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Microbiology & parasitology topic template

Revised: 14 May 2020
Copyright: 2020, PathologyOutlines.com, Inc.

    Example of well written Microbiology topic: Klebsiella oxytoca
    Example of well written Parasitology topic: Loa loa

    For ease of use, we put topic headings in the same order. Please put some text under each heading, but do not include obvious or repetitive information. If you think there is nothing to add, please write "not relevant to this topic", "repetitive with __ heading" or "unknown at this time" [i.e. if etiology is not known]. Do not delete any topic headings.


    Author 1

    Author name with degrees: ___________________________________________

    Author rank (M.D. candidate / Resident / Fellow / Instructor / Assistant, Associate or Full Professor): ___________________________________________

    Author leadership roles (maximum of 2) (ex: Director of Surgical Pathology, Vice Chair of Anatomic Pathology, Director of Cytopathology): ___________________________________________

    Author institution name: ___________________________________________

    Author institution city, state, zip code and country: ___________________________________________

    Author email address: ___________________________________________


    Author 2

    Author name with degrees: ___________________________________________

    Author rank (Assistant, Associate or Full Professor): ___________________________________________

    Author leadership roles (maximum of 2) (ex: Director of Surgical Pathology, Vice Chair of Anatomic Pathology, Director of Cytopathology): ___________________________________________

    Author institution name: ___________________________________________

    Author institution city, state, zip code and country: ___________________________________________

    Author email address: ___________________________________________



    Chapter name: Microbiology & parasitology

    Section and subsection (in the Table of Contents): ___________________________________________

    Topic name:___________________________________________



    Definition / general
    A 1 - 2 sentence summary of the topic.

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    Essential features
    This topic heading should be completed after the rest of the topic is finished and should duplicate the 3 - 5 most important points mentioned elsewhere in the topic. In other words, it should list what every pathologist should know about the topic or what would be in a Board Review book.

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    Epidemiology
    Who is susceptible to this pathogen - age, gender, geographic location, very strong causal connections (example: Kaposi sarcoma and HIV, HHV8); weaker associations are listed under clinical features.

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    Sites
    Parts of the body or organ typically affected.

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    Pathophysiology
    Step by step details of how the infection begins and progresses (if not obvious).

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    Diagrams
    Those that do not automatically fit in another section. Provide caption and figure legend.


    Clinical features
    Anything clinical not included above or below. Includes associations with other conditions.

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    Diagnosis
    Information on how a diagnosis is made including imaging modalities and procedures utilized. Do not include microscopic findings.

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    Laboratory
    Typical growth conditions, biochemical testing used for diagnosis, description of plated colonies.

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    Case reports
    List 3 - 5 quality case reports, preferably from the past 5 years (unless the diagnosis is exceedingly rare). The format should be written as "25 year old man with large retroperitoneal mass (PMID: XXXX)." We prefer case reports from free full text PubMed archived journals in English. To find case reports that meet this criteria, use the following PubMed search (fill in the diagnosis): DIAGNOSIS case reports[PT] free full text[SB] 2015:2020[DP] english[LA]. This search should also be utilized to find images that you are not able to provide, such as clinical, gross, cytology and molecular / cytogenetics. Please visit Dr. Pritt's blog as a source for cases: Creepy Dreadful Wonderful Parasites.

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    Treatment
    General modes of treatment. Drug dosages are usually not necessary - if you want to include them, please provide a reference.

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    Clinical images
    Infections in patients, agar plates. For images you submit, provide a brief 1 - 4 word caption to appear below the thumbnail of the image and a longer figure legend to appear when the image is opened. If you do not have your own images, refer to the Case reports section for how to provide links to journal images, and provide links with a brief 1 - 4 word caption.


    Gross description
    Description of the excised specimen.

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    Gross images
    Images of the excised specimen. For images you submit, provide a brief 1 - 4 word caption to appear below the thumbnail of the image and a longer figure legend to appear when the image is opened. If you do not have your own images, refer to the Case reports section for how to provide links to journal images, and provide links with a brief 1 - 4 word caption.


