Draft genome sequences of Mycolicibacterium peregrinum isolated from a pig with lymphadenitis and from soil on the same Japanese pig farm

Komatsu, Tetsuya; Ohya, Kenji; Sawai, Kotaro; Odoi, Justice Opare; Otsu, Keiko; Ota, Akinobu; Ito, Toshihiro; Kawai, Mikihiko; Maruyama, Fumito

doi:10.1186/s13104-019-4380-3

Cited by 6 publications

(6 citation statements)

References 31 publications

(32 reference statements)

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“…Mycolicibacterium peregrinum was the most frequently isolated RGM from the different wildlife species-sika deer, wild boar, Japanese monkey, Japanese weasel, masked palm civet, and raccoon dog-which strongly suggested that wildlife may acquire Mycolicibacterium peregrinum from their environment. Studies conducted in Japan revealed that the draft genome sequence of Mycolicibacterium peregrinum isolated from a pig affected with lymphadenitis shares close identity with that of Mycolicibacterium peregrinum isolated from the soil of the pig's environment (Komatsu et al 2019). Moreover, the fact that Mycolicibacterium peregrinum was isolated from other animals (e.g., lion; Panthera leo), and from drinking water (Gcebe and Hlokwe 2017;Mohajeri et al 2017) indicates that Mycolicibacterium peregrinum can inhabit several environments.…”

Section: Discussionmentioning

confidence: 99%

“…To provide more information on the ecology and etiology of NTM, we previously presented the genome sequences of Mycolicibacter virginiensis, Mycolicibacter senuensis, and Mycobacterium colombiense isolated from the environment surrounding pigs in Japan (Ito et al 2018a, b). In addition, we analyzed the genome sequences of Mycolicibacterium peregrinum isolated from the lymph nodes of a pig and from the surrounding soil by in silico DNA-DNA hybridization, and the results showed that the two isolates were 100% identical (Komatsu et al 2019), implying circulation of NTM between the animal and the surrounding environment. Although NTM cases have been recorded in both humans and animals, the focus has been on humans more than on animals, especially wildlife.…”

Section: Introductionmentioning

confidence: 99%

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Isolation and Antimicrobial Susceptibilities of Nontuberculous Mycobacteria From Wildlife in Japan

Odoi

Ohya

Moribe

et al. 2020

Journal of Wildlife Diseases

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Nontuberculous mycobacteria (NTM) are opportunistic pathogens of humans and animals and are transmitted among the environment, wildlife, livestock, and humans. The aim of this study was to investigate the rate of isolation and antimicrobial susceptibility of NTM in wildlife. In total, 178 samples of feces ( n=131) and tissues ( n=47) were collected from 11 wildlife species in Gifu Prefecture and Mie Prefecture, Japan, between June 2016 and October 2018. We isolated NTM from 15.3% (20/131) of fecal samples using Ogawa medium, and isolates were identified by sequencing the rpoB and hsp65 genes. The rpoB sequences were compared with those from other strains of human and environmental origin. The NTM isolates were obtained from sika deer ( Cervus nippon), wild boar ( Sus scrofa), Japanese monkey ( Macaca fuscata), raccoon dog ( Nyctereutes procyonoides), masked palm civet ( Paguma larvata), and Japanese weasel ( Mustela itatsi) and were classified as rapidly growing mycobacteria (RGM) and slowly growing mycobacteria (SGM). The 12 RGM identified were Mycolicibacterium peregrinum ( n=5), Mycolicibacterium fortuitum ( n=3), Mycolicibacterium septicum ( n=3), and Mycolicibacterium thermoresistibile ( n=1), and the eight SGM were Mycobacterium paraense ( n=4), Mycolicibacter arupensis ( n=2), Mycolicibacter virginiensis ( n=1), and Mycobacterium nebraskense ( n=1). The NTM from wildlife showed ≥99% similarity with strains from different sources including humans. The RGM were susceptible to the antimicrobial agents tested except for M. fortuitum, which was resistant to azithromycin and clarithromycin. The SGM showed multiple drug resistance qualities but were susceptible to amikacin, clarithromycin, and rifabutin. These results indicate that wildlife may be reservoir hosts of NTM in Japan. The presence of antimicrobial-resistant NTM in wildlife suggests that the trends of NTM antimicrobial susceptibility in wildlife should be monitored.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Isolation and Antimicrobial Susceptibilities of Nontuberculous Mycobacteria From Wildlife in Japan

