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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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2
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Ahmadi A, Khezri A, Nørstebø H, Ahmad R. A culture-, amplification-independent, and rapid method for identification of pathogens and antibiotic resistance profile in bovine mastitis milk. Front Microbiol 2023; 13:1104701. [PMID: 36687564 PMCID: PMC9852903 DOI: 10.3389/fmicb.2022.1104701] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 12/19/2022] [Indexed: 01/07/2023] Open
Abstract
Introduction Rapid and accurate diagnosis of causative pathogens in mastitis would minimize the imprudent use of antibiotics and, therefore, reduce the spread of antimicrobial resistance. Whole genome sequencing offers a unique opportunity to study the microbial community and antimicrobial resistance (AMR) in mastitis. However, the complexity of milk samples and the presence of a high amount of host DNA in milk from infected udders often make this very challenging. Methods Here, we tested 24 bovine milk samples (18 mastitis and six non-mastitis) using four different commercial kits (Qiagens' DNeasy® PowerFood® Microbial, Norgens' Milk Bacterial DNA Isolation, and Molzyms' MolYsis™ Plus and Complete5) in combination with filtration, low-speed centrifugation, nuclease, and 10% bile extract of male bovine (Ox bile). Isolated DNA was quantified, checked for the presence/absence of host and pathogen using PCR and sequenced using MinION nanopore sequencing. Bioinformatics analysis was performed for taxonomic classification and antimicrobial resistance gene detection. Results The results showed that kits designed explicitly for bacterial DNA isolation from food and dairy matrices could not deplete/minimize host DNA. Following using MolYsis™ Complete 5 + 10% Ox bile + micrococcal nuclease combination, on average, 17% and 66.5% of reads were classified as bovine and Staphylococcus aureus reads, respectively. This combination also effectively enriched other mastitis pathogens, including Escherichia coli and Streptococcus dysgalactiae. Furthermore, using this approach, we identified important AMR genes such as Tet (A), Tet (38), fosB-Saur, and blaZ. We showed that even 40 min of the MinION run was enough for bacterial identification and detecting the first AMR gene. Conclusion We implemented an effective method (sensitivity of 100% and specificity of 92.3%) for host DNA removal and bacterial DNA enrichment (both gram-negative and positive) directly from bovine mastitis milk. To the best of our knowledge, this is the first culture- and amplification-independent study using nanopore-based metagenomic sequencing for real-time detection of the pathogen (within 5 hours) and the AMR profile (within 5-9 hours), in mastitis milk samples. These results provide a promising and potential future on-farm adaptable approach for better clinical management of mastitis.
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Affiliation(s)
- Asal Ahmadi
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Abdolrahman Khezri
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | | | - Rafi Ahmad
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway,Institute of Clinical Medicine, Faculty of Health Sciences, UiT–The Arctic University of Norway, Tromsø, Norway,*Correspondence: Rafi Ahmad,
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Muacevic A, Adler JR. Clinical and Laboratory Features of Enteric Fever in Children and Antibiotic Sensitivity Pattern in a Tertiary Care Hospital of a Low- and Middle-Income Country. Cureus 2022; 14:e30784. [PMID: 36320797 PMCID: PMC9614183 DOI: 10.7759/cureus.30784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/27/2022] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND Globally, enteric fever (EF) significantly gives rise to an appalling death toll. It is an endemic illness in Bangladesh and South Asia. The condition manifests in a wide range of clinical features in children. Nowadays, antibiotic resistance is an international stumbling block that hampers the appropriate treatment and outcome of EF. OBJECTIVE The study evaluated the clinical and laboratory characteristics and antibiotic sensitivity pattern of Salmonella enterica in children. METHODS This prospective research was conducted at Delta Medical College and Hospital, Dhaka, Bangladesh, from January 2017 to December 2019. A total of 200 pediatric cases of EF were included in this study who were either culture positive or had significantly raised Widal test titer for Salmonella with suggestive clinical features. RESULTS All the patients had a fever, and most had coated tongue, vomiting, abdominal pain, organomegaly, and diarrhea. Among the selected 200 cases of EF, 43.5% were Salmonella typhi culture-positive. A high erythrocyte sedimentation rate (ESR) was observed in a substantial number (53%) of patients. Ceftriaxone was the most sensitive (100%) antibiotic through laboratory analysis, followed by cefotaxime (95.1%). Among the oral antibiotics used, cefixime (92.8%) was the most sensitive. CONCLUSION EF in children can present with varied clinical manifestations. Selective antibiotic treatment according to sensitivity patterns is crucial for effective illness management and will reduce morbidity and mortality in the pediatric population.
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Choy RKM, Bourgeois AL, Ockenhouse CF, Walker RI, Sheets RL, Flores J. Controlled Human Infection Models To Accelerate Vaccine Development. Clin Microbiol Rev 2022; 35:e0000821. [PMID: 35862754 PMCID: PMC9491212 DOI: 10.1128/cmr.00008-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The timelines for developing vaccines against infectious diseases are lengthy, and often vaccines that reach the stage of large phase 3 field trials fail to provide the desired level of protective efficacy. The application of controlled human challenge models of infection and disease at the appropriate stages of development could accelerate development of candidate vaccines and, in fact, has done so successfully in some limited cases. Human challenge models could potentially be used to gather critical information on pathogenesis, inform strain selection for vaccines, explore cross-protective immunity, identify immune correlates of protection and mechanisms of protection induced by infection or evoked by candidate vaccines, guide decisions on appropriate trial endpoints, and evaluate vaccine efficacy. We prepared this report to motivate fellow scientists to exploit the potential capacity of controlled human challenge experiments to advance vaccine development. In this review, we considered available challenge models for 17 infectious diseases in the context of the public health importance of each disease, the diversity and pathogenesis of the causative organisms, the vaccine candidates under development, and each model's capacity to evaluate them and identify correlates of protective immunity. Our broad assessment indicated that human challenge models have not yet reached their full potential to support the development of vaccines against infectious diseases. On the basis of our review, however, we believe that describing an ideal challenge model is possible, as is further developing existing and future challenge models.
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Affiliation(s)
- Robert K. M. Choy
- PATH, Center for Vaccine Innovation and Access, Seattle, Washington, USA
| | - A. Louis Bourgeois
- PATH, Center for Vaccine Innovation and Access, Seattle, Washington, USA
| | | | - Richard I. Walker
- PATH, Center for Vaccine Innovation and Access, Seattle, Washington, USA
| | | | - Jorge Flores
- PATH, Center for Vaccine Innovation and Access, Seattle, Washington, USA
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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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Kariuki F, Getanda P, Nyachieo A, Juma G, Kinyanjui P, Kamau J. Evaluation of the detection of staA, viaB and sopE genes in Salmonella spp. using the polymerase chain reaction (PCR). Arch Microbiol 2021; 204:25. [DOI: 10.1007/s00203-021-02654-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 10/07/2021] [Accepted: 10/08/2021] [Indexed: 11/24/2022]
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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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Mahendradas P, Kawali A, Luthra S, Srinivasan S, Curi AL, Maheswari S, Ksiaa I, Khairallah M. Post-fever retinitis - Newer concepts. Indian J Ophthalmol 2020; 68:1775-1786. [PMID: 32823394 PMCID: PMC7690479 DOI: 10.4103/ijo.ijo_1352_20] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/09/2020] [Accepted: 07/20/2020] [Indexed: 12/18/2022] Open
Abstract
Post-fever retinitis (PFR) is an infectious or para-infectious uveitic entity caused by bacterial or viral agents and seen mainly in tropical countries. Systemic symptoms such as joint pain, skin rash are common during the febrile stage. On the basis of only clinical presentation, it is difficult to pin-point the exact etiology for PFR. Serological investigations, polymerase chain reaction, and knowledge of concurrent epidemics in the community may help to identify the etiological organism. Bacterial causes of PFR such as rickettsia and typhoid are treated with systemic antibiotics, with or without systemic steroid therapy, whereas PFR of viral causes such as chikungunya, dengue, West Nile virus, and Zika virus have no specific treatment and are managed with steroids. Nevertheless, many authors have advocated mere observation and the uveitis resolved with its natural course of the disease. In this article, we have discussed the clinical features, pathogenesis, investigations, and management of PFR.
