Characterization of multi-drug resistantMycobacterium tuberculosisfrom immigrants residing in the USA using Ion Torrent full-gene sequencing

Daum, Luke T.; Fischer, Gerald W.; Sromek, J.; Khubbar, Manjeet; Hunter, Paul; Gradus, M. Stephen; Bhattacharyya, Sanjib

doi:10.1017/s0950268813002409

Cited by 19 publications

(13 citation statements)

References 12 publications

(17 reference statements)

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“…The absence of a wild type band is suggestive of one of two scenarios -either it is a silent mutation that does not lead to an amino acid change, or a mutation not detected by LPA/an unknown gene. 22 We report rifampicin monoresistance of 5.7% (five samples), which was corroborated by Xpert MTB/Rif assay. Of these, three were non-viable and did not grow on culture.…”

Section: Lpa Compared To Xpert (Mtb/rif) For the Diagnosis Of Tubercusupporting

confidence: 52%

The diagnostic utility of line probe assays for multidrug-resistant tuberculosis

Ninan

Gowri

Christopher

et al. 2016

Pathogens and Global Health

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Owing to the burden of multidrug-resistant tuberculosis, molecular techniques have been approved by the WHO for the rapid diagnosis of the same. The objectives of this prospective, diagnostic study, conducted at Christian Medical College, a tertiary care center in South India, were to compare the performance of line probe assay (GenoTypeMTBDRplus) with culture, as well as the Xpert MTB/Rif assay on sputum samples. Ninety-one consecutive suspects of multidrug-resistant pulmonary tuberculosis patients from January 2013 to June 2013 were enrolled in this study and the results of line probe assay compared to culture and Xpert MTB/Rif. Compared to culture, the assay demonstrated a sensitivity and specificity of 81.5% (95%CI 67.4-91.1%) and 87.5% (95%CI 71-96.5%) for the detection of tuberculosis, with sensitivity and specificity of 100% (95%CI 85.2-100%) and 93.8% (95%CI 69.8-99.8%), respectively, for rifampicin resistance. For isoniazid resistance, sensitivity and specificity were 89.3% (95%CI 71.8-97.7%) and 100% (95%CI 71.5-100%), respectively. Compared to Xpert MTB/Rif assay, the assay showed a sensitivity of 80% (95%CI 68.2-88.9%) and specificity of 100% (95%CI 85.8-100%) for the detection of tuberculosis a sensitivity of 94.3% (95%CI 80.8-99.3%) and specificity of 94.1% (95%CI 71.3-99.9%) for rifampicin resistance was attained. This assay performed well on smear positive samples, but poorly on smear negative and scanty samples, and can serve as a rapid diagnostic tool, particularly in isoniazid monoresistant cases of tuberculosis, which are not diagnosed by Xpert MTB/Rif.

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Section: Lpa Compared To Xpert (Mtb/rif) For the Diagnosis Of Tubercusupporting

confidence: 52%

The diagnostic utility of line probe assays for multidrug-resistant tuberculosis

Ninan

Gowri

Christopher

et al. 2016

Pathogens and Global Health

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“…Since its invention by Rothberg et al (2011), Ion Torrent sequencing technology has been successfully applied to complete genomic sequencing, such as in Clostridium sp. BL8 (with Ion Torrent PGM™) (Marathe et al, 2014), and clear characterization of drug-resistant genes, such as in Mycobacterium tuberculosis (Daum et al, 2014). Results can be obtained within five days, comparable to the turnaround time required by current drug sensitivity testing (DST) (Daum et al, 2014).…”

Section: Whole Genome Sequencing Is a Feasible Way To Investigate Thementioning

confidence: 97%

“…BL8 (with Ion Torrent PGM™) (Marathe et al, 2014), and clear characterization of drug-resistant genes, such as in Mycobacterium tuberculosis (Daum et al, 2014). Results can be obtained within five days, comparable to the turnaround time required by current drug sensitivity testing (DST) (Daum et al, 2014). PacBio single-molecule real-time technology has frequently been used to perform whole-genome sequencing of many microorganisms, such as Neisseria gonorrhea (with the PacBio RSII platform), a Gram-negative β proteobacterium responsible for the sexually transmitted infection gonorrhea (Abrams et al, 2015).…”

Section: Whole Genome Sequencing Is a Feasible Way To Investigate Thementioning

confidence: 99%

Antibiotic resistance mechanisms of Myroides sp.

Yuan

et al. 2016

J. Zhejiang Univ. Sci. B

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Bacteria of the genus Myroides (Myroides spp.) are rare opportunistic pathogens. Myroides sp. infections have been reported mainly in China. Myroides sp. is highly resistant to most available antibiotics, but the resistance mechanisms are not fully elucidated. Current strain identification methods based on biochemical traits are unable to identify strains accurately at the species level. While 16S ribosomal RNA (rRNA) gene sequencing can accurately achieve this, it fails to give information on the status and mechanisms of antibiotic resistance, because the 16S rRNA sequence contains no information on resistance genes, resistance islands or enzymes. We hypothesized that obtaining the whole genome sequence of Myroides sp., using next generation sequencing methods, would help to clarify the mechanisms of pathogenesis and antibiotic resistance, and guide antibiotic selection to treat Myroides sp. infections. As Myroides sp. can survive in hospitals and the environment, there is a risk of nosocomial infections and pandemics. For better management of Myroides sp. infections, it is imperative to apply next generation sequencing technologies to clarify the antibiotic resistance mechanisms in these bacteria.

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“…It is operationally feasible to process PS-MTM specimens with PCR in ,7 days from expectoration, even if referred to remotely located laboratories. 19 Samples collected in PS-MTM are compatible with most extraction systems, and PM-PCR works well with several real-time platforms (S V Omar, unpublished data). In other settings, the collection of sputum for PS-MTM/PM-PCR detection could be followed by molecular analysis for drug resistance to further guide treatment.…”

Section: Discussionmentioning

confidence: 99%

Molecular detection of Mycobacterium tuberculosis from sputum transported in PrimeStore® from rural settings

Daum¹,

Peters

Fourie

et al. 2015

int j tuberc lung dis

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Characterization of multi-drug resistantMycobacterium tuberculosisfrom immigrants residing in the USA using Ion Torrent full-gene sequencing

Cited by 19 publications

References 12 publications

The diagnostic utility of line probe assays for multidrug-resistant tuberculosis

The diagnostic utility of line probe assays for multidrug-resistant tuberculosis

Antibiotic resistance mechanisms of Myroides sp.

Molecular detection of <I>Mycobacterium tuberculosis</I> from sputum transported in PrimeStore<SUP>®</SUP> from rural settings

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