PeerJ Preprints: Epidemiologyhttps://peerj.com/preprints/index.atom?journal=peerj&subject=4300Epidemiology articles published in PeerJ PreprintsAflatoxins in Uganda: an encyclopedic review of the etiology, epidemiology, detection, quantification, exposure assessment, reduction and controlhttps://peerj.com/preprints/279632019-09-162019-09-16Timothy OmaraWinfred NassaziTom OmuteAburu AwathFortunate LakerRaymond KalukusuBashir MusauBrenda V NakabuyeSarah KagoyaGeorge OtimEddie Adupa
Uganda is predominantly an agricultural country where farming employ more than 60% of the population. Aflatoxins remain a scourge in the country, unprecedentedly reducing the value of agricultural foods and in high enough exposure levels, implicated for hepatocellular carcinoma, stunted growth in children and untimely deaths. This review synthetizes the country’s major findings in relation to the mycotoxin’s etiology, epidemiology, detection, quantification, exposure assessment, control and reduction in different matrices. It also highlights some of the management strategies for aflatoxin control that could be adopted in Uganda. Review results indicate that aflatoxins in Uganda is majorly produced by Aspergillus flavus and A. parasiticus and have been reported in maize (Zea mays L.), sorghum (Sorghum bicolor L.), sesame (Sesamum indicum), beans (Phaseolus vulgaris L.), sunflower (Helianthus annus), millet (Eleusine coracana), a bovine milk-based product, peanuts (Arachis hypogaea L.) and cassava (Manihot esculenta) with the highest content reported in cassava, beans and peanuts. The causes and proliferation of aflatoxigenic contamination of Ugandan foods have been largely due to poor pre-, peri- and post-harvest activities, poor government legislation, lack of awareness and low levels of education among farmers, agri-entreprenuers and consumers on the plague. Aflatoxin B1 is the most prevalent aflatoxin in Uganda. There is still limited research on aflatoxins in Uganda because the surveillance, reduction and control carry prohibitive costs. A few exposure assessments have been done especially in human sera and dependence on a single or a related set of foods with little diet diversity has exacerbated the risk of exposure to aflatoxins in Uganda because most of the staple foods are aflatoxin-prone. On the detection, control and reduction, these are still marginal, though some devoted scholars have devised and validated a sensitive portable device for on-site aflatoxin detection in maize as well as shown that starter cultures used for making some cereal-based beverages have the potential to bind aflatoxins. More effort should be geared towards awareness creation through training of farmers and traders in the cereal value chain as well as developing capacity to monitor aflatoxins. Vaccination against Hepatitis B and Hepatitis A should be emphasized to reduce the risk of development of liver cancer among the populace.
Uganda is predominantly an agricultural country where farming employ more than 60% of the population. Aflatoxins remain a scourge in the country, unprecedentedly reducing the value of agricultural foods and in high enough exposure levels, implicated for hepatocellular carcinoma, stunted growth in children and untimely deaths. This review synthetizes the country’s major findings in relation to the mycotoxin’s etiology, epidemiology, detection, quantification, exposure assessment, control and reduction in different matrices. It also highlights some of the management strategies for aflatoxin control that could be adopted in Uganda. Review results indicate that aflatoxins in Uganda is majorly produced by Aspergillus flavus and A. parasiticus and have been reported in maize (Zea mays L.), sorghum (Sorghum bicolor L.), sesame (Sesamum indicum), beans (Phaseolus vulgaris L.), sunflower (Helianthus annus), millet (Eleusine coracana), a bovine milk-based product, peanuts (Arachis hypogaea L.) and cassava (Manihotesculenta) with the highest content reported in cassava, beans and peanuts. The causes and proliferation of aflatoxigenic contamination of Ugandan foods have been largely due to poor pre-, peri- and post-harvest activities, poor government legislation, lack of awareness and low levels of education among farmers, agri-entreprenuers and consumers on the plague. Aflatoxin B1 is the most prevalent aflatoxin in Uganda. There is still limited research on aflatoxins in Uganda because the surveillance, reduction and control carry prohibitive costs. A few exposure assessments have been done especially in human sera and dependence on a single or a related set of foods with little diet diversity has exacerbated the risk of exposure to aflatoxins in Uganda because most of the staple foods are aflatoxin-prone. On the detection, control and reduction, these are still marginal, though some devoted