Mycobacterium tuberculosis Beijing genotype strains associated with febrile response to treatment.

DNA fingerprinting has demonstrated predominance of the Beijing genotype among Mycobacterium tuberculosis strains isolated in Southeast Asia. We prospectively examined the occurrence of Beijing genotype strains in tuberculosis patients in Indonesia. Early in treatment, patients infected with Beijing genotype strains more often had fever unrelated to disease severity, toxicity, or drug resistance, indicating that Beijing genotype strains may have specific pathogenic properties

Mycobacterium canettii, the smooth variant of M. tuberculosis, isolated from a Swiss patient exposed in Africa.

An exceptionally smooth and glossy morphotype of Mycobacterium tuberculosis complex was isolated from a 56-year-old Swiss patient with mesenteric tuberculosis. Direct 16S rRNA sequence analysis of the hypervariable signature gene regions revealed a 100% homology to the specific M. tuberculosis complex sequence. Spoligotyping and restriction fragment length polymorphism analyses using the insertion sequences IS6110 and IS1081 and the polymorphic GC-rich sequence as additional genetic markers identified the isolate as the novel taxon M. canettii. Like a Somali child with a similar case, this patient probably contracted the infection in Africa, which raises questions about the geographic distribution of M. canettii

Tuberculose in Nederland 2012

Op de gedrukte exemplaren van het rapport is het nummer 15000204. Het rapportnummer heeft een 0 te weinig; na versturing van de rapporten is dit pas opgemerktIn 2012 werden 958 patiënten met tuberculose gemeld aan het Nederlands Tuberculose Register (NTR). Dit komt overeen met een incidentie van tuberculose van 5,7 per 100.000 inwoners. Ten opzichte van 2011 en 2010 is de incidentie met respectievelijk vier procent en tien procent afgenomen. Sinds 2002 is het aantal tbc-patiënten in Nederland met 32% gedaald. In 2012 werd bij 53 procent van de gemelde patiënten longtuberculose geconstateerd. Het aantal patiënten met longtuberculose (pulmonale tbc) daalt sneller dan het aantal met extrapulmonale tbc (tuberculose buiten de longen). Het percentage extrapulmonale gevallen was het hoogste onder tbc-patiënten die in het buitenland zijn geboren. De meest voorkomende vorm van extrapulmonale tuberculose was tuberculose van de perifere lymfklieren. Achttien procent (177) van de tbc-patiënten in 2012 had sputumpositieve longtuberculose, de meest besmettelijke vorm van tuberculose. De incidentie van sputumpositieve longtuberculose in 2012 was 1,1 per 100.000 inwoners. Tuberculose komt in Nederland vaker voor bij personen geboren in het buitenland (eerstegeneratieallochtonen) en tweedegeneratieallochtonen. Bijna drie kwart van het aantal tbc-patiënten in 2012 was geboren in het buitenland (73%). Van de groep eerstegeneratieallochtonen met tuberculose in Nederland was de groep Somaliërs net als voorgaande jaren het grootste (170). Het percentage tbc-patiënten afkomstig uit Somalië was daarmee even groot als het percentage autochtone Nederlanders met tuberculose (18 procent), maar de incidentie onder Somaliërs in Nederland is bijna 500 maal hoger dan onder autochtone Nederlanders (respectievelijk 1,3 en 691 per 100.000 inwoners). Multiresistente tuberculose Het aantal patiënten met multiresistente tuberculose (MDR-tbc) in Nederland schommelt de laatste vijf jaar tussen tien en twintig patiënten; dat is 1-2% van het totaal aantal patiënten. In 2012 werden elf patiënten met multiresistente tuberculose gediagnosticeerd. Eén van de elf patiënten met mulitresistente tuberculose was afkomstig uit Nederland, de tien andere patiënten uit het buitenland. Resultaat van de behandeling Van alle in 2011 geregistreerde tbc-patiënten voltooide 87% de tbc-behandeling met succes. Bij nieuwe patiënten met longtuberculose was dit