Tuberculosis: A Clinical Practice Guide

Laboratory Diagnosis of Tuberculosis

Author(s): Rafael Laniado-Laborín

Pp: 41-58 (18)

DOI: 10.2174/9789811488511120010009

* (Excluding Mailing and Handling)

Abstract

Although sputum microscopy remains the most widely used diagnostic method worldwide, given its low sensitivity (50-80%) and specificity (it does not distinguish M. tuberculosis from nontuberculous mycobacteria), more rapid, sensitive, and specific methods are required nowadays. Culture for mycobacteria continues to be the gold standard due to its higher sensitivity and specificity, and because it also allows the detection of strains resistant to antituberculosis drugs; however, even with liquid culture media, at least one month of processing is required to obtain results. Therefore, rapid genotyping methods (e.g., Xpert and line-probe assays known as LPAs) have replaced phenotypic methods by allowing the identification of species and the presence of mutations associated with resistance in less than 24 hours. The Xpert, an automated real-time PCR system, can identify the presence of mutations associated with rifampin resistance in less than two hours, with a sensitivity higher than 70% in patients with negative microscopy. LPAs allow species identification and the presence of mutations associated with resistance to isoniazid, rifampin, fluoroquinolones, and second-line injectables in less than 24 hours. Progressively, the complete sequencing of the Mycobacterium tuberculosis genome has been integrated into the diagnostic protocol, allowing the identification of all mutations associated with resistance for all antituberculosis drugs. Phenotypic methods (microscopy and cultures) continue to play an essential role in the follow-up of patients who are already under treatment.


Keywords: Cultures, Diagnosis, Genome sequencing, LPA, MGIT, Microscopy, Tuberculosis, Xpert.Cultures, Diagnosis, Genome sequencing, LPA, MGIT, Microscopy, Tuberculosis, Xpert.