scholars have devised and validated a sensitive portable device for on-site aflatoxin detection in maize as well as shown that starter cultures used for making some cereal-based beverages have the potential to bind aflatoxins. More effort should be geared towards awareness creation through training of farmers and traders in the cereal value chain as well as developing capacity to monitor aflatoxins. Vaccination against Hepatitis B and Hepatitis A should be emphasized to reduce the risk of development of liver cancer among the populace.STROBE-MR: Guidelines for strengthening the reporting of Mendelian randomization studieshttps://peerj.com/preprints/278572019-07-152019-07-15George Davey SmithNeil M DaviesNiki DimouMatthias EggerValentina GalloRobert GolubJulian PT HigginsClaudia LangenbergElizabeth W LoderJ Brent RichardsRebecca C RichmondVeronika W SkrivankovaSonja A SwansonNicholas J TimpsonAnne Tybjaerg-HansenTyler J VanderWeeleBenjamin AR WoolfJames Yarmolinsky
While the number of studies using Mendelian randomization (MR) methods has grown exponentially in the last decade, the quality of reporting of these studies often has been poor. Similar to other reporting guidelines such as CONSORT (Consolidated Standards of Reporting Trials) for randomised trials and STROBE (STrenghtening the Reporting of Observational studies in Epidemiology) for observational studies in epidemiology, the STROBE-MR working group aims to provide guidance to authors on how to improve reporting of MR studies and help readers, reviewers, and journal editors to evaluate the quality of the presented evidence.
Empirical evidence indicates that many reports of MR studies do not clearly state or examine the various assumptions of MR methods and report insufficient details on the data sources, which makes it hard to evaluate the quality and reliability of the results. The STROBE-MR guidance covers both one sample and two sample MR studies. At present, the draft checklist consists of 20 items, organized into the title and abstract, introduction, methods, results and discussion sections of articles.
As these guidelines aim to reach the entire MR community, we would like to give everyone the opportunity to contribute their comments. The following draft of the STROBE-MR checklist is open for public discussion and all feedback will be taken into account during its next revision. For feedback, please use the comment section below this post on PeerJ Preprints.
We hope the final guidelines will serve the entire community and contribute to improving the reporting of MR studies in the future.
While the number of studies using Mendelian randomization (MR) methods has grown exponentially in the last decade, the quality of reporting of these studies often has been poor. Similar to other reporting guidelines such as CONSORT (Consolidated Standards of Reporting Trials) for randomised trials and STROBE (STrenghtening the Reporting of Observational studies in Epidemiology)for observational studies in epidemiology, the STROBE-MR working group aims to provide guidance to authors on how to improve reporting of MR studies and help readers, reviewers, and journal editors to evaluate the quality of the presented evidence.Empirical evidence indicates that many reports of MR studies do not clearly state or examine the various assumptions of MR methods and report insufficient details on the data sources, which makes it hard to evaluate the quality and reliability of the results. The STROBE-MR guidance covers both one sample and two sample MR studies. At present, the draft checklist consists of 20 items, organized into the title and abstract, introduction, methods, results and discussion sections of articles.As these guidelines aim to reach the entire MR community, we would like to give everyone the opportunity to contribute their comments. The following draft of the STROBE-MR checklist is open for public discussion and all feedback will be taken into account during its next revision. For feedback, please use the comment section below this post on PeerJ Preprints.We hope the final guidelines will serve the entire community and contribute to improving the reporting of MR studies in the future.Report of candidatus Mycoplasma haematoparvum and Mycoplasma haemocanis canine natural infections in Massambaba restinga, Brazilhttps://peerj.com/preprints/278052019-06-162019-06-16Marcia Gonçalves MirandaBruno AlberigiFlavya Mendes-de-AlmeidaAlexandre José Rodrigues BendasNadia AlmosnyJonimar Pereira PaivaNorma Vollmer Labarthe
Background: Tick-borne diseases are frequent in the Southeastern section of Brazil. The most prevalent canine parasites diagnosed are Ehrlichia canis, Babesia gibsoni, Babesia canis and Anaplasma platys, although Mycoplasma haemocanis and candidatus Mycoplasma haematoparvum have been registered in the country.