percentage iets lager (85%). Patiënten met multiresistente tuberculose voltooiden minder vaak de behandeling. Van de elf MDR-tbc-patiënten gediagnosticeerd in 2010 voltooiden zeven (64%) de behandeling met succes, één patiënt (9%) brak de behandeling voortijdig af, één patiënt zette de behandeling in het buitenland voort, één patiënt is overleden aan een andere oorzaak dan tuberculose en van één patiënt is het behandelresultaat (nog) niet bekend. Sterfte aan tuberculose Van de tbc-patiënten geregistreerd in het NTR in 2011 en 2012 overleden respectievelijk achttien (1,8%) en zes personen (0,6%) aan tuberculose. Patiënten met ernstige comorbiditeit hebben grotere kans op sterfte aan tuberculose. In 2012 overleed één persoon met diabetes, twee personen met een maligniteit en één persoon met nierinsufficiëntie aan tuberculose. Latente tbc-infectie (LTBI) In 2012 zijn 1.293 nieuwe gevallen van LTBI geregistreerd. Bij 855 personen werd de diagnose bij bron- en contactonderzoek vastgesteld. In 2011 startten in totaal 1.027 van de 1.297 personen (79%) een preventieve behandeling. Van hen voltooide 84% de LTBI-behandeling met succes. Delay Op grond van de gegevens in het NTR is de gemiddelde duur van het diagnostisch delay in de periode 2005-2012 niet toegenomen, hoewel bij illegalen, dak- en thuislozen, en drugs- en alcoholverslaafden wel aanwijzingen zijn voor een langer patient delay. Bij ruim een kwart van de patiënten die passief worden gevonden is wel sprake van een 'te lang' of 'ongunstig delay'. Voor doctor delay geldt hetzelfde: er is bij ruim een kwart van de patiënten die passief worden gevonden sprake van een 'te lang' of 'ongunstig delay'. Case finding In totaal 15% van alle tbc-patiënten werd in 2012 gevonden door actieve opsporing door de afdeling tbc-bestrijding van de GGD. Het percentage tbc-patiënten dat gevonden wordt door screening van risicogroepen zoals nieuwe immigranten, asielzoekers, drugsverslaafden en dak- en thuislozen neemt al langere tijd af. In de jaren 1993-1998 werd 14% van de tbc-patiënten gevonden door screening, maar in 2012 was dit nog maar 8%. Het percentage patiënten gevonden via bron- en contactonderzoek was in 2012 hetzelfde als in voorgaande jaren (7%). Tbc-patiënten met verminderde weerstand Het percentage tbc-patiënten met een co-infectie met hiv was 3% in 2012. Het percentage tbc-patiënten die op co-infectie met hiv werden getest nam toe van 28% in 2008 naar 49% in 2011, maar is in 2012gestagneerd (47%). Van patiënten uit risicogebieden zoals sub-Sahara Afrika was in 59% van de gevallen de hiv-status bekend. Het aantal tbc-patiënten die behandeld worden met TNF-alfaremmers neemt toe. In 2012 betrof het achttien (1,9%) patiënten. Transmissie en clustersurveillance Van de patiënten met kweekpositieve tuberculose clusterde de helft met een voorgaande patiënt. Bij een derde van de clusterende patiënten was sprake van recente clustering, een mogelijk gevolg van recente transmissie in Nederland. In 2012 vertoonden vier van de clusters een groei van meer dan vijf patiënten. De laatste jaren zijn er minder snelgroeiende clusters, een teken dat transmissie van M. tuberculosis in Nederland afneemt of dat de bestrijdingsmaatregelen effectief zijn.In 2012 958 cases of tuberculosis (TB) were reported to the Netherlands Tuberculosis Register (NTR). The incidence rate was 5.7 per 100,000 population. Since 2002 the number of TB patients in the Netherlands declined with 32%. In 2012 53% of the notified cases was diagnosed with pulmonary tuberculosis. Over the years the number of patients with extrapulmonary TB declined less than the number with pulmonary TB. The percentage extrapulmonary cases is highest among foreign-born TB patients. Tuberculosis of the extra thoracic lymph nodes is the most common site of disease in extrapulmonary cases. 