PONE-D-21-37969The aetiology and clinical characteristics of cryptococcal infections in Far North Queensland, tropical AustraliaPLOS ONE

Dear Dr. Hanson,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. The manuscript has received a mixed review, and it requires significant revisions. Especially, serious are the concerns regarding the use of questionable statistics and lots of speculation.

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Michal A Olszewski, DVM, PhD

Academic Editor

PLOS ONE

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Partly

Reviewer #2: Yes

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: Yes

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3. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

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4. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: Yes

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5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: This paper reports the retrospective experience with 49 patients hospitalized in Northern Queensland with cryptococcosis. The report centers around 32 cases in which the isolate was identified by species: C neoformans or C. gattii. No novel findings were encountered. The higher prevalence of immunosuppressed patients with C. neoformans than C. gattii in Australia was confirmed. Some of the other difference between the two species in other reports were not found, in part due to the small sample size, such as more infections confined to the lung or more mass lesions in the brain among C. gattii cases.

The paper is burdened with masses of data that cannot be interpreted. The speculated connection between the higher prevalence of C. gattii cases in the last half of the year and flowering in Eucalyptus trees is specious. The lower, though normal, lymphocyte counts in the peripheral blood of C. neoformans patients is an example of applying a p value of 0.05 to more than 20 comparisons and finding one value of 0.04. There are larger and more detailed analyses of MRI and CT images, antifungal susceptibility and clinical descriptions of cryptococcosis in Australia than in this report. The long and speculative Discussion in the paper needs drastic shortening. The authors might consider deleting the data on the 17 cases with unspeciated isolates and minimizing speculation. If further analyses can provide insights into how cryptococcosis might differ in indigenous Australians, that might be instructive. Cairns has an experience with that population. Just because no difference was found doesn’t mean there were no differences.

Reviewer #2: In this manuscript, Sim et al. summarized the etiology, epidemiology and clinical course of cryptococcal infections in Far North Queensland between 1999 and 2019. During this period, infections with both Cryptococcus gattii and C. neoformans were identified. Individuals infected with C. gattii were less likely to be immunocompromised compared to patients with C. neoformans. Interestingly, they found that nearly 90% of the C. gattii infections had CNS involvement. Patients with C. gattii infections were more likely to be current or former smoker than patients with C. neoformans. Furthermore, more than 50% of the patients had a history of hazardous alcohol use. These clinical data are interesting; however, the manuscript will definitively benefit from an expanded mechanistic discussion on these clinical observations.

Comments

1) In this manuscript, 90% of the C. gattii infections had CNS involvement. Recent mouse studies showed that the primary target organ of C. gattii is different from that of C. neoformans. C. gattii grows faster in the lung and is primarily linked to pulmonary diseases (Pubmed PMID: 22570277). The authors should expand the discussion on this point.

2) Patients with C. gattii infections more likely to be smoker. It would be nice to have more discussion about that point.

3) It is also interesting that more than 50% of the patients had a history of hazardous alcohol use. The authors should discuss more on the potential mechanisms behind this observation. Actually, recent studies have shown that Liver cirrhosis is an independent risk factor of cryptococcal meningitis (Pubmed PMID: 25747471) and that liver macrophages play a prominent role to filter disseminating Cryptococcal yeast cells (Pubmed PMID: 31594939).

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Reviewer #1: No

Reviewer #2: No

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Attachments

Attachment

Submitted filename: Comments PLOS One 2021.docx

PONE-D-21-37969R1The aetiology and clinical characteristics of cryptococcal infections in Far North Queensland, tropical AustraliaPLOS ONE

Dear Dr. Hanson,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

Both reviewers found the manuscript to improve significantly; however, there are a few issues that are unresolved per Reviewer 1, which can be corrected by editorial changes in the manuscript. Especially, please omit speculations and address other limitations that the reviewer 1 has identified. 

Please submit your revised manuscript by Apr 02 2022 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

Please include the following items when submitting your revised manuscript:

• A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.
• A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.
• An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols.

We look forward to receiving your final version of the revised manuscript, shortely.

Kind regards,

Michal A Olszewski, DVM, PhD

Academic Editor

PLOS ONE

Journal Requirements:

Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice.

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #1: (No Response)

Reviewer #2: All comments have been addressed

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2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Partly

Reviewer #2: Yes

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: I Don't Know

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4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

**********

5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: Yes

**********

6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: This is better manuscript. However, the following issues should be addressed.

This is a report of 49 patients with cryptococcosis, of whom 16 may have had infection confined to the lung (table 2). Most analyses were done on a subset of 32 patients in whom the Cryptococcus was speciated as neoformans or gattii. Of the 32, 4 had isolated pulmonary disease. Though the diagnosis, management and outcome differs for cryptococcosis confined to the lung, that distinction does not appear in analysis of management or outcome. This should be corrected.

25.change wording to “clinical course of 49 cryptococcal infections”. Please insert total number of case so number of 32 in next line is in perspective

29-30 . omit speculation about flowering of trees because this new speculation does not have sufficient confirmation in the paper and may mislead readers (see below)

31 and 52-53 wording suggests that cryptococcomas may benefit by neurosurgery, presumably meaning resection. This is not true and is misleading.

93 a map of Australia is readily available to readers outside this manuscript and is unnecessary

138. Chart reviews about smoking and alcohol use find either no mention, simple mention or quantitation (pack years of cigarettes, amount of alcohol). Lines 109-110 indicate that “no mention”’ was tallied as no use. Cultural expectations may factor into that question. For example, was an indigenous patient more likely to be asked? The authors should be cautious in chart review interpretations, such as smokers being more common.

141 table 1 would benefit by a column with the results of the 17 patients with an unspeciated isolate. Readers don’t know how much bias is introduced by omitting a third of the cohort

171-172 This reference to the season of diagnosis correlating with tree flowering has several important limitations that are not adequately taken into account when the authors put this speculation in the abstract. As pointed out in lines 311-312 the time from exposure to clinical infection with C. gattii is unknown. However, it is thought to be from months to many years. This tentative conclusion is based on finding cases of C. gattii in patients who have left known endemic areas years previously. A long incubation period would help explain why there are no case clusters. Even in the Vancouver Island outbreak, there was no temporal relationship between time on the island and onset of symptoms. C. gattii has been isolated from dozens of tree species around the world but exposure history to such trees has not been correlated with disease, a similar situation with C. neoformans and weathered pigeon droppings. Nor has anyone correlated exposure to flowering of any tree nor flowering to isolation of the fungus from the tree. The authors should not put in the abstract (lines 29-30) their speculation that exposure to a flowering eucalyptus tree might lead to C. gattii infection.

Fig.3 There are many possible reasons for differing seasons at diagnosis but recent exposure is not the most likely.

Fig. 4 A similar reservation exists about geographic location. The location of a patient at time of diagnosis depends on population mobility. For example, an indigenous population may be less mobile. Location of C. gattii cases in rural areas may be a function of mobility.

Fig 6 and table 3 include drugs not recommended for treatment and don’t contribute to any conclusions.

Reviewer #2: (No Response)

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7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy.

Reviewer #1: No

Reviewer #2: No

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The aetiology and clinical characteristics of cryptococcal infections in Far North Queensland, tropical Australia

PONE-D-21-37969R2

Dear Dr. Hanson,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

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Kind regards,

Michal A Olszewski, DVM, PhD

Academic Editor

PLOS ONE