Recurrent Cholera Outbreaks in Sub-Saharan Africa: Moving beyond Epidemiology to Understand the Environmental Reservoirs and Drivers

Round 1

Reviewer 1 Report

A review article titled “Recurrent Cholera Outbreaks in sub-Saharan Africa” Moving beyond Epidemiology to Understand the Environmental Reservoirs and Drivers” addresses an interesting point and offers a unique and different perspective. Overall, article is well written, and authors collected sufficient number of references. Specific comments, of relatively minor nature, are specified below.

Line 35: Spell out DRC.

Line 46: Vibrio cholerae instead.

Line 53: Same comment as above.

Lines 70-71: Please provide a citation(s) for this statement.

Lines 73-75: Same comment as above.

Line 80: Spell out ENSO.

Lines 111-162: Figure 2 should be cited in this section.

Line 117: Vibrio cholerae instead.

Line 118: Remove one “in”.

Line 120: “…at both sites.” instead.

Line 133: Vibrio cholerae instead of “cholera”.

Line 142: “It is also likely that excessive…”?

Line 146: “Antibiotic resistant bacteria” instead of antimicrobial resistance?

Line 175: “…same study, authors concluded…”?

Line 175: “low discharges” of what? Please elaborate.

Line 190: “Indeed, contrary to dual peak…” instead?

Lines 194-195: This statement appears to contradict the previous sentences stating that annual peak occurs during wet summer season? Please clarify?

Line 259: “exist” instead of “abounds”?

Lines 259-260: “Here, ten key research questions are raised for future research directions under two…” instead?

Table 1. While most of the research questions have been addressed in the text, it seems to me that #2 and #6 have not been explored as well as others. I would suggest addressing it briefly in the appropriate section(s).

Line 266: “buttresses” instead of “buttress”?

Conflict of interest statement: since authors declared no conflict of interest, second part of the statement seems to be out of place?

Author Response

Review 1

A review article titled “Recurrent Cholera Outbreaks in sub-Saharan Africa” Moving beyond Epidemiology to Understand the Environmental Reservoirs and Drivers” addresses an interesting point and offers a unique and different perspective. Overall, article is well written, and authors collected sufficient number of references. Specific comments, of relatively minor nature, are specified below.

Thank you for the comments, they helped to improve the manuscript. We have addressed the specific comments you raised below.

Line 35: Spell out DRC.

We corrected to Democratic Republic of Congo.

Line 46: Vibrio cholerae instead.

We corrected to Vibrio cholerae.

Line 53: Same comment as above.

We corrected to V. cholerae.

Lines 70-71: Please provide a citation(s) for this statement.

A reference was added [20] - S. Almagro-moreno, R.K. Taylor, Cholera: Environmental Reservoirs and Impact on Disease Transmission, Microbiol. Spectr. 1 (2013) 1–12).

Lines 73-75: Same comment as above.

A reference was added [19] - S. Rebaudet, B. Sudre, B. Faucher, R. Piarroux, Cholera in Coastal Africa: A Systematic Review of Its Heterogeneous Environmental Determinants, J. Infect. Dis. 208 (2013) S98–S106.

Line 80: Spell out ENSO.

A correction was made as follows; El Niño-Southern Oscillation.

Lines 111-162: Figure 2 should be cited in this section.

A citation to Figure 2 was added in Line 115.

Line 117: Vibrio cholerae instead.

We corrected to V. cholerae.

Line 118: Remove one “in”.

The second ‘in’ was removed.

Line 120: “…at both sites.” instead.

Since there were only two countries and several sites were rephrased to: ‘both countries’.

Line 133: Vibrio cholerae instead of “cholera”.

We corrected to Vibrio cholerae.

Line 142: “It is also likely that excessive…”?

We removed the phrase and edited the sentence to “Excessive groundwater abstraction during the dry season may lower groundwater levels in shallow wells and boreholes relative to that of on-site sanitation systems; thus, increasing risk of groundwater contamination.”

Line 146: “Antibiotic resistant bacteria” instead of antimicrobial resistance?

We changed the term to antibiotic resistant bacteria.

Line 175: “…same study, authors concluded…”?

We changed others to authors.

Line 175: “low discharges” of what? Please elaborate.

We edited the phrase to low river discharges. The authors of the study reported dual peaks coinciding with low river discharges in spring season and high river flows in autumn.

Line 190: “Indeed, contrary to dual peak…” instead?

We removed the word due.