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Affiliation(s)
- Padmamalini Mahendradas
- Department of Uveitis and Ocular Immunology, Narayana Nethralaya, Bengaluru, Karnataka, India
| | - Ankush Kawali
- Department of Uveitis and Ocular Immunology, Narayana Nethralaya, Bengaluru, Karnataka, India
| | | | - Sanjay Srinivasan
- Department of Uveitis and Ocular Immunology, Narayana Nethralaya, Bengaluru, Karnataka, India
| | - Andre L Curi
- National Institute of Infectious Diseases-INI-FIOCRUZ, Rio de Janeiro – Brazil
| | | | - Imen Ksiaa
- Department of Ophthalmology, FattoumaBourguiba University Hospital, Faculty of Medicine, University of Monastir, Monastir, Tunisia
| | - Moncef Khairallah
- Department of Ophthalmology, FattoumaBourguiba University Hospital, Faculty of Medicine, University of Monastir, Monastir, Tunisia
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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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Kaur A, Ruhela A, Sharma P, Khariwal H, Seth S, Kumar A, Kapil A, Elangovan R, Kalyanasundaram D. Simultaneous and high sensitive detection of Salmonella typhi and Salmonella paratyphi a in human clinical blood samples using an affordable and portable device. Biomed Microdevices 2019; 21:95. [PMID: 31707575 DOI: 10.1007/s10544-019-0441-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Enteric fever is one of the leading causes of infection and subsequent fatality (greater than 1.8 million) (WHO 2018), especially in the developing countries due to contaminated water and food inter twinned with unhygienic practices. Clinical gold standard technique of culture-based method followed by biochemical tests demand 72+ hours for diagnosis while newly developed techniques (like PCR, RT-PCR, DNA microarray etc.) suffer from high limit of detection or involve high-cost infrastructure or both. In this work, a quick and highly specific method, SMOL was established for simultaneous detection of Salmonella paratyphi A and Salmonella typhi in clinical blood samples. SMOL consists of (i) pre-concentration of S. typhi and S. paratyphi A cells using magnetic nanoparticles followed by (ii) cell lysis and DNA extraction (iii) amplification of select nucleic acids by LAMP technique and (iv) detection of amplified nucleic acids using an affordable portable device (costs less than $70). To identify the viability of target cells at lower concentrations, the samples were processed at two different time periods of t = 0 and t = 4 h. Primers specific for the SPA2539 gene in S. paratyphi A and STY2879 gene in S. typhi were used for LAMP. Within 6 h SMOL was able to detect positive and negative samples from 55 human clinical blood culture samples and detect the viability of the cells. The results were concordant with culture and biochemical tests as well as by qPCR. Statistical power analysis yielded 100%. SMOL results were concordant with culture and biochemical tests as well as by qPCR. The sensitive and affordable system SMOL will be effective for poor resource settings.
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Affiliation(s)
- Avinash Kaur
- Centre for Biomedical Engineering, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Ankur Ruhela
- Centre for Biomedical Engineering, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Priyanka Sharma
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Harshit Khariwal
- Department of Electrical Engineering, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Sagar Seth
- Department of Physics, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Adarsh Kumar
- Department of Electrical Engineering, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Arti Kapil
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Ravikrishnan Elangovan
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi, 110016, India
| | - Dinesh Kalyanasundaram
- Centre for Biomedical Engineering, Indian Institute of Technology Delhi, New Delhi, 110016, India. .,Department of Biomedical Engineering, All India Institute of Medical Sciences, New Delhi, 110029, India.
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Sivasankar C, Jha NK, Ghosh R, Shetty PH. Anti quorum sensing and anti virulence activity of tannic acid and it's potential to breach resistance in Salmonella enterica Typhi / Paratyphi A clinical isolates. Microb Pathog 2019; 138:103813. [PMID: 31654777 DOI: 10.1016/j.micpath.2019.103813] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 09/16/2019] [Accepted: 10/18/2019] [Indexed: 11/28/2022]
Abstract
Salmonella enterica Typhi and Paratyphi A are food borne pathogens causing typhoid, which is one of the most important food borne disease in the developing world. S. Typhi and S. Paratyphi A are of much concern as multi drug resistance has been on the rise. The current study is aimed to screen phytochemicals for anti quorum sensing (QS) activity against S. Typhi and S. Paratyphi A. Upon screening with swarming assay, tannic acid (TA) showed highest anti-QS activity with minimal concentration of 400μg/ml. The anti-QS activity of TA was confirmed with C. violaceum ATCC 12,472. TA showed 38-43% and 35-50% of inhibition in cell surface hydrophobicity and EPS production respectively. Through FTIR analysis, it has been observed that EPS of treated cells has a considerable change in protein and peptide. TA has also exhibited drastic reduction in the surfactant production as high as 85-90%. Blood sensitivity and antibiotic sensitivity assay revealed that TA significantly sensitizes the S. Typhi and S. Paratyphi A cells to immune components in human blood and antibiotics. It has reduced the resistance of S. Typhi and S. Paratyphi A cells against amikacin, ampicillin, ciprofloxacin, azithromycin, chloramphenicol and gentamycin, thus revitalized the usage of these antibiotics against drug resistant S. Typhi and S. Paratyphi A infections. The consistency of anti-QS potential of TA was further evaluated and established with another eight clinical isolates of S. Typhi and S. Paratyphi A. Thus TA has been proved as a promising anti QS agent that can be developed as a therapeutic combination against S. Typhi and S. Paratyphi A.
