Draft Genome Sequences of Four Axenic Mycoplasma genitalium Strains Isolated from Denmark, Japan, and Australia

McGowin, Chris L.; Ma, Liang; Jensen, Jørgen Skov; Mancuso, Miriam; Hamasuna, Ryoichi; Adegboye, David; Martín, David H.

doi:10.1128/jb.01478-12

Cited by 10 publications

(6 citation statements)

References 11 publications

(9 reference statements)

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“…Phylogenetic analysis was performed using the isolates read data (this study) and the published [ 22 ] genomes of samples M2321, M6280, M6320 and M2288 (accession numbers [GenBank: CP003770–3], respectively). Fastq data was generated from published genomes by simulating short-read data in silico .…”

Section: Methodsmentioning

confidence: 99%

“…Despite their importance to human health, there are only 5 fully sequenced M. genitalium genomes to date, largely because of the fastidious nature and slow growth of the organism. They include the recent draft genomes of four M. genitalium strains isolated from patients in Denmark, Japan, and Australia [ 22 ], which were obtained from axenic cultures raised from single colonies and took up to a year to grow from a swab or urine specimens; a procedure normally involving 2 to 15 passages in Vero cells [ 23 , 24 ]. To increase our understanding of the population framework and diversity of M. genitalium we sequenced a set of 21 geographically and temporally diverse M. genitalium strains (1 of them with three isolates from the same patient) as well as other 5 strains available from the ATCC.…”

Section: Introductionmentioning

confidence: 99%

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Mycoplasma genitalium: whole genome sequence analysis, recombination and population structure

et al. 2017

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BackgroundAlthough Mycoplasma genitalium is a common sexually transmitted pathogen causing clinically distinct diseases both in male and females, few genomes have been sequenced up to now, due mainly to its fastidious nature and slow growth. Hence, we lack a robust phylogenetic framework to provide insights into the population structure of the species. Currently our understanding of the nature and diversity of M. genitalium relies on molecular tests targeting specific genes or regions of the genome and knowledge is limited by a general under-testing internationally. This is set against a background of drug resistance whereby M. genitalium has developed resistance to mainly all therapeutic antimicrobials.ResultsWe sequenced 28 genomes of Mycoplasma genitalium from temporally (1980–2010) and geographically (Europe, Japan, Australia) diverse sources. All the strain showed essentially the same genomic content without any accessory regions found. However, we identified extensive recombination across their genomes with a total of 25 regions showing heightened levels of SNP density. These regions include the MgPar loci, associated with host interactions, as well as other genes that could also be involved in this role. Using these data, we generated a robust phylogeny which shows that there are two main clades with differing degrees of genomic variability. SNPs found in region V of 23S rRNA and parC were consistent with azithromycin/erythromycin and fluoroquinolone resistances, respectively, and with their phenotypic MIC data.ConclusionsThe sequence data here generated is essential for designing rational approaches to type and track Mycoplasma genitalium as antibiotic resistance increases. It represents a first approach to its population genetics to better appreciate the role of this organism as a sexually transmitted pathogen.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4399-6) contains supplementary material, which is available to authorized users.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Mycoplasma genitalium: whole genome sequence analysis, recombination and population structure

et al. 2017

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“…These comprised four plant glycolytic parasite species ( Candidatus Phytoplasma asteris [53], Candidatus Phytoplasma austrailense [54], Candidatus Phytoplasma mali [55], Candidatus Phytoplasma solani [56], Candidatus Phytoplasma strawberry [57]), five animal glycolytic parasite species ( Mycoplasma conjunctivae [58], Mycoplasma genitalium [59], Mycoplasma haemocanis [60], Mycoplasma hyopneumoniae [61], Mycoplasma parvum [62]) and seven parasite species known to obtain energy from catabolism of amino acids or amino sugars ( Mycoplasma arthritidis [63], Mycoplasma capricolum [PRJNA16208], Mycoplasma fermentans [64], Mycoplasma hominis [23], Mycoplasma penetrans [65], Mycoplasma putrefaciens [66], Mycoplasma synoviae [67]). A further four parasite species were used for testing the predictive capacity of the model for synonymous codon use ( Mycoplasma crocodyli [68], Mycoplasma hyorhinis [69], Mycoplasma leachii [70], Mycoplasma mycoides [70]).…”

Section: Methodsmentioning

confidence: 99%

Dietary nitrogen alters codon bias and genome composition in parasitic microorganisms

