Transmission and drug-resistance of tuberculosis in Luodian revealed by whole genome sequencing based molecular epidemiology study

2020 ◽  
Author(s):  
Mei Liu ◽  
Peng Xu ◽  
Xingwei Liao ◽  
Qing Li ◽  
Wei Chen ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Interquartile Range ◽  
Beijing Genotype ◽  
Limited Area ◽  
Whole Genome ◽  
Effective Prevention ◽  
Lineage 2 ◽  
Cluster Rate

Abstract BACKGROUND Tuberculosis (TB) caused by Mycobacterium tuberculosis (MTB), remains a severe public health problem globally. Guizhou has the fourth highest TB report rate of pulmonary TB around China. Uncovering the current status of TB epidemic, and distinguishing disease caused by recent or remote infections are the key issue to formulate effective prevention and control strategy. However, these data are limited in Guizhou. In this study, we aimed to investigate the transmission and drug-resistance profiles of TB in Luodian, a highest TB incidence and resources limited area in Guizhou, China. METHODS During 22 May 2018 to 21 April 2019, individuals with positive MTB culture were enrolled, all of them accepted the standardized interview. MTB isolates were performed whole genome sequencing. The prevalence of MTB genotypes, the genomic cluster rate and drug-resistance conferring mutations were analyzed based on the sequencing data. RESULTS A total of 107 cases were enrolled, of which 64.5% were male, and the median age of the patients was 51 years old (interquartile range, 40–65 years old). 84% patient were new case while 16% were retreated cases. All cases excepted three came from nine towns, and 55.1% of cases were from Longping and Bianyang. The phylogeny tree showed that 53.3% of strains were Lineage 2 (Beijing genotype), while 46.7% were Lineage 4 (Euro-American genotype). Among Lineage 2 strains, 66.7% were modern Beijing. Seven clusters with genomic distance within 12 SNVs were identified. The clusters included 14 strains, accounting for a cluster rate of 13.1%. The distance of clustered cases was between 2.1 to 71 kilometers (Km), with a media distance of 14 Km (interquartile range, 2.8–38 Km). Cases of two clusters came from the same town. Based on the gene mutations associated to drug-resistance, we predicted that 4.8% was resistant to isoniazid, 3.7% to rifampicin, 3.7% to streptomycin, and only one strain (0.9%) was multidrug resistance (MDR). CONLUSIONS: The study found high transmission and low drug-resistance rate in Luodian, and sublineages of modern Beijing branch had recent expansion in Luodian. this work also may serve as a genomic baseline to study the evolution and spread of MTB in Guizhou.

scholarly journals Transmission of Multidrug/Rifampicin-Resistant Mycobacterium Tuberculosis in Chongqing, China: A Retrospective Observational Study Using Whole-Genome Sequencing

2021 ◽  
Author(s):  
Bing Zhao ◽  
Chunfa Liu ◽  
Jiale Fan ◽  
Aijing Ma ◽  
Wencong He ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Resistance Mutations ◽  
Treatment Information ◽  
Recent Transmission ◽  
Drugs Analysis ◽  
Lineage 2 ◽  
And Cluster Analysis

Abstract Background: Multidrug/rifampicin-resistant tuberculosis (MDR/RR-TB) is a global barrel for ‘Stop TB plan’. China has the second highest MDR/RR-TB burden in whole world wide. Understanding the transmission dynamic is facilitated for disease control. Methods: Whole genome sequencing (WGS) data from patients of Chongqing tuberculosis control institute were used for phylogenetic classifications, resistance predictions, and cluster analysis as indicator for recent transmission (RT). Factors associated with MDR/RR-TB were defined by a logistic regression model. Results: A total of 223 cases of MDR/RR-TB were recorded between Jan 1, 2018 and Dec 31, 2020, and 200 cases obtained relevant treatment information. The patients who are older than 55 year old were more likely to suffering from death. 178 MDR/RR strains were obtained WGS data, 152 were classified as lineage 2 strains. 80 (44.9%, 80 of 178) strains were in 20 genomic clusters that differed by 12 or fewer single nucleotide polymorphisms (SNPs), indicating RT. Patients who were infected with lineage 2 strains is a significant factor driving the epidemic towards MDR/RR-TB. Resistance mutations of first-line tuberculosis drugs analysis found that 79 (98.8%) of all 80 strains defined as RT have same mutations among each clusters totally. 55% (44 of 80) of the MDR/RR-TB strains accumulated additional drug resistance mutations along the transmission chain, especially fluoroquinolones (FQs) (63.6%, 28 of 44). Conclusions: The age is the most significant factor that causes death of MDR/RR-TB patients. RT of MDR/RR strains is not only drove the MDR/RR-TB epidemic, but also accumulated more serious resistance along the transmission chains.

scholarly journals Comprehensive Whole-Genome Sequencing and Reporting of Drug Resistance Profiles on Clinical Cases of Mycobacterium tuberculosis in New York State