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      • 13. app/Models/UserAccess/UserAccess.php:1266
      • 14. app/Http/Controllers/ChapterController.php:1518
      • 15. vendor/laravel/framework/src/Illuminate/Routing/Controller.php:54
      • 16. vendor/laravel/framework/src/Illuminate/Routing/ControllerDispatcher.php:43
      • 17. vendor/laravel/framework/src/Illuminate/Routing/Route.php:260
    • (select j.user_access_id,j.volume_id,j.user_id,j.from_ip,j.to_ip,j.type,j.track,"Trial Access" as access_base_text, CASE j.type WHEN 111 THEN true ELSE false END as terms_popup, "S" as content_download_type, null as restricted_user_access_key, null as restricted_user_access_type, CASE j.track WHEN 0 THEN false ELSE true END as tracksAccessByVolume,"chapter" as access_level, j.chapter_id from `user_access_chapter_trail` as `j` inner join `user_access_info` as `info` on `j`.`user_access_id` = `info`.`user_access_id` where ((j.from_ip <= 59081319 and j.to_ip >=59081319 )) and ((j.from_date <= 1740526723 and j.to_date >= 1740526723 and j.perpetual= 0) or (j.from_date is null and j.to_date is null and j.perpetual= 1)) and j.chapter_id = 14368) union (select j.user_access_id,j.volume_id,j.user_id,j.from_ip,j.to_ip,j.type,j.track,"Subscribed" as access_base_text, false as terms_popup, "S" as content_download_type, null as restricted_user_access_key, null as restricted_user_access_type, CASE j.track WHEN 0 THEN false ELSE true END as tracksAccessByVolume,"chapter" as access_level, j.chapter_id from `user_access_chapter_corporate` as `j` inner join `user_access_info` as `info` on `j`.`user_access_id` = `info`.`user_access_id` where ((j.from_ip <= 59081319 and j.to_ip >=59081319 )) and ((j.from_date <= 1740526723 and j.to_date >= 1740526723 and j.perpetual= 0) or (j.from_date is null and j.to_date is null and j.perpetual= 1)) and j.chapter_id = 14368) union (select j.user_access_id,j.volume_id,j.user_id,j.from_ip,j.to_ip,j.type,j.track,"Token Based Access" as access_base_text, false as terms_popup, "R" as content_download_type, j.uc_id as restricted_user_access_key, "v" as restricted_user_access_type, CASE j.track WHEN 0 THEN false ELSE true END as tracksAccessByVolume,"chapter" as access_level, j.chapter_id from `user_access_chapter_token` as `j` inner join `user_access_info` as `info` on `j`.`user_access_id` = `info`.`user_access_id` where ((j.from_ip <= 59081319 and j.to_ip >=59081319 )) and ((j.from_date <= 1740526723 and j.to_date >= 1740526723 and j.perpetual= 0) or (j.from_date is null and j.to_date is null and j.perpetual= 1)) and j.chapter_id = 14368)
      540μsalphaeurekaselec_live_10_06_2022UserAccess.php#1266
      Backtrace
      • 13. app/Models/UserAccess/UserAccess.php:1266
      • 14. app/Http/Controllers/ChapterController.php:1549
      • 15. vendor/laravel/framework/src/Illuminate/Routing/Controller.php:54
      • 16. vendor/laravel/framework/src/Illuminate/Routing/ControllerDispatcher.php:43
      • 17. vendor/laravel/framework/src/Illuminate/Routing/Route.php:260
    • select b.banner_link, b.banner_name, b.banner_script, b.banner_remarks, b.banner_file_name, b.banner_placement, bd.content_type, bd.content_id from `tbl_banner` as `b` inner join `tbl_banner_detail` as `bd` on `bd`.`banner_id` = `b`.`banner_id` inner join `users` as `u` on `u`.`id` = `b`.`updated_by` where `b`.`banner_ebook` = 1 and `bd`.`content_type` = 'B' and `bd`.`content_id` = 2923 and `b`.`banner_from_date` <= 1740526723 and `b`.`banner_to_date` >= 1740526723 and `b`.`banner_status` = 'A' order by `b`.`banner_id` desc
      1.07msalphaeurekaselec_live_10_06_2022Banner.php#95
      Bindings
      • 0: 1
      • 1: B
      • 2: 2923
      • 3: 1740526723
      • 4: 1740526723
      • 5: A
      Backtrace
      • 13. app/Models/Banner.php:95
      • 14. app/Http/helpers.php:404
      • 17. vendor/laravel/framework/src/Illuminate/Filesystem/Filesystem.php:124
      • 18. vendor/laravel/framework/src/Illuminate/View/Engines/PhpEngine.php:58
      • 19. vendor/laravel/framework/src/Illuminate/View/Engines/CompilerEngine.php:73
    • select count(*) as aggregate from `uc_cart_products` where cart_id='64f0eb46306a5c2bdf9116018a49c2c9'
      180μsalphaeurekaselec_live_10_06_2022Cart.php#271
      Backtrace
      • 15. app/Models/Cart.php:271
      • 16. view::layouts._header:260
      • 18. vendor/laravel/framework/src/Illuminate/Filesystem/Filesystem.php:124
      • 19. vendor/laravel/framework/src/Illuminate/View/Engines/PhpEngine.php:58
      • 20. vendor/laravel/framework/src/Illuminate/View/Engines/CompilerEngine.php:73
    App\Models\Keywords
    15Keywords.php#?
    App\Models\Chapter
    1Chapter.php#?
    App\Models\Ebook
    1Ebook.php#?
        _token
        Ml14tKUYcCTlWjsjwvCRUFR22jzmnFesSlvoxbe7
        uc_cart_id
        64f0eb46306a5c2bdf9116018a49c2c9
        _previous
        array:1 [ "url" => "https://alpha.eurekaselect.com/chapter/14368" ]
        _flash
        array:2 [ "old" => [] "new" => [] ]
        PHPDEBUGBAR_STACK_DATA
        []
        path_info
        /chapter/14368
        status_code
        200
        
        status_text
        OK
        format
        html
        content_type
        text/html; charset=UTF-8
        request_query
        []
        
        request_request
        []
        