18% (177) of all TB cases in 2012 was sputum-smear positive. The incidence rate of smear-positive pulmonary TB was 1.1 per 100,000 population. The majority of TB patients in the Netherlands was foreign-born (73%). As in previous years the largest population group with TB in 2012 was Somalian (170). The percentage of TB patients born in Somalia is in 2012 the same as the percentage native Dutch TB patients (18%). The incidence rate among people coming from Somalia is almost 500 times higher than the incidence rate of the native Dutch population (respectively 691 and 1.3 per 100,000 population). Multidrug-resistant tuberculosis In the last five years the number of patients with multidrug-resistant tuberculosis (MDR-TB) in the Netherlands varies between ten and twenty patients, 1-2% of the total number of TB patients. In 2012 eleven patients with MDR-TB were registered; ten were foreign-born. Treatment Outcome In 2011 87% of all TB patients completed treatment successfully. Of new cases with pulmonary TB 85% completed treatment successfully. Patients with MDR-TB completed treatment less often. Seven (64%) out of eleven MDR-TB-patients diagnosed in 2010 completed treatment successfully, one patient (9%) interrupted treatment, one patient continued treatment abroad, one patient died due to another cause than tuberculosis and of one patient treatment outcome is (still) unknown. TB-patients with co-morbidity or immune disorders The percentage of hiv-infected TB patients was 3% in 2012. The percentage TB patients tested for hiv increased from 28% in 2008 to 49% in 2011, but did not increase in 2012 (47%). Hiv-status was known in 59% of TB patients coming from sub-Saharan Africa, a hiv endemic area. The number of TB patients associated with TNF-alfa inhibitors treatment increases. In 2012 18 patients were registered (1.9%). Tuberculosis deaths Respectively 18 (1.8%) and 6 (0.6%) TB patients in 2011 and 2012 died due to tuberculosis. TB patients with serious co-morbidity have a higher risk of dying. In 2012 one person with diabetes, two persons with cancer and one person with renal insufficiency died due to tuberculosis. Respectively 20 (2.0%) and 20 (2.1%) TB patients in 2011 and 2012 died of other causes. Latent Tuberculosis Infection (LTBI) In 2012 1,293 new cases of LTBI were reported. 855 of these cases were detected through contact investigation. In 2011 1,027 of 1,297 cases (79%) started preventive treatment. Eighty-four percent of all persons with LTBI who received preventive treatment completed treatment successfully. Delay The mean length of the diagnostic delay over the years 2005-2012 did not increase, although undocumented TB patients, homeless TB patients, and drug and alcohol addicts with TB are associated with a longer patient delay. In more than a quarter of the passively detected cases a too long or 'unfavorable' patient delay was registered. This also applies to doctor delay; in more than a quarter of the passively detected cases a too long or 'unfavorable' delay was registered. Case finding Fifteen percent of all TB patients was detected by active case finding by the TB department of the Municipal Health Services. The percentage TB patients detected through screening of risk groups such as new immigrants, asylum seekers, drug addicts and homeless people has been decreasing for some time; in the years 1993-1998 14% of all TB patients was detected through screening, in 2012 only 8%. The number and percentage of cases found through contact investigation stayed more or less the same (7%). Transmission and cluster surveillance In 2012 50% of the cases with a positive culture belonged to a cluster. In one third of these cases recent clustering was registered, possibly as a result of recent transmission in the Netherlands. In 2012 four existing clusters showed growth of more than five patients. In the last few years there were no large outbreaks registered in the Netherlands