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Affiliation(s)
- Chandran Sivasankar
- Department of Food Science and Technology, Pondicherry University, Puducherry, 605014, India
| | - Nisha Kumari Jha
- Department of Food Science and Technology, Pondicherry University, Puducherry, 605014, India
| | - Ruchira Ghosh
- Department of Food Science and Technology, Pondicherry University, Puducherry, 605014, India
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Manore C, Graham T, Carr A, Feryn A, Jakhar S, Mukundan H, Highlander HC. Modeling and Cost Benefit Analysis to Guide Deployment of POC Diagnostics for Non-typhoidal Salmonella Infections with Antimicrobial Resistance. Sci Rep 2019; 9:11245. [PMID: 31375759 PMCID: PMC6677775 DOI: 10.1038/s41598-019-47359-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 07/05/2019] [Indexed: 12/03/2022] Open
Abstract
Invasive non-typhoidal Salmonella (NTS) is among the leading causes of blood stream infections in sub-Saharan Africa and other developing regions, especially among pediatric populations. Invasive NTS can be difficult to treat and have high case-fatality rates, in part due to emergence of strains resistant to broad-spectrum antibiotics. Furthermore, improper treatment contributes to increased antibiotic resistance and death. Point of care (POC) diagnostic tests that rapidly identify invasive NTS infection, and differentiate between resistant and non-resistant strains, may greatly improve patient outcomes and decrease resistance at the community level. Here we present for the first time a model for NTS dynamics in high risk populations that can analyze the potential advantages and disadvantages of four strategies involving POC diagnostic deployment, and the resulting impact on antimicrobial treatment for patients. Our analysis strongly supports the use of POC diagnostics coupled with targeted antibiotic use for patients upon arrival in the clinic for optimal patient and public health outcomes. We show that even the use of imperfect POC diagnostics can significantly reduce total costs and number of deaths, provided that the diagnostic gives results quickly enough that patients are likely to return or stay to receive targeted treatment.
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Affiliation(s)
- Carrie Manore
- Los Alamos National Laboratory, Theoretical Biology and Biophysics, Los Alamos, 87544, USA.
| | - Todd Graham
- University of Portland, Mathematics Department, Portland, 97203, USA
| | - Alexa Carr
- University of Portland, Mathematics Department, Portland, 97203, USA
| | - Alicia Feryn
- University of Portland, Mathematics Department, Portland, 97203, USA
| | - Shailja Jakhar
- Los Alamos National Laboratory, Chemistry, Los Alamos, 87544, USA
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Abstract
Purpose of review Enteric fever remains a major global-health concern, estimated to be responsible for between 11.9 and 26.9 million cases annually. Long-term prevention of enteric fever will require improved access to safe drinking water combined with investment in sanitation and hygiene interventions. In the short-to-medium term, new control strategies for typhoid fever have arrived in the form of typhoid Vi-conjugate vaccines (TCVs), offering hope that disease control can be achieved in the near future. Recent findings The diagnosis of enteric fever is complicated by its nonspecific clinical presentation, coupled with the low sensitivity of commonly used diagnostics. Investment in diagnostics has the potential to improve management, to refine estimates of disease burden and to facilitate vaccine impact studies. A new generation of reliable, diagnostic tests is needed that are simultaneously accessible, cost-effective, sensitive, and specific. The emergence and global dissemination of multidrug-resistant, fluoroquinolone-resistant, and extensively drug-resistant (XDR) strains of Salmonella Typhi emphasizes the importance of continued surveillance and appropriate antibiotic stewardship, integrated into a global strategy to address antimicrobial resistance (AMR). Current empirical treatment guidelines are out of date and should be updated to respond to local trends in AMR, so as to guide treatment choices in the absence of robust diagnostics and laboratory facilities. In September 2017, the WHO Strategic Advisory Group of Experts (SAGE) immunization recommended the programmatic use of TCVs in high burden countries. Ongoing and future studies should aim to study the impact of these vaccines in a diverse range of setting and to support the deployment of TCVs in high-burden countries. Summary The advent of new generation TCVs offers us a practical and affordable public-health tool that – for the first time – can be integrated into routine childhood immunization programmes. In this review, we advocate for the deployment of TCVs in line with WHO recommendations, to improve child health and limit the spread of antibiotic-resistant S. Typhi.
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Msefula CL, Olgemoeller F, Jambo N, Segula D, Van Tan T, Nyirenda TS, Nedi W, Kennedy N, Graham M, Henrion MYR, Baker S, Feasey N, Gordon M, Heyderman RS. Ascertaining the burden of invasive Salmonella disease in hospitalised febrile children aged under four years in Blantyre, Malawi. PLoS Negl Trop Dis 2019; 13:e0007539. [PMID: 31314752 PMCID: PMC6663031 DOI: 10.1371/journal.pntd.0007539] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 07/29/2019] [Accepted: 06/10/2019] [Indexed: 11/19/2022] Open
Abstract
Typhoid fever is endemic across sub-Saharan Africa. However, estimates of the burden of typhoid are undermined by insufficient blood volumes and lack of sensitivity of blood culture. Here, we aimed to address this limitation by exploiting pre-enrichment culture followed by PCR, alongside routine blood culture to improve typhoid case detection. We carried out a prospective diagnostic cohort study and enrolled children (aged 0-4 years) with non-specific febrile disease admitted to a tertiary hospital in Blantyre, Malawi from August 2014 to July 2016. Blood was collected for culture (BC) and real-time PCR after a pre-enrichment culture in tryptone soy broth and ox-bile. DNA was subjected to PCR for invA (Pan-Salmonella), staG (S. Typhi), and fliC (S. Typhimurium) genes. A positive PCR was defined as invA plus either staG or fliC (CT<29). IgM and IgG ELISA against four S. Typhi antigens was also performed. In total, 643 children (median age 1.3 years) with nonspecific febrile disease were enrolled; 31 (4.8%) were BC positive for Salmonella (n = 13 S. Typhi, n = 16 S. Typhimurium, and n = 2 S. Enteritidis). Pre-enrichment culture of blood followed by PCR identified a further 8 S. Typhi and 15 S. Typhimurium positive children. IgM and IgG titres to the S. Typhi antigen STY1498 (haemolysin) were significantly higher in children that were PCR positive but blood culture negative compared to febrile children with all other non-typhoid illnesses. The addition of pre-enrichment culture and PCR increased the case ascertainment of invasive Salmonella disease in children by 62-94%. These data support recent burden estimates that highlight the insensitivity of blood cultures and support the targeting of pre-school children for typhoid vaccine prevention in Africa. Blood culture with real-time PCR following pre-enrichment should be used to further refine estimates of vaccine effectiveness in typhoid vaccine trials.
