Evaluation of Whole-Genome Sequence Method to Diagnose Resistance of 13 Anti-tuberculosis Drugs and Characterize Resistance Genes in Clinical Multi-Drug Resistance Mycobacterium tuberculosis Isolates From China.

Abstract:

:Background: Whole-genome sequencing (WGS) is a viable and financially feasible tool for timely and comprehensive diagnosis of drug resistance in developed countries. With the increase in the incidence of multidrug-resistant tuberculosis (MDR-TB), second-line anti-TB drugs are gaining importance. However, genetic resistance to second-line anti-TB drugs based on WGS has not been fully studied. Methods: We randomly selected 100 MDR-TB and 10 non-MDR-TB isolates from a hospital in Zhejiang Province, China. Drug susceptibility tests against 13 anti-TB drugs were performed, and 34 drug resistance-related genes were analyzed using WGS in all isolates. For each drug, the accuracy, sensitivity, specificity, and positive and negative predictive values of WGS were compared with those of the conventional drug susceptibility test. Results: The overall sensitivity and specificity for WGS were respectively, 99.0 and 100.0% for isoniazid (INH), 99.0 and 100.0% for rifampicin (RIF), 94.8 and 65.3% for ethambutol (EMB), 86.2 and 84.4% for pyrazinamide (PZA), 95.6 and 95.6% for levofloxacin (LFX), 89.5 and 65.3% for moxifloxacin (MFX), 91.3 and 95.1% for streptomycin (SM), 90.9 and 99.0% for kanamycin, 90.9 and 100.0% for amikacin, 88.9 and 98.0% for capreomycin, 87.0 and 85.1% for prothionamide (PTO), 85.7 and 99.0% for para-aminosalicylic acid (PAS), and 66.7 and 95.9% for clofazimine (CLO). Conclusions: WGS is a promising approach to predict resistance to INH, RIF, PZA, LFX, SM, second-line injectable drugs (SLIDs), and PTO with satisfactory accuracy, sensitivity, and specificity of over 85.0%. The specificity of WGS in diagnosing resistance to EMB, and high-level resistance to MFX (2.0 mg/L) needs to be improved.

journal_name

Front Microbiol

authors

Chen X,He G,Wang S,Lin S,Chen J,Zhang W

doi

10.3389/fmicb.2019.01741

subject

Has Abstract

pub_date

2019-07-31 00:00:00

pages

1741

issn

1664-302X

journal_volume

10

pub_type

杂志文章
  • Human Microbe-Disease Association Prediction With Graph Regularized Non-Negative Matrix Factorization.

    abstract::A microbe is a microscopic organism which may exists in its single-celled form or in a colony of cells. In recent years, accumulating researchers have been engaged in the field of uncovering microbe-disease associations since microbes are found to be closely related to the prevention, diagnosis, and treatment of many ...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2018.02560

    authors: He BS,Peng LH,Li Z

    更新日期:2018-11-01 00:00:00

  • The mgtCBR mRNA Leader Secures Growth of Salmonella in Both Host and Non-host Environments.

    abstract::Upon intracellular cues, bacterial mRNA leaders often form secondary structures that determine expression of a downstream protein-coding region(s), thereby providing bacteria with a mechanism to control the amounts of necessary proteins in the right locales. Here we describe a polycistronic mRNA leader that secures ba...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2019.02831

    authors: Park M,Kim H,Nam D,Kweon DH,Shin D

    更新日期:2019-12-06 00:00:00

  • Genomic Characterization of Flavobacterium psychrophilum Serotypes and Development of a Multiplex PCR-Based Serotyping Scheme.

    abstract::Flavobacterium psychrophilum is a devastating bacterial pathogen of salmonids reared in freshwater worldwide. So far, serological diversity between isolates has been described but the underlying molecular factors remain unknown. By combining complete genome sequence analysis and the serotyping method proposed by Loren...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2017.01752

    authors: Rochat T,Fujiwara-Nagata E,Calvez S,Dalsgaard I,Madsen L,Calteau A,Lunazzi A,Nicolas P,Wiklund T,Bernardet JF,Duchaud E

    更新日期:2017-09-12 00:00:00

  • Alpine Snow Algae Microbiome Diversity in the Coast Range of British Columbia.

