % specific; sensitivity (91.4 % vs. 81.5 %) and efficiency (93.6 % vs. 86.4 %) of Q-PCR were better, but statistically not significant (p > 0.1) than N-PCR. The positive and negative likelihood ratios of Q-PCR were ∞ and 0.09 which indicated the potential clinical utility of Q-PCR for typhoid diagnosis. Q-PCR was more rapid than N-PCR (2 h vs. 6 h) in obtaining test results. Conclusions This study demonstrates for the first time that TaqMan-based Q-PCR assay performs more favorably than N-PCR for direct detection of S. Typhi DNA in blood samples. Direct and quantitative blood Q-PCR is a rapid and reliable method for diagnosis of typhoid fever.
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Affiliation(s)
- Surojit Das
- Bacteriology Division, National Institute of Cholera and Enteric Diseases, P-33, CIT Road, Scheme XM, Beliaghata, P.O. Box 177, Kolkata, 700010, West Bengal, India
| | - Ujjwayini Ray
- Microbiology Division, Apollo Gleneagles Hospitals, Kolkata, West Bengal, India
| | - Irfaan Akhter
- Clinical Division, Dr. B. C. Roy Memorial Post Graduate Institute of Pediatric Sciences, Kolkata, West Bengal, India
| | - Arka Chattopadhyay
- Department of Instrumentation and Electronics Engineering, Jadavpur University, Kolkata, West Bengal, India
| | - Dilip Kumar Paul
- Clinical Division, Dr. B. C. Roy Memorial Post Graduate Institute of Pediatric Sciences, Kolkata, West Bengal, India
| | - Shanta Dutta
- Bacteriology Division, National Institute of Cholera and Enteric Diseases, P-33, CIT Road, Scheme XM, Beliaghata, P.O. Box 177, Kolkata, 700010, West Bengal, India.
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Rehman A, Sarwar Y, Raza ZA, Hussain SZ, Mustafa T, Khan WS, Ghauri MA, Haque A, Hussain I. Metal nanoparticle assisted polymerase chain reaction for strain typing of Salmonella Typhi. Analyst 2016; 140:7366-72. [PMID: 26381602 DOI: 10.1039/c5an01286d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Salmonella enterica serotype Typhi (S. Typhi) is the causative agent of typhoid fever and remains a major health threat in most of the developing countries. The prompt diagnosis of typhoid directly from the patient's blood requires high level of sensitivity and specificity. Some of us were the first to report PCR based diagnosis of typhoid. This approach has since then been reported by many scientists using different genomic targets. Since the number of bacteria circulating in the blood of a patient can be as low as 0.3 cfu ml(-1), there is always a room for improvement in diagnostic PCR. In the present study, the role of different types of nanoparticles was investigated to improve the existing PCR based methods for diagnosis and strain typing of S. Typhi (targeting Variable Number of Tandem Repeats [VNTR]) by using optimized PCR systems. Three different types of nanoparticles were used i.e., citrate stabilized gold nanoparticles, rhamnolipid stabilized gold and silver nanoparticles, and magnetic iron oxide nanoparticles. The non-specific amplification was significantly reduced in VNTR typing when gold and silver nanoparticles were used in an appropriate concentration. More importantly, the addition of nanoparticles decreased the non-specificity to a significant level in the case of multiplex PCR thus further validating the reliability of PCR for the diagnosis of typhoid.
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Affiliation(s)
- Asma Rehman
- Nanobiotech Group, National Institute for Biotechnology & Genetic Engineering (NIBGE), Jhang Road, Faisalabad, Pakistan
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Development of a Simple, Peripheral-Blood-Based Lateral-Flow Dipstick Assay for Accurate Detection of Patients with Enteric Fever. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2016; 23:403-409. [PMID: 26961857 DOI: 10.1128/cvi.00690-15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Accepted: 02/29/2016] [Indexed: 11/20/2022]
Abstract
Enteric fever is a systemic infection caused by typhoidal strains of Salmonella enterica and is a significant cause of mortality and morbidity in many parts of the world, especially in resource-limited areas. Unfortunately, currently available diagnostic tests for enteric fever lack sensitivity and/or specificity. No true clinically practical gold standard for diagnosing patients with enteric fever exists. Unfortunately, microbiologic culturing of blood is only 30 to 70% sensitive although 100% specific. Here, we report the development of a lateral-flow immunochromatographic dipstick assay based on the detection of Salmonella enterica serovar Typhi (S Typhi) lipopolysaccharide (LPS)-specific IgG in lymphocyte culture secretion. We tested the assay using samples from 142 clinically suspected enteric fever patients, 28 healthy individuals residing in a zone where enteric fever is endemic, and 35 patients with other febrile illnesses. In our analysis, the dipstick detected all blood culture-confirmed S Typhi cases (48/48) and 5 of 6 Salmonella enterica serovar Paratyphi A blood cultured-confirmed cases. The test was negative in all 35 individuals febrile with other illnesses and all 28 healthy controls from the zone of endemicity. The test was positive in 19 of 88 individuals with suspected enteric fever but with negative blood cultures. Thus, the dipstick had a sensitivity of 98% compared to blood culture results and a specificity that ranged from 78 to 100% (95% confidence interval [CI], 70 to 100%), depending on the definition of a true negative. These results suggest that this dipstick assay can be very useful for the detection of enteric fever patients especially in regions of endemicity.
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Iyer P, Barreto SG, Sahoo B, Chandrani P, Ramadwar MR, Shrikhande SV, Dutt A. Non-typhoidal Salmonella DNA traces in gallbladder cancer. Infect Agent Cancer 2016. [PMID: 26941832 DOI: 10.1186/s13027-016-0057-x57] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND We earlier proposed a genetic model for gallbladder carcinogenesis and its dissemination cascade. However, the association of gallbladder cancer and 'inflammatory stimulus' to drive the initial cascade in the model remained unclear. A recent study suggested infection with Salmonella can lead to changes in the host signalling pathways in gallbladder cancer. FINDINGS We examined the whole exomes of 26 primary gall bladder tumour and paired normal samples for presence of 143 HPV (Human papilloma virus) types along with 6 common Salmonella serotypes (S. typhi Ty2, S. typhi CT18, S. typhimurium LT2, S. choleraesuis SCB67, S. paratyphi TCC, and S. paratyphi SPB7) using a computational subtraction pipeline based on the HPVDetector, we recently described. Based on our evaluation of 26 whole exome gallbladder primary tumours and matched normal samples: association of typhoidal Salmonella species were found in 11 of 26 gallbladder cancer samples, and non-typhoidal Salmonella species in 12 of 26 gallbladder cancer, with 6 samples were found co-infected with both. CONCLUSIONS We present the first evidence to support the association of non-typhoidal Salmonella species along with typhoidal strains in gallbladder cancer. Salmonella infection in the chronic carrier state fits the role of the 'inflammatory stimulus' in the genetic model for gallbladder carcinogenesis that may play a role in gallbladder cancer analogous to Helicobacter pylori in gastric cancer.