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Affiliation(s)
- Chisomo L. Msefula
- Pathology Department, College of Medicine, University of Malawi, Blantyre, Malawi
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi
- * E-mail:
| | - Franziska Olgemoeller
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi
- Department of Paediatrics, Queen Elizabeth Central Hospital, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Ndaru Jambo
- Pathology Department, College of Medicine, University of Malawi, Blantyre, Malawi
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi
- University of Liverpool, Liverpool, United Kingdom
| | - Dalitso Segula
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi
- Department of Internal Medicine, Queen Elizabeth Central Hospital, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Trinh Van Tan
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Tonney S. Nyirenda
- Pathology Department, College of Medicine, University of Malawi, Blantyre, Malawi
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Wilfred Nedi
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Neil Kennedy
- Department of Paediatrics, Queen Elizabeth Central Hospital, College of Medicine, University of Malawi, Blantyre, Malawi
- Centre for Medical Education, Queens University, Belfast, United Kingdom
| | - Matthew Graham
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Marc Y. R. Henrion
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Stephen Baker
- The Department of Medicine, The University of Cambridge, Cambridge, United Kingdom
| | - Nicholas Feasey
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Melita Gordon
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi
- University of Liverpool, Liverpool, United Kingdom
| | - Robert S. Heyderman
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi
- Division of Infection & Immunity, University College London, London, England, United Kingdom
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Tsuchiya Y, Loza E, Villa-Gomez G, Trujillo CC, Baez S, Asai T, Ikoma T, Endoh K, Nakamura K. Metagenomics of Microbial Communities in Gallbladder Bile from Patients with Gallbladder Cancer or Cholelithiasis. Asian Pac J Cancer Prev 2018; 19:961-967. [PMID: 29693356 PMCID: PMC6031792 DOI: 10.22034/apjcp.2018.19.4.961] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Salmonella typhi and Helicobacter infections have been shown to increase risk of gallbladder cancer (GBC), but findings have been inconsistent. Other bacterial infections may also be associated with GBC. However, information on microbial pathogens in gallbladder bile of GBC patients is scarce. We aimed to investigate the microbial communities in gallbladder bile of patients with GBC and cholelithiasis (CL). Seven GBC patients and 30 CL patients were enrolled in this study. Genomic DNA was extracted from bile and the V3-V4 region of 16S rRNA was amplified. The sequencing results were compared with the 16S database, and the bacteria were identified by homology searches and phylogenetic analysis. DNA was detected in the bile of three GBC (42.9%; Bolivia, 1; Chile, 2) and four CL patients (13.3%; Bolivia, 1; Chile, 3). Of the 37 patients, 30 (81.1%) were negative and unable to analyze. Salmonella typhi and Helicobacter sp. were not detected in bile from any GBC patients. As the predominant species, Fusobacterium nucleatum, Escherichia coli, and Enetrobacter sp. were detected in bile from GBC patients. Those in bile from CL patients were Escherichia coli, Salmonella sp., and Enerococcus gallinarum. Escherichia coli was detected in bile samples from both GBC and CL patients. Whether the bacteria detected in bile from GBC patients would associated with the development of GBC warrant further investigation.
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Affiliation(s)
- Yasuo Tsuchiya
- Division of Preventive Medicine, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
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Abstract
BACKGROUND Differentiating both typhoid (Salmonella Typhi) and paratyphoid (Salmonella Paratyphi A) infection from other causes of fever in endemic areas is a diagnostic challenge. Although commercial point-of-care rapid diagnostic tests (RDTs) for enteric fever are available as alternatives to the current reference standard test of blood or bone marrow culture, or to the widely used Widal Test, their diagnostic accuracy is unclear. If accurate, they could potentially replace blood culture as the World Health Organization (WHO)-recommended main diagnostic test for enteric fever. OBJECTIVES To assess the diagnostic accuracy of commercially available rapid diagnostic tests (RDTs) and prototypes for detecting Salmonella Typhi or Paratyphi A infection in symptomatic persons living in endemic areas. SEARCH METHODS We searched the Cochrane Infectious Diseases Group Specialized Register, MEDLINE, Embase, Science Citation Index, IndMED, African Index Medicus, LILACS, ClinicalTrials.gov, and the World Health Organization (WHO) International Clinical Trials Registry Platform (ICTRP) up to 4 March 2016. We manually searched WHO reports, and papers from international conferences on Salmonella infections. We also contacted test manufacturers to identify studies. SELECTION CRITERIA We included diagnostic accuracy studies of enteric fever RDTs in patients with fever or with symptoms suggestive of enteric fever living in endemic areas. We classified the reference standard used as either Grade 1 (result from a blood culture and a bone marrow culture) or Grade 2 (result from blood culture and blood polymerase chain reaction, or from blood culture alone). DATA COLLECTION AND ANALYSIS Two review authors independently extracted the test result data. We used a modified QUADAS-2 extraction form to assess methodological quality. We performed a meta-analysis when there were sufficient studies for the test and heterogeneity was reasonable. MAIN RESULTS Thirty-seven studies met the inclusion criteria and included a total of 5080 participants (range 50 to 1732). Enteric fever prevalence rates in the study populations ranged from 1% to 75% (median prevalence 24%, interquartile range (IQR) 11% to 46%). The included studies evaluated 16 different RDTs, and 16 studies compared two or more different RDTs. Only three studies used the Grade 1 reference standard, and only 11 studies recruited unselected febrile patients. Most included studies were from Asia, with five studies from sub-Saharan Africa. All of the RDTs were designed to detect S.Typhi infection only.Most studies evaluated three RDTs and their variants: TUBEX in 14 studies; Typhidot (Typhidot, Typhidot-M, and TyphiRapid-Tr02) in 22 studies; and the Test-It Typhoid immunochromatographic lateral flow assay, and its earlier prototypes (dipstick, latex agglutination) developed by the Royal Tropical Institute, Amsterdam (KIT) in nine studies. Meta-analyses showed an average sensitivity of 78% (95% confidence interval (CI) 71% to 85%) and specificity of 87% (95% CI 82% to 91%) for TUBEX; and an average sensitivity of 69% (95% CI 59% to 78%) and specificity of 90% (95% CI 78% to 93%) for all Test-It Typhoid and prototype tests (KIT). Across all forms of the Typhidot test, the average sensitivity was 84% (95% CI 73% to 91%) and specificity was 79% (95% CI 70% to 87%). When we based the analysis on the 13 studies of the Typhidot test that either reported indeterminate test results or where the test format means there are no indeterminate results, the average sensitivity was 78% (95% CI 65% to 87%) and specificity was 77% (95% CI 66% to 86%). We did not identify any difference in either sensitivity or specificity between TUBEX, Typhidot, and Test-it Typhoid tests when based on comparison to the 13 Typhidot studies where indeterminate results are either reported or not applicable. If TUBEX and Test-it Typhoid are compared to all Typhidot studies, the sensitivity of Typhidot was higher than Test-it Typhoid (15% (95% CI 2% to 28%), but other comparisons did not show a difference at the 95% level of CIs.In a hypothetical cohort of 1000 patients presenting with fever where 30% (300 patients) have enteric fever, on average Typhidot tests reporting indeterminate results or where tests do not produce indeterminate results will miss the diagnosis in 66 patients with enteric fever, TUBEX will miss 66, and Test-It Typhoid and prototype (KIT) tests will miss 93. In the 700 people without enteric fever, the number of people incorrectly diagnosed with enteric fever would be 161 with Typhidot tests, 91 with TUBEX, and 70 with Test-It Typhoid and prototype (KIT) tests. The CIs around these estimates were wide, with no difference in false positive results shown between tests.The quality of the data for each study was evaluated using a standardized checklist called QUADAS-2. Overall, the certainty of the evidence in the studies that evaluated enteric fever RDTs was low. AUTHORS' CONCLUSIONS In 37 studies that evaluated the diagnostic accuracy of RDTs for enteric fever, few studies were at a low risk of bias. The three main RDT tests and variants had moderate diagnostic accuracy. There was no evidence of a difference between the average sensitivity and specificity of the three main RDT tests. More robust evaluations of alternative RDTs for enteric fever are needed.