2017 ◽  
Vol 55 (6) ◽  
pp. 1871-1882 ◽  
Author(s):  
Joseph Shea ◽  
Tanya A. Halse ◽  
Pascal Lapierre ◽  
Matthew Shudt ◽  
Donna Kohlerschmidt ◽  
...  
Keyword(s):  
New York ◽  
Drug Resistance ◽  
Mycobacterium Tuberculosis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Predictive Value ◽  
New York State ◽  
Whole Genome ◽  
Content Type ◽  
York State

ABSTRACTWhole-genome sequencing (WGS) is a newer alternative for tuberculosis (TB) diagnostics and is capable of providing rapid drug resistance profiles while performing species identification and capturing the data necessary for genotyping. Our laboratory developed and validated a comprehensive and sensitive WGS assay to characterizeMycobacterium tuberculosisand otherM. tuberculosiscomplex (MTBC) strains, composed of a novel DNA extraction, optimized library preparation, paired-end WGS, and an in-house-developed bioinformatics pipeline. This new assay was assessed using 608 MTBC isolates, with 146 isolates during the validation portion of this study and 462 samples received prospectively. In February 2016, this assay was implemented to test all clinical cases of MTBC in New York State, including isolates and early positive Bactec mycobacterial growth indicator tube (MGIT) 960 cultures from primary specimens. Since the inception of the assay, we have assessed the accuracy of identification of MTBC strains to the species level, concordance with culture-based drug susceptibility testing (DST), and turnaround time. Species identification by WGS was determined to be 99% accurate. Concordance between drug resistance profiles generated by WGS and culture-based DST methods was 96% for eight drugs, with an average resistance-predictive value of 93% and susceptible-predictive value of 96%. This single comprehensive WGS assay has replaced seven molecular assays and has resulted in resistance profiles being reported to physicians an average of 9 days sooner than with culture-based DST for first-line drugs and 32 days sooner for second-line drugs.

scholarly journals Independent Microevolution Mediated by Mobile Genetic Elements of IndividualClostridium difficileIsolates from Clade 4 Revealed by Whole-Genome Sequencing

mSystems ◽  
2019 ◽  
Vol 4 (2) ◽  
Author(s):  
Yuan Wu ◽  
Chen Liu ◽  
Wen-Ge Li ◽  
Jun-Li Xu ◽  
Wen-Zhu Zhang ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Clostridium Difficile ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Mobile Genetic Elements ◽  
High Rate ◽  
Whole Genome ◽  
Content Type ◽  
Genetic Elements ◽  
Sequence Types

ABSTRACTHorizontal gene transfer of mobile genetic elements (MGEs) accounts for the mosaic genome ofClostridium difficile, leading to acquisition of new phenotypes, including drug resistance and reconstruction of the genomes. MGEs were analyzed according to the whole-genome sequences of 37C. difficileisolates with a variety of sequence types (STs) within clade 4 from China. Great diversity was found in each transposon even within isolates with the same ST. Two novel transposons were identified in isolates ZR9 and ZR18, of which approximately one third to half of the genes showed heterogenous origins compared with the usual intestinal bacterial genes. Most importantly,catD, known to be harbored by Tn4453a/b, was replaced byaac(6′) aph(2′′)in isolates 2, 7, and 28. This phenomenon illustrated the frequent occurrence of gene exchanges betweenC. difficileand other enterobacteria with individual heterogeneity. Numerous prophages and CRISPR arrays were identified inC. difficileisolates of clade 4. Approximately 20% of spacers were located in prophage-carried CRISPR arrays, providing a new method for typing and tracing the origins of closely related isolates, as well as in-depth studies of the mechanism underlying genome remodeling. The rates of drug resistance were obviously higher than those reported previously around the world, although all isolates retained high sensitivity to vancomycin and metronidazole. The increasing number ofC. difficileisolates resistant to all antibiotics tested here suggests the ease with which resistance is acquiredin vivo. This study gives insights into the genetic mechanism of microevolution within clade 4.IMPORTANCEMobile genetic elements play a key role in the continuing evolution ofClostridium difficile, resulting in the emergence of new phenotypes for individual isolates. On the basis of whole-genome sequencing analysis, we comprehensively explored transposons, CRISPR, prophage, and genetic sites for drug resistance within clade 4C. difficileisolates with different sequence types. Great diversity in MGEs and a high rate of multidrug resistance were found within this clade, including new transposons, Tn4453a/bwithaac(6′) aph(2′′)instead ofcatD, and a relatively high rate of prophage-carried CRISPR arrays. These findings provide important new insights into the mechanism of genome remodeling within clade 4 and offer a new method for typing and tracing the origins of closely related isolates.

scholarly journals Whole-Genome Sequencing for Drug Resistance Profile Prediction inMycobacterium tuberculosis

