Comparative genome analysis of Mycoplasma pneumoniae

Abstract

BackgroundMycoplasma pneumoniae is a common pathogen that causes upper and lower respiratory tract infections in people of all ages, responsible for up to 40 % of community-acquired pneumonias. It also causes a wide array of extrapulmonary infections and autoimmune phenomena. Phylogenetic studies of the organism have been generally restricted to specific genes or regions of the genome, because whole genome sequencing has been completed for only 4 strains. To better understand the physiology and pathogenicity of this important human pathogen, we performed comparative genomic analysis of 15 strains of M. pneumoniae that were isolated between the 1940s to 2009 from respiratory specimens and cerebrospinal fluid originating from the USA, China and England.ResultsIllumina MiSeq whole genome sequencing was performed on the 15 strains and all genome sequences were completed. Results from the comparative genomic analysis indicate that although about 1500 SNP and indel variants exist between type1 and type 2 strains, there is an overall high degree of sequence similarity among the strains (>99 % identical to each other). Within the two subtypes, conservation of most genes, including the CARDS toxin gene and arginine deiminase genes, was observed. The major variation occurs in the P1 and ORF6 genes associated with the adhesin complex. Multiple hsdS genes (encodes S subunit of type I restriction enzyme) with variable tandem repeat copy numbers were found in all 15 genomes.ConclusionsThese data indicate that despite conclusions drawn from 16S rRNA sequences suggesting rapid evolution, the M. pneumoniae genome is extraordinarily stable over time and geographic distance across the globe with a striking lack of evidence of horizontal gene transfer.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1801-0) contains supplementary material, which is available to authorized users.

CReasPy-cloning: a method for simultaneous cloning and engineering of megabase-sized genomes in yeast using the CRISPR-Cas9 system

“…To demonstrate the effectiveness of the CREASPY-cloning strategy, we cloned with a high efficiency the genome of Mycoplasma pneumoniae M129 20 in yeast, while simultaneously deleting a gene encoding for a virulence factor. Analysis showed that the cloned genome was intact and essentially error-free.…”

Genomic determination of minimum multi-locus sequence typing schemas to represent the genomic phylogeny of Mycoplasma hominis

“…Of the entire pan-genome, the core genome represents 55% of all genes. This level of similarity between M. hominis strains is in stark contrast to M. pneumoniae where over 99% identity has been observed between the genomes [30]. Congruence of the M. hominis pan-genome to other Mycoplasma species was assessed by comparison to M. pneumoniae (strain M129) and U. parvum serovar 3 (strain AF222894, ATCC 700970).…”

Comparison of Mycoplasma pneumoniae Genome Sequences from Strains Isolated from Symptomatic and Asymptomatic Patients

“…This sequence was derived from laboratory strain M129. Since 2013, several other genomic sequences have been published (Lluch-Senar et al, 2015; Simmons et al, 2013; Xiao et al, 2015). Most of these sequences were obtained in two independent studies.…”

“…Most of these sequences were obtained in two independent studies. One of these studies reported the comparative genome analysis of 15 M. pneumoniae strains isolated form respiratory tract samples and cerebrospinal fluid samples collected from patients between 1940 and 2009 in the USA, China, and England (Xiao et al, 2015). The other study reported the sequences of 23 clinical M. pneumoniae strains isolated between 1964 and 2011 in six different countries (Lluch-Senar et al, 2015).…”

“…In both studies, the genomes of M. pneumoniae strains seem very stable over time and at different locations in the world. The sequences of these studies show a low number of non-synonymous single-nucleotide polymorphisms, but a high rate of variation among repetitive elements (Lluch-Senar et al, 2015; Xiao et al, 2015). …”