Genomic characterization of Nontuberculous Mycobacteria

Fedrizzi, Tarcisio; Meehan, Conor J.; Grottola, Antonella; Giacobazzi, Elisabetta; Serpini, Giulia Fregni; Tagliazucchi, Sara; Fabio, Anna; Bettua, Clotilde; Bertorelli, Roberto; Sanctis, Veronica De; Rumpianesi, Fabio; Pecorari, Monica; Jousson, Olivier; Tortoli, Enrico; Segata, Nicola

doi:10.1038/srep45258

Cited by 182 publications

(218 citation statements)

References 77 publications

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“…Input genomes for pan-genome construction were first annotated using Prokka [31]. We identified homologous gene clusters at an amino acid identity threshold of 80% [32][33][34][35]. Panand core genome curves were generated via 30 input order permutations (similar to the approach in the GET_HOMOLOGUES pan-genome pipeline [36].…”

Section: Pan-genome Reconstructionmentioning

confidence: 99%

Disentangling the impact of environmental and phylogenetic constraints on prokaryotic strain diversity

Maistrenko¹,

Mende

Lϋetge

et al. 2019

Preprint

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Microbial organisms inhabit virtually all environments and encompass a vast biological diversity. The pan-genome concept aims to facilitate an understanding of diversity within defined phylogenetic groups. Hence, pan-genomes are increasingly used to characterize the strain diversity of prokaryotic species. To understand the interdependency of pan-genome features (such as numbers of core and accessory genes) and to study the impact of environmental and phylogenetic constraints on the evolution of conspecific strains, we computed pan-genomes for 155 phylogenetically diverse species using 7000 high-quality genomes. We show that many pan-genome features such as functional diversity and core genome nucleotide diversity are correlated to each other. Further, habitat flexibility as approximated by species ubiquity is associated with several pan-genome features, particularly core genome size. In general, environment had a stronger impact on pan-genome features than phylogenetic signal. Similar environmental preferences led to convergent evolution of pangenomic features in distant phylogenetic clades. For example, the soil environment promotes expansion of pan-genome size, while host-associated habitats lead to its reduction.

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Section: Pan-genome Reconstructionmentioning

confidence: 99%

Disentangling the impact of environmental and phylogenetic constraints on prokaryotic strain diversity

Maistrenko¹,

Mende

Lϋetge

et al. 2019

Preprint

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“…This ranges, in A, B and M, from 15 to 36. In contrast, in a recent study [19] from our laboratory evaluating genomes of 41 species belonging to the genus Mycobacterium we detected an average of 1027.35 unique genes per species (median 832). This is two magnitude orders higher in comparison with the quoted differences in A, B and M from Adekambi et al…”

mentioning

confidence: 55%

Mycobacterium abscessus, a taxonomic puzzle

Tortoli

Kohl

Trovato

et al. 2018

International Journal of Systematic and Evolutionary Microbiology

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We read with interest the paper of Adekambi and coworkers [1] suggesting the reinstatement of Mycobacterium abscessus subsp. abscessus (A), M. abscessus subsp. massiliense (M) and M. abscessus subsp. bolletii (B) as independent species.This paper is in clear contradiction with our own recent work [2] published in 2016.The claim of the authors (1st page) that postgenomic analysis 'unambiguously supports the reinstatement of species' seems to us at least highly questionable; in none of the studies they cited in their paper [3][4][5][6][7][8], with the exception of one study [9] done in collaboration with the same authors, is the status of subspecies questioned.A major argument supporting the suggestion of Adekambi et al. was published by him in 2008 [10]. The major conclusions of this work were that 1) an rpoB gene similarity 97.7 % correlates with a DNA-DNA Hybridization (DDH) <70 %; and 2) the DDH may be inferred by the formula: 5.98(rpoB similarity)-2516.1.In the 3840 bp sequence of the rpoB gene obtained when the sequences of the type strains of A, B and M (deposited by Adekambi et al. in GenBank; AY147164, AY859692 and AY593981), have been cut to start and end at the same nucleotide positions, we obtained the following similarity values: A versus M=98.07 %; A v B=97.86 %; M v B=98.51 %; each of them corresponding to DDH>70 %.Adekambi et al. questioned our data produced, performing the wet lab DDH test with five replicates [11]. Instead they proposed results (Table 2 of [10]) inferred from rpoB similarity using the above mentioned formula. In our view, it is not valid to replace a complex assay that takes into account the whole genome (which is still considered the gold standard), with a formula based on just a single gene.Bioinformatic algorithms are available and validated in multiple studies, which can be used to infer the DDH from genomic data. The best known, in addition to Average Nucleotide Identity (ANI) [12], are the Genome to Genome Distance (GGD) [13,14] and the Genomic Signature-Delta Difference (GS-DD) [15].In our work we calculated the GGD, which is the equivalent in silico of DDH, using the software available at http://ggdc. dsmz.de/ggdc.php and obtained the following DDH-equivalent results: A v M=84.7 %; A v B=86.10 %; M v B=87.70 %; all clearly >70 % and not supportive of the status of independent species [12].We also calculated the GS-DD using the software available at www.cmbl.uga.edu/software/delta-differences.html, which again did not support the hypothesis of independent species (Table 1).We disagree, furthermore, in the assertion of Adekambi at al. (third page) in which we are said to have stated that ANI values >98.3 % are needed to support the status of subspecies. Fig. 1 of our paper [2] reports the results of our analysis of 46 genomes (43 clinical isolates+3 type strains) showing the ANI variability which, among strains belonging to the three taxa (A, B and M), ranged from 96.6 to 97.6 %. Within each single taxon (A or B or M), this variability ranged from 98.5 to 99.9 %. Therefore ...

