Molecular epidemiology and drug-resistance of tuberculosis in Luodian revealed by whole genome sequencing

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.

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

10.21203/rs.3.rs-26012/v1 ◽

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.

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Whole-Genome Sequencing Applied to the Molecular Epidemiology of Shiga Toxin-Producing Escherichia coli O157:H7 in Argentina: TABLE 1

Genome Announcements ◽

10.1128/genomea.01341-16 ◽

2016 ◽

Vol 4 (6) ◽

Cited By ~ 1

Author(s):

Claudia Carolina Carbonari ◽

Nahuel Fittipaldi ◽

Sarah Teatero ◽

Taryn B. T. Athey ◽

Luis Pianciola ◽

...

Keyword(s):

Escherichia Coli ◽

Molecular Epidemiology ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Shiga Toxin ◽

Whole Genome ◽

Escherichia Coli O157 ◽

Genome Sequences ◽

High Quality ◽

Human Infections

Shiga toxin-producing Escherichia coli strains are worldwide associated with sporadic human infections and outbreaks. In this work, we report the availability of high-quality draft whole-genome sequences for 19 O157:H7 strains isolated in Argentina.

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

mSystems ◽

10.1128/msystems.00252-18 ◽

2019 ◽

Vol 4 (2) ◽

Cited By ~ 4

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.

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Whole-Genome Sequencing for Drug Resistance Profile Prediction inMycobacterium tuberculosis

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.02175-18 ◽

2019 ◽

Vol 63 (4) ◽

Cited By ~ 11

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.

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

Genome Medicine ◽

10.1186/s13073-019-0660-8 ◽

2019 ◽

Vol 11 (1) ◽

Cited By ~ 10

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

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Whole genome sequencing of clinical strains of Mycobacterium tuberculosis from Mumbai, India: A potential tool for determining drug-resistance and strain lineage

Tuberculosis ◽

10.1016/j.tube.2017.08.002 ◽

2017 ◽

Vol 107 ◽

pp. 63-72 ◽

Cited By ~ 17

Author(s):

Anirvan Chatterjee ◽

Kayzad Nilgiriwala ◽

Dhananjaya Saranath ◽

Camilla Rodrigues ◽

Nerges Mistry

Keyword(s):

Drug Resistance ◽

Mycobacterium Tuberculosis ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome ◽

Clinical Strains ◽

Potential Tool

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Comparative Genome Analysis of Extended-Spectrum-β-Lactamase-Producing Escherichia coli Sequence Type 131 Strains from Nepal and Japan

mSphere ◽

10.1128/msphere.00289-16 ◽

2016 ◽

Vol 1 (5) ◽

Cited By ~ 6

Author(s):

Tohru Miyoshi-Akiyama ◽

Jatan Bahadur Sherchan ◽

Yohei Doi ◽

Maki Nagamatsu ◽

Jeevan B. Sherchand ◽

...

Keyword(s):

Molecular Epidemiology ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Sequence Type ◽

Whole Genome ◽

Asian Countries ◽

Content Type ◽

E Coli ◽

Global Spread ◽

Low Prevalence

ABSTRACT The global spread of ESBL-E. coli has been driven in large part by pandemic sequence type 131 (ST131). A recent study suggested that, within E. coli ST131, certain sublineages have disseminated worldwide with little association with their geographical origin, highlighting the complexity of the epidemiology of this pandemic clone. ST131 bacteria have also been classified into four virotypes based on the distribution of certain virulence genes. Information on virotype distribution in Asian ST131 strains is limited. We conducted whole-genome sequencing of ESBL-E. coli ST131 strains collected in Nepal and Japan, two Asian countries with a high and low prevalence of ESBL-E. coli, respectively. We systematically compared these ST131 genomes with those reported from other regions to gain insights into the molecular epidemiology of their spread and found the distinct phylogenetic characteristics of the spread of ESBL-E. coli ST131 in these two geographical areas of Asia. The global spread of extended-spectrum-β-lactamase (ESBL)-producing Escherichia coli (ESBL-E. coli) has largely been driven by the pandemic sequence type 131 (ST131). This study aimed to determine the molecular epidemiology of their spread in two Asian countries with contrasting prevalence. We conducted whole-genome sequencing (WGS) of ESBL-E. coli ST131 strains collected prospectively from Nepal and Japan, two countries in Asia with a high and low prevalence of ESBL-E. coli, respectively. We also systematically compared these genomes with those reported from other regions using publicly available WGS data for E. coli ST131 strains. Further, we conducted phylogenetic analysis of these isolates and all genome sequence data for ST131 strains to determine sequence diversity. One hundred five unique ESBL-E. coli isolates from Nepal (February 2013 to July 2013) and 76 isolates from Japan (October 2013 to September 2014) were included. Of these isolates, 54 (51%) isolates from Nepal and 11 (14%) isolates from Japan were identified as ST131 by WGS. Phylogenetic analysis based on WGS suggested that the majority of ESBL-E. coli ST131 isolates from Nepal clustered together, whereas those from Japan were more diverse. Half of the ESBL-E. coli ST131 isolates from Japan belonged to virotype C, whereas half of the isolates from Nepal belonged to a virotype other than virotype A, B, C, D, or E (A/B/C/D/E). The dominant sublineage of E. coli ST131 was H30Rx, which was most prominent in ESBL-E. coli ST131 isolates from Nepal. Our results revealed distinct phylogenetic characteristics of ESBL-E. coli ST131 spread in the two geographical areas of Asia, indicating the involvement of multiple factors in its local spread in each region. IMPORTANCE The global spread of ESBL-E. coli has been driven in large part by pandemic sequence type 131 (ST131). A recent study suggested that, within E. coli ST131, certain sublineages have disseminated worldwide with little association with their geographical origin, highlighting the complexity of the epidemiology of this pandemic clone. ST131 bacteria have also been classified into four virotypes based on the distribution of certain virulence genes. Information on virotype distribution in Asian ST131 strains is limited. We conducted whole-genome sequencing of ESBL-E. coli ST131 strains collected in Nepal and Japan, two Asian countries with a high and low prevalence of ESBL-E. coli, respectively. We systematically compared these ST131 genomes with those reported from other regions to gain insights into the molecular epidemiology of their spread and found the distinct phylogenetic characteristics of the spread of ESBL-E. coli ST131 in these two geographical areas of Asia.

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