Methods: When two clinically healthy dogs from a suburban area of the state of Rio de Janeiro, Brazil with history of being heavily infested with ticks were examined at Idexx Reference Laboratories, California for tick panel check.
Results: One dog harbored DNA of candidatus Mycoplasma haematoparvum and the other DNA of Mycoplasma haemocanis.
Conclusions: These results suggest that monitoring for tick infestations and tick-borne parasites must be permanent in southeastern Brazil, especially due to global climate changes which may contribute to spread and increase the number of infections in the Country.
Background: Tick-borne diseases are frequent in the Southeastern section of Brazil. The most prevalent canine parasites diagnosed are Ehrlichia canis, Babesia gibsoni, Babesia canis and Anaplasma platys, although Mycoplasma haemocanis and candidatusMycoplasmahaematoparvum have been registered in the country.Methods: When two clinically healthy dogs from a suburban area of the state of Rio de Janeiro, Brazil with history of being heavily infested with ticks were examined at Idexx Reference Laboratories, California for tick panel check.Results: One dog harbored DNAof candidatus Mycoplasma haematoparvum and the other DNAof Mycoplasma haemocanis. Conclusions:These results suggest that monitoring for tick infestations and tick-borne parasites must be permanent in southeastern Brazil, especially due to global climate changes which may contribute to spread and increase the number of infections in the Country.Epidemiological scenario of Dengue in the state of Manipur during the last 3 yearshttps://peerj.com/preprints/277862019-06-062019-06-06Leimapokpam Shivadutta SinghRajkumar Manojkumar SinghHuidrom Lokhendro Singh
Background. In recent years, Dengue has been emerging as a global health problem with approximately 2.5 billion people being affected by it .In the last 50 years, the incidence of dengue infection has increased 30-fold, and the World Health Organization (WHO) has estimated that 96 million cases of dengue occur annually. The epidemiology of dengue fever (DF) is complex in the Indian subcontinent as all the four serotypes are circulating. And there is no systematic epidemiological study done on dengue cases in Manipur, a north-eastern state of India. This study is therefore done to report observations on dengue cases from a virus diagnostic and research laboratory of Manipur to present an epidemiological scenario of the state for the last three years. Method. We used the dengue data extracted from the laboratory register of Viral Research and Diagnostic Laboratory (VRDL) from 2016 to 2018. All suspected outpatient and inpatients dengue cases from public and private health services are included in the VRDL database whose informed consent were obtained. We evaluated the overall features of the data for generating seasonal pattern, geographical pattern, gender wise distribution, age wise distribution and seroprevelance pattern of dengue cases for the study period from 2016 to 2018. Results. A total of 1689 cases of suspected patients of dengue virus infection were tested for dengue ELISA test and 272(16.10%) samples were found to be seropositive. The month wise distribution of dengue cases is quite an interesting as the three years of study shows variant pattern in observation. In all the three years dengue seropositive cases were seen higher in male population. But there is no significant value to the positivity of dengue seropositive towards male than female (The chi-square statistic is 2.1314.The p-value is .344481. The result is not significant at p < .05.). Conclusion. Our study presents a comparative epidemiological study on seroprevelance of dengue in the state of Manipur from the year 2016 to 2018. The findings in the present study extend the knowledge of the geographical distribution and seroprevelance of dengue in the state of Manipur for the last three years. This is an attempt to present epidemiological dengue seroprevelance in the state of Manipur which in future would be a reference from public health concerns for taking up necessary action plan to curtail the spread of dengue.