    Microscopic (histologic) description
    List microscopic diagnostic criteria first, if they exist. Then common and uncommon histologic features, associated features and microscopic grading criteria if applicable. Include classification systems here or under clinical features.

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    Microscopic (histologic) images
    The author must take and submit high quality representative micro images. Include low and high power H&E images and relevant immunostains and special stains. For each image, submit both a caption and a figure legend in the manuscript word document. Do not include your name, twitter handle, institution or logo on the image. The caption will appear below the thumbnail of the image and should be 1 - 4 words describing the image findings, such as "cytologic atypia", "chronic inflammation", "epithelioid cells", "chromogranin" or "AE1 / AE3". Do not use captions such as "Case 1", "Various images", "H&E", "100x" or the diagnosis. The figure legend will appear when the image is open and must contain all relevant information including site, procedure, diagnosis, key histologic findings and stain if other than H&E. Do not use figure legends such as "Case 1" or "Representative images". Please visit Dr. Pritt's blog as a source for micro images: Creepy Dreadful Wonderful Parasites.


    Cytology description
    Cytologic features and limitations.

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    Cytology images
    Cytology images, if clinically appropriate. For images you submit, provide a brief 1 - 4 word caption to appear below the thumbnail of the image and a longer figure legend to appear when the image is opened. If you do not have your own images, refer to the Case reports section for how to provide links to journal images, and provide links with a brief 1 - 4 word caption. Include preparation, i.e. Pap, Diff-Quik, cell block, H&E touch, H&E smear. Contact us if you need help obtaining images.


    Peripheral smear description
    Description of blood smear.

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    Peripheral smear images
    Peripheral smear images with caption and figure legend for each image.


    Positive stains
    Provide a list of the names of relevant IHC and special stains that are positive at least 50% of the time. Begin each bullet with the name(s) of the stain(s). List those most commonly used first. If not uniformly positive, provide percentage of cases. List staining patterns if uncommon.

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    Molecular / cytogenetics description
    Description of DNA / RNA findings based on testing via sequencing, PCR, FISH, CISH, ISH, cytogenetics, etc.

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    Molecular / cytogenetics images
    Images of FISH, CISH, ISH, electropherogram, PCR gels, karyograms, etc. For images you submit, provide a brief 1 - 4 word caption to appear below the thumbnail of the image and a longer figure legend to appear when the image is opened. If you do not have your own images, refer to the Case reports section for how to provide links to journal images, and provide links with a brief 1 - 4 word caption.


    Videos
    Links to YouTube or other sites. Provide caption for each video.


    Differential diagnosis
    List names of entities in order from most to least important. Use short, concise bullets to include the most important differentiating features that are present or absent in the differential diagnosis entity, not the topic diagnosis. Do not describe features found in the topic diagnosis. We will link to the entity on our site.

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    Additional references
    General references for this topic not included above.

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    Board Review Question(s)
    Prepare 2 board review style questions that highlight important content from this topic. If the topic describes a very rare entity, 1 question testing basic information is sufficient. If the topic describes a very common entity, 3 questions testing basic information are suggested. These are not actual questions from the Pathology boards but review questions written in a similar format. The questions should test basic, essential diagnostic concepts that all pathologists should know rather than minor details. The topic needs to contain all information relevant to correct and incorrect answers. The first question must contain an image of the entity followed by a multiple choice question, such as "Which of the following is true about XXX tumor/disease?" The image can be reused from the topic. Do not use the format "Which of the following is false?" Questions should have only one answer. Do not use responses "all of the above", "none of the above", "A and C", etc. This question will be part of our Board Review page so the reader will not know the topic with which it is associated. Therefore you must make the organ clear in the question and the diagnosis clear in the answer. The second question may have an image associated with it but an image is not required. Click here for examples.


    Board Review Answer(s)
    Answers to the Question(s) above, sorted alphabetically by the first letter in the answer.