A comparison of capillary electrophoresis and direct sequencing in upstream conserved sequence region analysis of Pneumocystis jirovecii strains

Jarboui, Mohamed Ali; Mseddi, F.; Sellami, H.; Sellami, A.; Mahfoudh, N.; Makni, F.; Makni, H.; Àyadi, A.

doi:10.1099/jmm.0.045336-0

Cited by 5 publications

(5 citation statements)

References 22 publications

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“…The number of repeats can be determined by PCR amplification of the VNTR-containing region followed by high-resolution denaturing gel electrophoresis (300) (Fig. 8) or fluorescence capillary electrophoresis (371). A major benefit of this method is the high sensitivity for detection of a minor population in mixed populations, which can be seen in up to 92% of patients with PCP (see Table S1 in the supplemental material).…”

Section: Epidemiology Of Pneumocystis Methods For Molecular Typingmentioning

confidence: 99%

“…Isolates with the same number of repeat units can have different distribution patterns of repeat types. Application of this VNTR method to different PCP patient populations worldwide has found that the number of repeat units varies from 2 to 6, with 2, 3, and 4 repeats being the most common (300,319,(371)(372)(373)(374). The 6-repeat allele contains only one repeat pattern, while all other alleles reported, to date, harbor two or more different repeat patterns.…”

Section: Epidemiology Of Pneumocystis Methods For Molecular Typingmentioning

confidence: 99%

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A Molecular Window into the Biology and Epidemiology of Pneumocystis spp

2018

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, a unique atypical fungus with an elusive lifestyle, has had an important medical history. It came to prominence as an opportunistic pathogen that not only can cause life-threatening pneumonia in patients with HIV infection and other immunodeficiencies but also can colonize the lungs of healthy individuals from a very early age. The genus includes a group of closely related but heterogeneous organisms that have a worldwide distribution, have been detected in multiple mammalian species, are highly host species specific, inhabit the lungs almost exclusively, and have never convincingly been cultured, making a fascinating but difficult-to-study organism. Improved molecular biologic methodologies have opened a new window into the biology and epidemiology of. Advances include an improved taxonomic classification, identification of an extremely reduced genome and concomitant inability to metabolize and grow independent of the host lungs, insights into its transmission mode, recognition of its widespread colonization in both immunocompetent and immunodeficient hosts, and utilization of strain variation to study drug resistance, epidemiology, and outbreaks of infection among transplant patients. This review summarizes these advances and also identifies some major questions and challenges that need to be addressed to better understand biology and its relevance to clinical care.

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Section: Epidemiology Of Pneumocystis Methods For Molecular Typingmentioning

confidence: 99%

Section: Epidemiology Of Pneumocystis Methods For Molecular Typingmentioning

confidence: 99%

A Molecular Window into the Biology and Epidemiology of Pneumocystis spp

2018

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“…UCS is known to have a highly variable number of tandem repeats in the intron in P. jirovecii (19,39,40). In this study, we demonstrated for the first time the presence of inter-and intrastrain variations in tandem repeats in the intron of UCSs in P. carinii and P. oryctolagi.…”

Section: Figmentioning

confidence: 51%

Diversity and Complexity of the Large Surface Protein Family in the Compacted Genomes of MultiplePneumocystisSpecies

Chen

Huang

et al. 2020

mBio

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Pneumocystis, a major opportunistic pathogen in patients with a broad range of immunodeficiencies, contains abundant surface proteins encoded by a multicopy gene family, termed the major surface glycoprotein (Msg) gene superfamily. This superfamily has been identified in all Pneumocystis species characterized to date, highlighting its important role in Pneumocystis biology. In this report, through a comprehensive and in-depth characterization of 459 msg genes from 7 Pneumocystis species, we demonstrate, for the first time, the phylogeny and evolution of conserved domains in Msg proteins and provide a detailed description of the classification, unique characteristics, and phylogenetic relatedness of five Msg families. We further describe, for the first time, the relative expression levels of individual msg families in two rodent Pneumocystis species, the substantial variability of the msg repertoires in P. carinii from laboratory and wild rats, and the distinct features of the expression site for the classic msg genes in Pneumocystis from 8 mammalian host species. Our analysis suggests multiple functions for this superfamily rather than just conferring antigenic variation to allow immune evasion as previously believed. This study provides a rich source of information that lays the foundation for the continued experimental exploration of the functions of the Msg superfamily in Pneumocystis biology. IMPORTANCE Pneumocystis continues to be a major cause of disease in humans with immunodeficiency, especially those with HIV/AIDS and organ transplants, and is being seen with increasing frequency worldwide in patients treated with immunode-