Background. In recent years, Dengue has been emerging as a global health problem with approximately 2.5 billion people being affected by it .In the last 50 years, the incidence of dengue infection has increased 30-fold, and the World Health Organization (WHO) has estimated that 96 million cases of dengue occur annually. The epidemiology of dengue fever (DF) is complex in the Indian subcontinent as all the four serotypes are circulating. And there is no systematic epidemiological study done on dengue cases in Manipur, a north-eastern state of India. This study is therefore done to report observations on dengue cases from a virus diagnostic and research laboratory of Manipur to present an epidemiological scenario of the state for the last three years. Method. We used the dengue data extracted from the laboratory register of Viral Research and Diagnostic Laboratory (VRDL) from 2016 to 2018. All suspected outpatient and inpatients dengue cases from public and private health services are included in the VRDL database whose informed consent were obtained. We evaluated the overall features of the data for generating seasonal pattern, geographical pattern, gender wise distribution, age wise distribution and seroprevelance pattern of dengue cases for the study period from 2016 to 2018. Results. A total of 1689 cases of suspected patients of dengue virus infection were tested for dengue ELISA test and 272(16.10%) samples were found to be seropositive. The month wise distribution of dengue cases is quite an interesting as the three years of study shows variant pattern in observation. In all the three years dengue seropositive cases were seen higher in male population. But there is no significant value to the positivity of dengue seropositive towards male than female (The chi-square statistic is 2.1314.The p-value is .344481. The result is not significant at p < .05.). Conclusion. Our study presents a comparative epidemiological study on seroprevelance of dengue in the state of Manipur from the year 2016 to 2018. The findings in the present study extend the knowledge of the geographical distribution and seroprevelance of dengue in the state of Manipur for the last three years. This is an attempt to present epidemiological dengue seroprevelance in the state of Manipur which in future would be a reference from public health concerns for taking up necessary action plan to curtail the spread of dengue.PICO and Risk Of bias Navigator for Evidence Based Medicinehttps://peerj.com/preprints/276842019-06-022019-06-02Tomohide YamadaYoshinobu KondoRyo Momosaki
Evidence-based medicine (EBM) involves determining treatment that matches the needs of each patient by integrating the best and latest available “scientific evidence” and “clinical skills”. Systematic review and meta-analysis refer to the process of searching databases and performing statistical analysis to integrate the results of multiple independent studies conducted in the past. The results obtained provide the highest quality evidence, which has become the foundation of various clinical guidelines. Systematic review and meta-analysis are conducted in the following sequence: 1) formulation of a hypothesis, 2) searching databases for articles, 3) selection of research articles, 4) evaluation of bias for each study, 5) integration of the results, 6) verification of bias, and 7) evaluation of the quality of the meta-analysis. Especially regarding 2) article searches and 3) article selection, it is usual for two or more researchers to independently conduct a comprehensive search of databases and extract all the articles that meet the eligibility criteria. Generally, each researcher must evaluate thousands of research articles one by one, making the whole process very time-consuming. In addition, articles may be missed since the search is done manually, and the results tend to be arbitrary. Moreover, updating the information requires a lot of time and effort. Generally, it takes one to two years to complete a single systematic review and meta-analysis. As a result, many reviews are obsolete or missing. Therefore, development of software that could contribute to labor saving and automation of systematic review has been advocated. PICORON-EBM aims to shorten the time required for assessment of PICO and Risk of Bias by natural language processing. Strengths: 1. Quick and Easy operation. 2. You can add and delete any keywords to your area of interest.
URL: http://www.picoron.com/
Evidence-based medicine (EBM) involves determining treatment that matches the needs of each patient by integrating the best and latest available “scientific evidence” and “clinical skills”. Systematic review and meta-analysis refer to the process of searching databases and performing statistical analysis to integrate the results of multiple independent studies conducted in the past. The results obtained provide the highest quality evidence, which has become the foundation of various clinical guidelines. Systematic review and meta-analysis are conducted in the following sequence: 1) formulation of a hypothesis, 2) searching databases for articles, 3) selection of research articles, 4) evaluation of bias for each study, 5) integration of the results, 6) verification of bias, and 7) evaluation of the quality of the meta-analysis. Especially regarding 2) article searches and 3) article selection, it is usual for two or more researchers to independently conduct a comprehensive search of databases and extract all the articles that meet the eligibility criteria. Generally, each researcher must evaluate thousands of research articles one by one, making the whole process very time-consuming. In addition, articles may be missed since the search is done manually, and the results tend to be arbitrary. Moreover, updating the information requires a lot of time and effort. Generally, it takes one to two years to complete a single systematic review and meta-analysis. As a result, many reviews are obsolete or missing. Therefore, development of software that could contribute to labor saving and automation of systematic review has been advocated. PICORON-EBM aims to shorten the time required for assessment of PICO and Risk of Bias by natural language processing. Strengths: 1. Quick and Easy operation. 2. You can add and delete any keywords to your area of interest.URL: http://www.picoron.com/Automated data extraction software for medical summary using text mining (T-Library)https://peerj.com/preprints/276852019-06-022019-06-02Tomohide YamadaYoshinobu KondoRyo Momosaki
The electronic medical record (EMR) is a source of clinical information and is used for clinical research. Clinical researchers leverage this information by employing staffs to manually extracting data from the unstructured text. This process can be both error-prone and labor-intensive.