2019 ◽  
Vol 63 (4) ◽  
Author(s):  
Sebastian M. Gygli ◽  
Peter M. Keller ◽  
Marie Ballif ◽  
Nicolas Blöchliger ◽  
Rico Hömke ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Critical Concentration ◽  
Drug Susceptibility Testing ◽  
Quality Data ◽  
Whole Genome ◽  
Resistance Mutations ◽  
Content Type ◽  
Agar Dilution

ABSTRACTWhole-genome sequencing allows rapid detection of drug-resistantMycobacterium tuberculosisisolates. However, the availability of high-quality data linking quantitative phenotypic drug susceptibility testing (DST) and genomic data have thus far been limited. We determined drug resistance profiles of 176 genetically diverse clinicalM. tuberculosisisolates from the Democratic Republic of the Congo, Ivory Coast, Peru, Thailand, and Switzerland by quantitative phenotypic DST for 11 antituberculous drugs using the BD Bactec MGIT 960 system and 7H10 agar dilution to generate a cross-validated phenotypic DST readout. We compared DST results with predicted drug resistance profiles inferred by whole-genome sequencing. Classification of strains by the two phenotypic DST methods into resistotype/wild-type populations was concordant in 73 to 99% of cases, depending on the drug. Our data suggest that the established critical concentration (5 mg/liter) for ethambutol resistance (MGIT 960 system) is too high and misclassifies strains as susceptible, unlike 7H10 agar dilution. Increased minimal inhibitory concentrations were explained by mutations identified by whole-genome sequencing. Using whole-genome sequences, we were able to predict quantitative drug resistance levels for the majority of drug resistance mutations. Predicting quantitative levels of drug resistance by whole-genome sequencing was partially limited due to incompletely understood drug resistance mechanisms. The overall sensitivity and specificity of whole-genome-based DST were 86.8% and 94.5%, respectively. Despite some limitations, whole-genome sequencing has the potential to infer resistance profiles without the need for time-consuming phenotypic methods.

scholarly journals Deciphering drug resistance in Mycobacterium tuberculosis using whole-genome sequencing: progress, promise, and challenges

2019 ◽  
Vol 11 (1) ◽  
Author(s):  
Keira A. Cohen ◽  
Abigail L. Manson ◽  
Christopher A. Desjardins ◽  
Thomas Abeel ◽  
Ashlee M. Earl
Keyword(s):  
Drug Resistance ◽  
Mycobacterium Tuberculosis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome

scholarly journals Drug resistance profile and clonality of Plasmodium falciparum parasites in Cape Verde: the 2017 malaria outbreak

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Silvania Da Veiga Leal ◽  
Daniel Ward ◽  
Susana Campino ◽  
Ernest Diez Benavente ◽  
Amy Ibrahim ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Plasmodium Falciparum ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Family Members ◽  
Cape Verde ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data ◽  
High Level

Abstract Background Cape Verde is an archipelago located off the West African coast and is in a pre-elimination phase of malaria control. Since 2010, fewer than 20 Plasmodium falciparum malaria cases have been reported annually, except in 2017, when an outbreak in Praia before the rainy season led to 423 autochthonous cases. It is important to understand the genetic diversity of circulating P. falciparum to inform on drug resistance, potential transmission networks and sources of infection, including parasite importation. Methods Enrolled subjects involved malaria patients admitted to Dr Agostinho Neto Hospital at Praia city, Santiago island, Cape Verde, between July and October 2017. Neighbours and family members of enrolled cases were assessed for the presence of anti-P. falciparum antibodies. Sanger sequencing and real-time PCR was used to identify SNPs in genes associated with drug resistance (e.g., pfdhfr, pfdhps, pfmdr1, pfk13, pfcrt), and whole genome sequencing data were generated to investigate the population structure of P. falciparum parasites. Results The study analysed 190 parasite samples, 187 indigenous and 3 from imported infections. Malaria cases were distributed throughout Praia city. There were no cases of severe malaria and all patients had an adequate clinical and parasitological response after treatment. Anti-P. falciparum antibodies were not detected in the 137 neighbours and family members tested. No mutations were detected in pfdhps. The triple mutation S108N/N51I/C59R in pfdhfr and the chloroquine-resistant CVIET haplotype in the pfcrt gene were detected in almost all samples. Variations in pfk13 were identified in only one sample (R645T, E668K). The haplotype NFD for pfmdr1 was detected in the majority of samples (89.7%). Conclusions Polymorphisms in pfk13 associated with artemisinin-based combination therapy (ACT) tolerance in Southeast Asia were not detected, but the majority of the tested samples carried the pfmdr1 haplotype NFD and anti-malarial-associated mutations in the the pfcrt and pfdhfr genes. The first whole genome sequencing (WGS) was performed for Cape Verdean parasites that showed that the samples cluster together, have a very high level of similarity and are close to other parasites populations from West Africa.

Sign in / Sign up

Export Citation Format

Share Document