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“…UCS is known to have a highly variable number of tandem repeats in the intron in P. jirovecii (20, 39, 40). In this study, we demonstrated for the first time the presence of inter- and intra-strain variations in tandem repeats in the intron of UCS in P. carinii and P. oryctolagi.…”

Section: Discussionmentioning

confidence: 99%

Diversity and complexity of the large surface protein family in the compacted genomes of variousPneumocystisspecies

Chen

Huang

et al. 2019

Preprint

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Supplemental Materials: 1 Text file (Text S1) 43 2 Tables (S1-S2) 44 13 Figures (S1-S13) 45 8 Data Sets (Msg sequences for different families) 46 47 48 Pneumocystis, a major opportunistic pathogen in patients with a broad range of 49 immunodeficiencies, contains abundant surface proteins encoded by a multi-copy gene family, 50 termed the major surface glycoprotein (Msg) gene superfamily. This superfamily has been 51 identified in all Pneumocystis species characterized to date, highlighting its important role in 52 Pneumocystis biology. In this report, through a comprehensive and in-depth characterization of 53 459 msg genes from 7 Pneumocystis species, we demonstrate, for the first time, the phylogeny 54 and evolution of conserved domains in Msg proteins, and provide detailed description of the 55 classification, unique characteristics and phylogenetic relatedness of five Msg families. We 56 further describe the relative expression levels of individual msg families in two rodent 57 Pneumocystis species, the substantial variability of the msg repertoires in P. carinii from 58 laboratory and wild rats, and the distinct features of the expression site for the classic msg 59 genes in Pneumocystis from 8 mammalian host species. Our analysis suggests a wide variety 60 of functions for this superfamily, not only conferring antigenic variation to allow immune evasion 61 but also mediating life-stage development, optimizing cell mobility and adhesion, and adapting 62 to specific host niches or environmental conditions. This study provides a rich source of 63 information that lays the foundation for the continued experimental exploration of the functions 64 of the Msg superfamily in Pneumocystis biology. 66Pneumocystis continues to be a major cause of disease in humans with 67 immunodeficiencies, especially those with HIV/AIDS and organ transplants, and is being seen 68 with increasing frequency in patients treated with immunodepleting monoclonal antibodies. As 69 an atypical fungus, Pneumocystis has highly adapted to the mammalian lung environment (1), 70 with a high level of host specificity; P. jirovecii infects humans, P. carinii infects Norway rats 71 (Rattus norvegicus), and P. murina infects house mice (Mus musculus). In addition, 72Pneumocystis cell walls are structurally unique and differ significantly from typical fungal cell 73 walls that are comprised of polysaccharides (mainly glucan and chitin) and highly mannosylated 74 proteins. Both genomic and experimental analyses have shown the absence of chitin and outer 75 chain N-mannans in Pneumocystis cell walls (1). Furthermore, beta-1,3-glucan is absent in the 76 trophic form while present but masked in the cyst form of Pneumocystis (2). 77An integral component of the Pneumocystis cell wall in both the cyst and trophic forms is 78 the major surface glycoprotein (Msg) (also known as gp95, gp115, gp120 and gpA) (3-8). Ever 79 since its identification in 1982 (9), Msg has been a focus of research, in part because it is the 80 most abundant Pneumocystis protein as as...

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A comparison of capillary electrophoresis and direct sequencing in upstream conserved sequence region analysis of Pneumocystis jirovecii strains

Cited by 5 publications

References 22 publications

A Molecular Window into the Biology and Epidemiology of Pneumocystis spp

A Molecular Window into the Biology and Epidemiology of Pneumocystis spp

Diversity and Complexity of the Large Surface Protein Family in the Compacted Genomes of MultiplePneumocystisSpecies

Diversity and complexity of the large surface protein family in the compacted genomes of variousPneumocystisspecies

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