Discussion
This study characterized S. Typhi isolated from cases of typhoid fever collected by the Sivigila National Surveillance System and laboratory from across Colombia between 2012–2015. Our work demonstrates that there is a substantial burden of typhoid fever in Colombia [22]. The disease epidemiology in this Latin American country appears to be highly variable, with typhoid associated with sustained transmission in some regions and short-term outbreaks in other departments. We additionally found that typhoid is broadly distributed and caused by multiple genotypes, of which the majority may be constrained to Colombia and do not appear to circulate between other Latin American countries.
We identified a particularly high burden of typhoid in Cucutá city in Norte de Santander department and in other more remote locations including Antioquia, Meta, and Huila, indicating both urban and rural disease transmission. Similar observations have been made in Sub-Saharan Africa [24]. Colombia has been classified as a country with an intermediate burden of typhoid fever (1.2 to 2.0 cases per 100,000 people/year) [4,5,25]. However, it is known that epidemics of typhoid fever can arise sporadically in Latin America [26]; therefore, we suspect the underreporting of disease in the national data capturing system as the national surveillance system is unlikely to capture the full extent of the disease burden in Colombia. Furthermore, given the geographical landscape of Colombia, there is the potential for a lack of typhoid reporting in many rural locations, leading to a shortfall in disease notification of these cases to the central surveillance system. Our data were enriched for organisms arising from the major cities in well-connected departments. This lack of an equal distribution of clinical laboratories across the country is likely to induce substantial bias in any conclusion regarding the distribution of typhoid in Colombia. Many rural locations do not have access to standardized blood culturing systems or a resident clinical microbiologist to identify infecting organisms [27]. The highest density of laboratories with the ability to perform blood culture can be found in Nariño, Boyacá, Atlántico, Bolívar, Valle del Cauca, Santander, Antioquia, and Bogotá. Whereas, the lowest density of clinical laboratories with the ability to perform blood culture is in the departments of Vaupes, San Andres and Providence, Guainía, Quindío, Vichada, Guaviare, Amazonas, and Putumayo. Furthermore, almost half the cases were isolated as part of the national contributory health insurance scheme, suggesting bias towards those that can afford to pay for improved healthcare services. The lack of a surveillance system that encompasses the entire country, the use of non-standardized protocols, and an inconsistent health insurance system may also limit case numbers being detected and reported [28].
We observed that the majority S. Typhi isolates from this study were pan-susceptible to the tested antimicrobials, with MDR and fluoroquinolone resistance phenotypes being uncommon. Consequently, our data suggest that traditional first-line antimicrobials and the fluoroquinolones are likely to remain largely effective for the treatment of typhoid fever in Colombia [29]. Local treatment guidelines for typhoid do not yet exist in Colombia and use standard of care empirical treatment for a patient suspected to have typhoid fever, which is typically a third-generation cephalosporin, such as ceftriaxone. However, many hospitals follow the guidelines of the WHO and then switch to a fluoroquinolone when S. Typhi has been isolated from blood [30]. We identified no ESBL producing S. Typhi; other ESBL producing Salmonella have been reported from Latin America, but unlike the epidemiology of S. Typhi outside of the region, drug resistance appears not to be an issue [31,32]. This observation is probably associated with a lack of H58 (genotype 4.3.1) S. Typhi outside of Asia and Africa. The integration of whole genome sequencing (WGS) with conventional epidemiology has been shown to be highly valuable in the detection of outbreaks, strengthening AMR surveillance, and public health investigations [33]. Our future direction aims to introduce WGS in our current surveillance network to monitor for the emergence of H58 S. Typhi in Latin America and continue to track the local spread of other AMR genotypes.
This study identified specific geographical regions that may be hot spots of S. Typhi in Colombia. For instance, Cucutá in Norte de Santander department and two localized clusters across Antioquia (spanning Apartadó, Carepa, Chigorodo, Itsmina, Medellin, Murindo, Riosucio, Turbo, and Vigia del Fuerte) exhibited extensive case clustering of specific genotypes. These locations have a propensity for poor sanitation and are the hubs for recent massive displacement of provincial workers in a low sociodemographic population of indigenous people and immigrants [34]. The more recent typhoid epidemiology in Colombia (and other Latin American countries) may be highly volatile as a consequence of the Venezuelan migratory situation. Indeed, this highest minimum incidence was identified in Norte de Santander, which lies on the border with Venezuela. However, due to the limitations of data collection and a porous border we were only able to identify two patients that were confirmed to have entered Colombia from the state of Táchira, Venezuela. This crisis has induced a convergence of social and public health problems and should be the targeted for the provision of appropriate public health interventions and future research initiatives [35].