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Affiliation(s)
- Lalith Wijedoru
- Liverpool School of Tropical MedicineDepartment of Clinical SciencesLiverpoolUKL3 5QA
| | - Sue Mallett
- University of BirminghamInstitute of Applied Health SciencesEdgbastonBirminghamUKB15 2TT
| | - Christopher M Parry
- Liverpool School of Tropical MedicineDepartment of Clinical SciencesLiverpoolUKL3 5QA
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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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Divyashree S, Nabarro LEB, Veeraraghavan B, Rupali P. Enteric fever in India: current scenario and future directions. Trop Med Int Health 2016; 21:1255-1262. [DOI: 10.1111/tmi.12762] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- S. Divyashree
- Department of Infectious Disease; Christian Medical College; Vellore India
| | - L. E. B. Nabarro
- Department of Infectious Disease; Christian Medical College; Vellore India
- Public Health England; London UK
| | - B. Veeraraghavan
- Department of Microbiology; Christian Medical College; Vellore India
| | - P. Rupali
- Department of Infectious Disease; Christian Medical College; Vellore India
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20
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Tennant SM, Toema D, Qamar F, Iqbal N, Boyd MA, Marshall JM, Blackwelder WC, Wu Y, Quadri F, Khan A, Aziz F, Ahmad K, Kalam A, Asif E, Qureshi S, Khan E, Zaidi AK, Levine MM. Detection of Typhoidal and Paratyphoidal Salmonella in Blood by Real-time Polymerase Chain Reaction. Clin Infect Dis 2016; 61 Suppl 4:S241-50. [PMID: 26449938 DOI: 10.1093/cid/civ726] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND The gold standard for diagnosis of enteric fever caused by Salmonella Typhi or Salmonella Paratyphi A or B is bone marrow culture. However, because bone marrow aspiration is highly invasive, many hospitals and large health centers perform blood culture instead. As blood culture has several limitations, there is a need for novel typhoid diagnostics with improved sensitivity and more rapid time to detection. METHODS We developed a clyA-based real-time polymerase chain reaction (qPCR) method to detect Salmonella Typhi and Salmonella Paratyphi A simultaneously in blood. The sensitivity and specificity of this probeset was first evaluated in vitro in the laboratory and then in a typhoid-endemic population, in Karachi, Pakistan, and in healthy US volunteers. RESULTS We optimized a DNA extraction and real-time PCR-based method that could reliably detect 1 colony-forming unit/mL of Salmonella Typhi. The probe set was able to detect clinical Salmonella Typhi and Salmonella Paratyphi A strains and also diarrheagenic Escherichia coli, but not invasive E. coli or other invasive bacteria. In the field, the clyA qPCR diagnostic was 40% as sensitive as blood culture. However, when qPCR-positive specimens were considered to be true positives, blood culture only exhibited 28.57% sensitivity. Specificity was ≥90% for all comparisons and in the healthy US volunteers. qPCR was significantly faster than blood culture in terms of detection of typhoid and paratyphoid. CONCLUSIONS Based on lessons learned, we recommend that future field trials of this and other novel diagnostics that detect typhoidal and nontyphoidal Salmonella employ multiple methodologies to define a "positive" sample.
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Affiliation(s)
- Sharon M Tennant
- Center for Vaccine Development Department of Medicine, University of Maryland, Baltimore
| | - Deanna Toema
- Center for Vaccine Development Department of Medicine, University of Maryland, Baltimore
| | | | - Najeeha Iqbal
- Department of Paediatrics and Child Health Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
| | - Mary Adetinuke Boyd
- Center for Vaccine Development Department of Pediatrics, University of Maryland, Baltimore
| | - Joanna M Marshall
- Center for Vaccine Development Department of Medicine, University of Maryland, Baltimore
| | - William C Blackwelder
- Center for Vaccine Development Department of Medicine, University of Maryland, Baltimore
| | - Yukun Wu
- Center for Vaccine Development Department of Medicine, University of Maryland, Baltimore
| | | | - Asia Khan
- Department of Paediatrics and Child Health
| | | | | | - Adil Kalam
- Department of Paediatrics and Child Health
| | | | | | - Erum Khan
- Department of Pathology and Microbiology, Aga Khan University, Karachi, Pakistan
| | | | - Myron M Levine
- Center for Vaccine Development Department of Medicine, University of Maryland, Baltimore Department of Pediatrics, University of Maryland, Baltimore
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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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Al-Emran HM, Hahn A, Baum J, Cruz Espinoza LM, Deerin J, Im J, Ibrango S, Kabore LP, von Kalckreuth V, Konings F, Marks F, Sampo E, Panzner U, Park SE, Pak GD, Schütt-Gerowitt H, Vinnemeier CD, Warren M, Soura AB. DiagnosingSalmonella entericaSerovar Typhi Infections by Polymerase Chain Reaction Using EDTA Blood Samples of Febrile Patients From Burkina Faso. Clin Infect Dis 2016; 62 Suppl 1:S37-41. [DOI: 10.1093/cid/civ770] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Gibani MM, Jin C, Darton TC, Pollard AJ. Control of Invasive Salmonella Disease in Africa: Is There a Role for Human Challenge Models? Clin Infect Dis 2015; 61 Suppl 4:S266-71. [PMID: 26449941 PMCID: PMC4596929 DOI: 10.1093/cid/civ673] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Invasive Salmonella disease in Africa is a major public health concern. With evidence of the transcontinental spread of the Salmonella Typhi H58 haplotype, improved estimates of the burden of infection and understanding of the complex interplay of factors affecting disease transmission are needed to assist with efforts aimed at disease control. In addition to Salmonella Typhi, invasive nontyphoidal Salmonella are increasingly recognized as an important cause of febrile illness and mortality in sub-Saharan Africa. Human experimental oral challenge studies with Salmonella can be used as a model to offer unique insights into host-pathogen interactions as well as a platform to efficiently test new diagnostic and vaccine candidates. In this article, we review the background and use of human challenge studies to date and discuss how findings from these studies may lead to progress in the control of invasive Salmonella disease in Africa.
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Affiliation(s)
- Malick M Gibani
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the National Institute for Health Research Oxford Biomedical Research Centre, United Kingdom
| | - Celina Jin
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the National Institute for Health Research Oxford Biomedical Research Centre, United Kingdom
| | - Thomas C Darton
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the National Institute for Health Research Oxford Biomedical Research Centre, United Kingdom
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford and the National Institute for Health Research Oxford Biomedical Research Centre, United Kingdom
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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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Mehmood K, Sundus A, Naqvi IH, Ibrahim MF, Siddique O, Ibrahim NF. Typhidot - A blessing or a menace. Pak J Med Sci 2015; 31:439-43. [PMID: 26101507 PMCID: PMC4476358 DOI: 10.12669/pjms.312.5934] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 07/14/2014] [Accepted: 12/15/2014] [Indexed: 11/24/2022] Open
Abstract
Objectives: Typhoid remain an increasing problem in Third world countries like Pakistan. A reliable, easy and affordable rapid diagnostic test is a need for our clinicians, many of whom consider Typhidot to be promising. Typhidot has been used as the only tool to diagnose typhoid fever by general practitioners and consultants despite its low sensitivity and specificity causing misdiagnosis and treatment. We therefore conducted this study to evaluate the sensitivity and specificity of Typhidot in patients with fever. Methods: A retrospective analysis of a total of 145 febrile patients was done. Blood culture and Typhidot along with other relevant investigations had been performed in each case. Sensitivity, specificity and the association of Typhidot to the diagnosis was found using SPSS v16.0. Results: Out of 145 patients, 15(10.3%) had positive blood culture for Salmonella typhi, 7 (4.8%) had positive culture for salmonella paratyphi and 94(64.8%) had positive culture for other organisms. Twenty nine (20%) patients had negative culture results. Forty seven (32.4%) patients had only IgM positive on Typhidot, 7(4.8%) had both IgM and IgG positive and 91(62.8%) had both IgM and IgG negative. Amongst the 130 patients with diseases other than typhoid, 50(38.5%) showed a positive Typhidot result. Amongst the 15 patients with typhoid, 11(73.3%) showed a negative Typhidot result. The sensitivity of Typhidot was found to be 26.7% and the specificity was 61.5%. The Positive Predictive Value (PPV) was 7.4% and the Negative Predictive Value (NPV) was 87.9%. Conclusion: Even though Typhidot is rapid, easy and affordable, its use should be discouraged due to low sensitivity and specificity and insignificant (p=0.067) association to the disease.