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Affiliation(s)
- Prajish Iyer
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai India
| | - Savio George Barreto
- Department of Gastrointestinal Surgery, Gastrointestinal Oncology, and Bariatric Surgery, Medanta Institute of Digestive and Hepatobiliary Sciences, Medanta, The Medicity, Gurgaon, India
| | - Bikram Sahoo
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai India
| | - Pratik Chandrani
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai India
| | - Mukta R Ramadwar
- Department of Pathology, Tata Memorial Centre, Ernest Borges Marg, Parel, Mumbai, India
| | - Shailesh V Shrikhande
- Department of Gastrointestinal and Hepato-Pancreato-Biliary Surgical Oncology, Tata Memorial Centre, Ernest Borges Marg, Parel, Mumbai, India
| | - Amit Dutt
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai India
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Zhou L, Jones C, Gibani MM, Dobinson H, Thomaides-Brears H, Shrestha S, Blohmke CJ, Darton TC, Pollard AJ. Development and Evaluation of a Blood Culture PCR Assay for Rapid Detection of Salmonella Paratyphi A in Clinical Samples. PLoS One 2016; 11:e0150576. [PMID: 26930553 PMCID: PMC4773247 DOI: 10.1371/journal.pone.0150576] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 02/17/2016] [Indexed: 01/15/2023] Open
Abstract
Background Enteric fever remains an important cause of morbidity in many low-income countries and Salmonella Paratyphi A has emerged as the aetiological agent in an increasing proportion of cases. Lack of adequate diagnostics hinders early diagnosis and prompt treatment of both typhoid and paratyphoid but development of assays to identify paratyphoid has been particularly neglected. Here we describe the development of a rapid and sensitive blood culture PCR method for detection of Salmonella Paratyphi A from blood, potentially allowing for appropriate diagnosis and antimicrobial treatment to be initiated on the same day. Methods Venous blood samples from volunteers experimentally challenged orally with Salmonella Paratyphi A, who subsequently developed paratyphoid, were taken on the day of diagnosis; 10 ml for quantitative blood culture and automated blood culture, and 5 ml for blood culture PCR. In the latter assay, bacteria were grown in tryptone soy broth containing 2.4% ox bile and micrococcal nuclease for 5 hours (37°C) before bacterial DNA was isolated for PCR detection targeting the fliC-a gene of Salmonella Paratyphi A. Results An optimized broth containing 2.4% ox bile and micrococcal nuclease, as well as a PCR test was developed for a blood culture PCR assay of Salmonella Paratyphi A. The volunteers diagnosed with paratyphoid had a median bacterial burden of 1 (range 0.1–6.9) CFU/ml blood. All the blood culture PCR positive cases where a positive bacterial growth was shown by quantitative blood culture had a bacterial burden of ≥ 0.3 CFU/ ml blood. The blood culture PCR assay identified an equal number of positive cases as automated blood culture at higher bacterial loads (≥0.3 CFU/ml blood), but utilized only half the volume of specimens. Conclusions The blood culture PCR method for detection of Salmonella Paratyphi A can be completed within 9 hours and offers the potential for same-day diagnosis of enteric fever. Using 5 ml blood, it exhibited a lower limit of detection equal to 0.3 CFU/ml blood, and it performed at least as well as automated blood culture at higher bacterial loads (≥0.3 CFU/ml blood) of clinical specimens despite using half the volume of blood. The findings warrant its further study in endemic populations with a potential use as a novel diagnostic which fills the present gap of paratyphoid diagnostics.
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Affiliation(s)
- Liqing Zhou
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
- * E-mail:
| | - Claire Jones
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Malick M. Gibani
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Hazel Dobinson
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Helena Thomaides-Brears
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Sonu Shrestha
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Christoph J. Blohmke
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Thomas C. Darton
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Andrew J. Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
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Ulcerative Colitis and Its Association with Salmonella Species. Interdiscip Perspect Infect Dis 2016; 2016:5854285. [PMID: 26904116 PMCID: PMC4745578 DOI: 10.1155/2016/5854285] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 12/21/2015] [Indexed: 12/28/2022] Open
Abstract
Ulcerative colitis (UC) is characterized by presence of ulcer in colon and bloody diarrhea. The present study explores the possibility of association between Salmonella and ulcerative colitis. The present study comprised 59 cases of UC, 28 of colon cancer (CC), 127 of irritable bowel syndrome (IBS), and 190 of healthy control. The serological study was done by Widal and Indirect Haemagglutination Assay (IHA) for ViAb. Nested PCR was performed targeting fliC, staA, and stkG gene for Typhi and Paratyphi A, respectively. A total of 15.3% patients were positive for Salmonella “O” antigen among them 18.6% UC, 35.5% CC, 12.6% IBS, and 15.3% healthy control. A total of 36.9% patients were positive for “H” antigen including 39.0%, 57.1%, and 67.7% UC, CC, and IBS, respectively. About 1.73% show positive agglutination for AH antigen including 3.4%, 3.6%, and 1.6%, UC, CC, and IBS. A total of 10.89% were positive for ViAb. While 6.8% of UC, 10.7% of CC, 11.0% of IBS, and 12.1% of healthy subjects were positive for the antibody, the PCR positivity rates for Salmonella specific sequences were 79.7% in UC, 53.6% in CC, 66.1% in IBS, and 16.3% in healthy controls. The present study suggested that higher prevalence of Salmonella might play important role in etiopathogenesis of UC, IBS, and CC.