This software (T-Library) is a software which automatically extracts key clinical data from patient records and can potentially help healthcare providers and researchers save money, make treatment decisions and manage clinical trials.
This software saves labor for data transcription in clinical research. This is a vital step toward getting researchers rapid access to the information they need. This is also the attempt to cluster patients’ morbid states and establish accurate and constantly updated risk engine of complications’ crises, using deep learning.
Strengths: 1) Quick and Easy operation
URL: http://www.picoron.com/tlibrary/
The electronic medical record (EMR) is a source of clinical information and is used for clinical research. Clinical researchers leverage this information by employing staffs to manually extracting data from the unstructured text. This process can be both error-prone and labor-intensive.This software (T-Library) is a software which automatically extracts key clinical data from patient records and can potentially help healthcare providers and researchers save money, make treatment decisions and manage clinical trials.This software saves labor for data transcription in clinical research. This is a vital step toward getting researchers rapid access to the information they need. This is also the attempt to cluster patients’ morbid states and establish accurate and constantly updated risk engine of complications’ crises, using deep learning.Strengths: 1) Quick and Easy operationURL: http://www.picoron.com/tlibrary/Bayesian meta-analysis of studies with rare events: Do the choice of prior distributions and the exclusion of studies without events in both arms matter?https://peerj.com/preprints/277322019-05-152019-05-15Soheila AghlmandiPeter JüniJames CarpenterMarcel Zwahlen
Randomized controlled trials (RCTs) analyzing serious adverse events often observe low incidence and might even observe zero events in either or both of the treatment and control arms. In the meta-analysis of RCTs of adverse events, it is unclear whether trials with zero events in both arms provide any information for the summary risk ratio (RR) or odds ratio (OR). Studies with zero events in both arms are usually excluded in both frequentist and Bayesian meta-analysis. We used a fully probabilistic approach—a Bayesian framework—for the meta-analysis of studies with rare events, and systematically assessed whether exclusion of studies with no events in both arms produced different results compared to keeping all studies in the meta-analysis. We did this by conducting a simulation study in which we assessed the bias in the point estimate of the log(OR) and the coverage of the 95% posterior interval for the log(OR) for different analytical decisions and choices in fixed effect and random effects meta-analysis. We used simulated data generated from a known fixed effect or random effects data scenario (each scenario with a 1000 meta-analysis data-set). We found that the uniform and Jeffrey’s prior on the baseline risk in the control group leads to biased results and a reduced coverage, and that setting the prior distribution on the log(odds) scale worked better. We also found nearly identical results regardless of whether studies with no events in both arms were excluded or not.
Randomized controlled trials (RCTs) analyzing serious adverse events often observe low incidence and might even observe zero events in either or both of the treatment and control arms. In the meta-analysis of RCTs of adverse events, it is unclear whether trials with zero events in both arms provide any information for the summary risk ratio (RR) or odds ratio (OR). Studies with zero events in both arms are usually excluded in both frequentist and Bayesian meta-analysis. We used a fully probabilistic approach—a Bayesian framework—for the meta-analysis of studies with rare events, and systematically assessed whether exclusion of studies with no events in both arms produced different results compared to keeping all studies in the meta-analysis. We did this by conducting a simulation study in which we assessed the bias in the point estimate of the log(OR) and the coverage of the 95% posterior interval for the log(OR) for different analytical decisions and choices in fixed effect and random effects meta-analysis. We used simulated data generated from a known fixed effect or random effects data scenario (each scenario with a 1000 meta-analysis data-set). We found that the uniform and Jeffrey’s prior on the baseline risk in the control group leads to biased results and a reduced coverage, and that setting the prior distribution on the log(odds) scale worked better. We also found nearly identical results regardless of whether studies with no events in both arms were excluded or not.Do wastewater treatment plants increase antibiotic resistant bacteria or genes in the environment? Protocol for a systematic reviewhttps://peerj.com/preprints/277272019-05-132019-05-13Daloha Rodríguez-MolinaPetra MangHeike SchmittMariana Carmen ChifiriucKatja RadonLaura Wengenroth
Background. Antibiotic resistance is a global public health threat. Water from human activities is collected at wastewater treatment plants where processes often do not sufficiently neutralize antibiotic resistant bacteria and genes, which are further shed into the local environment. This protocol outlines the steps to conduct a systematic review based on the Population, Exposure, Comparator and Outcome (PECO) framework, aiming at answering the question Are antimicrobial-resistant enterobacteriaceae and antimicrobial resistance genes present (O) in air and water samples (P) taken either near or downstream or downwind or down-gradient from wastewater treatment plants (E), as compared to air and water samples taken either further away or upstream or upwind or up-gradient from such wastewater treatment plant (C)? Presence of antimicrobial-resistant bacteria and genes will be quantitatively measured by extracting their prevalence or concentration, depending on the reviewed study.