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Affiliation(s)
- Khalid Mehmood
- Dr. Khalid Mehmood, FRCP, Head of Department, Medical Unit 3, Civil Hospital Karachi, Pakistan
| | - Ayesha Sundus
- Dr. Ayesha Sundus, MBBS, House Officer, Civil Hospital Karachi, Pakistan
| | - Iftikhar Haider Naqvi
- Dr. Iftikhar Haider Naqvi, FCPS, Assistant Professor, Medical Unit 3, Civil Hospital Karachi, Pakistan
| | - Mohammad Faisal Ibrahim
- Dr. Mohammad Faisal Ibrahim, MBBS, Graduate Medical Student, Dow University of Health Sciences, Karachi, Pakistan
| | - Osama Siddique
- Dr. Osama Siddique, MBBS, Graduate Medical Student, Dow University of Health Sciences, Karachi, Pakistan
| | - Nida Faisal Ibrahim
- Dr. Nida Faisal Ibrahim, MBBS, Graduate Medical Student, Dow University of Health Sciences, Karachi, Pakistan
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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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A novel technique for detecting antibiotic-resistant typhoid from rapid diagnostic tests. J Clin Microbiol 2015; 53:1758-60. [PMID: 25762768 PMCID: PMC4400746 DOI: 10.1128/jcm.00531-15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 03/03/2015] [Indexed: 01/28/2023] Open
Abstract
Fluoroquinolone-resistant typhoid is increasing. An antigen-detecting rapid diagnotic test (RDT) can rapidly diagnose typhoid from blood cultures. A simple, inexpensive molecular technique performed with DNA from positive RDTs accurately identified gyrA mutations consistent with phenotypic susceptibility testing results. Field diagnosis combined with centralized molecular resistance testing could improve typhoid management and surveillance in low-resource settings.
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Ganesan V, Harish BN, Menezes GA, Parija SC. Detection of Salmonella in Blood by PCR using iroB gene. J Clin Diagn Res 2014; 8:DC01-3. [PMID: 25584214 DOI: 10.7860/jcdr/2014/9191.5086] [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: 03/09/2014] [Accepted: 09/10/2014] [Indexed: 11/24/2022]
Abstract
BACKGROUND Salmonella, a genus of more than 2500 serological variants (serovars), includes many organisms that can cause human disease. Enteric fever remains an important public health problem in developing countries. Non typhoidal Salmonella generally produce a self limited gastroenteritis in healthy individuals whereas in extremes of age and immunocompromised cause severe fatal disease. The protean manifestations make this disease a true diagnostic challenge. AIM The present study was carried out to optimize PCR for detecting the Salmonella genus using iroB gene and evaluate its use in the rapid diagnosis of typhoid and non typhoidal salmonellosis. MATERIALS AND METHODS The study was carried out between August 2009 and July 2011 on blood samples from patients attending JIPMER hospital, Pondicherry, India with clinical suspicion of enteric fever and salmonellosis. Whole blood was used DNA extraction and conventional PCR done with iroB and fliC primers. Blood culture and Widal test were performed for all the patients. STATISTICAL ANALYSIS Performed using Fischer's exact test with Graphpad Instat 3. RESULTS PCR results were compared with blood culture. Sensitivity and specificity of PCR with fliC gene are 95.6% and 93.3% respectively. Sensitivity and specificity of PCR with iroB gene are 96.6% and 93.3% respectively CONCLUSION With iroB gene, additional cases of Salmonella Paratyphi A and non typhoidal Salmonella were detected when compared to fliC gene.
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Affiliation(s)
- Vithiya Ganesan
- Assistant Professor, Department of Microbiology, Velammal Medical College Hospital and Research Institute , Madurai, India
| | - Belgode Narasimha Harish
- Head of the Department, Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Science and Research , Puducherry, India
| | - Godfred Antony Menezes
- Assistant Professor, College of Applied Medical Sciences, University of Ha'il, Ha'il , Kingdom of Saudi Arabia (KSA)
| | - Subash Chandra Parija
- Dean, Jawaharlal Institute of Postgraduate Medical Science and Research , Puducherry, India
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Chattopadhyay S, Dey SK, Maiti PK, Dolai D. A novel tool for capture and detection of typhoid fever using Ag-labeled nanocomposites. J Biol Inorg Chem 2014; 19:1377-84. [DOI: 10.1007/s00775-014-1199-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Accepted: 09/26/2014] [Indexed: 11/30/2022]
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Rani N, Vajpayee P, Bhatti S, Singh S, Shanker R, Gupta KC. Quantification of Salmonella Typhi in water and sediments by molecular-beacon based qPCR. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2014; 108:58-64. [PMID: 25042245 DOI: 10.1016/j.ecoenv.2014.06.033] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 06/27/2014] [Accepted: 06/27/2014] [Indexed: 06/03/2023]
Abstract
A molecular-beacon based qPCR assay targeting staG gene was designed for specific detection and quantification of S. Typhi and validated against water and sediment samples collected from the river Ganga, Yamuna and their confluence on two days during Mahakumbha mela 2012-2013 (a) 18 December, 2012: before six major religious holy dips (Makar Sankranti, Paush Poornima, Mauni Amavasya, Basant Panchami, Maghi Poornima and Mahashivratri) (b) 10 February, 2013: after the holy dip was taken by over 3,00,00,000 devotees led by ascetics of Hindu sects at Sangam on 'Mauni Amavasya' (the most auspicious day of ritualistic mass bathing). The assay could detect linearly lowest 1 genomic equivalent per qPCR and is highly sensitive and selective for S. Typhi detection in presence of non specific DNA from other bacterial strains including S. Paratyphi A and S. Typhimurium. It has been observed that water and sediment samples exhibit S. Typhi. The mass holy dip by devotees significantly affected the water and sediment quality by enhancing the number of S. Typhi in the study area. The qPCR developed in the study might be helpful in planning the intervention and prevention strategies for control of enteric fever outbreaks in endemic regions.