Lines 194-195: This statement appears to contradict the previous sentences stating that annual peak occurs during wet summer season? Please clarify?

The rainy season in the part of South Africa studied is from November to March; thus, the statement agrees with the previous one.

We clarified the statement as follows;

For example, peak cholera outbreaks in South Africa occur in January and February during the wet season reflecting its relationship with rainfall peaks and relatively high temperatures.

Line 259: “exist” instead of “abounds”?

We replaced abounds with exist.

Lines 259-260: “Here, ten key research questions are raised for future research directions under two…” instead?

We agree and removed (1).

Table 1. While most of the research questions have been addressed in the text, it seems to me that #2 and #6 have not been explored as well as others. I would suggest addressing it briefly in the appropriate section(s).

Thank you for the comment. Question 2 is addressed in Lines 112-128, particularly L115-118.

We added the following paragraph related to Question 6:

Some studies have shown that people infected with HIV/AIDS, malaria and tuberculosis often have weakened immunity, and are more susceptible to co-infections with other infectious diseases [64]. Therefore, cholera outbreaks in SSA could be linked to other epidemics such as malaria, tuberculosis and HIV/AIDS. However, further research is needed to investigate whether co-infections promote cholera outbreaks.   

Line 266: “buttresses” instead of “buttress”?

We considered the comment. The statement refers to the previous point, and since ‘these’ is plural and ‘this’ is singular we revised to; This further buttresses….

Conflict of interest statement: since authors declared no conflict of interest, second part of the statement seems to be out of place?

We removed the redundant sentence.

Author Response File: Author Response.docx

Reviewer 2 Report

The authors present a concise call to action for expanded efforts to use integrative approaches in studying the ecology and environmental drivers of cholera in Africa. The call is well justified and the presentation is clearly written, with the enumeration of specific questions for recommended future studies serving as a useful organizing element. A suggested addition to this presentation would be a discussion of the potential for the European Environment and Epidemiology (E3) Network (which was established to facilitate precisely the types of connections between environment and epidemiology suggested by the authors but for studies focusing on Europe) to serve as a model for the establishment of an equivalent system for Africa. Do the authors believe that the E3 Network provides a good model for an equivalent system in Africa? If yes, then it would be useful to address what steps and resources would facilitate such a system being established and maintained in Africa and to highlight specific features of the E3 that should be emulated or prioritized. If not, then it would be helpful for the authors to provide a discussion of alternative mechanisms for facilitating collaboration or interactions between researchers who might be activated to engage (or are already engaging) in the types of studies being recommended by the authors in their call to action.

For reference, E3 Network page: https://e3geoportal.ecdc.europa.eu/SitePages/Home.aspx

Author Response

Reviewer 2

The authors present a concise call to action for expanded efforts to use integrative approaches in studying the ecology and environmental drivers of cholera in Africa. The call is well justified and the presentation is clearly written, with the enumeration of specific questions for recommended future studies serving as a useful organizing element. A suggested addition to this presentation would be a discussion of the potential for the European Environment and Epidemiology (E3) Network (which was established to facilitate precisely the types of connections between environment and epidemiology suggested by the authors but for studies focusing on Europe) to serve as a model for the establishment of an equivalent system for Africa. Do the authors believe that the E3 Network provides a good model for an equivalent system in Africa? If yes, then it would be useful to address what steps and resources would facilitate such a system being established and maintained in Africa and to highlight specific features of the E3 that should be emulated or prioritized. If not, then it would be helpful for the authors to provide a discussion of alternative mechanisms for facilitating collaboration or interactions between researchers who might be activated to engage (or are already engaging) in the types of studies being recommended by the authors in their call to action.

For reference, E3 Network page: https://e3geoportal.ecdc.europa.eu/SitePages/Home.aspx

Thank you for the insightful comment. We added Lines 273-286 on E3 Network and its applicability in Africa:

 The current knowledge gaps on understanding the role of environmental reservoirs and drivers in proliferation and transmission of V. cholerae are probably caused by the lack of connection between epidemiological and environmental science studies. In Europe, the European Environment and Epidemiology (E3) Network was established to bridge the gap between epidemiological and environmental data; thus, providing a link between environmental drivers and infectious diseases [62]. There is need for establishing a similar network of researchers and organizations in Africa that aims at promoting collaboration and sharing of epidemic monitoring, environmental monitoring and characterization, and demographics and socio-economic data. For example, such a network could collate data on socio-economic and environmental factors that drive susceptibility to cholera in communities impacted by other infectious diseases such as tuberculosis, malaria and HIV/AIDS. However, success in such a network could be hindered by lack of research resources in low-income countries impacted by cholera. Hence, the African-European Partnership for Neglected Infectious Diseases recommended collaboration between African and European researchers as well as governmental support in endemic countries [63].

