Whole genome sequencing assisted outbreak investigation of Salmonella enteritidis, at a hospital in South Africa, September 2022
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Health authorities were notified of a suspected outbreak of foodborne disease in a hospital in South Africa, where staff and patients reported acute onset of abdominal cramps, diarrhoea, fever and rigours after eating a chicken pasta meal. The aim of this report is to discuss the use of whole genome sequencing (WGS) analysis of bacterial isolates to support an epidemiological investigation. An epidemiological investigation led by the Infection Control Manager of the hospital and supported by an outbreak response team was conducted. Standard microbiological procedures were used to process stool samples and culture/identify diarrhoeal pathogens. Bacterial cultures were investigated using WGS performed using Illumina NextSeq technology, and WGS data were analysed using multiple bioinformatics tools, including those available at the Center for Genomic Epidemiology and EnteroBase. Core genome multilocus sequence typing (cgMLST) was used to investigate the phylogeny of isolates. Forty-nine cases were identified, with stool samples collected from 21 cases, and nontyphoidal Salmonella isolated from 19 out of 21 (90%) of the samples. All isolates were identified as Salmonella enterica serovar Enteritidis and differed from each other by ≤2 allele differences on cgMLST, indicating that isolates are highly genetically related. Delays in testing of food retention samples rendered the negative test results of limited value. A case–control study was conducted; eating chicken pasta was strongly associated with developing gastroenteritis (Odds Ration (OR) = 15.4, Chi-Square test with Yates correction p value = 0.02). The epidemiological evidence suggests that the chicken pasta was the likely vehicle of transmission in this outbreak, although the source of S. enterica serovar Enteritidis remains unknown.
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The authors have addressed all the concerns raised by the reviewers satisfactorily and the manuscript is ready for publication. I suggest to introduce paragraph in the abstract prior to publishing for ease of reading.
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The reviewers and I agree that the premise of the paper is interesting and sound. The reviewers have raised some concerns that will need to be addressed in a revision.
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Comments to Author
The authors describe an outbreak caused by Salmonella in a hospital in South Africa. They conducted: 1. an epidemiological investigation 2. a whole-genome sequencing (WGS) of outbreak-associated Salmonella isolates as well as relevant controls obtained during the same year in South Africa Results of part two of the paper are very convincing. WGS was able to clearly differentiate the outbreak-associated isolates from unrelated Salmonella ser Enteritidis isolates circulating in the population during the outbreak. The reviewer is unaware of similar uses of WGS in the past. Therefore, the authors could add some references and discuss stability of the markers over the very short period of the outbreak (days). The epidemiological investigation has some flaws which should be addressed. - The title / …
Comments to Author
The authors describe an outbreak caused by Salmonella in a hospital in South Africa. They conducted: 1. an epidemiological investigation 2. a whole-genome sequencing (WGS) of outbreak-associated Salmonella isolates as well as relevant controls obtained during the same year in South Africa Results of part two of the paper are very convincing. WGS was able to clearly differentiate the outbreak-associated isolates from unrelated Salmonella ser Enteritidis isolates circulating in the population during the outbreak. The reviewer is unaware of similar uses of WGS in the past. Therefore, the authors could add some references and discuss stability of the markers over the very short period of the outbreak (days). The epidemiological investigation has some flaws which should be addressed. - The title / description of Table 1 needs improvement. It needs to state that the Table deals with cases. It is not clear what "epidemiological link only" (second line, 30 cases) means. - Figure 1 only contains 46 cases, three missing. If this was because of unknown date of onset this should be stated. If yes, the authors might wish to remove these patients from the study since it is unclear if they belong to the outbreak. - case-control-study: how were controls recruited and selected? This is a very important detail, because it might introduce a significant bias (the reviewer is of course convinced that the conclusions are very plausible anyway), but a case-control study has to follow methodical rigor! - omit Table 3 and give results in text; chi square can also be calculated with Yates correction giving substantially the same results (confidence interval for OR is not needed). Omit unnecessary digits from OR and p-level data. OR is 15.4 and p is 0.02 - the sentence in lines 178/179 is unclear The whole section on food safety investigation can be omitted, just stating what was analysed and that results were negative; it is no surprise that Salmonella was not found in the kitchen The authors might wish to consider additional details for future investigations. The most probable source for Salmonella in this outbreak was the chicken meat. Details of the preparation (thorough cooking of the meat, recipe) and hot holding of the finished pasta dish are the most important points to consider.
Please rate the manuscript for methodological rigour
Satisfactory
Please rate the quality of the presentation and structure of the manuscript
Good
To what extent are the conclusions supported by the data?