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Affiliation(s)
- Neetika Rani
- Environmental Microbiology, Environmental Toxicology Group, CSIR-Indian Institute of Toxicology Research, Post Box 80, M.G. Marg, Lucknow 226001, India; Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Poornima Vajpayee
- Environmental Microbiology, Environmental Toxicology Group, CSIR-Indian Institute of Toxicology Research, Post Box 80, M.G. Marg, Lucknow 226001, India.
| | - Saurabh Bhatti
- Environmental Microbiology, Environmental Toxicology Group, CSIR-Indian Institute of Toxicology Research, Post Box 80, M.G. Marg, Lucknow 226001, India; Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Smriti Singh
- Environmental Microbiology, Environmental Toxicology Group, CSIR-Indian Institute of Toxicology Research, Post Box 80, M.G. Marg, Lucknow 226001, India
| | - Rishi Shanker
- Environmental Microbiology, Environmental Toxicology Group, CSIR-Indian Institute of Toxicology Research, Post Box 80, M.G. Marg, Lucknow 226001, India; Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Kailash Chand Gupta
- Environmental Microbiology, Environmental Toxicology Group, CSIR-Indian Institute of Toxicology Research, Post Box 80, M.G. Marg, Lucknow 226001, India; Academy of Scientific and Innovative Research (AcSIR), New Delhi, India.
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Mandal J, Akhter MZ, Kabir MS, Ahsan S. Development of a multiplex polymerase chain reaction protocol for the simultaneous detection of Salmonella enterica serovar Typhi and Class 1 integron. ASIAN PACIFIC JOURNAL OF TROPICAL DISEASE 2014. [DOI: 10.1016/s2222-1808(14)60732-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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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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Abstract
PURPOSE OF REVIEW Infection caused by ingestion of human-restricted Salmonella enterica serovars Typhi and Paratyphi predominantly affects the most impoverished sections of society. In this review, we describe recent advances made in estimating the burden of illness and the important role improved diagnostic tests may have in controlling infection and report the development of a new human challenge model of typhoid infection. RECENT FINDINGS Typhoid continues to be a major cause of morbidity, particularly in children and young adults in south east Asia, although accurate assessments are still hindered by the lack of reliable surveillance data. Recent reports of high rates of infection in Africa and the dominance of paratyphoid in several geographic areas are of particular concern. Diagnosis of enteric fever remains frustrated by the nonspecific clinical presentation of cases and the lack of test sensitivity. Methods to improve diagnostic accuracy are hindered by the incomplete understanding of immunobiological mechanisms of infection and lack of a suitable animal infection model. SUMMARY Enteric fever is a major global problem, the burden of which has only partially been recognized. Control strategies utilizing cheap accurate diagnostics and effective vaccines are urgently required, and their development should be accelerated by the use of a human challenge model.
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Waddington CS, Darton TC, Pollard AJ. The challenge of enteric fever. J Infect 2014; 68 Suppl 1:S38-50. [DOI: 10.1016/j.jinf.2013.09.013] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2013] [Indexed: 11/27/2022]
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Zhang J, Wei L, Kelly P, Freeman M, Jaegerson K, Gong J, Xu B, Pan Z, Xu C, Wang C. Detection of Salmonella spp. using a generic and differential FRET-PCR. PLoS One 2013; 8:e76053. [PMID: 24146814 PMCID: PMC3797804 DOI: 10.1371/journal.pone.0076053] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2013] [Accepted: 08/17/2013] [Indexed: 11/20/2022] Open
Abstract
To facilitate the detection of Salmonella and to be able to rapidly and conveniently determine the species/subspecies present, we developed and tested a generic and differential FRET-PCR targeting their tetrathionate reductase response regulator gene. The differential pan-Salmonella FRET-PCR we developed successfully detected seven plasmids that contained partial sequences of S. bongori and the six S. enterica subspecies. The detection limit varied from ∼5 copies of target gene/per PCR reaction for S. enterica enterica to ∼200 for S. bongori. Melting curve analysis demonstrated a Tm of ∼68°C for S. enterica enterica, ∼62.5°C for S. enterica houtenae and S. enterica diarizonae, ∼57°C for S. enterica indica, and ∼54°C for S. bongori, S. enterica salamae and S. enterica arizonae. The differential pan-Salmonella FRET-PCR also detected and determined the subspecies of 4 reference strains and 47 Salmonella isolated from clinically ill birds or pigs. Finally, we found it could directly detect and differentiate Salmonella in feline (5/50 positive; 10%; one S. enterica salamae and 4 S. enterica enterica) and canine feces (15/114 positive; 13.2%; all S. enterica enterica). The differential pan-Salmonella FRET-PCR failed to react with 96 non-Salmonella bacterial strains. Our experiments show the differential pan-Salmonella FRET-PCR we developed is a rapid, sensitive and specific method to detect and differentiate Salmonella.
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Affiliation(s)
- Jilei Zhang
- Yangzhou University College of Veterinary Medicine, Yangzhou, Jiangsu, P. R. China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, P. R. China
| | - Lanjing Wei
- Yangzhou University College of Veterinary Medicine, Yangzhou, Jiangsu, P. R. China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, P. R. China
| | - Patrick Kelly
- Ross University School of Veterinary Medicine, Basseterre, St. Kitts and Nevis
| | - Mark Freeman
- Virginia-Maryland Regional College of Veterinary Medicine, Blacksburg, Virginia, United States of America
| | - Kirsten Jaegerson
- Ross University School of Veterinary Medicine, Basseterre, St. Kitts and Nevis
| | - Jiansen Gong
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, P. R. China
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, Jiangsu, P. R. China
| | - Bu Xu
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, P. R. China
- Poultry Institute, Chinese Academy of Agricultural Sciences, Yangzhou, Jiangsu, P. R. China
| | - Zhiming Pan
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, P. R. China
- Yangzhou University College of Bioscience and Biotechnology, Yangzhou, Jiangsu, P. R. China
| | - Chuanling Xu
- Yangzhou University College of Veterinary Medicine, Yangzhou, Jiangsu, P. R. China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, P. R. China
| | - Chengming Wang
- Yangzhou University College of Veterinary Medicine, Yangzhou, Jiangsu, P. R. China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, P. R. China
- * E-mail:
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Frickmann H, Hänle A, Essig A, Dekker D, Boahen K, Acquah S, Sarpong N, Adu-Sarkodie Y, Schwarz NG, May J, Marks F, Hagen RM, Poppert S. Fluorescence in situ hybridization (FISH) for rapid identification of Salmonella spp. from agar and blood culture broth--an option for the tropics? Int J Med Microbiol 2013; 303:277-84. [PMID: 23642903 DOI: 10.1016/j.ijmm.2013.04.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Revised: 04/02/2013] [Accepted: 04/07/2013] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Salmonella enterica is an important cause of diarrhea with the potential to cause systemic infection including sepsis, particularly in the tropics. Sepsis in particular requires quick and reliable identification to allow a rapid optimization of antibiotic therapy. We describe the establishment and evaluation of fluorescence in situ hybridization (FISH) as a rapid and easy-to-perform molecular identification procedure from agar and blood culture broths. METHODS Two newly developed FISH probes with specificity for Salmonella spp. were evaluated with 10 reference strains, 448 clinical isolates of Gram-negative bacteria from Germany and Ghana including 316 Salmonella spp. strains, and 39 environmental Salmonella spp. isolates from rivers and streams in Ghana. One FISH probe was further tested with 207 pre-incubated blood culture broths from Germany with Gram-negative rod-shaped bacteria in Gram stain. RESULTS Evaluation of the newly designed FISH probes demonstrated sensitivity of 99.2% and specificity of 98.4% for clinical isolates, sensitivity of 97.4% for environmental Salmonella spp. isolates, and sensitivity of 100% and specificity of 99.5% for blood culture materials. CONCLUSIONS FISH proved to be highly reliable for a rapid identification of Salmonella spp. directly from pre-incubated blood culture broths as well as after growth on agar. The inexpensive and easy-to-perform procedure is particularly suitable for resource-limited areas where more sophisticated procedures are not available.
