Comprehensive bioinformatics analysis of Mycoplasma pneumoniae genomes to investigate underlying population structure and type-specific determinants

Diaz, Maureen H.; Desai, Heta P.; Morrison, Shatavia S.; Benitez, Alvaro J.; Wolff, Bernard J.; Caravas, Jason; Read, Timothy D.; Dean, Deborah; Winchell, Jonas M.

doi:10.1371/journal.pone.0174701

Cited by 24 publications

(32 citation statements)

References 67 publications

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“…The SNP approach is widely used in the study of antimicrobial resistance and genetic diversity and is not limited to M. pneumoniae (26)(27)(28). This study is consistent with previous studies investigating SNPs within M. pneumoniae (20,21). Variant calling against M129 of P1 subtypes showed substantially fewer variants compared to P1 type 2 in both nonsynonymous SNPs and total variants.…”

Section: Discussionsupporting

confidence: 92%

“…Therefore, we did not subgroup based on phylogenetic associations. In the study done by Diaz et al (21), subgroup 'Type 1U' (which authors designated as ubiquitous) was the group containing majority of the P1 subtype 1 isolates. In contrast to their findings, phylogenetic analysis in this study demonstrated that the isolates within the same subgroup type 1U was divided into two large groups.…”

Section: Discussionmentioning

confidence: 99%

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Comparative Genomics of Mycoplasma pneumoniae isolated from Children with Pneumonia: South Korea, 2010-2016

Lee

Seong

Shin

et al. 2019

Preprint

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Background Mycoplasma pneumoniae is a common cause of respiratory tract infections in children and adults. This study applied high-throughput whole genome sequencing (WGS) technologies to analyze the genomes of 30 M. pneumoniae strains isolated from children with pneumonia in South Korea during the two epidemics from 2010 to 2016 in comparison with a global collection of 48 M. pneumoniae strains which includes seven countries ranging from 1944 to 2017. Results The 30 Korean strains had approximately 40% GC content and ranged from 815,686 to 818,669 base pairs, coding for a total of 809 to 828 genes. Overall, BRIG revealed 99% to > 99% similarity among strains. The genomic similarity dropped to approximately 95% in the P1 type 2 strains when aligned to the reference M129 genome, which corresponded to the region of the p1 gene. MAUVE detected four subtype-specific insertions (three in P1 type 1 and one in P1 type 2), of which were all hypothetical proteins except for one tRNA insertion in all P1 type 1 strains. The phylogenetic associations of 30 strains were generally consistent with the multilocus sequence typing results. eBURST analysis demonstrated two clonal complexes which are accordant with the known P1 typing, with higher diversity among P1 type 2 strains. The phylogenetic tree constructed with 78 genomes including 48 genomes outside Korea formed three clusters, in which the sequence type 3 strains from Korea were divided into two P1 type 1 clusters. Conclusions The comparative genome analysis of the 78 M. pneumoniae strains including 30 strains from Korea by WGS reveals structural diversity and phylogenetic associations, even though the similarity across the strains was very high.

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Section: Discussionsupporting

confidence: 92%

Section: Discussionmentioning

confidence: 99%

Comparative Genomics of Mycoplasma pneumoniae isolated from Children with Pneumonia: South Korea, 2010-2016

Lee

Seong

Shin

et al. 2019

Preprint

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“…Watkins et al analyzed five patients with Stevens‐Johnson Sydrome (SJS) infected with Mp and described a unique MLVA type M3‐X‐6‐2 that contributed to the development of SJS. Diaz et al performed whole genome sequencing analysis of 107 M. pneumoniae isolates but did not analyze clinical information. In our previous study, we noted that locus Mpn13 was associated with the P1 genotype .…”

Section: Discussionmentioning

confidence: 99%

Molecular and clinical characteristics of severe Mycoplasma pneumoniae pneumonia in children