    abstract::Snow algae blooms contain bacteria, fungi, and other microscopic organisms. We surveyed 55 alpine snow algae blooms, collecting a total of 68 samples, from 12 mountains in the Coast Range of British Columbia, Canada. We used microscopy and rDNA metabarcoding to document biodiversity and query species and taxonomic ass...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2020.01721

    authors: Yakimovich KM,Engstrom CB,Quarmby LM

    更新日期:2020-07-28 00:00:00

  • Analysis of Two Complementary Single-Gene Deletion Mutant Libraries of Salmonella Typhimurium in Intraperitoneal Infection of BALB/c Mice.

    abstract::Two pools of individual single gene deletion (SGD) mutants of S. Typhimurium 14028s encompassing deletions of 3,923 annotated non-essential ORFs and sRNAs were screened by intraperitoneal (IP) injection in BALB/c mice followed by recovery from spleen and liver 2 days post infection. The relative abundance of each muta...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2015.01455

    authors: Silva-Valenzuela CA,Molina-Quiroz RC,Desai P,Valenzuela C,Porwollik S,Zhao M,Hoffman RM,Andrews-Polymenis H,Contreras I,Santiviago CA,McClelland M

    更新日期:2016-01-05 00:00:00

  • Diversity and Composition of Airborne Fungal Community Associated with Particulate Matters in Beijing during Haze and Non-haze Days.

    abstract::To assess the diversity and composition of airborne fungi associated with particulate matters (PMs) in Beijing, China, a total of 81 PM samples were collected, which were derived from PM2.5, PM10 fractions, and total suspended particles during haze and non-haze days. The airborne fungal community in these samples was ...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2016.00487

    authors: Yan D,Zhang T,Su J,Zhao LL,Wang H,Fang XM,Zhang YQ,Liu HY,Yu LY

    更新日期:2016-04-14 00:00:00

  • A Burkholderia thailandensis DedA Family Membrane Protein Is Required for Proton Motive Force Dependent Lipid A Modification.

    abstract::The DedA family is a conserved membrane protein family found in most organisms. A Burkholderia thailandensis DedA family protein, named DbcA, is required for high-level colistin (polymyxin E) resistance, but the mechanism awaits elucidation. Modification of lipopolysaccharide lipid A with the cationic sugar aminoarabi...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2020.618389

    authors: Panta PR,Doerrler WT

    更新日期:2021-01-12 00:00:00

  • Response of bacterioplankton to iron fertilization of the Southern Ocean, Antarctica.

    abstract::Ocean iron fertilization is an approach to increase CO2 sequestration. The Indo-German iron fertilization experiment "LOHAFEX" was carried out in the Southern Ocean surrounding Antarctica in 2009 to monitor changes in bacterial community structure following iron fertilization-induced phytoplankton bloom of the seawate...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2015.00863

    authors: Singh SK,Kotakonda A,Kapardar RK,Kankipati HK,Sreenivasa Rao P,Sankaranarayanan PM,Vetaikorumagan SR,Gundlapally SR,Nagappa R,Shivaji S

    更新日期:2015-08-26 00:00:00

  • Analysis of Indian SARS-CoV-2 Genomes Reveals Prevalence of D614G Mutation in Spike Protein Predicting an Increase in Interaction With TMPRSS2 and Virus Infectivity.

    abstract::Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, has emerged as a global pandemic worldwide. In this study, we used ARTIC primers-based amplicon sequencing to profile 225 SARS-CoV-2 genomes from India. Phylogenetic analysis of 202 high-quality assem...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2020.594928

    authors: Raghav S,Ghosh A,Turuk J,Kumar S,Jha A,Madhulika S,Priyadarshini M,Biswas VK,Shyamli PS,Singh B,Singh N,Singh D,Datey A,Avula K,Smita S,Sabat J,Bhattacharya D,Kshatri JS,Vasudevan D,Suryawanshi A,Dash R,Senapati

    更新日期:2020-11-23 00:00:00

  • Enterotoxigenicity and Antimicrobial Resistance of Staphylococcus aureus Isolated from Retail Food in China.