Reviewer 3 Report

Journal: Challenges

Review

Title: Recurrent Cholera Outbreaks in sub-Saharan Africa: Moving beyond Epidemiology to Understand the Environmental Reservoirs and Drivers

In this manuscript, a review on often-overlooked issues in cholera research is proposed, stimulating discussion concerning related research aspects and fostering introduction of cross-disciplinary approach on researches concerning cholera and other water-borne diseases in sub-Saharan Africa and beyond.

In the Introduction section, the review reports information on sub-Saharan Africa cholera outbreaks. The aspect of the predominance of epidemiological studies is highlighted along with the scarciry of information on ecology of cholera in Africa, in particular concerning environmental drivers and reservoirs of cholera.

The review intends to offer a broader view on the concerns related to cholera in Africa, in particular in the sub-Saharan area, by stimulating a more cross-disciplinary research including comprehensive hydrology, environmental science and climatic science studies, which are often overlooked in studies related to cholara.

The review focusses on three specific aspects: 1) evidence nature and dynamics of recent cholera outbreaks in sub-Saharan Africa; 2) highlight the role of environmental drivers and reservoirs in influencing the dinamics of cholera outbreaks; 3) point out future research directions and evidence the need to use emerging research tools to better understand the cholera dynamics.

Continuing, the review describes how to integrate different aspects of environmental sciences into cholera research, starting from the comprehension of environmental drivers and reservoirs. In an outbreak, the etiological agent of cholera, Vibrio cholerae, is discharged directly into the environment through human excretions and municipal wastewater effluent. Aquatic systems act as a sink of the V. cholerae, where bacteria may persist and proliferate and then enter the human body through consumption of contaminated water and food. Climate changes and variability, and climate teleconnections, drive dynamics of cholera and other water borne diseases. In addition to the climatic and atmospheric aspects, the role of aquatic systems and hydrology system must be included in cholera diffusion. All these aspects suggest that research of enviromental sciences are of fundamental importance in order to combat cholera epidemics. Moreover, epidemiological forensic, could be included, as well as environmental disciplines such as hydrologgy, atmospheric climatic sciences and soils sciences.

Another fundamental of cholera ecology is represented by environmental reservoirs of cholera where the V. cholerae inhabits, grows and proliferates to be potentially released causing human disease outbreaks. The persistence and proliferation of the bacterium V. cholerae is promoted by including brackish, riverine, estuarine waters and salinity. Aquatic organisms, both of saline and fresh waters, harbour V. cholerae. Climatic teleconnections are also aspects important to be developed concenring studies of human and animal diseases.

The emerging researches tools to be exploited and descriptions of future directions were then reported. New tools of research include new methods in genomic and microbiological analyses, remote sensing, data analytics and process modelling. Relationships between long-term hydroclimatic data corresponding to historical data on cholera outbreaks are deficient and need to be improved in the future.

Computer science related to data analyses could moreover give important insights to predict cholera behaviour and cholera outbreaks. Moreover, data mining, the process of looking at large banks of information to generate new information, could give extremely important and innovative information on cholera dynamics.

Future researches on cholera in general and on cholera in SSA in particular, need be directed beyond traditional epiedmiological studies, including other relevant disciplines and research tools. Two thematic areas are of fundamental importance for future research directions: 1) environmental reservoirs and drivers, and 2) development of predictive tools.

The emergent aspect from this approach is that cholera research in SSA and other regions should move beyon epidemiology and include other allied disciplines. Again, emerging research tools comprehending remote sensing and GIS, genomics and advanced data analytics will give high value to these studies.

This review represents an important base to stimulate discussion and promote a shift to interdisciplinarity and to new methodological aspects.

