Whole genome sequencing uncovers a novel IND-16 metallo-β-lactamase from an extensively drug-resistant Chryseobacterium indologenes strain J31

Aim: This study aims to characterize clinical strains of Acinetobacter baumannii with an extensively drug-resistant phenotype. Methods: VITEK® 2, Etest® method and broth microdilution method for colistin were used. PCR analysis and multilocus sequence typing Pasteur scheme were performed to identify bla-OXA genes and genetic relatedness, respectively. Whole-genome sequencing analysis was used to characterize three isolates. Results: All the isolates were susceptible only to polymyxins. blaOXA-23-like gene was the only acquired carbapenemase gene in 88.2% of the isolates. Multilocus sequence typing identified various sequence types: ST2, ST19, ST195, ST577 and ST632. Two new sequence types, namely, ST1279 and ST1280, were detected by whole-genome sequencing. Conclusion: This study showed that carbapenem-resistant A. baumannii isolates causing infections in intensive care units almost exclusively produce OXA-23, underlining their frequent spread in Italy.

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Genome Sequencing of Polydrug-, Multidrug-, and Extensively Drug-Resistant Mycobacterium tuberculosis Strains from South India

Microbiology Resource Announcements ◽

10.1128/mra.01388-18 ◽

2019 ◽

Vol 8 (12) ◽

Author(s):

Sivakumar Shanmugam ◽

Narender Kumar ◽

Dina Nair ◽

Mohan Natrajan ◽

Srikanth Prasad Tripathy ◽

...

Keyword(s):

Mycobacterium Tuberculosis ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

South India ◽

Sequence Data ◽

Whole Genome ◽

Drug Resistant ◽

Resistance Mutations ◽

Content Type ◽

Extensively Drug Resistant

The genomes of 16 clinical Mycobacterium tuberculosis isolates were subjected to whole-genome sequencing to identify mutations related to resistance to one or more anti-Mycobacterium drugs. The sequence data will help in understanding the genomic characteristics of M. tuberculosis isolates and their resistance mutations prevalent in South India.

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Whole Genome Sequencing Based Characterization of Extensively Drug-Resistant Mycobacterium tuberculosis Isolates from Pakistan

PLoS ONE ◽

10.1371/journal.pone.0117771 ◽

2015 ◽

Vol 10 (2) ◽

pp. e0117771 ◽

Cited By ~ 38

Author(s):

Asho Ali ◽

Zahra Hasan ◽

Ruth McNerney ◽

Kim Mallard ◽

Grant Hill-Cawthorne ◽

...

Keyword(s):

Mycobacterium Tuberculosis ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome ◽

Drug Resistant ◽

Extensively Drug Resistant

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Whole genome analysis of extensively drug-resistant Acinetobacter bau-mannii clinical isolates in Thailand

Infectious Disorders - Drug Targets ◽

10.2174/1871526520999201116201911 ◽

2020 ◽

Vol 20 ◽

Author(s):

Peechanika Chopjitt ◽

Anusak Kerdsin ◽

Dan Takeuchi ◽

Rujirat Hatrongjit ◽

Parichart Boueroy ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Acinetobacter Baumannii ◽