Seward

Kelly

2016

Genome Biol

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BackgroundGenomes are composed of long strings of nucleotide monomers (A, C, G and T) that are either scavenged from the organism’s environment or built from metabolic precursors. The biosynthesis of each nucleotide differs in atomic requirements with different nucleotides requiring different quantities of nitrogen atoms. However, the impact of the relative availability of dietary nitrogen on genome composition and codon bias is poorly understood.ResultsHere we show that differential nitrogen availability, due to differences in environment and dietary inputs, is a major determinant of genome nucleotide composition and synonymous codon use in both bacterial and eukaryotic microorganisms. Specifically, low nitrogen availability species use nucleotides that require fewer nitrogen atoms to encode the same genes compared to high nitrogen availability species. Furthermore, we provide a novel selection-mutation framework for the evaluation of the impact of metabolism on gene sequence evolution and show that it is possible to predict the metabolic inputs of related organisms from an analysis of the raw nucleotide sequence of their genes.ConclusionsTaken together, these results reveal a previously hidden relationship between cellular metabolism and genome evolution and provide new insight into how genome sequence evolution can be influenced by adaptation to different diets and environments.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-1087-9) contains supplementary material, which is available to authorized users.

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“…However, the short read length and high data volume from NGS technologies create problems for assembling highly repetitive sequences (44). In our genome sequencing studies of M. genitalium (45) and Pneumocystis (L. Ma et al, unpublished data; also http://www.broadinstitute .org/annotation/genome/Pneumocystis_group.2/MultiHome .html), we found that it is impossible to assemble highly repetitive sequences (Ͼ1.5 kb) using short reads generated by the 454 and Illumina platforms. One potential alternative approach is the newly developed PacBio SMRT sequencing technology, which is able to generate sequence reads longer than 3 kb (46).…”

Section: Figmentioning

confidence: 99%

Extensive Variation and Rapid Shift of the MG192 Sequence in Mycoplasma genitalium Strains from Patients with Chronic Infection

Mancuso

Williams

et al. 2014

Infect Immun

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e Mycoplasma genitalium causes persistent urogenital tract infection in humans. Antigenic variation of the protein encoded by the MG192 gene has been proposed as one of the mechanisms for persistence. The aims of this study were to determine MG192 sequence variation in patients with chronic M. genitalium infection and to analyze the sequence structural features of the MG192 gene and its encoded protein. Urogenital specimens were obtained from 13 patients who were followed for 10 days to 14 months. The variable region of the MG192 gene was PCR amplified, subcloned into plasmids, and sequenced. Sequence analysis of 220 plasmid clones yielded 97 unique MG192 variant sequences. MG192 sequence shift was identified between sequential specimens from all but one patient. Despite great variation of the MG192 gene among and within clinical specimens from different patients, MG192 sequences were more related within M. genitalium specimens from an individual patient than between patients. The MG192 variable region consisted of 11 discrete subvariable regions with different degrees of variability. Analysis of the two most variable regions (V4 and V6) in five sequential specimens from one patient showed that sequence changes increased over time and that most sequences were present at only one time point, suggesting immune selection. Topology analysis of the deduced MG192 protein predicted a surface-exposed membrane protein. Extensive variation of the MG192 sequence may not only change the antigenicity of the protein to allow immune evasion but also alter the mobility and adhesion ability of the organism to adapt to diverse host microenvironments, thus facilitating persistent infection.A s a sexually transmitted human pathogen, Mycoplasma genitalium causes nongonococcal urethritis (NGU) in men and is associated with genital tract inflammatory diseases in women, including endometritis, cervicitis, pelvic inflammatory disease, and tubal factor infertility (reviewed in reference 1). Additionally, there are increasing numbers of studies suggesting that M. genitalium increases the risk of HIV-1 acquisition and/or transmission (2-4). Like other pathogenic mycoplasmas, M. genitalium is capable of causing chronic infections, as has been documented in cultured human endocervical epithelial cells (5), in animal models (6, 7), in men with NGU (8, 9), and in women with cervicitis (10). The mechanisms for persistence remain poorly understood.The MgPa operon in the M. genitalium genome encodes three proteins, MG190 (mgpA), MG191 (mgpB or P140), and MG192 (mgpC or P110). The latter two are the known major adhesion proteins located on the surface of the terminal structure of M. genitalium, which plays a major role in the attachment of the organism to host epithelial cells (11,12). Both proteins are highly antigenic and capable of eliciting strong antibody responses in M. genitalium-infected patients and experimentally infected animals (6,(12)(13)(14), suggesting an important role in pathogenesis. According to the genome sequence of M. genital...

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Draft Genome Sequences of Four Axenic Mycoplasma genitalium Strains Isolated from Denmark, Japan, and Australia

Cited by 10 publications

References 11 publications

Mycoplasma genitalium: whole genome sequence analysis, recombination and population structure

Mycoplasma genitalium: whole genome sequence analysis, recombination and population structure

Dietary nitrogen alters codon bias and genome composition in parasitic microorganisms

Extensive Variation and Rapid Shift of the MG192 Sequence in Mycoplasma genitalium Strains from Patients with Chronic Infection

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