        request_headers
        0 of 0
        array:17 [ "x-https" => array:1 [ 0 => "1" ] "host" => array:1 [ 0 => "alpha.eurekaselect.com" ] "priority" => array:1 [ 0 => "u=0, i" ] "cookie" => array:1 [ 0 => "wayfindertarget=eyJpdiI6InlNaXFhcis0cld0YW1lYjZ3cE9QNVE9PSIsInZhbHVlIjoidi9qNFc5MHlsQ2pSRmd0ZHNaUDRXOVVVWks4NU8zdFNyQWppbG9DZ3ZpQT0iLCJtYWMiOiJiMzI5NjAxNTRjMTA0NWEzZTkyNTRkMDU4ZGQ5Mzk1NmIzMDNlNzgwZjY0OTJhZGQ4NTVkZWMwODVkMWNkMThkIiwidGFnIjoiIn0%3Dwayfindertarget=eyJpdiI6InlNaXFhcis0cld0YW1lYjZ3cE9QNVE9PSIsInZhbHVlIjoidi9qNFc5MHlsQ2pSRmd0ZHNaUDRXOVVVWks4NU8zdFNyQWppbG9DZ3ZpQT0iLCJtYWMiOiJiMzI5NjAxNTRjMTA0" ] "accept-encoding" => array:1 [ 0 => "gzip, deflate, br, zstd" ] "sec-fetch-dest" => array:1 [ 0 => "document" ] "sec-fetch-user" => array:1 [ 0 => "?1" ] "sec-fetch-mode" => array:1 [ 0 => "navigate" ] "sec-fetch-site" => array:1 [ 0 => "none" ] "accept" => array:1 [ 0 => "text/html,application/xhtml+xml,application/xml;q=0.9,image/avif,image/webp,image/apng,*/*;q=0.8,application/signed-exchange;v=b3;q=0.7" ] "user-agent" => array:1 [ 0 => "Mozilla/5.0 AppleWebKit/537.36 (KHTML, like Gecko; compatible; ClaudeBot/1.0; +claudebot@anthropic.com)" ] "upgrade-insecure-requests" => array:1 [ 0 => "1" ] "sec-ch-ua-platform" => array:1 [ 0 => ""Windows"" ] "sec-ch-ua-mobile" => array:1 [ 0 => "?0" ] "sec-ch-ua" => array:1 [ 0 => ""HeadlessChrome";v="129", "Not=A?Brand";v="8", "Chromium";v="129"" ] "cache-control" => array:1 [ 0 => "no-cache" ] "pragma" => array:1 [ 0 => "no-cache" ] ]
        request_cookies
        0 of 0
        array:1 [ "wayfindertarget" => null ]
        response_headers
        0 of 0
        array:5 [ "content-type" => array:1 [ 0 => "text/html; charset=UTF-8" ] "cache-control" => array:1 [ 0 => "no-cache, private" ] "date" => array:1 [ 0 => "Tue, 25 Feb 2025 23:38:43 GMT" ] "set-cookie" => array:2 [ 0 => "XSRF-TOKEN=eyJpdiI6IlU1ZzVJSkJNTS9hMSs0OVoreVI0MEE9PSIsInZhbHVlIjoiRXJDTVNoaWxTUzNleEVGSmV4ZnNGSHVlY1pvcWdzcUpzKzhOa1RDYk9VaXMvQ0pUQVhHUURTL3Y2dG5XVG9zQktFOXpHcTJ3OTJGSWlJb2VBVzIyeUdZbDkzN2pxMis5elphK0FpNXpLNyt1UCs3WXVZTGwzRFk2NHRjaWxwVk8iLCJtYWMiOiI1OTMzMDE3NWJhZDNkY2I4YWRkMTkxNDNlMWFlZGNmN2I1ZTczOGZkZGE0NTFjMjhlNGE2MDRkNmY5ZTQzYmIzIiwidGFnIjoiIn0%3D; expires=Fri, 28 Feb 2025 11:38:43 