    abstract::Staphylococcus aureus is one of the most common causes of zoonotic agent in the world, which are attributable to the contamination of food with enterotoxins. In this study, a total of 1,150 S. aureus isolates were cultured from 27,000 retail foods items from 203 cities of 24 provinces in China in 2015 and were test fo...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2017.02256

    authors: Wang W,Baloch Z,Jiang T,Zhang C,Peng Z,Li F,Fanning S,Ma A,Xu J

    更新日期:2017-11-21 00:00:00

  • Is Meropenem as a Monotherapy Truly Incompetent for Meropenem-Nonsusceptible Bacterial Strains? A Pharmacokinetic/Pharmacodynamic Modeling With Monte Carlo Simulation.

    abstract::Infections due to meropenem-nonsusceptible bacterial strains (MNBSs) with meropenem minimum inhibitory concentrations (MICs) ≥ 16 mg/L have become an urgent problem. Currently, the optimal treatment strategy for these cases remains uncertain due to some limitations of currently available mono- and combination therapy ...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2019.02777

    authors: Song X,Wu Y,Cao L,Yao D,Long M

    更新日期:2019-11-29 00:00:00

  • Association of targeted multiplex PCR with resequencing microarray for the detection of multiple respiratory pathogens.

    abstract::A large number of viral and bacterial organisms are responsible for community-acquired pneumonia (CAP) which contributes to substantial burden on health management. A new resequencing microarray (RPM-IVDC1) associated with targeted multiplex PCR was recently developed and validated for multiple respiratory viruses det...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2015.00532

    authors: Shen H,Zhu B,Wang S,Mo H,Wang J,Li J,Zhang C,Zeng H,Guan L,Shi W,Zhang Y,Ma X

    更新日期:2015-05-28 00:00:00

  • Respiratory virus modulation of host nucleocytoplasmic transport; target for therapeutic intervention?

    abstract::The respiratory diseases caused by rhinovirus, respiratory syncytial virus, and influenza virus represent a large social and financial burden on healthcare worldwide. Although all three viruses have distinctly unique properties in terms of infection and replication, they share the ability to exploit/manipulate the hos...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章,评审

    doi:10.3389/fmicb.2015.00848

    authors: Caly L,Ghildyal R,Jans DA

    更新日期:2015-08-14 00:00:00

  • Coral-Associated Bacterial Diversity Is Conserved across Two Deep-Sea Anthothela Species.

    abstract::Cold-water corals, similar to tropical corals, contain diverse and complex microbial assemblages. These bacteria provide essential biological functions within coral holobionts, facilitating increased nutrient utilization and production of antimicrobial compounds. To date, few cold-water octocoral species have been ana...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2016.00458

    authors: Lawler SN,Kellogg CA,France SC,Clostio RW,Brooke SD,Ross SW

    更新日期:2016-04-05 00:00:00

  • Role of Two-Component System Response Regulator bceR in the Antimicrobial Resistance, Virulence, Biofilm Formation, and Stress Response of Group B Streptococcus.

    abstract::Group B Streptococcus (GBS; Streptococcus agalactiae) is a leading cause of sepsis in neonates and pregnant mothers worldwide. Whereas the hyper-virulent serogroup III clonal cluster 17 has been associated with neonatal disease and meningitis, serogroup III ST283 was recently implicated in invasive disease among non-p...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2019.00010

    authors: Yang Y,Luo M,Zhou H,Li C,Luk A,Zhao G,Fung K,Ip M

    更新日期:2019-01-23 00:00:00

  • Induction of Protective Immunity against Toxoplasma gondii in Mice by Nucleoside Triphosphate Hydrolase-II (NTPase-II) Self-amplifying RNA Vaccine Encapsulated in Lipid Nanoparticle (LNP).

    abstract::RNA-based vaccine represents an irresistible and safe immunization strategy with decreasing theoretical risks of genomic integration and malignant cell transformation. To our knowledge, however, there is no report about development of RNA vaccine against Toxoplasma gondii infection. We have previously demonstrated tha...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2017.00605

    authors: Luo F,Zheng L,Hu Y,Liu S,Wang Y,Xiong Z,Hu X,Tan F

    更新日期:2017-04-05 00:00:00

  • Determination of Temperature Dependent Growth Parameters in Psychrotrophic Pathogen Bacteria and Tentative Use of Mean Kinetic Temperature for the Microbiological Control of Food.