Yan

Xue

Zhao

et al. 2019

Pediatric Pulmonology

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Objectives: To analyze the molecular and the clinical characteristics of Mycoplasma pneumoniae (Mp) pneumonia (MPP) and to explore the related factors predicting severe MPP (SMPP).Methods: A total of 423 pediatric cases of MPP were retrospectively analyzed, in 2013-2017, in Beijing, China. Clinical information was collected from the medical records. Mp-positive specimens were characterized using P1 typing and multiple locus variable-number tandem repeat analysis (MLVA). The macrolide resistanceassociated mutations were also detected.Results: The predominant genotype was P1-1 (88.2%) and M4-5-7-2 (87.5%), whereas percentages of type P1-2 and M3-5-6-2 increased across the 5-year period. The mutation rate of genotype M4-5-7-2 (365/370, 98.6%) was significantly higher than that of the genotype M3-5-6-2 (15/48, 32.25%; P = 0.000). Overall, 180 (42.6%) of the 423 Mp-positive patients were coinfected with other pathogens. Respiratory syncytial virus coinfection (24/180, 13.3%) was more common in cases typed M3-5-6-2 (4/23, 17.4%) than that of M4-5-7-2 (20/155, 12.9%; P = 0.038). Pleural effusion accounted for 52.6% (169/321) of the observed complications. In the mono-infection cases, cases typed M3-5-6-2 (56%, 14/25) were significantly (P = 0.020) associated with pleural effusion compared with those typed M4-5-7-2 (32.6%, 70/215); 84% (21/ 25) of specimens typed M3-5-6-2 were diagnosed as SMPP, whereas 63.7% (137/ 215) of specimens typed M4-5-7-2 were diagnosed as SMPP (P = 0.043). Conclusions:In our study, we proposed for the first time that the mono-infection patients with Mp typed M3-5-6-2 appear to have a higher risk for progressing to SMPP. MLVA typing can provide hints on the clinical characteristics of Mpp.

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“…In China, only 5 ( (32) recently reported that strains with 3 tandem repeats in the Mpn 16 region formed a distinct subgroup named as 1N within the P1 type 1 branch by phylogenetic analysis using the M. pneumoniae core genome. Therefore, the increase in MLVA type 4-5-7-3 may represent the emergence of a new subtype of M. pneumoniae P1 type 1 (32).…”

Section: Discussionmentioning

confidence: 99%

Multiple-Locus Variable-Number Tandem-Repeat Analysis of <i>Mycoplasma pneumoniae</i> Isolates between 2004 and 2014 in Yamagata, Japan: Change in Molecular Characteristics during an 11-year Period

et al. 2017

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SUMMARY:Multiple-locus variable-number tandem-repeat analysis (MLVA) typing was performed for Mycoplasma pneumoniae strains isolated between 2004 and 2014 in Yamagata, Japan. The results were examined by considering the combination of the P1 type and prevalence of macrolide resistanceassociated mutations. Four-locus (Mpn13-16) MLVA classified 347 strains into 9 MLVA types, including 3 major types: 3-5-6-2, 4-5-7-2, and 4-5-7-3. All type 3-5-6-2 strains (77 strains) were P1 type 2 variants (2a or 2c), while types 4-5-7-2 (181 strains) and 4-5-7-3 (75 strains) were P1 type 1. MLVA type 4-5-7-2 strains circulated and were dominant until 2010, accounting for 88.4 of the 121 strains isolated between 2004 and 2010. The prevalence of types 4-5-7-3 and 3-5-6-2 strains increased rapidly in 2011 and 2012, respectively, resulting in cocirculation of 3 MLVA types, including type 4-5-7-2, between 2011 and 2013. The prevalence of macrolide resistance-associated mutations in MLVA types 4-5-7-2, 4-5-7-3, and 3-5-6-2 strains was 59.7 (108 181), 25.3 (19 75), and 0 (0 77), respectively. Because the prevalence of macrolide resistance-associated mutations differed by current MLVA types in Yamagata, continued surveillance combined with molecular typing and identification of macrolide resistanceassociated mutations is necessary.

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Comprehensive bioinformatics analysis of Mycoplasma pneumoniae genomes to investigate underlying population structure and type-specific determinants

Cited by 24 publications

References 67 publications

Comparative Genomics of Mycoplasma pneumoniae isolated from Children with Pneumonia: South Korea, 2010-2016

Comparative Genomics of Mycoplasma pneumoniae isolated from Children with Pneumonia: South Korea, 2010-2016

Molecular and clinical characteristics of severe Mycoplasma pneumoniae pneumonia in children

Multiple-Locus Variable-Number Tandem-Repeat Analysis of <i>Mycoplasma pneumoniae</i> Isolates between 2004 and 2014 in Yamagata, Japan: Change in Molecular Characteristics during an 11-year Period

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