Development of a multiplex taqMan real-time PCR assay for typing of Mycoplasma pneumoniae based on type-specific indels identified through whole genome sequencing

Wolff, Bernard J.; Benitez, Alvaro J.; Desai, Heta P.; Morrison, Shatavia S.; Diaz, Maureen H.; Winchell, Jonas M.

doi:10.1016/j.diagmicrobio.2016.11.013

Cited by 7 publications

(9 citation statements)

References 25 publications

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“…[ 11 ] as a type 1-specific insertion sequence consisting of genes encoding hypothetical proteins and a single tRNA gene. Three small indels (13–15 bp) previously identified as unique to either type 1 or type 2 isolates [ 54 ] were confirmed in all newly sequenced genomes (n = 67). To confirm the apparent absence of these segments was not due to lack of Illumina sequencing reads, we performed multiple sequence alignments of only closed genomes (n = 34) ( Table 1 ).…”

Section: Resultssupporting

confidence: 55%

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

et al. 2017

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Mycoplasma pneumoniae is a significant cause of respiratory illness worldwide. Despite a minimal and highly conserved genome, genetic diversity within the species may impact disease. We performed whole genome sequencing (WGS) analysis of 107 M. pneumoniae isolates, including 67 newly sequenced using the Pacific BioSciences RS II and/or Illumina MiSeq sequencing platforms. Comparative genomic analysis of 107 genomes revealed >3,000 single nucleotide polymorphisms (SNPs) in total, including 520 type-specific SNPs. Population structure analysis supported the existence of six distinct subgroups, three within each type. We developed a predictive model to classify an isolate based on whole genome SNPs called against the reference genome into the identified subtypes, obviating the need for genome assembly. This study is the most comprehensive WGS analysis for M. pneumoniae to date, underscoring the power of combining complementary sequencing technologies to overcome difficult-to-sequence regions and highlighting potential differential genomic signatures in M. pneumoniae.

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Section: Resultssupporting

confidence: 55%

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

et al. 2017

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“…P1 typing. The specimens that were PCR positive for M. pneumoniae were classified into two main genomic groups corresponding to P1 types 1 and 2 using a multiplex real-time PCR assay for detection of type-specific short genomic regions identified through whole-genome sequencing as previously described (47).…”

Section: Methodsmentioning

confidence: 99%

Molecular Characterization of Mycoplasma pneumoniae Infections in Two Rural Populations of Thailand from 2009 to 2012

et al. 2017

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Studies on Mycoplasma pneumoniae in Thailand have focused on urban centers and have not included molecular characterization. In an attempt to provide a more comprehensive understanding of this organism, we conducted a systematic random sampling to identify 3,000 nasopharyngeal swab specimens collected from January 2009 through July 2012 during population-based surveillance for influenzalike illness in two rural provinces. M. pneumoniae was detected by real-time PCR in 175 (5.8%) specimens. Genotyping was performed using the major adhesion protein (P1) and multilocus variable-number tandem-repeat analysis (MLVA). Of the 157 specimens typed, 97 were P1 type 1 and 60 were P1 type 2. Six different MLVA profiles were identified in 149 specimens, with 4/5/7/2 (40%) and 3/5/6/2 (26%) predominating. There was no discrete seasonality to M. pneumoniae infections. Examination of the 23S rRNA sequence for known polymorphisms conferring macrolide resistance revealed that all 141 tested to possess the genotype associated with macrolide susceptibility.

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“…Mycoplasma pneumoniae is also a significant cause of respiratory diseases including CAP for all ages [153]. Mycoplasma pneumoniae pneumonia may be altered by the level of host cell-mediated immunity [154].…”

Section: Neutrophils In Infectious Pneumoniamentioning

confidence: 99%

Advanced Role of Neutrophils in Common Respiratory Diseases

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Pang

Wang

et al. 2017

Journal of Immunology Research

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Respiratory diseases, always being a threat towards the health of people all over the world, are most tightly associated with immune system. Neutrophils serve as an important component of immune defense barrier linking innate and adaptive immunity. They participate in the clearance of exogenous pathogens and endogenous cell debris and play an essential role in the pathogenesis of many respiratory diseases. However, the pathological mechanism of neutrophils remains complex and obscure. The traditional roles of neutrophils in severe asthma, chronic obstructive pulmonary diseases (COPD), pneumonia, lung cancer, pulmonary fibrosis, bronchitis, and bronchiolitis had already been reviewed. With the development of scientific research, the involvement of neutrophils in respiratory diseases is being brought to light with emerging data on neutrophil subsets, trafficking, and cell death mechanism (e.g., NETosis, apoptosis) in diseases. We reviewed all these recent studies here to provide you with the latest advances about the role of neutrophils in respiratory diseases.

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Development of a multiplex taqMan real-time PCR assay for typing of Mycoplasma pneumoniae based on type-specific indels identified through whole genome sequencing

Cited by 7 publications

References 25 publications

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

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

Molecular Characterization of Mycoplasma pneumoniae Infections in Two Rural Populations of Thailand from 2009 to 2012

Advanced Role of Neutrophils in Common Respiratory Diseases

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