Genome Sequencing ◽

Efflux Pump ◽

Multidrug Resistant ◽

Whole Genome ◽

Drug Resistant ◽

Resistant Genes ◽

Extensively Drug Resistant ◽

Antibiotic Efflux

Background:: Acinetobacter baumannii is recognized as a majority opportunistic nosocomial pathogen and caus-ing hospital-acquired infection worldwide. The increasing prevalence of extensively drug-resistant Acinetobacter baumannii (XDRAB) has become a rising concern in healthcare facilities and has impeded public health due to limitation of therapeutic options and are associated with high morbidity and mortality as well as longer hospitalization. Whole-genome sequencing of highly multidrug resistant A. baumannii will increase understanding of resistant mechanisms, the emergence of novel re-sistance, genetic relationships among the isolates, source tracking, and treatment decisions in selected patients. Objective:: This study revealed the genomic analysis to explore blaOXA-23 harboring XDRAB isolates in Thailand. Methods:: Whole-genome sequencing of the two XDRAB isolates was carried out on a HiSeq2000 Illumina platform and susceptibility on antimicrobials was conducted. Results:: Both isolates revealed sequence types of international, clone II-carrying, multiple antimicrobial-resistant genes—ST195 and ST451. They were resistant to antimicrobial agents in all drug classes tested for Acinetobacter spp. They carried 18 antimicrobial-resistant genes comprising of 4 -lactamase genes (blaOXA-23, blaOXA-66, blaTEM-1D, blaADC-25), 4 aminogly-coside-resistant genes (armA, aph(3')-Ia, aph(3'')-Ib, aph(6)-Id), 3 macrolide-resistant genes (amvA, mphE, msrE), 1 sulfon-amide-resistant gene (sul-2), 2 tetracycline-resistant genes (tetB, tetR), 1 resistant-nodulation-cell division (RND) antibiotic efflux pump gene cluster, 2 major facilitator superfamily (MFS) antibiotic efflux pump genes (abaF, abaQ), and 1 small multidrug-resistant (SMR) antibiotic efflux pump gene (abeS). Mutation of gyrA (S81L) occurred in both isolates. Conclusions:: Whole-genome sequencing revealed both blaOXA-23 harboring XDRAB isolates were clustered under interna-tional clone II with difference STs and carrying multiple antimicrobial-resistant genes conferred their resistance to antimi-crobial agents. Inactivation of antimicrobials and target modification by enzymes, and pumping antibiotics by efflux pump are mainly resistance mechanism of the XDRAB in this study.

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Whole-Genome Sequencing Analysis of Serially Isolated Multi-Drug and Extensively Drug Resistant Mycobacterium tuberculosis from Thai Patients

PLoS ONE ◽

10.1371/journal.pone.0160992 ◽

2016 ◽

Vol 11 (8) ◽

pp. e0160992 ◽

Cited By ~ 9

Author(s):

Kiatichai Faksri ◽

Jun Hao Tan ◽

Areeya Disratthakit ◽

Eryu Xia ◽

Therdsak Prammananan ◽

...

Keyword(s):

Mycobacterium Tuberculosis ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome ◽

Sequencing Analysis ◽

Drug Resistant ◽

Extensively Drug Resistant

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Transmitted Extended-Spectrum Extensively Drug-Resistant Tuberculosis in Beijing, China, with Discordant Whole-Genome Sequencing Analysis Results

Journal of Clinical Microbiology ◽

10.1128/jcm.00891-15 ◽

2015 ◽

Vol 53 (8) ◽

pp. 2781-2784 ◽

Cited By ~ 9

Author(s):

Hao Li ◽

Masood ur Rehman Kayani ◽

Yunting Gu ◽

Xiaobo Wang ◽

Ting Zhu ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome ◽

Sequencing Analysis ◽

Drug Resistant ◽

Resistant Disease ◽

Resistant Tuberculosis ◽

Extensively Drug Resistant ◽

Extended Spectrum ◽

Beijing China

Drug resistance to tuberculosis remains a major public health threat. Here, we report two cases of extended-spectrum extensively drug-resistant (XXDR) tuberculosis showing resistance to most first- and second-line agents. The results of a correlation of whole-genome sequencing (WGS) and phenotypic testing were discordant, suggesting that overreliance on WGS may miss clinically relevant resistance in extensively drug-resistant disease.

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Molecular Epidemiological Analysis of ST11-K64 Extensively Drug-Resistant Klebsiella pneumoniae Infections Outbreak in Intensive Care and Neurosurgery Units Based on Whole-Genome Sequencing

Frontiers in Microbiology ◽

10.3389/fmicb.2021.709356 ◽

2021 ◽

Vol 12 ◽

Author(s):

Liuxin Xiong ◽

Lebin Su ◽

Hanqing Tan ◽

Wansha Zhao ◽

Shuying Li ◽

...

