Epidemiology and Whole Genome Sequence Typing of Globally Emerging, Multidrug-Resistant Candida auris

Abstract Candida auris is an emergent yeast pathogen, easily transmissible between patients and with high percent of multidrug resistant strains. Here we present a draft genome sequence of the first known Russian strain of C. auris, isolated from a case of candidemia. The strain clustered within South Asian C. auris clade and seemingly represented an independent event of dissemination from the original species range. Observed fluconazole resistance was probably due to F105L and K143R mutations in ERG11.

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Whole-Genome Sequence of a Multidrug-Resistant Mycobacterium tuberculosis Beijing Sequence Type 10 Isolate from an Outbreak in Thailand

Genome Announcements ◽

10.1128/genomea.00803-14 ◽

2014 ◽

Vol 2 (4) ◽

Cited By ~ 3

Author(s):

O. O. Coker ◽

S. M. Regmi ◽

P. Suriyaphol ◽

K. Chininmanu ◽

T. Prammananan ◽

...

Keyword(s):

Mycobacterium Tuberculosis ◽

Genome Sequence ◽

Multidrug Resistant ◽

Sequence Type ◽

Whole Genome Sequence ◽

Whole Genome

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Molecular epidemiology of Candida auris in Qatar using whole genome sequence data

Access Microbiology ◽

10.1099/acmi.cc2021.po0171 ◽

2021 ◽

Vol 3 (12) ◽

Author(s):

Husam Salah ◽

Sathyavathi Sundararaju ◽

Lamya Dalil ◽

Patrick Tang ◽

Walid Al-Wali ◽

...

Keyword(s):

Sequence Data ◽

Multidrug Resistant ◽

Hospital Environment ◽

Whole Genome Sequence ◽

Whole Genome ◽

Resistance Mutations ◽

Candida Auris ◽

East Region ◽

Echinocandin Resistance ◽

Middle East Region

Candida auris is an emerging, multidrug resistant fungal pathogen that has become a public health threat worldwide. Candida auris spreads easily among patients within and between hospitals, and the incidence of infections has increased substantially in the last decade. Multiple C. auris outbreaks have been reported worldwide including India, USA and United Kingdom. Infections and outbreaks caused by C. auris have also been reported in the Middle East region including Kuwait, Oman, Saudi Arabia, and Qatar; however, the origin of these isolates is largely unknown. This study uses whole genome sequencing (WGS) data to determine the epidemiology and the drug resistance mutations from C. auris in Qatar. Forty samples isolated from the patients and the hospital environment were sequenced by Illumina Nextseq. Core genome SNPs revealed that all isolates belonged to the Indian lineage, which could be originated from the expatriate labour from South Asia. The genetic variability among the isolates was low but comprised of more than one genetic cluster. The environmental isolates were identical to the clinical isolates, and the isolates from patients of different hospitals/outbreaks clustered together, suggesting the transmission of C. auris could be linked to infected/colonized patients and the hospital environment. Mutations associated with azole and echinocandin resistance were discussed.

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Whole genome sequence of Klebsiella pneumoniae U25, a hypermucoviscous, multidrug resistant, biofilm producing isolate from India

Memórias do Instituto Oswaldo Cruz ◽

10.1590/0074-02760150423 ◽

2016 ◽

Vol 111 (2) ◽

pp. 144-146 ◽

Cited By ~ 12

Author(s):

Zumaana Rafiq ◽

Nithin Sam ◽

Rama Vaidyanathan

Keyword(s):

Klebsiella Pneumoniae ◽

Genome Sequence ◽

Multidrug Resistant ◽

Whole Genome Sequence ◽

Whole Genome

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Characterization of florfenicol resistance genes in the coagulase-negative Staphylococcus (CoNS) isolates and genomic features of a multidrug-resistant Staphylococcus lentus strain H29

10.21203/rs.3.rs-52544/v1 ◽

2020 ◽

Author(s):

Chongyang Wu ◽

Xueya Zhang ◽

Jialei Liang ◽

Qiaoling Li ◽

Hailong Lin ◽

...

Keyword(s):