    abstract::Temperature is the main factor to control the microbial growth in perishable foods. The psychrotrophic pathogen bacteria are microorganisms of concern for food products with extended shelf life in chilling conditions. The aims of this work were two. Firstly, to evaluate growth behavior of Aeromonas hydrophila DSM-3018...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2018.03023

    authors: De Silvestri A,Ferrari E,Gozzi S,Marchi F,Foschino R

    更新日期:2018-12-05 00:00:00

  • In-depth Profiling of MvfR-Regulated Small Molecules in Pseudomonas aeruginosa after Quorum Sensing Inhibitor Treatment.

    abstract::Pseudomonas aeruginosa is a Gram-negative bacterium, which causes opportunistic infections in immuno-compromised individuals. Due to its multiple resistances toward antibiotics, the development of new drugs is required. Interfering with Quorum Sensing (QS), a cell-to-cell communication system, has shown to be highly e...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2017.00924

    authors: Allegretta G,Maurer CK,Eberhard J,Maura D,Hartmann RW,Rahme L,Empting M

    更新日期:2017-05-24 00:00:00

  • Impacts of Fertilization Regimes on Arbuscular Mycorrhizal Fungal (AMF) Community Composition Were Correlated with Organic Matter Composition in Maize Rhizosphere Soil.

    abstract::The understanding of the response of arbuscular mycorrhizal fungi (AMF) community composition to fertilization is of great significance in sustainable agriculture. However, how fertilization influences AMF diversity and composition is not well-established yet. A field experiment located in northeast China in typical b...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2016.01840

    authors: Zhu C,Ling N,Guo J,Wang M,Guo S,Shen Q

    更新日期:2016-11-16 00:00:00

  • Biocatalytic desulfurization of thiophenic compounds and crude oil by newly isolated bacteria.

    abstract::Microorganisms possess enormous highly specific metabolic activities, which enable them to utilize and transform nearly every known chemical class present in crude oil. In this context, one of the most studied biocatalytic processes is the biodesulfurization (BDS) of thiophenic sulfur-containing compounds such as benz...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2015.00112

    authors: Mohamed Mel-S,Al-Yacoub ZH,Vedakumar JV

    更新日期:2015-02-13 00:00:00

  • New developments in the study of the microbiota of raw-milk, long-ripened cheeses by molecular methods: the case of Grana Padano and Parmigiano Reggiano.

    abstract::Microorganisms are an essential component of cheeses and play important roles during both cheese manufacture and ripening. Both starter and secondary flora modify the physical and chemical properties of cheese, contributing and reacting to changes that occur during the manufacture and ripening of cheese. As the compos...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2013.00036

    authors: Neviani E,Bottari B,Lazzi C,Gatti M

    更新日期:2013-02-28 00:00:00

  • Meta-Analysis of Vaginal Microbiome Data Provides New Insights Into Preterm Birth.

    abstract::Preterm birth (PTB) is defined as the birth of an infant before 37 weeks of gestational age. It is the leading cause of perinatal morbidity and mortality worldwide. In this study, we present a comprehensive meta-analysis of vaginal microbiome in PTB. We integrated raw longitudinal 16S rRNA vaginal microbiome data from...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2020.00476

    authors: Kosti I,Lyalina S,Pollard KS,Butte AJ,Sirota M

    更新日期:2020-04-08 00:00:00

  • Nutrient Stoichiometry Shapes Microbial Community Structure in an Evaporitic Shallow Pond.

    abstract::Nutrient availability and ratios can play an important role in shaping microbial communities of freshwater ecosystems. The Cuatro Ciénegas Basin (CCB) in Mexico is a desert oasis where, perhaps paradoxically, high microbial diversity coincides with extreme oligotrophy. To better understand the effects of nutrients on ...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2017.00949

    authors: Lee ZM,Poret-Peterson AT,Siefert JL,Kaul D,Moustafa A,Allen AE,Dupont CL,Eguiarte LE,Souza V,Elser JJ