Revisions

Line 35: “… reported in seven SSA countries; Cameroon … and Zambia” at this point six SSA countries were reported. It could be better to include Zimbabwe in the list of countries (i.e. “… Kenya, Mozambique, Zambia and Zimbabwe) or eliminate the conjunction “and” in the list of the previous six countries and after that talking of cholera outbreaks in Zimbabwe;

Line 35: “DRC” the Democtaric Republic of Congo, when reporting for the first time the name of the country, it could be better to include the name per extenso;

Line 38: “… case fatality ratios (CRF) …” change to ““… case fatality ratios (CFR) …”;

Line 129: Figure 2, please cite clearly Fig.2 in the text; 

Line 215: “microbial” change to “microbiological”;

Line 215: The importance of genomic studies by using phylogenetics tools and bioinformatics has been evidenced in the review. It is true that by using this approach it is possible to have a very broad view of the Vibro cholerae species behaviour and distribution. Nevertheless, a more specific approach, meaning sampling of sediment, water or aquatic organisms present into the cosatal areas, to be used for culturing and isolation of autochthonous bacteria of the species V. cholerae, and storage of isolated strains in refrigerator at -80°C, could give important information. In fact it would be possible to have and to maintain a bank of strains of V. cholerae to be analyzed not only from the genetic point of view, but also from the physiological point of view, for instance on the presence of specific chitin receptors, suggesting a preference for V. cholerae to adhere to aquatic organisms (i.e. copepods)or antibiotic-resistance. Although culturable bacteria in general represent a low percentage as respect to the whole microbial community and to information collected by genetic tools (i.e. metagenomic approach), isolated bacteria could give important information on V. cholerae adaptation, suggesting for eventual information on the site of origin of the same bacteria. Microbiological approach is not an “old” one, each method gives different information, the aspect of microbiology could be included in the multidisciplinary approach highlighted in this review. The microbiological aspect could add interest to this review, eventually, the most recent techniques (including genetic specifically on the isolated bacterial strain, recent tools in microscopy, study of mechanisms of bacterial adhesion to different substrata) will be then used to study the isolated bacterial strains of V. cholerae. As an example, enclosed a paper that comprehends isolation of V. cholerae  (Saidou Kaboré, Philippe Cecchi, Thomas Mosser, Mylene Toubiana, Oumar Traoré, Aboubakar S. Ouattara, Alfred S. Traoré, Nicolas Barro, Rita R. Colwell, Patrick Monfort. (2018) Occurrence of Vibrio cholerae in water reservoirs of Burkina Faso. Research in Microbiology 169).

Line 340: “… V. cholera …” change to “… V. cholerae …”.

Author Response

Reviewer 3

In this manuscript, a review on often-overlooked issues in cholera research is proposed, stimulating discussion concerning related research aspects and fostering introduction of cross-disciplinary approach on researches concerning cholera and other water-borne diseases in sub-Saharan Africa and beyond.

In the Introduction section, the review reports information on sub-Saharan Africa cholera outbreaks. The aspect of the predominance of epidemiological studies is highlighted along with the scarciry of information on ecology of cholera in Africa, in particular concerning environmental drivers and reservoirs of cholera.

The review intends to offer a broader view on the concerns related to cholera in Africa, in particular in the sub-Saharan area, by stimulating a more cross-disciplinary research including comprehensive hydrology, environmental science and climatic science studies, which are often overlooked in studies related to cholara.

The review focusses on three specific aspects: 1) evidence nature and dynamics of recent cholera outbreaks in sub-Saharan Africa; 2) highlight the role of environmental drivers and reservoirs in influencing the dinamics of cholera outbreaks; 3) point out future research directions and evidence the need to use emerging research tools to better understand the cholera dynamics.

Continuing, the review describes how to integrate different aspects of environmental sciences into cholera research, starting from the comprehension of environmental drivers and reservoirs. In an outbreak, the etiological agent of cholera, Vibrio cholerae, is discharged directly into the environment through human excretions and municipal wastewater effluent. Aquatic systems act as a sink of the V. cholerae, where bacteria may persist and proliferate and then enter the human body through consumption of contaminated water and food. Climate changes and variability, and climate teleconnections, drive dynamics of cholera and other water borne diseases. In addition to the climatic and atmospheric aspects, the role of aquatic systems and hydrology system must be included in cholera diffusion. All these aspects suggest that research of enviromental sciences are of fundamental importance in order to combat cholera epidemics. Moreover, epidemiological forensic, could be included, as well as environmental disciplines such as hydrologgy, atmospheric climatic sciences and soils sciences.

Another fundamental of cholera ecology is represented by environmental reservoirs of cholera where the V. cholerae inhabits, grows and proliferates to be potentially released causing human disease outbreaks. The persistence and proliferation of the bacterium V. cholerae is promoted by including brackish, riverine, estuarine waters and salinity. Aquatic organisms, both of saline and fresh waters, harbour V. cholerae. Climatic teleconnections are also aspects important to be developed concenring studies of human and animal diseases.

