Study design and protocol
The research question is best addressed through a Scoping review, as it is broad and aims to map all the available evidence on the topic. This scoping review will be undertaken in line with the JBI methodology for scoping reviews.
Inclusion criteria
Types of water sources
For the purpose of this review, we will consider studies that included PCR-based microbial water quality assessment of improved drinking water sources. We will use standard definition of ‘improved drinking water source’ which is defined, by the WHO/UNICEF joint monitoring program, as a water source that, by nature of its construction, is adequately protected from outside contamination, particularly faecal matter [31]. This definition includes piped water in a dwelling, plot or yard, and other improved sources such as public taps or standpipes, tube wells or boreholes, protected dug wells, protected springs and rainwater collection. This review will not include water quality data in relation to the following ‘un-improved’ water sources: unprotected dug well, unprotected spring, cart with small tank/drum, tanker truck, and surface water (river, dam, lake, pond, stream, canal, irrigation channels). Although it is categorized as ‘un-improved’ in the above definition, bottled water will be considered in this review because the reason for its categorization as ‘un-improved’ (i.e., in relation to ‘water quantity’) is not relevant for the focus of this review which is on ‘water quality’.
Concept
The overarching concept of interest for this scoping review is microbial quality of drinking water in developing countries as determined by PCR-based methods. The PCR is a technique in molecular genetics that permits the analysis of any short sequence of DNA (or RNA) in samples containing only minute quantities of DNA or RNA. PCR is used to reproduce (amplify) selected sections of DNA or RNA for analysis [20]. Accordingly, this review will consider studies that identified, quantified and characterized diarrheagenic pathogens in drinking water using PCR techniques. Employed PCR detection methods and detection capacity, type of detected pathogens, detected gene numbers/copies, types and associated water borne diseases, will be explored.
Comparator
The comparators could be related to detection methodology (e.g. across different PCR tools) or other contributing factors such types of water sources (e.g. between piped water and other improved sources) or water treatment methods (between treated and untreated or across different water treatment techniques) or proximity to known contamination sources. Other comparators that may be identified along the review process will also be considered for the reporting.
Context
This review will include studies conducted within the context of low- and middle-income countries. The World Bank classification of economies according to 2019 gross national income (GNI) per capita will be used to identify this countries [32].
Types of studies
All studies that characterize diarrheagenic pathogens in improved water sources using PCR techniques and conducted in low- and middle-income countries since 2003 will be included in this review. These may include quantitative, and /or mixed method studies, cross-sectional studies, and intervention/experimental studies. Other relevant sources such as systematic reviews, theses, dissertations, unpublished and gray literature will also be included in this review. Conference items/abstracts will not be considered in this review to avoid potential duplication.
Search strategy
The literature search strategy consists of a 3 stage process, as recommended by the JBI [33]. In the first stage, an initial search will be undertaken in two databases (PubMed and SCOPUS). The initial search strategy for PubMed with the identified keywords is detailed in Table 1. In the second stage, titles and abstracts of the first stage articles will be reviewed to identify search terms. A full comprehensive search will be undertaken in the following databases: PubMed/Medline, Scopus, Web of Science, JBI, Cochrane Library, and Google Scholar. A gray literature search will be undertaken for unpublished studies in Google and ProQuest. In the third stage, the reference lists of the included sources literatures will be examined to identify additional sources. The search will be limited to English language.
Table 1
Search terms to be used for the preliminary search in Pubmed.
S. No
|
Query
|
1.
|
"polymerase chain reaction"[MeSH] OR Polymerase chain reaction[tw] OR PCR(tw)
|
2.
|
Detection (tw) OR Identification (tw) OR Characterization(tw)
|
3.
|
"diarrhea"[MeSH] OR "diarrhea"[tw] OR "diarrheas"[tw] OR "diarrhoea"[tw] OR "diarrhoeas"[tw]
|
4.
|
Pathogenic microbes (tw) OR "bacteria"[MeSH] OR Bacteria[Text Word] OR "escherichia coli"[MeSH s] OR E. coli[tw]OR "viruses"[MeSH] OR Virus[tw]OR Protozoa (tw)
|
5.
|
Improved water (tw) OR "drinking water"[MeSH] OR Drinking water[tw]
|
6.
|
Low- and middle-income countries (tw) OR Africa (tw) OR Asia (tw) OR Caribbean Countries (tw)
|
7.
|
1 AND 2 AND 3 AND 4 AND 5 AND 6
|
8.
|
Limit 7 to English
|
MeSH = Medical subject headings, tw = text word |
Study selection
All identified citations will be exported to Mendeley Desktop reference management software version 1.19.4 (Mendeley Ltd., Elsevier, Netherlands). After removing duplicates, the titles and abstracts of the identified studies will be reviewed by three independent reviewers (STG, NES and YMT). The documents without abstracts will be screened at the full text level. Then, the full text of selected studies will be retrieved and assessed in detail against the inclusion criteria by the same reviewers. Any disagreement between the three reviewers during the screening stage will be resolved through discussion or by the involvement of a fourth and fifth reviewer. For the screening of articles at full text level, rejection of an article will be decided by the review team upon suggestion of the first reader. At each stage, the number of studies excluded and the reasons for exclusion will be archived and reported in the final scoping review. The results of the search strategy and screening process will be reported in full in the final scoping review report and presented in a Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) flow diagram [34].
Data extraction
Data will be extracted by three independent reviewers (STG, NES and YMT) from studies included in the review using a prepared data extraction excel spreadsheet tool. For each study, authors’ name, place and year of publication, study period, date of search, and the country/region of the study, type of water source, water treatment technique, if any, sample type, data on sample size, types of PCR techniques used, result of included studies: detected type of pathogen/s, amount, detection capacity and associated water borne diseases will be extracted. The data extraction form will be pretested and revised as necessary during the review process. The reviewers will contact the authors for missing data and clarification of primary studies if required; such inclusions will be reported in the final scoping review. The particular study will be excluded if there is no response from the author/s.