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Iyer P, Barreto SG, Sahoo B, Chandrani P, Ramadwar MR, Shrikhande SV, Dutt A. Non-typhoidal Salmonella DNA traces in gallbladder cancer. Infect Agent Cancer 2016; 11:12. [PMID: 26941832 PMCID: PMC4776363 DOI: 10.1186/s13027-016-0057-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 02/23/2016] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND We earlier proposed a genetic model for gallbladder carcinogenesis and its dissemination cascade. However, the association of gallbladder cancer and 'inflammatory stimulus' to drive the initial cascade in the model remained unclear. A recent study suggested infection with Salmonella can lead to changes in the host signalling pathways in gallbladder cancer. FINDINGS We examined the whole exomes of 26 primary gall bladder tumour and paired normal samples for presence of 143 HPV (Human papilloma virus) types along with 6 common Salmonella serotypes (S. typhi Ty2, S. typhi CT18, S. typhimurium LT2, S. choleraesuis SCB67, S. paratyphi TCC, and S. paratyphi SPB7) using a computational subtraction pipeline based on the HPVDetector, we recently described. Based on our evaluation of 26 whole exome gallbladder primary tumours and matched normal samples: association of typhoidal Salmonella species were found in 11 of 26 gallbladder cancer samples, and non-typhoidal Salmonella species in 12 of 26 gallbladder cancer, with 6 samples were found co-infected with both. CONCLUSIONS We present the first evidence to support the association of non-typhoidal Salmonella species along with typhoidal strains in gallbladder cancer. Salmonella infection in the chronic carrier state fits the role of the 'inflammatory stimulus' in the genetic model for gallbladder carcinogenesis that may play a role in gallbladder cancer analogous to Helicobacter pylori in gastric cancer.
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Affiliation(s)
- Prajish Iyer
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai India
| | - Savio George Barreto
- Department of Gastrointestinal Surgery, Gastrointestinal Oncology, and Bariatric Surgery, Medanta Institute of Digestive and Hepatobiliary Sciences, Medanta, The Medicity, Gurgaon, India
| | - Bikram Sahoo
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai India
| | - Pratik Chandrani
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai India
| | - Mukta R. Ramadwar
- Department of Pathology, Tata Memorial Centre, Ernest Borges Marg, Parel, Mumbai, India
| | - Shailesh V. Shrikhande
- Department of Gastrointestinal and Hepato-Pancreato-Biliary Surgical Oncology, Tata Memorial Centre, Ernest Borges Marg, Parel, Mumbai, India
| | - Amit Dutt
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai India
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Storey HL, Huang Y, Crudder C, Golden A, de los Santos T, Hawkins K. A Meta-Analysis of Typhoid Diagnostic Accuracy Studies: A Recommendation to Adopt a Standardized Composite Reference. PLoS One 2015; 10:e0142364. [PMID: 26566275 PMCID: PMC4643909 DOI: 10.1371/journal.pone.0142364] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 10/21/2015] [Indexed: 01/09/2023] Open
Abstract
Novel typhoid diagnostics currently under development have the potential to improve clinical care, surveillance, and the disease burden estimates that support vaccine introduction. Blood culture is most often used as the reference method to evaluate the accuracy of new typhoid tests; however, it is recognized to be an imperfect gold standard. If no single gold standard test exists, use of a composite reference standard (CRS) can improve estimation of diagnostic accuracy. Numerous studies have used a CRS to evaluate new typhoid diagnostics; however, there is no consensus on an appropriate CRS. In order to evaluate existing tests for use as a reference test or inclusion in a CRS, we performed a systematic review of the typhoid literature to include all index/reference test combinations observed. We described the landscape of comparisons performed, showed results of a meta-analysis on the accuracy of the more common combinations, and evaluated sources of variability based on study quality. This wide-ranging meta-analysis suggests that no single test has sufficiently good performance but some existing diagnostics may be useful as part of a CRS. Additionally, based on findings from the meta-analysis and a constructed numerical example demonstrating the use of CRS, we proposed necessary criteria and potential components of a typhoid CRS to guide future recommendations. Agreement and adoption by all investigators of a standardized CRS is requisite, and would improve comparison of new diagnostics across independent studies, leading to the identification of a better reference test and improved confidence in prevalence estimates.
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Affiliation(s)
- Helen L. Storey
- Diagnostics Program, PATH, Seattle, Washington, United States of America
- * E-mail:
| | - Ying Huang
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Chris Crudder
- Diagnostics Program, PATH, Seattle, Washington, United States of America
| | - Allison Golden
- Diagnostics Program, PATH, Seattle, Washington, United States of America
| | - Tala de los Santos
- Diagnostics Program, PATH, Seattle, Washington, United States of America
| | - Kenneth Hawkins
- Diagnostics Program, PATH, Seattle, Washington, United States of America
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Salman M, Ali A, Jabbar A, Sarwar Y, Rahman M, Iqbal M, Haque A. Simplest identification, O-specific polysaccharide purification and antigenic evaluation of Salmonella enterica serovar Typhi Vi negative isolate. EXCLI JOURNAL 2015; 14:1078-84. [PMID: 26600755 PMCID: PMC4650959 DOI: 10.17179/excli2015-565] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 09/28/2015] [Indexed: 11/10/2022]
Abstract
Currently licensed typhoid vaccines are based on Vi capsular polysaccharides. Recent molecular reports from typhoid endemic countries state that Salmonella enterica serovar Typhi (S. Typhi) Vi negative strains occur naturally and cause typhoid fever which is indistinguishable from disease caused by Vi positive strains. Vaccine based on Vi polysaccharide may not protect patients if the invading S. Typhi are negative for Vi. The lipopolysaccharide (LPS) is an essential component of S. Typhi outer membrane in which O-specific polysaccharide (OSP) is a protective antigen and universal candidate for vaccine development. In this study, S. Typhi Vi negative isolates were discriminated from Vi positive isolates through a duplex PCR using primers of fliC-d (599bp) and tviA (495bp) genes. The LPS of S. Typhi Vi negative isolates was extracted by hot phenol method and OSP was purified by core hydrolysis. The yield of extracted LPS was 91 mg/L and that of purified OSP was 49.14 mg/L of culture broth. LPS showed ladder like appearance by zinc imidazole staining following SDS-PAGE. Whole cell challenged mice sera were used for in vitro antigenicity evaluation of the purified LPS and OSP. The antigenicity was found adequate by immunodiffusion assay. To our knowledge, this is the first report of purification and antigenic evaluation of LPS of a Vi negative S. Typhi isolate. The purified OSP from S. Typhi Vi negative isolate may be coupled with a carrier protein to produce universal low cost conjugate vaccine candidates for use in typhoid endemic regions.