The emerging researches tools to be exploited and descriptions of future directions were then reported. New tools of research include new methods in genomic and microbiological analyses, remote sensing, data analytics and process modelling. Relationships between long-term hydroclimatic data corresponding to historical data on cholera outbreaks are deficient and need to be improved in the future.

Computer science related to data analyses could moreover give important insights to predict cholera behaviour and cholera outbreaks. Moreover, data mining, the process of looking at large banks of information to generate new information, could give extremely important and innovative information on cholera dynamics.

Future researches on cholera in general and on cholera in SSA in particular, need be directed beyond traditional epiedmiological studies, including other relevant disciplines and research tools. Two thematic areas are of fundamental importance for future research directions: 1) environmental reservoirs and drivers, and 2) development of predictive tools.

The emergent aspect from this approach is that cholera research in SSA and other regions should move beyon epidemiology and include other allied disciplines. Again, emerging research tools comprehending remote sensing and GIS, genomics and advanced data analytics will give high value to these studies.

This review represents an important base to stimulate discussion and promote a shift to interdisciplinarity and to new methodological aspects.

Revisions

Line 35: “… reported in seven SSA countries; Cameroon … and Zambia” at this point six SSA countries were reported. It could be better to include Zimbabwe in the list of countries (i.e. “… Kenya, Mozambique, Zambia and Zimbabwe) or eliminate the conjunction “and” in the list of the previous six countries and after that talking of cholera outbreaks in Zimbabwe;

Thank you for the comment. The conjunction was used as a time contrast between the six countries and Zimbabwe.

Line 35: “DRC” the Democtaric Republic of Congo, when reporting for the first time the name of the country, it could be better to include the name per extenso;

Thank you for the comment. DRC was replaced with Democratic Republic of Congo.

Line 38: “… case fatality ratios (CRF) …” change to ““… case fatality ratios (CFR) …”;

We replaced CRF with CFR.

Line 129: Figure 2, please cite clearly Fig.2 in the text;

We cited Fig. 2 in Line 115.

Line 215: “microbial” change to “microbiological”;

We changed microbial to microbiological.

Line 215: The importance of genomic studies by using phylogenetics tools and bioinformatics has been evidenced in the review. It is true that by using this approach it is possible to have a very broad view of the Vibro cholerae species behaviour and distribution. Nevertheless, a more specific approach, meaning sampling of sediment, water or aquatic organisms present into the cosatal areas, to be used for culturing and isolation of autochthonous bacteria of the species V. cholerae, and storage of isolated strains in refrigerator at -80°C, could give important information. In fact it would be possible to have and to maintain a bank of strains of V. cholerae to be analyzed not only from the genetic point of view, but also from the physiological point of view, for instance on the presence of specific chitin receptors, suggesting a preference for V. cholerae to adhere to aquatic organisms (i.e. copepods) or antibiotic-resistance. Although culturable bacteria in general represent a low percentage as respect to the whole microbial community and to information collected by genetic tools (i.e. metagenomic approach), isolated bacteria could give important information on V. cholerae adaptation, suggesting for eventual information on the site of origin of the same bacteria. Microbiological approach is not an “old” one, each method gives different information, the aspect of microbiology could be included in the multidisciplinary approach highlighted in this review. The microbiological aspect could add interest to this review, eventually, the most recent techniques (including genetic specifically on the isolated bacterial strain, recent tools in microscopy, study of mechanisms of bacterial adhesion to different substrata) will be then used to study the isolated bacterial strains of V. cholerae. As an example, enclosed a paper that comprehends isolation of V. cholerae (Saidou Kaboré, Philippe Cecchi, Thomas Mosser, Mylene Toubiana, Oumar Traoré, Aboubakar S. Ouattara, Alfred S. Traoré, Nicolas Barro, Rita R. Colwell, Patrick Monfort. (2018) Occurrence of Vibrio cholerae in water reservoirs of Burkina Faso. Research in Microbiology 169).

Thank you for the comment. The following line was added: Furthermore, there is need for maintenance of V. cholerae banks that could be used for physiological analysis (e.g., characterization of chitin receptors associated with V. cholerae adherence to aquatic organisms) [52].

Line 340: “… V. cholera …” change to “… V. cholerae …”.

We changed to V. Cholerae.