Genome Sequence ◽

Resistance Genes ◽

Multidrug Resistant ◽

The Other ◽

Whole Genome Sequence ◽

Dilution Method ◽

Agar Dilution Method ◽

Coagulase Negative Staphylococcus ◽

Whole Genome ◽

Gene Arrays

Abstract BackgroundWith the wide use of florfenicol to prevent and treat the bacterial infection of domestic animals, the emergence of the florfenicol resistance bacteria is increasingly serious. It is very important to elucidate the molecular mechanism of the bacteria’s resistance to florfenicol. MethodsThe minimum inhibitory concentration (MIC) levels was determined by the agar dilution method, and polymerase chain reaction (PCR) was conducted to analyze the distribution of florfenicol resistance genes in 39 CoNS strains isolated from poultry and livestock animals and seafood. The whole genome sequence of one multidrug-resistant strain, Staphylococcus lentus H29, was characterized, and comparative genomics analysis of the resistance gene-related sequences was also performed. ResultsAs a result, the isolates from the animals showed a higher resistance rate (23/28, 82.1%) and much higher MIC levels of florfenicol than those from seafood. Twenty-seven animal isolates carried 37 florfenicol resistance genes (including 26 fexA , 6 cfr and 5 fexB genes), of which 1 carried a cfr gene, 16 carried a fexA gene, 5 carried both fexA and fexB genes and 5 carried both fexA and cfr genes. On the other hand, all 11 isolates from seafood were sensitive to florfenicol, and only 3 carried a fexA gene each. The whole genome sequence of S. lentus H29 was composed of a chromosome and two plasmids ( pH29-46 , pH29- 26) and harbored 11 resistance genes, including 6 genes [ cfr, fexA, ant(6)-Ia , aac A -aph D , mecA and mph(C) ] encoded on the chromosome, four genes [ cfr, fexA, aac A -aph D and tcaA ] on pH29-46 and one gene ( fosD ) on pH29-26. It was interested to find that the S. lentus H29 genome carried two identical copies of the gene arrays of radC - tnpABC - hp - fexA (5,671 bp) and IS 256 - cfr (2,690 bp), of which one copy of the two gene arrays was encoded on plasmid pH29-46, while the other was encoded on the chromosome. ConclusionsThe current study revealed the wide distribution of florfenicol resistance genes ( cfr, fexA and fexB ) in animal bacteria, and to the best of our knowledge, this is the first report of one CoNS strain carrying two identical copies of florfenicol resistance-related gene arrays.

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Whole-genome sequence to decipher the resistome of Chryseobacterium indologenes, a multidrug-resistant bacterium isolated from a cystic fibrosis patient in Marseille, France

10.26226/morressier.56d6be76d462b80296c9773f ◽

2016 ◽

Author(s):

Teresa Cimmino

Keyword(s):

Cystic Fibrosis ◽

Cystic Fibrosis Patient ◽

Genome Sequence ◽

Multidrug Resistant ◽

Resistant Bacterium ◽

Whole Genome Sequence ◽

Whole Genome ◽

Chryseobacterium Indologenes ◽

Multidrug Resistant Bacterium

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Characterization of florfenicol resistance genes in the coagulase-negative Staphylococcus (CoNS) isolates and genomic features of a multidrug-resistant Staphylococcus lentus strain H29

10.21203/rs.3.rs-52544/v2 ◽

2020 ◽

Author(s):

Chongyang Wu ◽

Xueya Zhang ◽

Jialei Liang ◽

Qiaoling Li ◽

Hailong Lin ◽

...

Keyword(s):

Genome Sequence ◽

Resistance Genes ◽

Multidrug Resistant ◽

The Other ◽

Whole Genome Sequence ◽

Dilution Method ◽

Agar Dilution Method ◽

Coagulase Negative Staphylococcus ◽

Whole Genome ◽

Gene Arrays

Abstract Background: With the wide use of florfenicol to prevent and treat the bacterial infection of domestic animals, the emergence of the florfenicol resistance bacteria is increasingly serious. It is very important to elucidate the molecular mechanism of the bacteria’s resistance to florfenicol.Methods: The minimum inhibitory concentration (MIC) levels were determined by the agar dilution method, and polymerase chain reaction (PCR) was conducted to analyze the distribution of florfenicol resistance genes in 39 CoNS strains isolated from poultry and livestock animals and seafood. The whole genome sequence of one multidrug resistant strain, Staphylococcus lentus H29, was characterized, and comparative genomics analysis of the resistance gene-related sequences was also performed.Results: As a result, the isolates from the animals showed a higher resistance rate (23/28, 82.1%) and much higher MIC levels to florfenicol than those from seafood. Twenty-seven animal isolates carried 37 florfenicol resistance genes (including 26 fexA, 6 cfr and 5 fexB genes) with one carrying a cfr gene, 16 each harboring a fexA gene, 5 with both a fexA and a fexB genes and the other 5 with both a fexA and a cfr genes. On the other hand, all 11 isolates from seafood were sensitive to florfenicol, and only 3 carried a fexA gene each. The whole genome sequence of S. lentus H29 was composed of a chromosome and two plasmids (pH29-46, pH29-26) and harbored 11 resistance genes, including 6 genes [cfr, fexA, ant(6)-Ia, aacA-aphD, mecA and mph(C)] encoded on the chromosome, 4 genes [cfr, fexA, aacA-aphD and tcaA] on pH29-46 and 1 gene (fosD) on pH29-26. We found that the S. lentus H29 genome carried two identical copies of the gene arrays of radC-tnpABC-hp-fexA (5,671 bp) and IS256-cfr (2,690 bp), of which one copy of the two gene arrays was encoded on plasmid pH29-46, while the other was encoded on the chromosome.Conclusions: The current study revealed the wide distribution of florfenicol resistance genes (cfr, fexA and fexB) in animal bacteria, and to the best of our knowledge, this is the first report that one S. lentus strain carried two identical copies of florfenicol resistance-related gene arrays.

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