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Affiliation(s)
- Muhammad Salman
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan affiliated with Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan ; Department of Biotechnology, Abdul Wali Khan University, Mardan
| | - Aamir Ali
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan affiliated with Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - Abdul Jabbar
- Department of Biotechnology, Mirpur University of Science & Technology (MUST), Mirpur, AJK, Pakistan
| | - Yasra Sarwar
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan affiliated with Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - Moazur Rahman
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan affiliated with Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - Mazhar Iqbal
- Health Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan affiliated with Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - Abdul Haque
- Department of Pathology, The University of Faisalabad, Faisalabad
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Crump JA, Sjölund-Karlsson M, Gordon MA, Parry CM. Epidemiology, Clinical Presentation, Laboratory Diagnosis, Antimicrobial Resistance, and Antimicrobial Management of Invasive Salmonella Infections. Clin Microbiol Rev 2015; 28:901-37. [PMID: 26180063 PMCID: PMC4503790 DOI: 10.1128/cmr.00002-15] [Citation(s) in RCA: 640] [Impact Index Per Article: 71.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Salmonella enterica infections are common causes of bloodstream infection in low-resource areas, where they may be difficult to distinguish from other febrile illnesses and may be associated with a high case fatality ratio. Microbiologic culture of blood or bone marrow remains the mainstay of laboratory diagnosis. Antimicrobial resistance has emerged in Salmonella enterica, initially to the traditional first-line drugs chloramphenicol, ampicillin, and trimethoprim-sulfamethoxazole. Decreased fluoroquinolone susceptibility and then fluoroquinolone resistance have developed in association with chromosomal mutations in the quinolone resistance-determining region of genes encoding DNA gyrase and topoisomerase IV and also by plasmid-mediated resistance mechanisms. Resistance to extended-spectrum cephalosporins has occurred more often in nontyphoidal than in typhoidal Salmonella strains. Azithromycin is effective for the management of uncomplicated typhoid fever and may serve as an alternative oral drug in areas where fluoroquinolone resistance is common. In 2013, CLSI lowered the ciprofloxacin susceptibility breakpoints to account for accumulating clinical, microbiologic, and pharmacokinetic-pharmacodynamic data suggesting that revision was needed for contemporary invasive Salmonella infections. Newly established CLSI guidelines for azithromycin and Salmonella enterica serovar Typhi were published in CLSI document M100 in 2015.
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Affiliation(s)
- John A Crump
- Centre for International Health, University of Otago, Dunedin, Otago, New Zealand Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Maria Sjölund-Karlsson
- Division of Foodborne, Waterborne, and Environmental Diseases, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Melita A Gordon
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, United Kingdom Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Christopher M Parry
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, United Kingdom Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
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Fan F, Yan M, Du P, Chen C, Kan B. Rapid and Sensitive Salmonella Typhi Detection in Blood and Fecal Samples Using Reverse Transcription Loop-Mediated Isothermal Amplification. Foodborne Pathog Dis 2015; 12:778-86. [PMID: 26270463 DOI: 10.1089/fpd.2015.1950] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Typhoid fever caused by Salmonella enterica serovar Typhi remains a significant public health problem in developing countries. Although the main method for diagnosing typhoid fever is blood culture, the test is time consuming and not always able to detect infections. Thus, it is very difficult to distinguish typhoid from other infections in patients with nonspecific symptoms. A simple and sensitive laboratory detection method remains necessary. The purpose of this study is to establish and evaluate a rapid and sensitive reverse transcription-based loop-mediated isothermal amplification (RT-LAMP) method to detect Salmonella Typhi infection. In this study, a new specific gene marker, STY1607, was selected to develop a STY1607-RT-LAMP assay; this is the first report of specific RT-LAMP detection assay for typhoid. Human-simulated and clinical blood/stool samples were used to evaluate the performance of STY1607-RT-LAMP for RNA detection; this method was compared with STY1607-LAMP, reverse transcription real-time polymerase chain reaction (rRT-PCR), and bacterial culture methods for Salmonella Typhi detection. Using mRNA as the template, STY1607-RT-LAMP exhibited 50-fold greater sensitivity than STY1607-LAMP for DNA detection. The STY1607-RT-LAMP detection limit is 3 colony-forming units (CFU)/mL for both the pure Salmonella Typhi samples and Salmonella Typhi-simulated blood samples and was 30 CFU/g for the simulated stool samples, all of which were 10-fold more sensitive than the rRT-PCR method. RT-LAMP exhibited improved Salmonella Typhi detection sensitivity compared to culture methods and to rRT-PCR of clinical blood and stool specimens from suspected typhoid fever patients. Because it can be performed without sophisticated equipment or skilled personnel, RT-LAMP is a valuable tool for clinical laboratories in developing countries. This method can be applied in the clinical diagnosis and care of typhoid fever patients as well as for a quick public health response.
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Affiliation(s)
- Fenxia Fan
- 1 State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention , Chinese Center for Disease Control and Prevention, Beijing, China .,2 Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases , Hangzhou, Zhejiang, China
| | - Meiying Yan
- 1 State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention , Chinese Center for Disease Control and Prevention, Beijing, China .,2 Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases , Hangzhou, Zhejiang, China
| | - Pengcheng Du
- 1 State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention , Chinese Center for Disease Control and Prevention, Beijing, China
| | - Chen Chen
- 1 State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention , Chinese Center for Disease Control and Prevention, Beijing, China
| | - Biao Kan
- 1 State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention , Chinese Center for Disease Control and Prevention, Beijing, China .,2 Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases , Hangzhou, Zhejiang, China
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Arabestani MR, Rastiany S, Kazemi S, Mousavi SM. Conventional, molecular methods and biomarkers molecules in detection of septicemia. Adv Biomed Res 2015; 4:120. [PMID: 26261822 PMCID: PMC4513309 DOI: 10.4103/2277-9175.158027] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 12/18/2014] [Indexed: 11/13/2022] Open
Abstract
Sepsis is a leading cause of morbidity and mortality in hospitalized patients worldwide and based on studies, 30–40% of all cases of severe sepsis and septic shock results from the blood stream infections (BSIs). Identifying of the disease, performing laboratory tests, and consequently treatment are factors that required for optimum management of BSIs. In addition, applying precise and immediate identification of the etiologic agent is a prerequisite for specific antibiotic therapy of pathogen and thereby decreasing mortality rates. The diagnosis of sepsis is difficult because clinical signs of sepsis often overlap with other noninfectious cases of systemic inflammation. BSIs are usually diagnosed by performing a series of techniques such as blood cultures, polymerase chain reaction-based methods, and biomarkers of sepsis. Extremely time-consuming even to take up to several days is a major limitation of conventional methods. In addition, yielding false-negative results due to fastidious and slow-growing microorganisms and also in case of antibiotic pretreated samples are other limitations. In comparison, molecular methods are capable of examining a blood sample obtained from suspicious patient with BSI and gave the all required information to prescribing antimicrobial therapy for detected bacterial or fungal infections immediately. Because of an emergency of sepsis, new methods are being developed. In this review, we discussed about the most important sepsis diagnostic methods and numbered the advantage and disadvantage of the methods in detail.