Previous studies have suggested that multiple S. Typhi PFGE patterns circulate at a regional level across Latin America [36,37]. A regional comparison between typhoid outbreaks in Argentina and Colombia found that many isolates shared highly similar restriction patterns [38]. In this study, two restriction patterns dominated, which included 36.6% of the isolates from outbreaks in the departments of Putumayo and Antioquia. More recently, we compared S. Typhi isolates from 2005–2008 from Argentina, Brazil, Colombia, and Chile and found that various PFGE patterns were exchanged between Colombia and Brazil [36]. Latterly, we compared S. Typhi isolates from Colombia with the PNLA&C database to identify shared PFGE patterns; two common Colombian restriction patterns were indistinguishable with organisms found in Argentina and Chile and were hypothesized to be associated with sustained regional circulation [37]. A study comparing organisms isolated between 1996 and 2016 in ten countries across the continent described 278 regional XbaI-PFGE patterns, of which 34 were shared between several countries [23]. In this broad Latin American study, Colombia possessed 23 XbaI-PFGE patterns that were identical to organisms isolated in Argentina, Brazil, Chile, Guatemala, Peru, and Venezuela. These studies suggest a high level of genetic diversity of S. Typhi circulating within individual countries in Latin America of which some variants have the ability to spread successfully across the region. Again, the adoption of WGS should facilitate a deeper understanding of the population structure and dynamics of S. Typhi in this region.
This study has limitations; due to the nature of the surveillance system(s). The data may be incomplete as cases are detected passively and particular departments may have a lack of facilities for diagnosing typhoid. Additionally, the population at risk and health seeking behavior were not assessed in our study making an accurate incidence estimation unfeasible. Furthermore, bacterial genotyping was limited to PGFE, which is no longer the gold standard method for genotyping S. Typhi. However, due the limitation of the capacity to perform WGS across Latin America, PFGE remains the currently preferred subtyping method by PNLA&C [39]. Despite these limitations, this study highlights that there is a significant burden of typhoid in Colombia and the political instability in Venezuela may place additional pressures on typhoid control in Latin America.
Our study provides a current perspective of typhoid fever in a Latin America country and highlights the importance of pathogen-specific surveillance to add insight into the epidemiology of typhoid in this region. Sustained surveillance and the adoption of WGS in high risk areas should aid in disease control, our ability to identify new AMR variants, and permit us follow specific clones and lineages in Colombia and across Latin America.
10.1371/journal.pntd.0008040.r001
Decision Letter 0
Azman
Andrew S.
Deputy Editor
2020
Andrew S. Azman
This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Submission Version
0
23 Sep 2019
Dear Professor Baker:
Thank you very much for submitting your manuscript "Endemic transmission of Salmonella enterica serovar Typhi in Colombia, 2012-2015" (#PNTD-D-19-01222) for review by PLOS Neglected Tropical Diseases. Your manuscript was fully evaluated at the editorial level and by independent peer reviewers. The reviewers appreciated the attention to an important problem, but raised some substantial concerns about the manuscript as it currently stands. These issues must be addressed before we would be willing to consider a revised version of your study. We cannot, of course, promise publication at that time.
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Reviewer's Responses to Questions
Key Review Criteria Required for Acceptance?
As you describe the new analyses required for acceptance, please consider the following:
Methods
-Are the objectives of the study clearly articulated with a clear testable hypothesis stated?
-Is the study design appropriate to address the stated objectives?
-Is the population clearly described and appropriate for the hypothesis being tested?
-Is the sample size sufficient to ensure adequate power to address the hypothesis being tested?
-Were correct statistical analysis used to support conclusions?
-Are there concerns about ethical or regulatory requirements being met?
Reviewer #1: The objectives of this study are clear, and the study design is appropriate. The population studied is described and the sample size large enough to draw conclusions. The statistical analysis appears appropriate and I have no ethical concerns.
Reviewer #2: Methods
1. Line 130. It is mentioned that certain areas of the country have strengthened their surveillance for typhoid fever. If those specific areas or departments can be cited that would be helpful.
2. Line 133: Defining “non-endemic” as “incidences lower than the national average” is not the usual usage and meaning of “endemicity”. Endemicity repetitive, predictable occurrence over time rather than relative incidence (incidence against a national average). Characterizing all regions below the national average as non-endemic could lead to under-reporting of endemicity and over-reporting of sporadic transmission. The U.S. CDC and W.H.O / P.A.H.O. have definitions of sporadic, endemic, hyperendemic transmission; as well as epidemic, outbreak, cluster, pandemic, etc.
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Results
-Does the analysis presented match the analysis plan?
-Are the results clearly and completely presented?
-Are the figures (Tables, Images) of sufficient quality for clarity?
Reviewer #1: The analysis matches the plan and the results are clear and clearly presented. I found the maps to be a little blurred.