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Affiliation(s)
- Hagen Frickmann
- Department of Tropical Medicine at the Bernhard-Nocht Institute, German Armed Forces Hospital of Hamburg, Germany.
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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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Zhou L, Pollard AJ. A novel method of selective removal of human DNA improves PCR sensitivity for detection of Salmonella Typhi in blood samples. BMC Infect Dis 2012; 12:164. [PMID: 22839649 PMCID: PMC3482578 DOI: 10.1186/1471-2334-12-164] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Accepted: 07/11/2012] [Indexed: 11/21/2022] Open
Abstract
Background Enteric fever is a major public health problem, causing an estimated 21million new cases and 216,000 or more deaths every year. Current diagnosis of the disease is inadequate. Blood culture only identifies 45 to 70% of the cases and is time-consuming. Serological tests have very low sensitivity and specificity. Clinical samples obtained for diagnosis of enteric fever in the field generally have <1 organism/ml of blood, so that even PCR-based methods, widely used for detection of other infectious diseases, are not a straightforward option in typhoid diagnosis. We developed a novel method to enrich target bacterial DNA by selective removal of human DNA from blood samples, enhancing the sensitivity of PCR tests. This method offers the possibility of improving PCR assays directly using clinical specimens for diagnosis of this globally important infectious disease. Methods Blood samples were mixed with ox bile for selective lysis of human blood cells and the released human DNA was then digested with addition of bile resistant micrococcal nuclease. The intact Salmonella Typhi bacteria were collected from the specimen by centrifugation and the DNA extracted with QIAamp DNA mini kit. The presence of Salmonella Typhi bacteria in blood samples was detected by PCR with the fliC-d gene of Salmonella Typhi as the target. Results Micrococcal nuclease retained activity against human blood DNA in the presence of up to 9% ox bile. Background human DNA was dramatically removed from blood samples through the use of ox bile lysis and micrococcal nuclease for removal of mammalian DNA. Consequently target Salmonella Typhi DNA was enriched in DNA preparations and the PCR sensitivity for detection of Salmonella Typhi in spiked blood samples was enhanced by 1,000 fold. Conclusions Use of a combination of selective ox-bile blood cell lysis and removal of human DNA with micrococcal nuclease significantly improves PCR sensitivity and offers a better option for improved typhoid PCR assays directly using clinical specimens in diagnosis of this globally important infection disease which we believe could be of importance in improving clinical care and providing effective evaluation of novel vaccines.
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Affiliation(s)
- Liqing Zhou
- Oxford Vaccine Centre, Department of Paediatrics, University of Oxford, Oxford, UK.
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Thriemer K, Ley B, Ame S, von Seidlein L, Pak GD, Chang NY, Hashim R, Schmied WH, Busch CJL, Nixon S, Morrissey A, Puri MK, Ali M, Ochiai RL, Wierzba T, Jiddawi MS, Clemens JD, Ali SM, Deen JL. The burden of invasive bacterial infections in Pemba, Zanzibar. PLoS One 2012; 7:e30350. [PMID: 22363426 PMCID: PMC3281825 DOI: 10.1371/journal.pone.0030350] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Accepted: 12/14/2011] [Indexed: 11/18/2022] Open
Abstract
Background We conducted a surveillance study to determine the leading causes of bloodstream infection in febrile patients seeking treatment at three district hospitals in Pemba Island, Zanzibar, Tanzania, an area with low malaria transmission. Methods All patients above two months of age presenting to hospital with fever were screened, and blood was collected for microbiologic culture and malaria testing. Bacterial sepsis and malaria crude incidence rates were calculated for a one-year period and were adjusted for study participation and diagnostic sensitivity of blood culture. Results Blood culture was performed on 2,209 patients. Among them, 166 (8%) samples yielded bacterial growth; 87 (4%) were considered as likely contaminants; and 79 (4%) as pathogenic bacteria. The most frequent pathogenic bacteria isolated were Salmonella Typhi (n = 46; 58%), followed by Streptococcus pneumoniae (n = 12; 15%). The crude bacteremia rate was 6/100,000 but when adjusted for potentially missed cases the rate may be as high as 163/100,000. Crude and adjusted rates for S. Typhi infections and malaria were 4 and 110/100,000 and 4 and 47/100,000, respectively. Twenty three (51%), 22 (49%) and 22 (49%) of the S.Typhi isolates were found to be resistant toward ampicillin, chloramphenicol and cotrimoxazole, respectively. Multidrug resistance (MDR) against the three antimicrobials was detected in 42% of the isolates. Conclusions In the presence of very low malaria incidence we found high rates of S. Typhi and S. pneumoniae infections on Pemba Island, Zanzibar. Preventive measures such as vaccination could reduce the febrile disease burden.
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Tennant SM, Zhang Y, Galen JE, Geddes CD, Levine MM. Ultra-fast and sensitive detection of non-typhoidal Salmonella using microwave-accelerated metal-enhanced fluorescence ("MAMEF"). PLoS One 2011; 6:e18700. [PMID: 21494634 PMCID: PMC3073000 DOI: 10.1371/journal.pone.0018700] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Accepted: 03/08/2011] [Indexed: 01/11/2023] Open
Abstract
Certain serovars of Salmonella enterica subsp. enterica cause invasive disease (e.g., enteric fever, bacteremia, septicemia, meningitis, etc.) in humans and constitute a global public health problem. A rapid, sensitive diagnostic test is needed to allow prompt initiation of therapy in individual patients and for measuring disease burden at the population level. An innovative and promising new rapid diagnostic technique is microwave-accelerated metal-enhanced fluorescence (MAMEF). We have adapted this assay platform to detect the chromosomal oriC locus common to all Salmonella enterica subsp. enterica serovars. We have shown efficient lysis of biologically relevant concentrations of Salmonella spp. suspended in bacteriological media using microwave-induced lysis. Following lysis and DNA release, as little as 1 CFU of Salmonella in 1 ml of medium can be detected in <30 seconds. Furthermore the assay is sensitive and specific: it can detect oriC from Salmonella serovars Typhi, Paratyphi A, Paratyphi B, Paratyphi C, Typhimurium, Enteritidis and Choleraesuis but does not detect Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae, Streptococcus pneumoniae, Haemophilus influenzae or Acinetobacter baumanii. We have also performed preliminary experiments using a synthetic Salmonella oriC oligonucleotide suspended in whole human blood and observed rapid detection when the sample was diluted 1∶1 with PBS. These pre-clinical data encourage progress to the next step to detect Salmonella in blood (and other ordinarily sterile, clinically relevant body fluids).
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Affiliation(s)
- Sharon M Tennant
- Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, Maryland, United States of America.
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