Methods. We will search PubMed, EMBASE, the Cochrane database and Web of Science for original articles published from 01-Jan-2000 to 03-Sep-2018 with language restriction. Articles will undergo a relevance and a design screening process. Data from eligible articles will be extracted by two independent reviewers. Further, we will perform a risk of bias assessment using a decision matrix. We will synthesize and present results in narrative and tabular form and will perform a meta-analysis if heterogeneity of results allows it.
Discussion. Antibiotic resistance in environmental samples around wastewater treatment plants may pose a risk of exposure to workers and nearby residents. Results from the systematic review outlined in this protocol will allow to estimate the extend of exposure, to inform policy making and help to design future studies.
Background. Antibiotic resistance is a global public health threat. Water from human activities is collected at wastewater treatment plants where processes often do not sufficiently neutralize antibiotic resistant bacteria and genes, which are further shed into the local environment. This protocol outlines the steps to conduct a systematic review based on the Population, Exposure, Comparator and Outcome (PECO) framework, aiming at answering the question Are antimicrobial-resistant enterobacteriaceae and antimicrobial resistance genes present (O) in air and water samples (P) taken either near or downstream or downwind or down-gradient from wastewater treatment plants (E), as compared to air and water samples taken either further away or upstream or upwind or up-gradient from such wastewater treatment plant (C)? Presence of antimicrobial-resistant bacteria and genes will be quantitatively measured by extracting their prevalence or concentration, depending on the reviewed study.Methods. We will search PubMed, EMBASE, the Cochrane database and Web of Science for original articles published from 01-Jan-2000 to 03-Sep-2018 with language restriction. Articles will undergo a relevance and a design screening process. Data from eligible articles will be extracted by two independent reviewers. Further, we will perform a risk of bias assessment using a decision matrix. We will synthesize and present results in narrative and tabular form and will perform a meta-analysis if heterogeneity of results allows it.Discussion. Antibiotic resistance in environmental samples around wastewater treatment plants may pose a risk of exposure to workers and nearby residents. Results from the systematic review outlined in this protocol will allow to estimate the extend of exposure, to inform policy making and help to design future studies.Available software for meta-analyses of genome-wide expression studieshttps://peerj.com/preprints/277082019-05-062019-05-06Diego A Forero
Advances in transcriptomic methods have led to a large number of published genome-wide expression studies (GWES), in humans and in model organisms. For several years, GWES involved the use of microarray platforms to compare genome-expression data for two or more groups of samples of interest. Meta-analysis of GWES is a powerful approach for the identification of differentially expressed genes in biological topics or diseases of interest, combining information from multiple primary studies. In this article, I review the main features of available software for carrying out meta-analysis of GWES. I describe seven packages from the Bioconductor platform and 5 packages from the CRAN platform. In addition, nine previously described programs and two online programs are reviewed. Finally, I discuss advantages and disadvantages of these available programs and propose key points for future developments.