Reviewer #2: 1. Of 468 S. Typhi isolates, 402 came from seven departments. The department of Norte de Santander accounted for 190 (47.3%) of these 402 isolates. This result immediately catches the attention of the reader.
2. Line 193-194, the statement “almost half of cases were affiliated to the national contributory health insurance scheme” is explained. If the authors are implying that this impacts surveillance, they should elaborate on this point. Also, “insurance scheme” is not discussed elsewhere, except itemized under Table 1.
3. Figure 1 should explain the quantitative significance of the dot size in the legend and/or caption. If the dot sizes have no absolute meaning and are listed in steadily decreasing order based on PFGE type prevalence, perhaps to assist in differentiation by both size and color, then that must be stated so that misinterpretation is avoided. Currently, it might be interpreted that one dot of -0115 represents a prevalence 25-times greater than one dot of -0155 (roughly gauging relative dot size). Also, does each dot represent a hospital/reporting site or a patient’s home coordinates?
4. Lines 205-206. Does Sivigila define “endemic”?
5. The first paragraphs of the Results discuss the number of cases by department and smaller administrative units. A table that presents: the mean annual population of each of these seven departments during the years 2012-2015 (derived from either the 2005 or 2018 census data); the mean number of S. Typhi cases over 2012-2015 and the mean annual incidence per 100,000 persons for those years, would be very helpful. Some departments, such as Norte de Santander, that have been the site of extensive legal and illegal immigration from Venezuela during 2014 and 2015 may have notable numbers of high-risk persons who are not reflected in the 2018 census. Nevertheless, whatever denominators are available should be used to calculate incidence rates. Then some of the figures can be modified to have spot maps based on incidence rather than just number of cases, should be crafted.
6. Line 234: Table 3 does not represent the result that is stated immediately prior and in reference to the table. Please check this.
7. Line 244-245: The sentence, “Notable, Group III contained the majority of organisms […] and nalidixic acid (n=10)” is misleading because Group III also contained 356 out of 402 characterized isolates. A percentage/proportion might be included in parentheses and a statistical test could be performed to support this association, if it is to be deemed “notable.” It should also be further discussed in the discussion section.
8. Figure 2: The four maps are inconsistent with the text (lines 236-247) and the figure 2 caption. See below.
Lines 236-247: Group 1 has 13 isolates in 6 departments. Group 2 has 27 isolates in 6 departments. Group 3 has 356 isolates in 14 departments. Group 4 has 6 isolates in 4 departments.
Figure 2 Caption: Group 1, purple, in 7 departments (should it be 6?). Group 2, yellow, in 6 departments. Group 3, orange (should it be green?), in 5 departments (should it be 14?). Group 4, green (should it be orange?), in 14 departments (should it be 4?).
There are several inconsistencies (numbers and colors) that need addressing.
The data contained within lines 265-274 could be better understood and discussed in a table or figure.
Lines 287-288: What are the “three most common Colombian pulsotypes” specifically according to Figure 5? They are not clearly labeled or identified, and the labels in Figure 5 do not match the labels in Figure 1 or Table 3.
9. It was not possible to download reference #22. Please check all citations and links carefully.
10. Line 197: “liquid corporal-secretions” should be changed to “normally sterile body fluids”.
11. Figure 1 caption – “Kerner” seems to be a misspelling of “Kernel”.
12. Figure 3 requires a scale on the map and again, “Kerner” seems to be a misspelling of “Kernel”.
13. Figure 4 caption: Lists cases by municipality, but the maps in Figure 4 do not label these municipalities.
14. Lines 276-288 “Colombian Salmonella Typhi in a Latin America framework”. In order to assess the relevance of this analysis the readers need to know how representative the isolates are for the other countries and how these isolates were obtained. Without this information it is hard to judge the relevance of comparing a few isolates from other countries in South America.
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Conclusions
-Are the conclusions supported by the data presented?
-Are the limitations of analysis clearly described?
-Do the authors discuss how these data can be helpful to advance our understanding of the topic under study?
-Is public health relevance addressed?
Reviewer #1: The conclusions are supported by the data and the limitations explored. There is discussion of how the data could be used and the public health implications.
Reviewer #2: 1. Line 300. “We identified a particularly high burden of typhoid in Cucutá”, the capital city of Norte de Santander department. This city has been an epicenter of Venezuelan migration. The isolates from Cucutá should be compared to Venezuelan isolates of S. Typhi, if the authors have some.
2. Do the authors have any way to differentiate which isolates came from Venezuelan immigrants and refugees? Minus the isolates from this city and this department, the total Colombia burden drops almost in half. So it is critical to attempt to ascertain how many of the typhoid cases derive from the Venezuelan refugee crisis.
3. Lines 317 – 330. This is an important and well written paragraph.
4. Lines 332 – 337. This paragraph addresses in detail the issues raised above with respect to the status of Venezuelan refugees in Cucutá and elsewhere in Norte de Santander.
