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The Evolution of Genotyping Strategies To Detect, Analyze, and Control Transmission of Tuberculosis

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  • Authors: Darío García De Viedma1,2,3, Laura Pérez-Lago4,5
  • Editors: Fernando Baquero6, Emilio Bouza7, J.A. Gutiérrez-Fuentes8, Teresa M. Coque9
  • VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: Department of Microbiology and Infectious Diseases, Gregorio Marañón General University Hospital, Madrid, Spain; 2: Instituto Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain; 3: CIBER Enfermedades respiratorias CIBERES, Spain; 4: Department of Microbiology and Infectious Diseases, Gregorio Marañón General University Hospital, Madrid, Spain; 5: Instituto Investigación Sanitaria Gregorio Marañón (IiSGM), Madrid, Spain; 6: Hospital Ramón y Cajal (IRYCIS), Madrid, Spain; 7: Hospital Ramón y Cajal (IRYCIS), Madrid, Spain; 8: Complutensis University, Madrid, Spain; 9: Hospital Ramón y Cajal (IRYCIS), Madrid, Spain
  • Source: microbiolspec October 2018 vol. 6 no. 5 doi:10.1128/microbiolspec.MTBP-0002-2016
  • Received 10 July 2016 Accepted 06 March 2018 Published 19 October 2018
  • Darío García de Viedma, [email protected]
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  • Abstract:

    The introduction of genotypic tools to analyze isolates has transformed our knowledge of the transmission dynamics of this pathogen. We discuss the development of the laboratory methods that have been applied in recent years to study the epidemiology of . This review integrates two approaches: on the one hand, it considers how genotyping techniques have evolved over the years; and on the other, it looks at how the way we think these techniques should be applied has changed. We begin by examining the application of fingerprinting tools to suspected outbreaks only, before moving on to universal genotyping schemes, and finally we describe the latest real-time strategies used in molecular epidemiology. We also analyze refined approaches to obtaining epidemiological data from patients and to increasing the discriminatory power of genotyping by techniques based on genomic characterization. Finally, we review the development of integrative solutions to reconcile the speed of PCR-based methods with the high discriminatory power of whole-genome sequencing in easily implemented formats adapted to low-resource settings. Our analysis of future considerations highlights the need to bring together the three key elements of high-quality surveillance of transmission in tuberculosis, namely, speed, precision, and ease of implementation.

  • Citation: García De Viedma D, Pérez-Lago L. 2018. The Evolution of Genotyping Strategies To Detect, Analyze, and Control Transmission of Tuberculosis. Microbiol Spectrum 6(5):MTBP-0002-2016. doi:10.1128/microbiolspec.MTBP-0002-2016.

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/content/journal/microbiolspec/10.1128/microbiolspec.MTBP-0002-2016
2018-10-19
2019-10-17

Abstract:

The introduction of genotypic tools to analyze isolates has transformed our knowledge of the transmission dynamics of this pathogen. We discuss the development of the laboratory methods that have been applied in recent years to study the epidemiology of . This review integrates two approaches: on the one hand, it considers how genotyping techniques have evolved over the years; and on the other, it looks at how the way we think these techniques should be applied has changed. We begin by examining the application of fingerprinting tools to suspected outbreaks only, before moving on to universal genotyping schemes, and finally we describe the latest real-time strategies used in molecular epidemiology. We also analyze refined approaches to obtaining epidemiological data from patients and to increasing the discriminatory power of genotyping by techniques based on genomic characterization. Finally, we review the development of integrative solutions to reconcile the speed of PCR-based methods with the high discriminatory power of whole-genome sequencing in easily implemented formats adapted to low-resource settings. Our analysis of future considerations highlights the need to bring together the three key elements of high-quality surveillance of transmission in tuberculosis, namely, speed, precision, and ease of implementation.