Strongly support
Do you have any concerns of possible image manipulation, plagiarism or any other unethical practices?
No
Is there a potential financial or other conflict of interest between yourself and the author(s)?
No
If this manuscript involves human and/or animal work, have the subjects been treated in an ethical manner and the authors complied with the appropriate guidelines?
Yes
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Comments to Author
In this work by Brummer et al., the authors trace the source of a disease outbreak in a hospital in South Africa to chicken pasta. Through WGS, they find that Salmonella Enteritidis is responsible for the outbreak, which they detected in 19 patient samples. Overall, the premise of the paper, results, and methods are sound. The authors include their raw sequencing data on Enterobase and ENA, making it publicly available. They use standard WGS and phylogenetic pipelines to identify S. Enteritidis as the key player in the outbreak. The tables and figures are simple but sufficient for this work. The organization and flow of the paper are clear, and the introduction is adequately cited. Below are some additional comments for the authors to consider in a minorly revised article: 1) The abstract should be …
Comments to Author
In this work by Brummer et al., the authors trace the source of a disease outbreak in a hospital in South Africa to chicken pasta. Through WGS, they find that Salmonella Enteritidis is responsible for the outbreak, which they detected in 19 patient samples. Overall, the premise of the paper, results, and methods are sound. The authors include their raw sequencing data on Enterobase and ENA, making it publicly available. They use standard WGS and phylogenetic pipelines to identify S. Enteritidis as the key player in the outbreak. The tables and figures are simple but sufficient for this work. The organization and flow of the paper are clear, and the introduction is adequately cited. Below are some additional comments for the authors to consider in a minorly revised article: 1) The abstract should be re-written in paragraph form instead of separate sections. 2) Line 111: Johannesburg has an extra capitalized O. 3) Table 1: "Unknown" under age is spelled wrong. 4) Some numbers in Table 1 seem incorrect. For example, for clinical staff (N=10), there were 2 females (which should be 20%, but the authors put 22%), and 7 males (which should be 70%, but the authors put 78%). If the authors are calculating these percentages by removing the 1 with unknown sex, they should state this in the table caption somewhere, otherwise, it could be confusing for readers. 5) Table 1: Please highlight why only 1 member of the kitchen staff had a sequenced sample. I think this is explained in line 123, but it is a bit subtle. Perhaps rephrase to "While the outbreak also impacted a large number of kitchen staff (n=24), only one had access to diagnostic services to have their stool sampled." 6) Figure 2: The numbers on the lines in the figure are very hard to see due to the light grey font; please fix.
Please rate the manuscript for methodological rigour
Good
Please rate the quality of the presentation and structure of the manuscript
Satisfactory
To what extent are the conclusions supported by the data?
Strongly support
Do you have any concerns of possible image manipulation, plagiarism or any other unethical practices?
No
Is there a potential financial or other conflict of interest between yourself and the author(s)?
No
If this manuscript involves human and/or animal work, have the subjects been treated in an ethical manner and the authors complied with the appropriate guidelines?
Yes
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Comments to Author
The results show that the source of the contamination was from inside the kitchen. Were all those involved in the preparation and serving of food, even those without symptoms, tested for salmonella in feces? It seems that in such epidemiological studies, all aspects should be taken into account, and even apparently healthy people should be sampled and the presence or absence of bacteria in their feces should be proven. It is possible that a person or people from the kitchen staff are chronic carriers and have caused food contamination.
Please rate the manuscript for methodological rigour
Satisfactory
Please rate the quality of the presentation and structure of the manuscript
Good
To what extent are the conclusions supported by the data?
Partia…
Comments to Author
The results show that the source of the contamination was from inside the kitchen. Were all those involved in the preparation and serving of food, even those without symptoms, tested for salmonella in feces? It seems that in such epidemiological studies, all aspects should be taken into account, and even apparently healthy people should be sampled and the presence or absence of bacteria in their feces should be proven. It is possible that a person or people from the kitchen staff are chronic carriers and have caused food contamination.
Please rate the manuscript for methodological rigour
Satisfactory
Please rate the quality of the presentation and structure of the manuscript
Good
To what extent are the conclusions supported by the data?
Partially support
Do you have any concerns of possible image manipulation, plagiarism or any other unethical practices?
No
Is there a potential financial or other conflict of interest between yourself and the author(s)?
No
If this manuscript involves human and/or animal work, have the subjects been treated in an ethical manner and the authors complied with the appropriate guidelines?
Yes
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