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“…The enrichment of mycobacterial MAGs with AMR traits in Dis systems can be attributed to several factors. For instance, mycobacteria are known to harbour intrinsic antibiotic resistance 76 and their colonization, survival, and persistence in DWDS and their resistance to disinfectants at low nutrient concentrations has been well documented 77–79 . Further, intracellular colonization of mycobacteria in protozoa may allow for survival and proliferation of these genera 80 and sheltering within biofilms can also enhance their survival 79,81–83 .…”

Section: Resultsmentioning

confidence: 99%

Disinfectant residuals in drinking water systems select for mycobacterial populations with intrinsic antimicrobial resistance

Sevillano¹,

Dai

Calus

et al. 2019

Preprint

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22Antimicrobial resistance (AMR) in drinking water has received less attention than 23 counterparts in the urban water cycle. While culture-based techniques or gene-centric 24 PCR have been used to probe the impact of treatment approaches (e.g., disinfection) on 25 AMR in drinking water, to our knowledge there is no systematic comparison of AMR 26 traits between disinfected and disinfectant residual-free drinking water systems. We use 27 metagenomics to assess the associations between disinfectant residuals and AMR 28 prevalence and its host association in full-scale drinking water distribution systems 29 (DWDSs). The differences in AMR profiles between DWDSs are associated with the 30 presence or absence of disinfectant. Further, AMR genes and mechanisms enriched in 31 disinfected systems are associated with drug classes primarily linked to nontuberculous 32 mycobacteria (NTM). Finally, evaluation of metagenome assembled genomes (MAGs) 33 of NTM indicates that they possess AMR genes conferring intrinsic resistance to key 34 antibiotics, whereas such NTM genomes were not detected in disinfectant residual free 35DWDSs. Thus, disinfection may not only influence the AMR profiles of the drinking 36 water microbiome but also select for NTM with intrinsic AMR. 37 38 39 Regulation compliant drinking water can contain low concentrations of chemicals and 41 microorganisms originating from source water, treatment process, distribution systems, 42 and premises plumbing 1,2 . While our understanding of chemical contaminants (e.g., 43 disinfection by-products (DBP) 3 ) and microbial populations 4-6 in treated drinking water 44 is increasing, the drinking water field has only recently started investigating emerging 45 biological contaminants 7 like antibiotic resistance bacteria (ARB) and antibiotic 46 resistance genes (ARG). Misuse of antibiotics and anthropogenic release of bioactive 47 compounds into the urban water cycle exacerbate the prevalence and persistence of 48 antimicrobial resistance (AMR) and can make engineered systems for water treatment 49 (i.e., wastewater and drinking water) critical points of AMR dissemination 8,9 . Drinking 50 water can constitute a potential exposure route to microorganisms with intrinsic and 51 acquired antibiotic resistance genes (i.e., resistome 10 ), and it is particularly concerning 52 if AMR traits are associated with waterborne pathogens 11 . 53 54Drinking water disinfection is one of the most important public health advances towards 55 elimination of waterborne diseases and remains the most widely used treatment strategy 56 today for pathogen control 12 . Typically, drinking water systems (DWS) maintain a 57 disinfectant residual, usually chlorine, in the drinking water distribution system 58 (DWDS) to minimize microbial growth. However, its unintended impacts (e.g., DBP 59 formation) have prompted the evaluation of alternative strategies to mitigate associated 60 risks. These range from the use of alternate disinfectants such as chloramines, to 61 advanced oxidation processes th...

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Genomic characterization of Nontuberculous Mycobacteria

Cited by 182 publications

References 77 publications

Disentangling the impact of environmental and phylogenetic constraints on prokaryotic strain diversity

Disentangling the impact of environmental and phylogenetic constraints on prokaryotic strain diversity

Mycobacterium abscessus, a taxonomic puzzle

Disinfectant residuals in drinking water systems select for mycobacterial populations with intrinsic antimicrobial resistance

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