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Figures

Image of FIGURE 1
FIGURE 1

Schematic representation of the chromosome of a hypothetical complex isolate with marked repetitive elements as targets for different typing methods. The principle of those methods is pictorially outlined. (1) In IS-RFLP typing, mycobacterial DNA is cleaved with the restriction endonuclease PvuII, and the resulting fragments are separated electrophoretically on an agarose gel, transferred onto a nylon membrane by Southern blotting, and hybridized to a probe complementary to the 3′ end of the IS (probe target), yielding a characteristic banding pattern in which every band represents a single IS element. (2) Spoligotyping relies upon PCR amplification of a single DR locus that harbors 36-bp DRs interspersed with unique 34- to 41-bp spacer sequences. The PCR products (red horizontal lines) are hybridized to a membrane containing 43 oligonucleotides corresponding to the spacers from H37Rv and BCG. The presence or absence of each of those 43 spacers in the DR region of the analyzed isolate will be represented as the pattern of positive or negative hybridization signals. (3) The VNTR loci or MIRUs are PCR-amplified, and the obtained products (yellow horizontal line) are sized on agarose gels to deduce the number of repeats in each individual locus. (4, 5) Two PCR-based typing methods, that is, DRE-PCR and amplityping, are designed to amplify DNA between clusters of IS and polymorphic GC-rich sequences (PGRS) or between clusters of IS elements, respectively. Different distances between the repetitive elements and their different copy numbers result in variability of banding patterns, composed of DNA fragments amplified (a to d) and produced for individual isolates. Other typing methods (less frequently used) are also shown: heminested inverse PCR (6) and ligation-mediated PCR (7). Figure reprinted and legend adapted from reference 83 , CC BY 3.0.

Source: microbiolspec October 2018 vol. 6 no. 5 doi:10.1128/microbiolspec.MTBP-0002-2016
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Image of FIGURE 2
FIGURE 2

Schematic representation of how the chronologies of transmission can be inferred from the analysis of SNPs from clustered isolates. Each dot represents a SNP. Each box represents a patient. (A) Hypothetical transmission involving five patients, each differing in one SNP with the closest isolate. Neither the directionality of the transmission nor the index case can be inferred. (B) Hypothetical transmission involving seven patients. If the epidemiological data allow us to determine the index case, the direction of transmission (indicated by arrows) can be deduced.

Source: microbiolspec October 2018 vol. 6 no. 5 doi:10.1128/microbiolspec.MTBP-0002-2016
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Image of FIGURE 3
FIGURE 3

Different networks of clusters based on the analysis of SNPs obtained from WGS. Each black dot represents a SNP. All the isolates sharing identical SNP composition are included in the same circle. The size of the circle is proportional to the number of isolates included. An example of star-like topology, expected for networks including superspreader case, can be found in the cluster with the central node highlighted in red (second line, leftside). Reprinted from reference 63 with permission from Elsevier CC-BY-4.0.

Source: microbiolspec October 2018 vol. 6 no. 5 doi:10.1128/microbiolspec.MTBP-0002-2016
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Image of FIGURE 4
FIGURE 4

Chart illustrating work flow between the clinical setting, the genome and analysis center, and the TB research laboratory. (1) Strain X is identified as belonging to an uncontrolled transmission cluster. Strains are analyzed from raw sequencing data (2) to detect polymorphisms at the genome sequencing center. (3) SNPs are detected after comparison of the strain X sequence with those of the reference strains. SNP1 is shared by the strains belonging to the cluster and is not present in the global strain collection. (4) The TB research laboratory will use the transmission cluster-specific SNP to design specific assays. An allele-specific-oligonucleotide PCR assay, TRAP, was chosen to distinguish between strains belonging to the cluster. Once the assay is validated, it is easily transferred to a local clinical setting (5) for screening of ongoing surveillance (both from culture and from direct samples) of the spread of the targeted highly transmissible strains and as support to the local TB control program. Reprinted from reference 68 with permission.

Source: microbiolspec October 2018 vol. 6 no. 5 doi:10.1128/microbiolspec.MTBP-0002-2016
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