Mycobacterium tuberculosis Beijing Genotype and Risk for Treatment Failure and Relapse, Vietnam

Among 2,901 new smear-positive tuberculosis cases in Ho Chi Minh City, Vietnam, 40 cases of treatment failure and 39 relapsing cases were diagnosed. All initial and follow-up Mycobacterium tuberculosis isolates of these case-patients had (nearly) identical restriction fragment length polymorphism patterns, and the Beijing genotype was a significant risk factor for treatment failure and relapse (odds ratio 2.8, 95% confidence interval 1.5 to 5.2)

Whole genome sequencing as the ultimate tool to diagnose tuberculosis

AbstractIn the past two decades, DNA techniques have been increasingly used in the laboratory diagnosis of tuberculosis (TB). The (sub) species of the Mycobacterium tuberculosis complex are usually identified using reverse line blot techniques. The resistance is predicted by the detection of mutations in genes associated with resistance. Nevertheless, all cases are still subjected to cumbersome phenotypic resistance testing. The production of a strain-characteristic DNA fingerprint, to investigate the epidemiology of TB, is done by the 24-locus variable number tandem repeat (VNTR) typing. However, most of the molecular techniques in the diagnosis of TB can eventually be replaced by whole genome sequencing (WGS). Many international TB reference laboratories are currently working on the introduction of WGS; however, standardization in the international context is lacking. The European Centre for Infectious Disease Prevention and Control in Stockholm, Sweden organizes a yearly round of quality control on VNTR typing and in 2015 for the first time also WGS. In this first proficiency study, only three out of eight international TB laboratories produced WGS results in line with those of the reference laboratory. The whole process of DNA isolation, purification, quantification, sequencing, and analysis/interpretation of data is still under development. In this presentation, many aspects will be covered that influence the quality and interpretation of WGS results. The turn-around-time, analysis, and utility of WGS will be discussed. Moreover, the experiences in the use of WGS in the molecular epidemiology of TB in The Netherlands are detailed. It can be concluded that many difficulties still have to be conquered. The state of the art is that bacteria still have to be cultured to have sufficient quality and quantity of DNA for succesful WGS. The quality of sequencing has improved significantly over the past 7years, and the detection of mutations has, therefore, become more reliable. The resistance mutations detected in WGS are in line with the ones visualized in reverse line blot techniques. The turnover in the genome of M. tuberculosis is very low, ∼0.3–0.5 mutations per genome per year. However, there is a wide variation in the occurrence of mutations per strain and genotype. Still, the resolution of WGS in epidemiological typing is higher than that in VNTR typing; previously suggested epidemiological links by VNTR typing are sometimes refuted on the basis of WGS. Although WGS offers the highest resolution in typing, in a country like The Netherlands, there are many strains with a limited genetic distance up to 100 mutations, without an apparent epidemiological link between the respective cases. These lookalikes are presumably even more prevalent in settings where predominant genotypes of M. tuberculosis are circulating. In summary, WGS seems to yield a more reliable prediction of resistance by the (lack of) detection of mutations in all 25 genes ever associated with resistance. This may within a short while prevent the need for many phenotypic resistance tests. Although more robust algorithms need to be developed, the recognition of the (sub) species in the M. tuberculosis complex seems possible. The first detailed studies on the population structure of M. tuberculosis strains in The Netherlands provide more resolution in typing but also an interesting observation that a part of the strains are genetically so conserved that they are separated by less than 100 mutations. This demands a more extended and accurate validation and understanding of the utility of WGS in the epidemiology of TB

Ziehl-Neelsen microscopy in the diagnosis of tuberculosis in settings of high human immunodeficiency virus prevalence

Objective: To determine the accuracy of Ziehl-Neelsen microscopy in the diagnosis of TB in setings of high HIV prevalence.Design: Cross-sectional descriptive study.Setting: Hospitals serving areas of high human immunodeficiency virus prevalence in western Kenya. The study was conducted between September 2007 and September 2009.Results: In total, 341/872 (39.1%) of the TB suspects were positive in ZN, 53.1% (181/341) of them culture positive. Only 3.8% (20/531) of the ZN smear negatives were culture positive. Of the 695 suspects evaluated for both Mycobacterium and HIV infection, 255 (36.7%) were ZN smear positive, 42.7% of them HIV positive. Out of the 440 ZN smear negatives, 37% were HIV positive. Similarly, 168 suspects were culture positive, 46.4% of them HIV positive. The HIV infection did not significantly reduce ZN smear positivity rate (P = 0.42) and culture sensitivity (P = 0.09). The ZN sensitivity and specificity were 88.1% and 79.7%, respectively. The predictive values were 58.0 (PPV), and 95.5% (NPV), respectively. However, the area under the ROC curve was 0.84, with 95% CI between 0.80-0.87 and P< 0.001). The ZN smear microscopy had a lesser ability to distinguish between TB and non-TB cases compared to culture.Conclusion: ZN microscopy causes a significant over-diagnosis of TB in settings of high HIV/AIDS prevalence. There is need for further studies on this subject taking into consideration the various confounding factors