Microbiological Laboratory Testing in the Diagnosis of Fungal Infections in Pulmonary and Critical Care Practice

The review process for official ATS documents is independent from the ATS journals’ review processes. The Documents Editor will perform an initial review of the document upon submission. If there are major flaws (e.g., not compliant with word limits, incorrect methodology used), the document will be returned to the authors with a description of what needs to be revised for the document to be ready for peer review. If the document is satisfactory, it will be sent for peer review by content experts. Peer reviewers are selected by the Documents Editor, with input from the relevant assembly chair. The authors’ preferred and non-preferred reviewers are also considered. Both domestic and international reviewers are typically sought, in order to solicit a diversity of opinions. Most documents are reviewed by four peer reviewers, although the exact number is at the discretion of the Documents Editor. Peer review generally takes three to five weeks. A decision letter will be issued following peer review, which is almost always a request for revisions. The decision letter includes comments from peer reviewers about content and from the Documents Editor about methodology and formatting/organization of the document. Authors are expected to consider each reviewer comment, make revisions deemed appropriate, and then resubmit the revised version of the document along with a point-by-point response to the reviewers’ comments. Resubmission of revised manuscripts is expected within three months from the date the decision letter. The revised document and the point-by-point responses will be reviewed by the Documents Editor and/or the peer reviewers. Following this review, another decision letter will be issued, which is usually either a request for additional modifications or notification that the document is being advanced to the Board of Directors to undergo further review and to be considered for approval. If any major conflicts between the Documents Editor and the chairs occur during the peer review process, the DDIC is responsible for making a decision about the appropriate course action. In cases where extreme conflict occurs, the ATS Executive Committee be called upon to intervene. Peer review is managed differently for multi-society projects. Following submission of the document, each society conducts its own peer review. The total number of reviewers and the time required for peer review are variable, although both tend to be greater with more societies involved. The lead society, as designated in the Memorandum of Understanding, collates the reviewer comments from all of the participating societies and then issues a single decision letter, which is usually a request for revisions. Authors are expected to consider each reviewer comment, make revisions deemed appropriate, and then resubmit the revised version of the document along with a point-by-point response to the reviewers’ comments to each society independently. Cycles of peer review, decision letters, revisions, and resubmission continue until all of the co-sponsoring societies agree that the document is ready to be advanced to the leadership of each society for approval. Once approved by the Documents Editor, the document (along with the peer reviewers’ comments, the Documents Editor’s comments, and the authors’ responses to those comments) is sent to the Board of Directors for further review and a vote for or against approval at the next Board of Directors meeting.

Critical Care, Infectious Disease, Pathology, Pediatrics, Pulmonology, Clinical Pathology, Pediatric Infectious Diseases, Pediatric Pulmonology, Pathology, Pediatrics, Pediatrics

The workplan specifies the purpose of the guideline product, target patient population, clinical outcomes of interest, key features of the systematic literature review, and a proposed timeline for completion. ATS staff, Chair, and possibly other panel members selected by the Chair (the Expert Panel Steering Committee), will typically draft the workplan for full panel review. A standard protocol worksheete is used for consistency. Once the Co‐Chairs have approved a first draft of the workplan, the plan will be shared with the full Expert Panel. At the discretion of the ATS Chief, Documents, the ATS leadership may review the plan to make suggestions for revision intended to clarify aspects of the goals for developing the guideline. These suggestions are sent to the Chair for review. Work on the systematic literature review can proceed upon the sign‐off of the Workplan by the Expert Panel. ATS applies the Grading, Recommendations, Assessment, Development, and Evaluation (GRADE) approach to formulating, writing, and grading recommendations. In brief, the first phase to execute is determining the scope of the guideline and specifying the manageable number of clinical questions to translate to clinical recommendations. The second phase (led by the methodologist) is to conduct the evidence synthesis: search the literature; select relevant studies, extract and pool data; and summarize the body of evidence. The final phase to execute is develop and grade recommendations based upon the evidence.

ATS uses the Evidence to Recommendations (EtR) framework. High: High confidence that the available evidence reflects the true magnitude and direction of the net effect (i.e., balance of benefits v harms) and that further research is very unlikely to change either the magnitude or direction of this net effect. Intermediate: Moderate confidence that the available evidence reflects the true magnitude and direction of the net effect. Further research is unlikely to alter the direction of the net effect; however, it might alter the magnitude of the net effect. Low: Low confidence that the available evidence reflects the true magnitude and direction of the net effect. Further research may change either the magnitude and/or direction this net effect. Very Low: Evidence is insufficient to discern the true magnitude and direction of the net effect. Further research may better inform the topic. The use of the consensus opinion of experts is reasonable to inform outcomes related to the topic.

ATS uses a formal consensus methodology based on the modified Delphi technique in clinically important areas where there is limited evidence or a lack of high‐quality evidence to inform clinical guidance recommendations. GRADE rates the certainty (also known as quality or confidence) in effect estimates for benefits and harms as high, moderate, low or very low, and the overall certainty is based on the lowest confidence of the outcomes critical for decision making. Recommendations are classified as strong (desirable consequences clearly do or do not outweigh undesirable consequences) or conditional (the balance of desirable and undesirable consequences is less certain). Alternative designations are conditional, discretionary, or contingent recommendations. A strong recommendation was made for an intervention when, following deliberations, the panel was certain that the desirable consequences of the intervention outweigh the undesirable consequences, likewise a strong recommendation would have been made against a proposed intervention if the panel was certain that the undesirable consequences of the intervention outweigh the desirable consequences. A strong recommendation indicates that almost all well-informed patients would choose to have or not to have the intervention. A conditional recommendation was made for an intervention when the panel was uncertain whether the desirable consequences of the intervention outweigh the undesirable consequences, likewise a conditional recommendation would have been made against a proposed intervention if the panel was uncertain that the undesirable consequences of the intervention outweigh the desirable consequences. Reasons for a conditional recommendation and thus uncertainty included low or very low quality of evidence, or the desirable and undesirable consequences being finely balanced, with underlying values and preferences playing an important role.

ATS provides funding for Guideline Development.

ATS Conflict of Interest Policy complies with the CMSS Code for Interactions with Companies. ATS requires no COI with Tobacco entity (includes manufacturer/dissemination of e-cigarettes).

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