Transmission of tuberculosis between foreign-born and Finnish-born populations in Finland, 2014–2017

We describe the epidemiology of tuberculosis (TB) and characterized Mycobacterium tuberculosis (M. tuberculosis) isolates to evaluate transmission between foreign-born and Finnish-born populations. Data on TB cases were obtained from the National Infectious Disease Register and denominator data on legal residents and their country of birth from the Population Information System. M. tuberculosis isolates were genotyped by spoligotyping and Mycobacterial Interspersed Repetitive Unit Variable Number Tandem Repeat (MIRU-VNTR). We characterized clusters by age, sex, origin and region of living which included both foreign-born cases and those born in Finland. During 2014–2017, 1015 TB cases were notified; 814 were confirmed by culture. The proportion of foreign-born cases increased from 33.3% to 39.0%. Foreign-born TB cases were younger (median age, 28 vs. 75 years), and had extrapulmonary TB or multidrug-TB more often than Finnish-born cases (P<0.01 for all comparisons). Foreign-born cases were born in 60 different countries; most commonly in Somalia (25.5%). Altogether 795 isolates were genotyped; 31.2% belonged to 80 different clusters (range, 2–13 cases/cluster). Fourteen (17.5%) clusters included isolates from both Finnish-born and foreign-born cases. An epidemiological link between cases was identified by (epidemiological) background information in two clusters. Although the proportion of foreign-born TB cases was considerable, our data suggests that transmission of TB between foreign and Finnish born population is uncommon.

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Standard Genotyping Overestimates Transmission of Mycobacterium tuberculosis among Immigrants in a Low-Incidence Country

Journal of Clinical Microbiology ◽

10.1128/jcm.00126-16 ◽

2016 ◽

Vol 54 (7) ◽

pp. 1862-1870 ◽

Cited By ~ 58

Author(s):

David Stucki ◽

Marie Ballif ◽

Matthias Egger ◽

Hansjakob Furrer ◽

Ekkehardt Altpeter ◽

...

Keyword(s):

Mycobacterium Tuberculosis ◽

Variable Number Tandem Repeat ◽

Variable Number ◽

Nucleotide Polymorphisms ◽

Foreign Born ◽

Single Nucleotide ◽

Content Type ◽

Weak Evidence ◽

High Incidence ◽

Low Incidence

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 520Mycobacterium tuberculosisisolates 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.

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The Prevalence of Virulence Determinants and Antibiotic Resistance Patterns in Methicillin—Resistant Staphylococcus aureus in a Nursing Home in Poland

Pathogens ◽

10.3390/pathogens10040427 ◽

2021 ◽

Vol 10 (4) ◽

pp. 427

Author(s):

Martyna Kasela ◽

Agnieszka Grzegorczyk ◽

Bożena Nowakowicz-Dębek ◽

Anna Malm

Keyword(s):

Staphylococcus Aureus ◽

Methicillin Resistant Staphylococcus Aureus ◽

Variable Number Tandem Repeat ◽

Multidrug Resistant ◽

Variable Number ◽

Pulse Field ◽

Virulence Determinants ◽

Gene Encoding ◽

Methicillin Resistant ◽

Pulse Field Gel Electrophoresis

Nursing homes (NH) contribute to the regional spread of methicillin-resistant Staphylococcus aureus (MRSA). Moreover, residents are vulnerable to the colonization and subsequent infection of MRSA etiology. We aimed at investigating the molecular and phenotypic characteristics of 21 MRSA collected from the residents and personnel in an NH (Lublin, Poland) during 2018. All MRSA were screened for 20 genes encoding virulence determinants (sea-see, eta, etb, tst, lukS-F-PV, eno, cna, ebpS, fib, bbp, fnbA, fnbB, icaADBC) and for resistance to 18 antimicrobials. To establish the relatedness and clonal complexes of MRSA in NH we applied multiple-locus variable-number tandem-repeat fingerprinting (MLVF), pulse field gel electrophoresis (PFGE), multilocus sequence typing (MLST) and staphylococcal cassette chromosome mec (SCCmec) typing. We identified four sequence types (ST) among two clonal complexes (CC): ST (CC22) known as EMRSA-15 as well as three novel STs—ST6295 (CC8), ST6293 (CC8) and ST6294. All tested MRSA were negative for sec, eta, etb, lukS-F-PV, bbp and ebpS genes. The most prevalent gene encoding toxin was sed (52.4%; n = 11/21), and adhesins were eno and fnbA (100%). Only 9.5% (n = 2/21) of MRSA were classified as multidrug-resistant. The emergence of novel MRSA with a unique virulence and the presence of epidemic clone EMRSA-15 creates challenges for controlling the spread of MRSA in NH.

