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首页> 外文期刊>Journal of Clinical Microbiology >Standard Genotyping Overestimates Transmission of Mycobacterium tuberculosis among Immigrants in a Low-Incidence Country
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Standard Genotyping Overestimates Transmission of Mycobacterium tuberculosis among Immigrants in a Low-Incidence Country

机译：标准基因分型法高估了低发病率国家移民中结核分枝杆菌的传播

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Immigrants from regions with a high incidence of tuberculosis (TB) are a risk group for TB in low-incidence countries such as Switzerland. In a previous analysis of a nationwide collection of 520 Mycobacterium tuberculosis isolates from 2000 to 2008, we identified 35 clusters comprising 90 patients based on standard genotyping (24-locus mycobacterial interspersed repetitive-unit–variable-number tandem-repeat [MIRU-VNTR] typing and spoligotyping). Here, we used whole-genome sequencing (WGS) to revisit these transmission clusters. Genome-based transmission clusters were defined as isolate pairs separated by ≤12 single nucleotide polymorphisms (SNPs). WGS confirmed 17/35 (49%) MIRU-VNTR typing clusters; the other 18 clusters contained pairs separated by >12 SNPs. Most transmission clusters (3/4) of Swiss-born patients were confirmed by WGS, as opposed to 25% (4/16) of the clusters involving only foreign-born patients. The overall clustering proportion was 17% (90 patients; 95% confidence interval [CI], 14 to 21%) by standard genotyping but only 8% (43 patients; 95% CI, 6 to 11%) by WGS. The clustering proportion was 17% (67/401; 95% CI, 13 to 21%) by standard genotyping and 7% (26/401; 95% CI, 4 to 9%) by WGS among foreign-born patients and 19% (23/119; 95% CI, 13 to 28%) and 14% (17/119; 95% CI, 9 to 22%), respectively, among Swiss-born patients. Using weighted logistic regression, we found weak evidence of an association between birth origin and transmission (adjusted odds ratio of 2.2 and 95% CI of 0.9 to 5.5 comparing Swiss-born patients to others). In conclusion, standard genotyping overestimated recent TB transmission in Switzerland compared to WGS, particularly among immigrants from regions with a high TB incidence, where genetically closely related strains often predominate. We recommend the use of WGS to identify transmission clusters in settings with a low incidence of TB.
机译：在瑞士等低发病率国家，结核病高发地区的移民是结核病的高危人群。在先前对2000年至2008年全国520株结核分枝杆菌分离物的分析中，我们基于标准的基因分型（24位分枝杆菌散布的重复单位-可变数目串联重复[MIRU-VNTR]打字和填字游戏）。在这里，我们使用全基因组测序（WGS）重新访问了这些传播簇。基于基因组的传播簇定义为被≤12个单核苷酸多态性（SNP）隔开的分离对。 WGS确认了17/35（49％）MIRU-VNTR分型簇;其他18个簇包含由> 12个SNP隔开的对。 WGS证实了大多数瑞士出生患者的传播簇（3/4），而仅涉及外国出生患者的簇中有25％（4/16）被证实。通过标准基因分型，总体聚类比例为17％（90名患者; 95％置信区间[CI]，14至21％），而WGS仅为8％（43名患者; 95％CI，6至11％）。根据标准基因分型，在国外出生的患者中，聚集率分别为17％（67/401; 95％CI，13％至21％）和WGS的7％（26/401; 95％CI，4％至9％），19％在瑞士出生的患者中分别为（23/119; 95％CI，13％至28％）和14％（17/119; 95％CI，9％至22％）。使用加权对数回归，我们发现出生起源与传播之间存在弱关联的证据（与瑞士出生的患者相比，调整后的优势比为2.2，95％CI为0.9-5.5）。总之，与WGS相比，瑞士的标准基因分型法高估了最近的结核病传播，特别是在结核病高发地区的移民中，遗传密切相关的菌株通常占主导地位。我们建议使用WGS来识别结核病发病率较低的环境中的传播群。

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