Advances in transcriptomic methods have led to a large number of published genome-wide expression studies (GWES), in humans and in model organisms. For several years, GWES involved the use of microarray platforms to compare genome-expression data for two or more groups of samples of interest. Meta-analysis of GWES is a powerful approach for the identification of differentially expressed genes in biological topics or diseases of interest, combining information from multiple primary studies. In this article, I review the main features of available software for carrying out meta-analysis of GWES. I describe seven packages from the Bioconductor platform and 5 packages from the CRAN platform. In addition, nine previously described programs and two online programs are reviewed. Finally, I discuss advantages and disadvantages of these available programs and propose key points for future developments.Dynamic time warping assessment and sensitive high resolution melting analysis for subtyping Salmonella isolates from the Northern Thailandhttps://peerj.com/preprints/276642019-04-192019-04-19Nuttachat WisittipanitChaiwat PulsrikarnSaranya WutthiosotSitthisak PinmongkhonkulKritchai Poonchareon
Background: Nontyphoidal Salmonella spp. transmitted through various routes are a major concern of food poisoning due to the consumption of contaminated food.
Objective: To establish a molecular-based protocol for simple and rapid subtyping of Salmonella isolates from various sources.
Materials and methods: Sensitive High-Resolution Melting-curve analysis (S-HRMa) and Dynamic Time Warping assessment (DTW) were applied for serotyping forty Salmonella spp. isolates from various origins and locations in seven provinces in the north of Thailand; the results were compared to those from conventional serotyping and ERIC- PCR.
Results: HRM serotyping of forty Salmonella spp. initially produced fourteen melting-curves with two predominant clusters: C1 (n=18) and C2 (n=9). Applying S-HRMa and serogroups generated twenty-five sensitive clusters. Conventional serotyping revealed that cluster C1 and C2 comprised of six different Salmonella serotypes with S. Weltevradent (n=14) as the predominant one. The S-HRMa also suggested the possible subtyping in some serotypes. In addition, DTW was performed to cluster those forty Salmonella spp. into twenty-eight clusters, assigned into different four clades corresponding to S-HRMa. The two clustering methods indicated that the S. Weltevreden was the predominant subtype (DTW4-S1, n=6). Three ERIC clusters at 92% similarity index also corresponded to the results of those two clustering methods. With important and related epidemiological data, S. Derby and S. Monophasic were suggested to be related to the slaughterhouse and swine. In this study, the ERIC cluster 10 comprising two Salmonella isolates of S. Weltevraden suggested the transmission route was likely to be farm-to-farm in the same province.
Conclusions: The DTW assessment and S-HRMa effectively increased the discrimatory power of clustering to the same level as that of ERIC - PCR and were a simple and rapid protocol to perform Salmonella subtyping for the epidemiological research.
Background: Nontyphoidal Salmonella spp. transmitted through various routes are a major concern of food poisoning due to the consumption of contaminated food.Objective: To establish a molecular-based protocol for simple and rapid subtyping of Salmonella isolates from various sources.Materials and methods: Sensitive High-Resolution Melting-curve analysis (S-HRMa) and Dynamic Time Warping assessment (DTW) were applied for serotyping forty Salmonella spp. isolates from various origins and locations in seven provinces in the north of Thailand; the results were compared to those from conventional serotyping and ERIC- PCR.Results: HRM serotyping of forty Salmonella spp. initially produced fourteen melting-curves with two predominant clusters: C1 (n=18) and C2 (n=9). Applying S-HRMa and serogroups generated twenty-five sensitive clusters. Conventional serotyping revealed that cluster C1 and C2 comprised of six different Salmonella serotypes with S. Weltevradent (n=14) as the predominant one. The S-HRMa also suggested the possible subtyping in some serotypes. In addition, DTW was performed to cluster those forty Salmonella spp. into twenty-eight clusters, assigned into different four clades corresponding to S-HRMa. The two clustering methods indicated that the S. Weltevreden was the predominant subtype (DTW4-S1, n=6). Three ERIC clusters at 92% similarity index also corresponded to the results of those two clustering methods. With important and related epidemiological data, S. Derby and S. Monophasic were suggested to be related to the slaughterhouse and swine. In this study, the ERIC cluster 10 comprising two Salmonella isolates of S. Weltevraden suggested the transmission route was likely to be farm-to-farm in the same province.Conclusions: The DTW assessment and S-HRMa effectively increased the discrimatory power of clustering to the same level as that of ERIC - PCR and were a simple and rapid protocol to perform Salmonella subtyping for the epidemiological research.