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Affiliation(s)
- Mohammad Reza Arabestani
- Brucellosis Research Center, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran ; Department of Microbiology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Sahar Rastiany
- Department of Microbiology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Sima Kazemi
- Department of Microbiology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Seyed Masoud Mousavi
- Department of Microbiology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
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Andrews JR, Ryan ET. Diagnostics for invasive Salmonella infections: Current challenges and future directions. Vaccine 2015; 33 Suppl 3:C8-15. [PMID: 25937611 DOI: 10.1016/j.vaccine.2015.02.030] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 02/03/2015] [Accepted: 02/08/2015] [Indexed: 10/23/2022]
Abstract
Invasive Salmonellosis caused by Salmonella enterica serotype Typhi or Paratyphi A, B, C, or invasive non-typhoidal Salmonella serotypes, is an immensely important disease cluster for which reliable, rapid diagnostic tests are not available. Blood culture remains the gold standard but is insensitive, slow, and resource-intensive. Existing molecular diagnostics have poor sensitivity due to the low organism burden in bodily fluids. Commercially available serologic tests for typhoidal Salmonella have had limited sensitivity and specificity. In high burden, resource-limited settings, reliance on clinical diagnosis or inaccurate tests often results in frequent, unnecessary treatment, which contributes selective pressure for the emergence of antimicrobial resistance. This practice also results in inadequate therapy for other etiologies of acute febrile illnesses, including leptospirosis and rickettsial infections. A number of novel serologic, molecular, transcriptomic and metabolomic approaches to diagnostics are under development. Target product profiles that outline specific needs may focus development and investment, and establish benchmarks for accuracy, cost, speed, and portability of new diagnostics. Of note, a critical barrier to diagnostic assay rollout will be the low cost and low perceived harm of empiric therapy on behalf of providers and patients, which leaves few perceived incentives to utilize diagnostics. Approaches that align incentives with societal goals of limiting inappropriate antimicrobial use, such as subsidizing diagnostics, may be essential for stimulating development and uptake of such assays in resource-limited settings. New diagnostics for invasive Salmonellosis should be developed and deployed alongside diagnostics for alternative etiologies of acute febrile illnesses to improve targeted use of antibiotics.
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Affiliation(s)
- Jason R Andrews
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, United States.
| | - Edward T Ryan
- Division of Infectious Diseases, Massachusetts General Hospital, Harvard Medical School, 55 Fruit Street, Boston, MA 02114, United States.
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Ahirwar SK, Pratap CB, Patel SK, Shukla VK, Singh IG, Mishra OP, Kumar K, Singh TB, Nath G. Acid exposure induces multiplication of Salmonella enterica serovar Typhi. J Clin Microbiol 2014; 52:4330-3. [PMID: 25320227 PMCID: PMC4313307 DOI: 10.1128/jcm.02275-14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 10/09/2014] [Indexed: 11/20/2022] Open
Abstract
Salmonella enterica serovar Typhi faces several environmental stresses while going through the stomach (acidic pH) to the small intestine (basic pH) and intracellularly in macrophages (acidic pH) in humans. The acidic pH followed by alkaline pH in the small intestine might be responsible for expression of certain stress-induced genes, resulting in not only better survival but also induction of multiplication and invasion of the bacterium in the small intestine. Based on this hypothesis, we developed a process wherein we exposed the blood, urine, and stool specimens from 90 acute typhoid fever patients and 36 chronic typhoid carriers to acidic pH to see the effect on isolation rate of S. Typhi. About 5 g of freshly passed unpreserved stool, a centrifuged deposit of 15 ml of urine, and 5 ml of blood clot were subjected to 5 ml of Luria-Bertani (LB) broth (pH 3.5) for 20 min, followed by enrichment in bile broth-selenite F broth. When the combined isolation from all 3 specimens, i.e., blood, urine, and stool, after acid exposure was considered, a total of 77.7% of the acute typhoid patients were observed to be positive for the isolation of the S. Typhi serotype, compared to 8.8% by the conventional method. Similarly, 42% (15/36) of chronic carriers yielded positive for S. Typhi growth after acid exposure, compared to 5.5% (2/36) by the conventional method. It therefore can be concluded that acid shock triggers the multiplication of the bacteria, resulting in better isolation rates from blood clot, stool, and urine specimens.
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Affiliation(s)
- Suneel Kumar Ahirwar
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Chandra Bhan Pratap
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Saurabh Kumar Patel
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Vijay K Shukla
- Department of General Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Indarjeet Gambhir Singh
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Om Prakash Mishra
- Department of Pediatrics, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Kailash Kumar
- Department of Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Tej Bali Singh
- Department of Community Medicine, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Gopal Nath
- Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
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Pratap CB, Kumar G, Patel SK, Shukla VK, Kumar K, Singh TB, Nath G. Mix-infection of S. Typhi and ParaTyphi A in Typhoid Fever and Chronic Typhoid Carriers: A Nested PCR Based Study in North India. J Clin Diagn Res 2014; 8:DC09-14. [PMID: 25584217 DOI: 10.7860/jcdr/2014/9167.5107] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 09/10/2014] [Indexed: 11/24/2022]
Abstract
INTRODUCTION Enteric fever is a systemic disease caused by Salmonella organism such as serotypes Typhi and ParaTyphi A, B, C. Salmonella ParaTyphi A contributes more than 50% of all the enteric fever cases and it has recently been projected as an emerging pathogen. MATERIALS AND METHODS The present study was aimed to detect Salmonella Typhi and ParaTyphi A in urine, blood and stool specimens collected from cases of enteric fever (110), chronic typhoid carriers (46) and healthy controls (75) to explore the possibility of mixed infection by nested PCR. A new nested PCR primer was designed targeting putative fimbrial protein (stkG) gene which is one of the fimbrial gene families to Salmonella ParaTyphi A and for S. Typhi already reported primers targeting flagellin (fliC) gene. RESULTS Large volume of urine specimens (15 ml) was found to be the best for detection of Salmonella serotypes. The urine sample was found to have mixed-infection by both the serotypes in 40.9% of the cases but lower in blood (27.3%) and stool (13.6%). CONCLUSION The present study concludes that occurrence of mixed infection may be quite frequent in typhoid and chronic typhoid carriers' individuals, although the reported recent rise in ParaTyphi A incidence may not be real.