Odoi

Ohya

Moribe

et al. 2020

Journal of Wildlife Diseases

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“…Additionally, in the NCBI database, there is a bias as only genomes of defined species are associated with plasmids. Moreover, despite several reports of Mycolicibacterium genomes [15][16][17][18][19][20][21][22][23][24][25][26], these studies rarely survey plasmids among their contigs. Thus, only a few plasmids have been reported in this genus, mainly from unrecognized genomes [2,14,[27][28][29][30].…”

Section: Introductionmentioning

confidence: 99%

Comprehensive in silico survey of the Mycolicibacterium mobilome reveals an as yet underexplored diversity

Morgado

Moreno-Vicente

2021

Microbial Genomics

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The mobilome plays a crucial role in bacterial adaptation and is therefore a starting point to understand and establish the gene flow occurring in the process of bacterial evolution. This is even more so if we consider that the mobilome of environmental bacteria can be the reservoir of genes that may later appear in the clinic. Recently, new genera have been proposed in the family Mycobacteriaceae , including the genus Mycolicibacterium , which encompasses dozens of species of agricultural, biotechnological, clinical and ecological importance, being ubiquitous in several environments. The current scenario in the Mycobacteriaceae mobilome has some bias because most of the characterized mycobacteriophages were isolated using a single host strain, and the few plasmids reported mainly relate to the genus Mycobacterium . To fill in the gaps in these issues, we performed a systematic in silico study of these mobile elements based on 242 available genomes of the genus Mycolicibacterium . The analyses identified 156 putative plasmids (19 conjugative, 45 mobilizable and 92 non-mobilizable) and 566 prophages in 86 and 229 genomes, respectively. Moreover, a contig was characterized by resembling an actinomycete integrative and conjugative element (AICE). Within this diversity of mobile genetic elements, there is a pool of genes associated with several canonical functions, in addition to adaptive traits, such as virulence and resistance to antibiotics and metals (mercury and arsenic). The type-VII secretion system was a common feature in the predicted plasmids, being associated with genes encoding virulent proteins (EsxA, EsxB, PE and PPE). In addition to the characterization of plasmids and prophages of the family Mycobacteriaceae , this study showed an abundance of these genetic elements in a dozen species of the genus Mycolicibacterium .

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“…This may contribute to their diversity and evolution or even to their success as opportunistic pathogens (33). Studies conducted in Japan suggest that livestock could acquire Mycolicibacterium peregrinum from their environment (34). Presence of Mycolicibacterium representatives containing a set of ARGs in the natural environment could be a reservoir of genes for potential development of resistance in pathogenic groups.…”

Section: Resultsmentioning

confidence: 99%

Genome-resolved insight into the reservoir of antibiotic resistance genes in an aquatic microbial community

Goodarzi

Asad

Mehrshad

2022

Preprint

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Aquatic microbial communities are an important reservoir of Antibiotic Resistance Genes. However, distribution and diversity of different ARG categories in environmental microbes with different ecological strategies is not yet well studied. Despite the potential exposure of the southern part of the Caspian Sea to the release of antibiotics, little is known about its natural resistome profile. We used a combination of Hidden Markov model (HMM), homology alignment and a deep learning approach for comprehensive screening of the diversity and distribution of ARGs in the Caspian Sea metagenomes at a genome resolution. Detected ARGs were classified into five antibiotic resistance categories including Prevention of access to target (44%), Modification/protection of targets (30%), Direct modification of antibiotics (22%), Stress resistance (3%), and Metal resistance (1%). The 102 detected ARG containing metagenome-assembled genomes of the Caspian Sea were dominated by representatives of Acidimicrobiia, Gammaproteobacteria and Actinobacteria classes. Comparative analysis revealed that the highly abundant, oligotrophic, and genome streamlined representatives of taxa Acidimicrobiia and Actinobacteria modify the antibiotics target via mutation to develop antibiotic resistance rather than carrying extra resistance genes. Our results help with understanding how the encoded resistance categories of each genome are aligned with their ecological strategies.

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Draft genome sequences of Mycolicibacterium peregrinum isolated from a pig with lymphadenitis and from soil on the same Japanese pig farm

Cited by 6 publications

References 31 publications

Isolation and Antimicrobial Susceptibilities of Nontuberculous Mycobacteria From Wildlife in Japan

Isolation and Antimicrobial Susceptibilities of Nontuberculous Mycobacteria From Wildlife in Japan

Comprehensive in silico survey of the Mycolicibacterium mobilome reveals an as yet underexplored diversity

Genome-resolved insight into the reservoir of antibiotic resistance genes in an aquatic microbial community

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