Comparative genome analyses of Mycobacteroides immunogenum reveals two potential novel subspecies

Abstract

Mycobacteroides immunogenum is an emerging opportunistic pathogen implicated in nosocomial infections. Comparative genome analyses may provide better insights into its genomic structure, functions and evolution. The present analysis showed that M. immunogenum has an open pan-genome. Approximately 36.8% of putative virulence genes were identified in the accessory regions of M. immunogenum . Phylogenetic analyses revealed two potential novel subspecies of M. immunogenum , supported by evidence from ANIb (average nucleotide identity using blast) and GGDC (Genome to Genome Distance Calculator) analyses. We identified 74 genomic islands (GIs) in Subspecies 1 and 23 GIs in Subspecies 2. All Subspecies 2-harboured GIs were not found in Subspecies 1, indicating that they might have been acquired by Subspecies 2 after their divergence. Subspecies 2 has more defence genes than Subspecies 1, suggesting that it might be more resistant to the insertion of foreign DNA and probably explaining why Subspecies 2 has fewer GIs. Positive selection analysis suggest that M. immunogenum has a lower selection pressure compared to non-pathogenic mycobacteria. Thirteen genes were positively selected and many were involved in virulence.

Pathology, microbiology, and genetic diversity associated with Erysipelothrix rhusiopathiae and novel Erysipelothrix spp. infections in southern sea otters (Enhydra lutris nereis)

“…The second isolate, 4724–06, shared 95.3% ANI and 59.1% GGD to isolate 4322–04 but increased similarity to E. rhusiopathiae type strains ATCC 19414 (ANI: 97.4%; dDDH: 78.3%), NCTC 8163 (ANI: 97.3%; dDDH: 78.6%) and NCTC 7999 (ANI: 97.3%; dDDH: 77.6%), with ANI (>95%; <98%) and dDDH (>70%; <80%) values in the subspecies range for the three E. rhusiopathiae type strains ( Bannantine et al, 2020 ; Choo et al, 2020 ; Pearce et al, 2021 ), suggesting isolate 4724-06 represents a novel subspecies. Herein, the name Erysipelothrix rhusiopathiae ohloneorum ssp.…”

“…NZ_OW659496) ( Table 2 ; Zhong et al, 2022 ). ANI values >96% and dDDH values >70% indicate the same species ( Auch et al, 2010 ; Meier-Kolthoff et al, 2013 ; Ciufo et al, 2018 ), while ANI values >98% and dDDH values >80% suggest the same subspecies ( Meier-Kolthoff et al, 2014 ; Bannantine et al, 2020 ; Choo et al, 2020 ; Pearce et al, 2021 ). At the genome level, isolate 4322–04 shared <95% ANI to E. rhusiopathiae type strain ATCC 19414 (94.7%) and isolates NCTC 8163 (94.7%) and NCTC 7999 (94.6%), while exhibiting <60% dDDH similarity to the same strains ( Table 3 ).…”

Premise Plumbing Pipe Materials and In-Building Disinfectants Shape the Potential for Proliferation of Pathogens and Antibiotic Resistance Genes

“…At week 30, monochloramine addition increased the normalized abundance of oxidative stress genes relative to all other disinfected conditions (Dunn’s test, p < 0.013). This is perhaps a result of the selective pressure incurred by monochloramine that favors mycobacteria, which tend to be disinfectant resistant , and to carry robust oxidative stress resistance mechanisms. , This effect was reversed by week 37 when disinfectants were removed. Nitrification/denitrification genes were more abundant in copper than PVC (Dunn’s test, p = 0.0031) and iron (Dunn’s test, p < 0.001) conditions (Figure S21), which are consistent with nitrogen-fixing Bradyrhizobium also being more prevalent in the copper conditions and indirectly stimulating nitrifiers/denitrifiers.…”

Genome characterisation and comparative analysis of Schaalia dentiphila sp. nov. and its subspecies, S. dentiphila subsp. denticola subsp. nov., from the human oral cavity

“…The 16S rRNA gene phylogeny was inferred with 16S rRNA gene sequences of twelve Schaalia type strains and Actinomyces naeslundii JCM 8349 T from the NCBI database. Similarly, multiple ( gene/loci ) sequence analyses were conducted according to previously described methods [ 19 ]. The sequences of five housekeeping genes, including atpA (ATP synthase subunit alpha), rpoB (RNA polymerase, β-subunit), pgi (glucose-6-phosphate isomerase), metG (methionyl-tRNA synthetase), and gyrA (DNA gyrase subunit A) were extracted from RAST genome annotation.…”

“…The threshold values for species delineation below 95—96% similarity for ANI and AAI, respectively. The threshold value above 96% and up to 99.5% similarity, indicates that the strains are the same species but potentially different subspecies [ 19 , 30 , 31 ].…”