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Affiliation(s)
- Chandra Bhan Pratap
- PhD Student, Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University , Varanasi, India
| | - Gopal Kumar
- Senior Resident, Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University , Varanasi, India
| | - Saurabh Kumar Patel
- PhD Student, Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University , Varanasi, India
| | - Vijay K Shukla
- Professor, Department of General Surgery, Institute of Medical Sciences, Banaras Hindu University , Varanasi, India
| | - Kailash Kumar
- Professor, Department of Medicine, Institute of Medical Sciences, Banaras Hindu University , Varanasi, India
| | - Tej Bali Singh
- Professor, Department of Community Medicine, Institute of Medical Sciences, Banaras Hindu University , Varanasi, India
| | - Gopal Nath
- Professor, Department of Microbiology, Institute of Medical Sciences, Banaras Hindu University , Varanasi, India
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Loonen AJM, Wolffs PFG, Bruggeman CA, van den Brule AJC. Developments for improved diagnosis of bacterial bloodstream infections. Eur J Clin Microbiol Infect Dis 2014; 33:1687-702. [PMID: 24848132 DOI: 10.1007/s10096-014-2153-4] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 04/30/2014] [Indexed: 12/26/2022]
Abstract
Bloodstream infections (BSIs) are associated with high mortality and increased healthcare costs. Optimal management of BSI depends on several factors including recognition of the disease, laboratory tests and treatment. Rapid and accurate identification of the etiologic agent is crucial to be able to initiate pathogen specific antibiotic therapy and decrease mortality rates. Furthermore, appropriate treatment might slow down the emergence of antibiotic resistant strains. Culture-based methods are still considered to be the "gold standard" for the detection and identification of pathogens causing BSI. Positive blood cultures are used for Gram-staining. Subsequently, positive blood culture material is subcultured on solid media, and (semi-automated) biochemical testing is performed for species identification. Finally, a complete antibiotic susceptibility profile can be provided based on cultured colonies, which allows the start of pathogen-tailored antibiotic therapy. This conventional workflow is extremely time-consuming and can take up to several days. Furthermore, fastidious and slow-growing microorganisms, as well as antibiotic pre-treated samples can lead to false-negative results. The main aim of this review is to present different strategies to improve the conventional laboratory diagnostic steps for BSI. These approaches include protein-based (MALDI-TOF mass spectrometry) and nucleic acid-based (polymerase chain reaction [PCR]) identification from subculture, blood cultures, and whole blood to decrease time to results. Pathogen enrichment and DNA isolation methods, to enable optimal pathogen DNA recovery from whole blood, are described. In addition, the use of biomarkers as patient pre-selection tools for molecular assays are discussed.
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Affiliation(s)
- A J M Loonen
- Laboratory for Molecular Diagnostics, Department of Medical Microbiology and Pathology, Jeroen Bosch Hospital, 's-Hertogenbosch, The Netherlands
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Book M, Lehmann LE, Zhang X, Stüber F. Monitoring infection: from blood culture to polymerase chain reaction (PCR). Best Pract Res Clin Anaesthesiol 2014; 27:279-88. [PMID: 24012238 DOI: 10.1016/j.bpa.2013.06.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Accepted: 06/28/2013] [Indexed: 01/14/2023]
Abstract
In patients with sepsis, diagnosis of blood stream infection (BSI) is a key concern to the therapist. Direct verification of pathogens in the blood stream executed by blood cultures (BC) still is regarded as the gold standard up to date. The quickest possible initiation of an appropriate antimicrobial therapy is a cornerstone of an effective therapy. Moreover, in this view BC can also serve to identify antimicrobial agents to target the pathogen. However, when employing BC the time needed until microbiological results are available ranges from 24 up to 72 h. Moreover, infections caused by multiple pathogens often remain undetected and concurrent antibiotic therapy may lower the overall sensitivity. Alternative pathogen characterization can be performed by polymerase chain reaction (PCR) based amplification methods. Results using PCR can be obtained within 6-8 h. Therefore, the time delay until an appropriate therapy can be reduced enormously. Moreover, these methods have the potential to enhance the sensitivity in the diagnosis of blood stream infections. Therefore, PCR based methods might be a valuable adjunct to present procedures of diagnosing bacteraemia.
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Affiliation(s)
- Malte Book
- University Department of Anaesthesiology and Pain Medicine, Inselspital, Freiburgstrasse, CH-3010 Bern, Switzerland.
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Fabre L, Le Hello S, Roux C, Issenhuth-Jeanjean S, Weill FX. CRISPR is an optimal target for the design of specific PCR assays for salmonella enterica serotypes Typhi and Paratyphi A. PLoS Negl Trop Dis 2014; 8:e2671. [PMID: 24498453 PMCID: PMC3907412 DOI: 10.1371/journal.pntd.0002671] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Accepted: 12/13/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Serotype-specific PCR assays targeting Salmonella enterica serotypes Typhi and Paratyphi A, the causal agents of typhoid and paratyphoid fevers, are required to accelerate formal diagnosis and to overcome the lack of typing sera and, in some situations, the need for culture. However, the sensitivity and specificity of such assays must be demonstrated on large collections of strains representative of the targeted serotypes and all other bacterial populations producing similar clinical symptoms. METHODOLOGY Using a new family of repeated DNA sequences, CRISPR (clustered regularly interspaced short palindromic repeats), as a serotype-specific target, we developed a conventional multiplex PCR assay for the detection and differentiation of serotypes Typhi and Paratyphi A from cultured isolates. We also developed EvaGreen-based real-time singleplex PCR assays with the same two sets of primers. PRINCIPAL FINDINGS We achieved 100% sensitivity and specificity for each protocol after validation of the assays on 188 serotype Typhi and 74 serotype Paratyphi A strains from diverse genetic groups, geographic origins and time periods and on 70 strains of bacteria frequently encountered in bloodstream infections, including 29 other Salmonella serotypes and 42 strains from 38 other bacterial species. CONCLUSIONS The performance and convenience of our serotype-specific PCR assays should facilitate the rapid and accurate identification of these two major serotypes in a large range of clinical and public health laboratories with access to PCR technology. These assays were developed for use with DNA from cultured isolates, but with modifications to the assay, the CRISPR targets could be used in the development of assays for use with clinical and other samples.
