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Genome sequencing of Mycobacterium pinnipedii strains: genetic characterization and evidence of superinfection in a South American sea lion (Otaria flavescens).

ABSTRACT: BACKGROUND:Mycobacterium pinnipedii, a member of the Mycobacterium tuberculosis Complex (MTBC), is capable of infecting several host species, including humans. Recently, ancient DNA from this organism was recovered from pre-Columbian mummies of Peru, sparking debate over the origin and frequency of tuberculosis in the Americas prior to European colonization. RESULTS:We present the first comparative genomic study of this bacterial species, starting from the genome sequencing of two M. pinnipedii isolates (MP1 and MP2) obtained from different organs of a stranded South American sea lion. Our results indicate that MP1 and MP2 differ by 113 SNPs (single nucleotide polymorphisms) and 46 indels, constituting the first report of a mixed-strain infection in a sea lion. SNP annotation analyses indicate that genes of the VapBC family, a toxin-antitoxin system, and genes related to cell wall remodeling are under evolutionary pressure for protein sequence change in these strains. OrthoMCL analysis with seven modern isolates of M. pinnipedii shows that these strains have highly similar proteomes. Gene variations were only marginally associated with hypothetical proteins and PE/PPE (proline-glutamate and proline-proline-glutamate, respectively) gene families. We also detected large deletions in ancient and modern M. pinnipedii strains, including a few occurring only in modern strains, indicating a process of genome reduction occurring over the past one thousand years. Our phylogenomic analyses suggest the existence of two modern clusters of M. pinnipedii associated with geographic location, and possibly host species, and one basal node associated with the ancient M. pinnipedii strains. Previously described MiD3 and MiD4 deletions may have occurred independently, twice, over the evolutionary course of the MTBC. CONCLUSION:The presence of superinfection (i.e. mixed-strain infection) in this sea lion suggests that M. pinnipedii is highly endemic in this population. Mycobacterium pinnipedii proteomes of the studied isolates showed a high degree of conservation, despite being under genomic decay when compared to M. tuberculosis. This finding indicates that further genomes need to be sequenced and analyzed to increase the chances of finding variably present genes among strains or that M. pinnipedii genome remodeling occurred prior to bacterial speciation.

SUBMITTER: Silva-Pereira TT

PROVIDER: S-EPMC6937676 | biostudies-literature | 2019 Dec

REPOSITORIES: biostudies-literature

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Genome sequencing of Mycobacterium pinnipedii strains: genetic characterization and evidence of superinfection in a South American sea lion (Otaria flavescens).

Silva-Pereira Taiana T TT Ikuta Cássia Y CY Zimpel Cristina K CK Camargo Naila C S NCS de Souza Filho Antônio F AF Ferreira Neto José S JS Heinemann Marcos B MB Guimarães Ana M S AMS

BMC genomics 20191230 1

<h4>Background</h4>Mycobacterium pinnipedii, a member of the Mycobacterium tuberculosis Complex (MTBC), is capable of infecting several host species, including humans. Recently, ancient DNA from this organism was recovered from pre-Columbian mummies of Peru, sparking debate over the origin and frequency of tuberculosis in the Americas prior to European colonization.<h4>Results</h4>We present the first comparative genomic study of this bacterial species, starting from the genome sequencing of two ...[more]

PMID: 31888476

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Project description:Respiratory mites of the genera Orthohalarachne and Halarachne (Acari: Halarachnidae) are causative agents of nasopharyngeal/nasopulmonary acariasis in pinnipeds and sea otters. Until now, these endoparasitic mites were mainly diagnosed via necropsies and invasive procedures. So far, non-invasive diagnostic techniques have neither been developed nor applied in free-ranging pinnipeds. In the current study, we aimed to evaluate the halarachnid mite infestation status of free-ranging "urban" South American sea lions Otaria flavescens in the city of Valdivia, Chile. Therefore, non-invasive sampling methods were used in the current study, e. g. by observation-based sampling of freshly expectorated nasal mucus in the animal environment. Further, collection devices were developed for target-oriented sampling of sneezed nasal mucus, including sterile petri dishes and stretched clingfilms mounted on telescopic rods. Applying these techniques, 26 individual sputum samples were collected. 11.5% of sputum samples proved positive for halarachnid larvae (in total, n = 7), which were morphologically identified as Orthohalarachne attenuata (n = 2) or Orthohalarachne diminuata (n = 5). In one of the individual sea lion mucus samples, both Orthohalarachne species were detected, thereby confirming a patent co-infestation in vivo. 16S rDNA-based molecular identification of individual Orthohalarachne spp. larvae confirmed morphological findings. For the first time, we here molecularly characterized Orthohalarachne spp. on the basis of three gene regions [18S, 28S and the internal transcribed spacer 1 (ITS1)]. Overall, current data include the successful application of non-invasive techniques to sample halarachnid mites from free-ranging synanthropic pinnipeds and contribute to the current knowledge on respiratory mites infesting South American sea lions by combining morphological and molecular methods to overcome challenges in species identification. This study should further serve as baseline study and calls for more research on occurrence, biology and health implications of orthohalarachnosis in free-living as well as captive pinnipeds.

Dataset Information

Genome sequencing of Mycobacterium pinnipedii strains: genetic characterization and evidence of superinfection in a South American sea lion (Otaria flavescens).

Publications

Genome sequencing of Mycobacterium pinnipedii strains: genetic characterization and evidence of superinfection in a South American sea lion (Otaria flavescens).

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