Whole-genome Phylogenetic Analysis of Complex from Clinical Respiratory Samples

Overview

Journal Microbiol Spectr

Date 2025 Jan 10

PMID 39792017

Authors

Chew Ka Lip

Joelle Go

Nur Aisyah Binte Abu Bakar

Sophie Octavia

Raymond Tzer Pin Lin

Jeanette W P Teo

Affiliations

Soon will be listed here.

Abstract

Importance: complex (MAC) infections are increasingly challenging to manage due to their complex species diversity and varied resistance patterns. This study underscores the genetic diversity within MAC, identifying at least eight species and subspecies among 203 clinical isolates, with subsp. (MAH) being most prevalent at 72.9%. Notably, genetic clustering was observed within MAH and subsp. , suggesting potential transmission routes within healthcare settings. Clarithromycin and amikacin resistance was found to be uncommon, aligning with the rarity of resistance-associated genetic mutations. These findings emphasize the need for enhanced infection control measures and routine susceptibility testing to tailor antibiotic therapies effectively.

References

Koh W, Hong G, Kim S, Jeong B, Park H, Jeon K . Treatment of refractory Mycobacterium avium complex lung disease with a moxifloxacin-containing regimen. Antimicrob Agents Chemother. 2013; 57(5):2281-5. PMC: 3632919. DOI: 10.1128/AAC.02281-12. View

Kim S, Jhun B, Moon S, Shin S, Jeon K, Kwon O . Mutations in and in Moxifloxacin-Resistant Mycobacterium avium Complex and Mycobacterium abscessus Complex Clinical Isolates. Antimicrob Agents Chemother. 2018; 62(9). PMC: 6125518. DOI: 10.1128/AAC.00527-18. View

van Tonder A, Ellis H, Churchward C, Kumar K, Ramadan N, Benson S . complex genomics and transmission in a London hospital. Eur Respir J. 2022; 61(4). PMC: 10116071. DOI: 10.1183/13993003.01237-2022. View

Busatto C, Vianna J, da Silva Junior L, Ramis I, da Silva P . Mycobacterium avium: an overview. Tuberculosis (Edinb). 2019; 114:127-134. DOI: 10.1016/j.tube.2018.12.004. View

Stamatakis A . RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. 2014; 30(9):1312-3. PMC: 3998144. DOI: 10.1093/bioinformatics/btu033. View

Daley C, Iaccarino J, Lange C, Cambau E, Wallace Jr R, Andrejak C . Treatment of nontuberculous mycobacterial pulmonary disease: an official ATS/ERS/ESCMID/IDSA clinical practice guideline. Eur Respir J. 2020; 56(1). PMC: 8375621. DOI: 10.1183/13993003.00535-2020. View

Fernandez-Pittol M, Batista-Arnau S, Roman A, Nicolas L, Oliver L, Gonzalez-Moreno O . Differences in Drug-Susceptibility Patterns between , , and Clinical Isolates: Prospective 8.5-Year Analysis by Three Laboratories. Antibiotics (Basel). 2023; 12(1). PMC: 9854862. DOI: 10.3390/antibiotics12010064. View

Kim S, Kim D, Moon S, Song J, Huh H, Lee N . Association between 16S rRNA gene mutations and susceptibility to amikacin in Mycobacterium avium Complex and Mycobacterium abscessus clinical isolates. Sci Rep. 2021; 11(1):6108. PMC: 7969740. DOI: 10.1038/s41598-021-85721-5. View

Simao F, Waterhouse R, Ioannidis P, Kriventseva E, Zdobnov E . BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics. 2015; 31(19):3210-2. DOI: 10.1093/bioinformatics/btv351. View

10.

Sommerstein R, Hasse B, Marschall J, Sax H, Genoni M, Schlegel M . Global Health Estimate of Invasive Mycobacterium chimaera Infections Associated with Heater-Cooler Devices in Cardiac Surgery. Emerg Infect Dis. 2018; 24(3):576-578. PMC: 5823345. DOI: 10.3201/eid2403.171554. View

11.

Hasan N, Davidson R, Epperson L, Kammlade S, Beagle S, Levin A . Population Genomics and Inference of Mycobacterium avium Complex Clusters in Cystic Fibrosis Care Centers, United States. Emerg Infect Dis. 2021; 27(11):2836-2846. PMC: 8544995. DOI: 10.3201/eid2711.210124. View

12.

Sirichoat A, Kaewprasert O, Hinwan Y, Faksri K . Phenotypic drug-susceptibility profiles and genetic analysis based on whole-genome sequencing of Mycobacterium avium complex isolates in Thailand. PLoS One. 2023; 18(11):e0294677. PMC: 10664917. DOI: 10.1371/journal.pone.0294677. View

13.

Maurer F, Pohle P, Kernbach M, Sievert D, Hillemann D, Rupp J . Differential drug susceptibility patterns of Mycobacterium chimaera and other members of the Mycobacterium avium-intracellulare complex. Clin Microbiol Infect. 2018; 25(3):379.e1-379.e7. DOI: 10.1016/j.cmi.2018.06.010. View

14.

Chang C, Chen L, Yu C, Hsueh P, Chien J . Different clinical features of patients with pulmonary disease caused by various Mycobacterium avium-intracellulare complex subspecies and antimicrobial susceptibility. Int J Infect Dis. 2020; 98:33-40. DOI: 10.1016/j.ijid.2020.06.019. View

15.

Letunic I, Bork P . Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res. 2016; 44(W1):W242-5. PMC: 4987883. DOI: 10.1093/nar/gkw290. View

16.

Wetzstein N, Kohl T, Andres S, Schultze T, Geil A, Kim E . Comparative analysis of phenotypic and genotypic antibiotic susceptibility patterns in Mycobacterium avium complex. Int J Infect Dis. 2020; 93:320-328. DOI: 10.1016/j.ijid.2020.02.059. View

17.

Kim S, Jhun B, Moon S, Jeon K, Kwon O, Huh H . Genetic mutations in linezolid-resistant Mycobacterium avium complex and Mycobacterium abscessus clinical isolates. Diagn Microbiol Infect Dis. 2018; 94(1):38-40. DOI: 10.1016/j.diagmicrobio.2018.10.022. View

18.

Lim A, Chotirmall S, Fok E, Verma A, De P, Goh S . Profiling non-tuberculous mycobacteria in an Asian setting: characteristics and clinical outcomes of hospitalized patients in Singapore. BMC Pulm Med. 2018; 18(1):85. PMC: 5964916. DOI: 10.1186/s12890-018-0637-1. View

19.

Bryant J, Grogono D, Rodriguez-Rincon D, Everall I, Brown K, Moreno P . Emergence and spread of a human-transmissible multidrug-resistant nontuberculous mycobacterium. Science. 2016; 354(6313):751-757. PMC: 5142603. DOI: 10.1126/science.aaf8156. View

20.

Nishiuchi Y, Tamura A, Kitada S, Taguri T, Matsumoto S, Tateishi Y . Mycobacterium avium complex organisms predominantly colonize in the bathtub inlets of patients' bathrooms. Jpn J Infect Dis. 2009; 62(3):182-6. View