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Affiliation(s)
- Laetitia Fabre
- Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, WHO Collaborative Center for Reference and Research on Salmonella, Institut Pasteur, Paris, France
| | - Simon Le Hello
- Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, WHO Collaborative Center for Reference and Research on Salmonella, Institut Pasteur, Paris, France
| | - Chrystelle Roux
- Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, WHO Collaborative Center for Reference and Research on Salmonella, Institut Pasteur, Paris, France
| | - Sylvie Issenhuth-Jeanjean
- Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, WHO Collaborative Center for Reference and Research on Salmonella, Institut Pasteur, Paris, France
| | - François-Xavier Weill
- Unité des Bactéries Pathogènes Entériques, Centre National de Référence des Escherichia coli, Shigella et Salmonella, WHO Collaborative Center for Reference and Research on Salmonella, Institut Pasteur, Paris, France
- * E-mail:
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Parry CM, Wijedoru L, Arjyal A, Baker S. The utility of diagnostic tests for enteric fever in endemic locations. Expert Rev Anti Infect Ther 2014; 9:711-25. [DOI: 10.1586/eri.11.47] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Khanam F, Sheikh A, Sayeed MA, Bhuiyan MS, Choudhury FK, Salma U, Pervin S, Sultana T, Ahmed D, Goswami D, Hossain ML, Mamun KZ, Charles RC, Brooks WA, Calderwood SB, Cravioto A, Ryan ET, Qadri F. Evaluation of a typhoid/paratyphoid diagnostic assay (TPTest) detecting anti-Salmonella IgA in secretions of peripheral blood lymphocytes in patients in Dhaka, Bangladesh. PLoS Negl Trop Dis 2013; 7:e2316. [PMID: 23951368 PMCID: PMC3708850 DOI: 10.1371/journal.pntd.0002316] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Accepted: 06/03/2013] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Rapid and reliable diagnostic assays for enteric (typhoid and paratyphoid) fever are urgently needed. We report the characterization of novel approach utilizing lymphocyte secretions, for diagnosing patients with enteric fever by the TPTest procedure. METHODOLOGY TPTest detects Salmonella-specific IgA responses in lymphocyte culture supernatant. We utilized TPTest in patients with suspected enteric fever, patients with other illnesses, and healthy controls. We also evaluated simplified modifications of TPTest for adaptation in laboratories with limited facilities and equipment. PRINCIPAL FINDINGS TPTest was positive in 39 (27 typhoid and 12 paratyphoid A) patients confirmed by blood culture and was negative in 74 healthy individuals. Among 32 individuals with other illnesses, 29 were negative by TPTest. Of 204 individuals with suspected enteric fever who were negative by blood culture, 44 were positive by TPTest and the patients were clinically indistinguishable from patients with confirmed bacteremia, except they were more likely to be under 5 years of age. We evaluated simplifications in TPTest, including showing that lymphocytes could be recovered using lysis buffer or buffy coat method as opposed to centrifugation, that incubation of cells at 37°C did not require supplemental CO2, and that results were available for majority of samples within 24 hours. Positive results by TPTest are transient and revert to negative during convalescence, supporting use of the test in endemic areas. The results can also be read using immunodot blot approach as opposed to ELISA. Since no true gold standard currently exists, we used a number of definitions of true positives and negatives. TPTest had sensitivity of 100% compared to blood culture, and specificity that ranged from 78-97% (73-100, 95% CI), depending on definition of true negative. CONCLUSION The TPTest is useful for identification of patients with enteric fever in an endemic area, and additional development of simplified TPTest is warranted.
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Affiliation(s)
- Farhana Khanam
- International Centre for Diarrhoeal Disease Research (icddr,b), Bangladesh, Dhaka, Bangladesh
| | - Alaullah Sheikh
- International Centre for Diarrhoeal Disease Research (icddr,b), Bangladesh, Dhaka, Bangladesh
| | - Md. Abu Sayeed
- International Centre for Diarrhoeal Disease Research (icddr,b), Bangladesh, Dhaka, Bangladesh
| | - Md. Saruar Bhuiyan
- International Centre for Diarrhoeal Disease Research (icddr,b), Bangladesh, Dhaka, Bangladesh
| | - Feroza Kaneez Choudhury
- International Centre for Diarrhoeal Disease Research (icddr,b), Bangladesh, Dhaka, Bangladesh
| | - Umme Salma
- International Centre for Diarrhoeal Disease Research (icddr,b), Bangladesh, Dhaka, Bangladesh
| | - Shahnaz Pervin
- Department of Microbiology, Dhaka Medical College and Hospital (DMCH), Dhaka, Bangladesh
| | - Tania Sultana
- International Centre for Diarrhoeal Disease Research (icddr,b), Bangladesh, Dhaka, Bangladesh
| | - Dilruba Ahmed
- International Centre for Diarrhoeal Disease Research (icddr,b), Bangladesh, Dhaka, Bangladesh
| | - Doli Goswami
- International Centre for Diarrhoeal Disease Research (icddr,b), Bangladesh, Dhaka, Bangladesh
| | - Md. Lokman Hossain
- International Centre for Diarrhoeal Disease Research (icddr,b), Bangladesh, Dhaka, Bangladesh
| | - K. Z. Mamun
- Department of Microbiology, Dhaka Medical College and Hospital (DMCH), Dhaka, Bangladesh
| | - Richelle C. Charles
- Division of Infectious Disease, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - W. Abdullah Brooks
- International Centre for Diarrhoeal Disease Research (icddr,b), Bangladesh, Dhaka, Bangladesh
| | - Stephen B. Calderwood
- Division of Infectious Disease, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, United States of America
| | | | - Edward T. Ryan
- Division of Infectious Disease, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Firdausi Qadri
- International Centre for Diarrhoeal Disease Research (icddr,b), Bangladesh, Dhaka, Bangladesh
- * E-mail:
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Walawalkar YD, Gaind R, Nayak V. Study on Salmonella Typhi occurrence in gallbladder of patients suffering from chronic cholelithiasis-a predisposing factor for carcinoma of gallbladder. Diagn Microbiol Infect Dis 2013; 77:69-73. [PMID: 23790418 DOI: 10.1016/j.diagmicrobio.2013.05.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Revised: 05/12/2013] [Accepted: 05/15/2013] [Indexed: 01/11/2023]
Abstract
Cholelithiasis is frequently associated with carcinoma of gallbladder, and the presence of Salmonella Typhi in gallbladder of patients suffering from cholelithiasis is implicated as a predisposing factor for carcinogenesis. This study was conducted on patients suffering from chronic cholelithiasis from a region in North India-endemic area for enteric fever with high incidence of gallstones and gallbladder cancer. Since culture studies rarely reveal the chronic Salmonella Typhi persistence, we use PCR assay to specifically amplify the H1-d flagellin gene sequence homologous with Salmonella Typhi. Seven cases (17.5%), none of which were positive for culture, showed positive PCR results for Salmonella Typhi, 4 (10%) of which were tissue, 2 bile (5%), and 1 gallstone (2.5%). The chronic existence of Salmonella Typhi in gallbladder disease was confirmed. Thus, the study would indicate the importance of vaccination so as to prevent chronic infection and need for early diagnostic tools to prevent any further complications.