GMT; Max-Age=216000; path=/; secure; samesite=laxXSRF-TOKEN=eyJpdiI6IlU1ZzVJSkJNTS9hMSs0OVoreVI0MEE9PSIsInZhbHVlIjoiRXJDTVNoaWxTUzNleEVGSmV4ZnNGSHVlY1pvcWdzcUpzKzhOa1RDYk9VaXMvQ0pUQVhHUURTL3Y2dG5XVG9zQktFOXpHc" 1 => "alphaeurekaselectnet_session=eyJpdiI6IlhFV0hiSVJQbXFEL2o4TDFpMWtKakE9PSIsInZhbHVlIjoiWVp5c1FvMHVmWERiNzZORFdjb3FSOGgzdUJkZ290TnhVQU9OOTBub3lsS3loRGZvVThkY01CdGF0dWN6MC9nSVZpQWhML2NULzF0RWFrVHlzZ3U3RFJianZ0b1JocVZoVWJCS3JGaVo0VDZTeWRyRG5lZnUrOWlCR1lFeTdIYWIiLCJtYWMiOiIxZTc3Yzk2NmJlZGNmOTg3ZWVhYWQ3M2Y2NzhmMGJkYzI3Y2NmZTY3Nzk0YmMwZWNjOWY0ZTM2MzdlZjYyN2MzIiwidGFnIjoiIn0%3D; path=/; secure; httponly; samesite=laxalphaeurekaselectnet_session=eyJpdiI6IlhFV0hiSVJQbXFEL2o4TDFpMWtKakE9PSIsInZhbHVlIjoiWVp5c1FvMHVmWERiNzZORFdjb3FSOGgzdUJkZ290TnhVQU9OOTBub3lsS3loRGZvVThkY01CdGF" ] "Set-Cookie" => array:2 [ 0 => "XSRF-TOKEN=eyJpdiI6IlU1ZzVJSkJNTS9hMSs0OVoreVI0MEE9PSIsInZhbHVlIjoiRXJDTVNoaWxTUzNleEVGSmV4ZnNGSHVlY1pvcWdzcUpzKzhOa1RDYk9VaXMvQ0pUQVhHUURTL3Y2dG5XVG9zQktFOXpHcTJ3OTJGSWlJb2VBVzIyeUdZbDkzN2pxMis5elphK0FpNXpLNyt1UCs3WXVZTGwzRFk2NHRjaWxwVk8iLCJtYWMiOiI1OTMzMDE3NWJhZDNkY2I4YWRkMTkxNDNlMWFlZGNmN2I1ZTczOGZkZGE0NTFjMjhlNGE2MDRkNmY5ZTQzYmIzIiwidGFnIjoiIn0%3D; expires=Fri, 28-Feb-2025 11:38:43 GMT; path=/; secureXSRF-TOKEN=eyJpdiI6IlU1ZzVJSkJNTS9hMSs0OVoreVI0MEE9PSIsInZhbHVlIjoiRXJDTVNoaWxTUzNleEVGSmV4ZnNGSHVlY1pvcWdzcUpzKzhOa1RDYk9VaXMvQ0pUQVhHUURTL3Y2dG5XVG9zQktFOXpHc" 1 => "alphaeurekaselectnet_session=eyJpdiI6IlhFV0hiSVJQbXFEL2o4TDFpMWtKakE9PSIsInZhbHVlIjoiWVp5c1FvMHVmWERiNzZORFdjb3FSOGgzdUJkZ290TnhVQU9OOTBub3lsS3loRGZvVThkY01CdGF0dWN6MC9nSVZpQWhML2NULzF0RWFrVHlzZ3U3RFJianZ0b1JocVZoVWJCS3JGaVo0VDZTeWRyRG5lZnUrOWlCR1lFeTdIYWIiLCJtYWMiOiIxZTc3Yzk2NmJlZGNmOTg3ZWVhYWQ3M2Y2NzhmMGJkYzI3Y2NmZTY3Nzk0YmMwZWNjOWY0ZTM2MzdlZjYyN2MzIiwidGFnIjoiIn0%3D; path=/; secure; httponlyalphaeurekaselectnet_session=eyJpdiI6IlhFV0hiSVJQbXFEL2o4TDFpMWtKakE9PSIsInZhbHVlIjoiWVp5c1FvMHVmWERiNzZORFdjb3FSOGgzdUJkZ290TnhVQU9OOTBub3lsS3loRGZvVThkY01CdGF" ] ]
        session_attributes
        0 of 0
        array:5 [ "_token" => "Ml14tKUYcCTlWjsjwvCRUFR22jzmnFesSlvoxbe7" "uc_cart_id" => "64f0eb46306a5c2bdf9116018a49c2c9" "_previous" => array:1 [ "url" => "https://alpha.eurekaselect.com/chapter/14368" ] "_flash" => array:2 [ "old" => [] "new" => [] ] "PHPDEBUGBAR_STACK_DATA" => [] ]
        ClearShow all
        Date ↕MethodURLData
        #12025-02-25 23:38:43GET/chapter/143681121917