5. Lines 341-358. To reiterate, without knowing more about the isolates from the other Latin American countries, including how they were selected, it is difficult for the reader to accept categorically the conclusions drawn by the authors. More information about these strains and softening of statements would strengthen the paper.
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Editorial and Data Presentation Modifications?
Use this section for editorial suggestions as well as relatively minor modifications of existing data that would enhance clarity. If the only modifications needed are minor and/or editorial, you may wish to recommend “Minor Revision” or “Accept”.
Reviewer #1: Line 126: sentence does not make sense. Do you mean ’Cases were defined as those with …’?
Line 131: Not sure what reiterative epidemiological behaviour is. Could this be clearer?
Line 197: What are liquid corporal-secretions?
Line 203 and line 205: How does the public health department define outbreaks, endemic and non-endemic?
Line 306: I could not see these discrepancies discussed in the results but may have missed it
Line 319: What are the recommended first line antbiotics for typhoid? Are there national guidelines?
Line 320: I could not see any results that confirmed that the extended spectrum cephalosporin resistant strain had an ESBL phenotype. It looks as if this strain was negative by PCR for blaSHV, blaTEM, and blaCTX-M?
Table 1
Please explain some of the variables (perhaps as a footnote): Regime type; Categories of health coverage; municipal centre and populated centre.
Reviewer #2: In the spirit of being helpful, the following typographical and grammatical edits are offered:
• Line 56: A period is missing at the end of the first sentence
• Line 59: “we aimed to add some insight” is informal
• Line 62: “widely is” should be changed to “is widely”
• Line 63: “major” should be written as “majority”
• Line 64: “epidemiology of typhoid of Colombia” should be rewritten to “epidemiology of typhoid in Colombia” or similar
• Line 64: “distinct to” should be written as “distinct from”
• Line 65: “organisms that circulating nationally” should be written as “organisms that are circulating nationally” or “organisms that circulate nationally”
• Line 83: misplaced comma between “disease, which”
• Line 302: Run-on sentence between “transmission, similar”
• Line 303: Missing articles; “currently classified as country with intermediate burden” should include “a” so it reads “as a country” and “an” so it reads “with an intermediate burden”
• Line 341: Change 5th word “the” to “that”
• Line 360: run-on sentence between “system(s)” and “the data”
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Summary and General Comments
Use this section to provide overall comments, discuss strengths/weaknesses of the study, novelty, significance, general execution and scholarship. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. If requesting major revision, please articulate the new experiments that are needed.
Reviewer #1: Typhoid fever was a major public health problem in Latin America in past decades but in recent years it has appears to have declined as a problem. This report is a useful reminder that for some countries and populations it remains an important disease. Importantly, unlike other regions of the world, antimicrobial resistance was uncommon and restricted to low levels of resistance to ampicillin and fluoroquinolones. A diversity of genetic types was described and limited overlap with genetic types in other Latin American countries. There was some evidence of areas with a higher incidence.
Detection of cases is dependent on a positive blood or bone marrow culture. It would be helpful to have some more detailed background information about the distribution of laboratories with the capacity for blood culture. Would most patients with a fever been investigated with a blood culture? In particular would blood cultures be performed in children and in smaller hospitals outside the main department centres or is it possible that there is under-ascertainment of cases in these groups?
Reviewer #2: The manuscript reports that over a 4-year period (2012-2015) in Colombia the national public health surveillance protocol for the identification of typhoid and paratyphoid fever yielded 468 confirmed cases of typhoid fever that had an archived Salmonella Typhi isolate. Notably, 420 of the 468 isolates originated from seven departments of Colombia, with 190/420 isolates coming from a single department, Norte de Santander, which borders Venezuela. Most cases occurred in the main metropolitan centers in the affected departments and 68.2% of aces were in persons > 15 years of age. Importantly, the vast majority of the isolates were sensitive to first-line antibiotics and none were H58 lineage. Pulse field gel electrophoresis (PFGE) was performed on 402 S. Typhi isolates allowing special distribution analyses to be carried out. These data shed light on some geographic areas and sub-populations in Colombia where typhoid fever remains a public health problem. These data do provide helpful information on typhoid fever in Colombia. Whilst the PFGE patterns if Colombian isolates are useful for analyzing relatedness among strains from within the same department and between different departments of Colombia, the attempt to relate the PFGE patterns to isolates from other Latin American countries was not particularly helpful because the source of the strains from other countries was not described in any detail.
Need a table that shows population, cases and incidence per 100,000 for the seven departments and for Cucutá”, the capital city of Norte de Santander department. This city has been an epicenter of Venezuelan migration. The isolates from Cucutá should be compared to Venezuelan isolates of S. Typhi, if the authors have some.
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