Keyword(s):

Klebsiella Pneumoniae ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genetic Relatedness ◽

Multiple Drug Resistance ◽

Multiple Drug ◽

Phenotypic Traits ◽

Whole Genome ◽

Drug Resistant ◽

Extensively Drug Resistant

Klebsiella pneumoniae (Kp) is the primary causative bacteria for nosocomial infections and hospital outbreaks. In particular, extensively drug-resistant K. pneumoniae (XDRKp) causes severe clinical infections in hospitalized patients. Here, we used pulsed-field gel electrophoresis (PFGE), drug susceptibility tests, and the whole-genome sequencing (WGS) technology to examine genetic relatedness and phenotypic traits of the strains isolated during an outbreak period. Based on PFGE, a distinct clones cluster comprised of eight XDRKp was observed. These strains were confirmed as ST11-K64 via multiple-locus sequence typing database of Kp. The strains also had genes related to the regulation of biofilm biosynthesis (type 1 & 3 fimbriae, type IV pili biosynthesis, RcsAB, and type VI secretion system) and multiple drug resistance (β-lactamase and aminoglycoside antibiotic resistance). WGS data based on core-single nucleotide polymorphisms and epidemiological investigation showed that the neurosurgery unit was likely the source of the outbreak, the strain was likely to have been transmitted to the ICU through patients. In addition, the two highly probable transmission routes were in the ICU (exposure through shared hospital beds) and the neurosurgery units (all cases were treated by the same rehabilitation physician and were most likely infected during the physical therapy). Notably, the bed mattress had played a crucial transmission role of this outbreak, served as a pathogen reservoir.

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THE CASE OF PRE-EXTENSIVELY DRUG-RESISTANT TUBERCULOSIS DETECTION BY USING THE WHOLE GENOME SEQUENCING M.TUBERCULOSIS

CHEST Journal ◽

10.1016/j.chest.2020.05.021 ◽

2020 ◽

Vol 157 (6) ◽

pp. A18

Author(s):

U. Kozhamkulov ◽

A. Akhmetova ◽

S. Rakhimova ◽

A. Akilzhanova ◽

A. Daniyarov ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome ◽

Drug Resistant ◽

Drug Resistant Tuberculosis ◽

Resistant Tuberculosis ◽

Extensively Drug Resistant

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Whole genome sequencing of clinical samples reveals extensively drug resistant tuberculosis (XDR TB) strains from the Beijing lineage in Nigeria, West Africa

Scientific Reports ◽

10.1038/s41598-021-96956-7 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Idowu B. Olawoye ◽

Jessica N. Uwanibe ◽

Chioma N. Kunle-Ope ◽

Olabisi F. Davies-Bolorunduro ◽

Temitope A. Abiodun ◽

...

Keyword(s):

West Africa ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genomic Sequence ◽

Public Health Problem ◽

Clinical Samples ◽

Antibiotics Resistance ◽

Whole Genome ◽

Drug Resistant ◽

Extensively Drug Resistant

AbstractMulti-drug (MDR) and extensively drug-resistant (XDR) tuberculosis (TB) continues to be a global public health problem especially in high TB burden countries like Nigeria. Many of these cases are undetected and go on to infect high risk individuals. Clinical samples from positive rifampicin resistant Xpert®MTB/Rif assay were subjected to direct whole genome sequencing and bioinformatics analysis to identify the full antibiotics resistance and lineage profile. We report two (2) XDR TB samples also belonging to the East-Asian/Beijing family of lineage 2 Mycobacterium tuberculosis complex from clinical samples in Nigeria. Our findings further reveal the presence of mutations that confer resistance to first-line drugs (rifampicin, isoniazid, ethambutol and pyrazanimide), second-line injectables (capreomycin, streptomycin, kanamycin and/or amikacin) and at least one of the fluoroquinolones (ofloxacin, moxifloxacin, levofloxacin and/or ciprofloxacin) in both samples. The genomic sequence data from this study not only provide the first evidence of XDR TB in Nigeria and West Africa, but also emphasize the importance of WGS in accurately detecting MDR and XDR TB, to ensure adequate and proper management treatment regimens for affected individuals. This will greatly aid in preventing the spread of drug resistance TB in high burden countries.

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