Whole genome sequencing and prediction of antimicrobial susceptibilities in non-tuberculous mycobacteria

Solanki, Priya; Lipman, Marc; McHugh, Timothy D; Satta, Giovanni

doi:10.3389/fmicb.2022.1044515

Cited by 5 publications

(3 citation statements)

References 62 publications

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“…Alongside culture-based techniques, speciation can be achieved using line probe assays, matrix-assisted laser desorption ionization–time-of-flight mass spectrometry or gene sequencing. 15 , 16 , 17 , 18 …”

Section: Diagnosismentioning

confidence: 99%

Non-tuberculous mycobacterial pulmonary disease (NTM-PD): Epidemiology, diagnosis and multidisciplinary management

Kumar,

Ponnuswamy,

Capstick

et al. 2024

Clinical Medicine

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Section: Diagnosismentioning

confidence: 99%

Non-tuberculous mycobacterial pulmonary disease (NTM-PD): Epidemiology, diagnosis and multidisciplinary management

Kumar,

Ponnuswamy,

Capstick

et al. 2024

Clinical Medicine

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“…Most NTMs are resistant to anti-TB drugs and antibiotics, further adding to the treatment challenge [5]. China has a high burden of TB, and the isolation rate of NTM is increasing.…”

Section: Introductionmentioning

confidence: 99%

Analysis of the types and characteristics of non-tuberculous mycobacteria in high endemic areas of tuberculosis

Li,

Lou,

et al. 2024

Preprint

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Objective: To understand the epidemiological, demographic and clinical characteristics of non-tuberculous mycobacterial lung disease (NTM-PD) in areas with high incidence of tuberculosis. Methods: A prospective surveillance study was conducted for non-tuberculous mycobacterial(NTM) at the Affiliated Hospital of Zunyi Medical University for five consecutive years. A total of 6259 culture-positive specimens grown on Roche medium between January 2017 and December 2021 were collected. After acid-fast staining, colony morphology, growth time, and p-nitrobenzoic acid detection, suspicious NTM strains were screened and identified by gene sequencing, and the dominant groups were subjected to drug sensitivity test. Results: A total of 107 suspected NTM colonies were screened from 6259 positive cultures, including 51 cases of NTM, 13 cases of MTB, and 43 cases of other bacteria. Among the 51 NTM positive patients, 43.1% were 45-65 years old. All the NTM positive specimens were derived from the respiratory tract. In 2017-2021, the isolation rate of NTM was the highest (1.18%) and the lowest (0.77%), and the main bacterial type was Mycobacterium abscessus (33.33%), followed by Mycobacterium intracellulare (27.45%), Mycobacterium chelates (11.76%), Mycobacterium kansasii (9.80%), Mycobacterium avium (7.84%), Mycobacterium gordonae (3.92%), Mycobacterium smegmatis (3.92%), and Mycobacterium bradyxanthum (1.96%). Other bacteria were dominated by Gordonia spp. The dominant NTM bacteria were Mycobacterium abscessus and Mycobacterium intracellulare, which had a high drug resistance rate. Middle-aged, male, bronchiectasis and serum albumin < 3.5 g/L were risk factors for NTM-PD. Conclusions: The trend of NTM infection rate is stable in this area, but the drug resistance rate is high. M. abscessus is the most common pathogen of NTM. Middle-aged, male patients with bronchiectasis and serum albumin < 3.5 g/L have a high risk of progressing to NTM-PD. In areas with a high incidence of TB, clinicians should make a differential diagnosis between suspected pulmonary TB and NTM infections.

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“…However, it has been pointed that M. abscessus subsp. abscessus (ABS) can develop inducible resistance even without T28 (7), and that although whole genome sequences (WGS) are useful for predicting resistance, they are not sufficient (8,9). We conducted whole-genome sequencing of M. abscessus subsp.…”

Section: Introductionmentioning

confidence: 99%

Worldwide spreading of pMAB625 plasmid encoding MMPL family transporter in multidrug-resistant clinical isolates ofMycobacterium abscessusby horizontal transfer

Ohse,

Yoshida,

Kamada

et al. 2024

Preprint

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In recent years, the number of infections caused by non-tuberculous mycobacteria has increased worldwide, and infections caused byMycobacterium abscessus(M. abscessus) are often difficult to treat due to their multidrug resistance. Research into the mechanisms of multidrug resistance inM. abscessushas focused on genetic mutations but not on genetic mobile elements such as plasmids. We performed a comparative genomic analysis of clinical isolates ofM. abscessuscollected from the same patient at different time points. Antimicrobial susceptibility testing showed that these clinical isolates had decreased susceptibility to carbapenem antibiotics compared to the type strain. Although the isolates had relatively few chromosomal mutations, they harboured three plasmids not found in the type strain. Two of the three plasmids encoded genes such as the ESX secretion system, and the other encoded the MMPL family transporter. We also mapped the sequence data from clinical isolates collected worldwide to these plasmid sequences. The data from 2.2% and 11.3% of isolates were mapped entirely to two of these plasmid sequences, respectively. These results indicate that these plasmids have been horizontally transferred among clinical isolates ofM. abscessusworldwide and provide new insights into the acquisition of multidrug resistance inM. abscessus.Graphical Abstract

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Whole genome sequencing and prediction of antimicrobial susceptibilities in non-tuberculous mycobacteria

Cited by 5 publications

References 62 publications

Non-tuberculous mycobacterial pulmonary disease (NTM-PD): Epidemiology, diagnosis and multidisciplinary management

Non-tuberculous mycobacterial pulmonary disease (NTM-PD): Epidemiology, diagnosis and multidisciplinary management

Analysis of the types and characteristics of non-tuberculous mycobacteria in high endemic areas of tuberculosis

Worldwide spreading of pMAB625 plasmid encoding MMPL family transporter in multidrug-resistant clinical isolates ofMycobacterium abscessusby horizontal transfer

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