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Affiliation(s)
- Yogesh D Walawalkar
- Department of Biological Sciences, Birla Institute of Technology & Science, Goa, India
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Ong SY, Pratap CB, Wan X, Hou S, Rahman AYA, Saito JA, Nath G, Alam M. The Genomic Blueprint of Salmonella enterica subspecies enterica serovar Typhi P-stx-12. Stand Genomic Sci 2013; 7:483-96. [PMID: 24019994 PMCID: PMC3764930 DOI: 10.4056/sigs.3286690] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Salmonella enterica subspecies enterica serovar Typhi is a rod-shaped, Gram-negative, facultatively anaerobic bacterium. It belongs to the family Enterobacteriaceae in the class Gammaproteobacteria, and has the capability of residing in the human gallbladder by forming a biofilm and hence causing the person to become a typhoid carrier. Here we present the complete genome of Salmonella enterica subspecies enterica serotype Typhi strain P-stx-12, which was isolated from a chronic carrier in Varanasi, India. The complete genome comprises a 4,768,352 bp chromosome with a total of 98 RNA genes, 4,691 protein-coding genes and a 181,431 bp plasmid. Genome analysis revealed that the organism is closely related to Salmonella enterica serovar Typhi strain Ty2 and Salmonella enterica serovar Typhi strain CT18, although their genome structure is slightly different.
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Affiliation(s)
- Su Yean Ong
- Centre for Chemical Biology, Universiti Sains Malaysia, Penang, Malaysia
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Khan S, Harish B, Menezes G, Acharya N, Parija S. Early diagnosis of typhoid fever by nested PCR for flagellin gene of Salmonella enterica serotype Typhi. Indian J Med Res 2012; 136:850-4. [PMID: 23287134 PMCID: PMC3573608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND & OBJECTIVES Typhoid fever caused by Salmonella Typhi continues to be a major health problem in spite of the use of antibiotics and the development of newer antibacterial drugs. Inability to make an early laboratory diagnosis and resort to empirical therapy, often lead to increased morbidity and mortality in cases of typhoid fever. This study was aimed to optimize a nested PCR for early diagnosis of typhoid fever and using it as a diagnostic tool in culture negative cases of suspected typhoid fever. METHODS Eighty patients with clinical diagnosis of typhoid fever and 40 controls were included in the study. The blood samples collected were subjected to culture, Widal and nested PCR targeting the flagellin gene of S. Typhi. RESULTS The sensitivity of PCR on blood was found to be 100 per cent whereas the specificity was 76.9 per cent. The positive predictive value (PPV) of PCR was calculated to be 76.9 per cent with an accuracy of 86 per cent. None of the 40 control samples gave a positive PCR. INTERPRETATION & CONCLUSIONS Due to its high sensitivity and specificity nested PCR can be used as a useful tool to diagnose clinically suspected, culture negative cases of typhoid fever.
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Affiliation(s)
- S. Khan
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education & Research, Puducherry, India
| | - B.N. Harish
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education & Research, Puducherry, India,Reprint requests: Dr B.N. Harish, Professor, Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education & Research, Puducherry 605 006, India e-mail:
| | - G.A. Menezes
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education & Research, Puducherry, India
| | - N.S. Acharya
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education & Research, Puducherry, India
| | - S.C. Parija
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Education & Research, Puducherry, India
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Evaluation of a simple blood culture amplification and antigen detection method for diagnosis of Salmonella enterica serovar typhi bacteremia. J Clin Microbiol 2012; 51:142-8. [PMID: 23100346 DOI: 10.1128/jcm.02360-12] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
In most areas where typhoid is endemic, laboratory diagnosis is not possible due to the lack of appropriate facilities. We investigated whether the combination of blood culture amplification of Salmonella enterica serovar Typhi with an S. Typhi antigen rapid diagnostic test (RDT) could be an accurate and inexpensive tool for the accelerated diagnosis of patients with acute typhoid in Laos. For a panel of 23 Gram-negative reference pathogens, the Standard Diagnostics (catalog no. 15FK20; Kyonggi-do, South Korea) RDT gave positive results for S. Typhi NCTC 8385, S. Typhi NCTC 786 (Vi negative), Salmonella enterica serovar Enteritidis (ATCC 13076), and Salmonella enterica serovar Ndolo NCTC 8700 (all group D). In a prospective study of 6,456 blood culture bottles from 3,028 patients over 15 months, 392 blood culture bottles (6.1%) from 221 (7.3%) patients had Gram-negative rods (GNRs) seen in the blood culture fluid. The sensitivity, negative predictive value, specificity, and positive predictive value were 96.7%, 99.5%, 97.9%, and 87.9%, respectively, for patients with proven S. Typhi bacteremia and 91.2%, 98.4%, 98.9%, and 93.9% for patients with group D Salmonella. The median (range) number of days between diagnosis by RDT and reference assays was 1 (-1 to +2) day for those with confirmed S. Typhi. The use of antigen-based pathogen detection in blood culture fluid may be a useful, relatively rapid, inexpensive, and accurate technique for the identification of important causes of bacteremia in the tropics.
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