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Profiling variable-number tandem repeat variation across populations using repeat-pangenome graphs

Nature Communications ◽

10.1038/s41467-021-24378-0 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Tsung-Yu Lu ◽

Katherine M. Munson ◽

Alexandra P. Lewis ◽

Qihui Zhu ◽

Luke J. Tallon ◽

...

Keyword(s):

Tandem Repeats ◽

Traditional Approach ◽

Variable Number Tandem Repeat ◽

Variable Number ◽

Population Diversity ◽

Protein Coding ◽

Short Reads ◽

Repeat Structure ◽

Continental Population ◽

Develop Software

AbstractVariable number tandem repeats (VNTRs) are composed of consecutive repetitive DNA with hypervariable repeat count and composition. They include protein coding sequences and associations with clinical disorders. It has been difficult to incorporate VNTR analysis in disease studies that use short-read sequencing because the traditional approach of mapping to the human reference is less effective for repetitive and divergent sequences. In this work, we solve VNTR mapping for short reads with a repeat-pangenome graph (RPGG), a data structure that encodes both the population diversity and repeat structure of VNTR loci from multiple haplotype-resolved assemblies. We develop software to build a RPGG, and use the RPGG to estimate VNTR composition with short reads. We use this to discover VNTRs with length stratified by continental population, and expression quantitative trait loci, indicating that RPGG analysis of VNTRs will be critical for future studies of diversity and disease.

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Reply to "Evaluation of Mycobacterial Interspersed Repetitive-Unit-Variable-Number Tandem-Repeat Genotyping as Performed in Laboratories in Canada, France, and the United States"

Journal of Clinical Microbiology ◽

10.1128/jcm.00233-12 ◽

2012 ◽

Vol 50 (5) ◽

pp. 1832-1832

Author(s):

J. L. de Beer ◽

D. van Soolingen

Keyword(s):

United States ◽

Tandem Repeat ◽

Variable Number Tandem Repeat ◽

The United States ◽

Variable Number

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Comparison of Multilocus Variable-Number Tandem-Repeat Analysis and Whole-Genome Sequencing for Investigation of Clostridium difficile Transmission

Journal of Clinical Microbiology ◽

10.1128/jcm.01095-13 ◽

2013 ◽

Vol 51 (12) ◽

pp. 4141-4149 ◽

Cited By ~ 48

Author(s):

D. W. Eyre ◽

W. N. Fawley ◽

E. L. Best ◽

D. Griffiths ◽

N. E. Stoesser ◽

...

Keyword(s):

Clostridium Difficile ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Tandem Repeat ◽

Variable Number Tandem Repeat ◽

Variable Number ◽

Whole Genome ◽

Repeat Analysis

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Potentially Human-Pathogenic Escherichia coli O26 in Norwegian Sheep Flocks

Applied and Environmental Microbiology ◽

10.1128/aem.00189-11 ◽

2011 ◽

Vol 77 (14) ◽

pp. 4949-4958 ◽

Cited By ~ 21

Author(s):

C. Sekse ◽

M. Sunde ◽

B.-A. Lindstedt ◽

P. Hopp ◽

T. Bruheim ◽

...

Keyword(s):

Escherichia Coli ◽

Variable Number Tandem Repeat ◽

Variable Number ◽

Human Pathogens ◽

Content Type ◽

Representative Sampling ◽

E Coli ◽

Pathogenic Escherichia Coli ◽

Close Relationship ◽

Large Survey

ABSTRACTA national survey ofEscherichia coliO26 in Norwegian sheep flocks was conducted, using fecal samples to determine the prevalence. In total, 491 flocks were tested, andE. coliO26 was detected in 17.9% of the flocks. One hundred forty-twoE. coliO26 isolates were examined for flagellar antigens (H typing) and four virulence genes, includingstxandeae, to identify possible Shiga toxin-producingE. coli(STEC) and enteropathogenicE. coli(EPEC). Most isolates (129 out of 142) were identified asE. coliO26:H11. They possessedeaeand may have potential as human pathogens, although only a small fraction were identified as STEC O26:H11, giving a prevalence in sheep flocks of only 0.8%. Correspondingly, the sheep flock prevalence of atypical EPEC (aEPEC) O26:H11 was surprisingly high (15.9%). The genetic relationship between theE. coliO26:H11 isolates was investigated by pulsed-field gel electrophoresis (PFGE) and multilocus variable number tandem repeat analysis (MLVA), identifying 63 distinct PFGE profiles and 22 MLVA profiles. Although the MLVA protocol was less discriminatory than PFGE and a few cases of disagreement were observed, comparison by partition mapping showed an overall good accordance between the two methods. A close relationship between a few isolates of aEPEC O26:H11 and STEC O26:H11 was identified, but all theE. coliO26:H11 isolates should be considered potentially pathogenic to humans. The present study consisted of a representative sampling of sheep flocks from all parts of Norway. This is the first large survey of sheep flocks focusing onE. coliO26 in general, including results of STEC, aEPEC, and nonpathogenic isolates.

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