    更新日期:2017-05-30 00:00:00

  • Methyl-Coenzyme M Reductase and Its Post-translational Modifications.

    abstract::The methyl-coenzyme M reductase (MCR) is a central enzyme in anaerobic microbial methane metabolism, which consists of methanogenesis and anaerobic oxidation of methane (AOM). MCR catalyzes the final step of methanogenesis and the first step of AOM to achieve the production and oxidation of methane, respectively. Besi...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章,评审

    doi:10.3389/fmicb.2020.578356

    authors: Chen H,Gan Q,Fan C

    更新日期:2020-10-09 00:00:00

  • Enzymatic Bioweathering and Metal Mobilization From Black Slate by the Basidiomycete Schizophyllum commune.

    abstract::Schizophyllum commune is a filamentous basidiomycete causing white-rot in many wood species with the help of a broad range of enzymes including multicopper oxidases such as laccases and laccase-like oxidases. Since these enzymes exhibit a broad substrate range, their ability to oxidatively degrade black slate was inve...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2018.02545

    authors: Kirtzel J,Madhavan S,Wielsch N,Blinne A,Hupfer Y,Linde J,Krause K,Svatoš A,Kothe E

    更新日期:2018-10-24 00:00:00

  • The Lp_3561 and Lp_3562 Enzymes Support a Functional Divergence Process in the Lipase/Esterase Toolkit from Lactobacillus plantarum.

    abstract::Lactobacillus plantarum species is a good source of esterases since both lipolytic and esterase activities have been described for strains of this species. No fundamental biochemical difference exists among esterases and lipases since both share a common catalytic mechanism. L. plantarum WCFS1 possesses a protein, Lp_...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2016.01118

    authors: Esteban-Torres M,Reverón I,Santamaría L,Mancheño JM,de Las Rivas B,Muñoz R

    更新日期:2016-07-19 00:00:00

  • Development of an Immunochromatographic Strip for Rapid Detection of Canine Adenovirus.

    abstract::Although canine adenovirus (CAdV) is highly prevalent in dogs, there is currently a lack of a quick diagnostic method. In this study, we developed a rapid immunochromatographic strip (ICS) assay using colloidal gold coupled to CAdV-2-specific monoclonal antibodies (mAbs). BALB/c mice were immunized with a purified CAd...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2019.02882

    authors: Wang S,Wen Y,An T,Duan G,Sun M,Ge J,Li X,Yang K,Cai X

    更新日期:2019-12-11 00:00:00

  • Role of Bacteriophages in the Implementation of a Sustainable Dairy Chain.

    abstract::The growing human population is currently facing an unprecedented challenge regarding global food sustainability. Thus, it is of paramount to maintain food production and quality while avoiding a negative impact on climate change and the environment at large. Along the food chain, several practices could compromise fu...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章,评审

    doi:10.3389/fmicb.2019.00012

    authors: Gutiérrez D,Fernández L,Rodríguez A,García P

    更新日期:2019-01-22 00:00:00

  • Gut Microbiome Contributes to Liver Fibrosis Impact on T Cell Receptor Immune Repertoire.

    abstract::Gut microbiota (GM) modifies the intrahepatic immune microenvironment, but the underlying mechanisms remain poorly understood. Liver fibrosis-associated imprinting is predicted to be reflected in GM. This study investigated the link between GM and the intrahepatic T cell receptor (TCR) immune repertoire (IR), and whet...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2020.571847

    authors: Liang Q,Zhang M,Hu Y,Zhang W,Zhu P,Chen Y,Xue P,Li Q,Wang K

    更新日期:2020-11-27 00:00:00

  • Deficiency in Lipoteichoic Acid Synthesis Causes a Failure in Executing the Colony Developmental Program in Bacillus subtilis.

    abstract::Colonies are an abundant form of bacterial multicellularity; however, relatively little is known about the initial stages of their construction. We have previously described that colony development of the soil bacterium Bacillus subtilis is a highly ordered process, typically initiating with the formation of extending...

    journal_title:Frontiers in microbiology

    pub_type: 杂志文章

    doi:10.3389/fmicb.2017.01991

    authors: Mamou G,Fiyaksel O,Sinai L,Ben-Yehuda S

    更新日期:2017-10-24 00:00:00