Contribution of the internal transcribed spacer regions to the detection and identification of human fungal pathogens.
Identifieur interne : 000556 ( Main/Exploration ); précédent : 000555; suivant : 000557Contribution of the internal transcribed spacer regions to the detection and identification of human fungal pathogens.
Auteurs : H. Trabelsi [Tunisie] ; S. Neji [Tunisie] ; I. Hadrich [Tunisie] ; N. Khemakhem [Tunisie] ; H. Sellami [Tunisie] ; F. Makni [Tunisie] ; A. Ayadi [Tunisie]Source :
- Current research in translational medicine [ 2452-3186 ] ; 2019.
Descripteurs français
- KwdFr :
- ADN fongique (génétique), ADN fongique (isolement et purification), Adolescent (MeSH), Adulte (MeSH), Adulte d'âge moyen (MeSH), Analyse de séquence d'ADN (méthodes), Bases de données d'acides nucléiques (MeSH), Champignons (génétique), Champignons (isolement et purification), Enfant (MeSH), Enfant d'âge préscolaire (MeSH), Espaceur de l'ADN ribosomique (analyse), Espaceur de l'ADN ribosomique (physiologie), Femelle (MeSH), Humains (MeSH), Jeune adulte (MeSH), Mycoses (diagnostic), Mycoses (microbiologie), Mycoses (épidémiologie), Mâle (MeSH), Nourrisson (MeSH), Phylogenèse (MeSH), Réaction de polymérisation en chaîne (méthodes), Sujet âgé (MeSH), Techniques de typage mycologique (méthodes), Tunisie (épidémiologie).
- MESH :
- analyse : Espaceur de l'ADN ribosomique.
- diagnostic : Mycoses.
- génétique : ADN fongique, Champignons.
- isolement et purification : ADN fongique, Champignons.
- microbiologie : Mycoses.
- méthodes : Analyse de séquence d'ADN, Réaction de polymérisation en chaîne, Techniques de typage mycologique.
- physiologie : Espaceur de l'ADN ribosomique.
- épidémiologie : Mycoses, Tunisie.
- Adolescent, Adulte, Adulte d'âge moyen, Bases de données d'acides nucléiques, Enfant, Enfant d'âge préscolaire, Femelle, Humains, Jeune adulte, Mâle, Nourrisson, Phylogenèse, Sujet âgé.
- Wicri :
- geographic : Tunisie.
English descriptors
- KwdEn :
- Adolescent (MeSH), Adult (MeSH), Aged (MeSH), Child (MeSH), Child, Preschool (MeSH), DNA, Fungal (genetics), DNA, Fungal (isolation & purification), DNA, Ribosomal Spacer (analysis), DNA, Ribosomal Spacer (physiology), Databases, Nucleic Acid (MeSH), Female (MeSH), Fungi (genetics), Fungi (isolation & purification), Humans (MeSH), Infant (MeSH), Male (MeSH), Middle Aged (MeSH), Mycological Typing Techniques (methods), Mycoses (diagnosis), Mycoses (epidemiology), Mycoses (microbiology), Phylogeny (MeSH), Polymerase Chain Reaction (methods), Sequence Analysis, DNA (methods), Tunisia (epidemiology), Young Adult (MeSH).
- MESH :
- chemical , analysis : DNA, Ribosomal Spacer.
- chemical , genetics : DNA, Fungal.
- chemical , isolation & purification : DNA, Fungal.
- chemical , physiology : DNA, Ribosomal Spacer.
- geographic , epidemiology : Tunisia.
- diagnosis : Mycoses.
- epidemiology : Mycoses.
- genetics : Fungi.
- isolation & purification : Fungi.
- methods : Mycological Typing Techniques, Polymerase Chain Reaction, Sequence Analysis, DNA.
- microbiology : Mycoses.
- Adolescent, Adult, Aged, Child, Child, Preschool, Databases, Nucleic Acid, Female, Humans, Infant, Male, Middle Aged, Phylogeny, Young Adult.
Abstract
Fungi are morphologically and phylogenetically diverse. There identification is largely based on phenotypic methods. Thus, related species, phenotypic variants and rare species may be unidentified. So, molecular methods have been introduced for identification of pathogenic molds to overcome these problems. In this study, we report the contribution of molecular tools (PCR sequencing) to identify fungal pathogens in both clinical and environmental samples. A total of 82 mold isolates were used (50 clinical samples and 32 environmental samples). PCR and direct sequencing, targeting the internal transcribed spacer (ITS) regions, were performed. We employed comparative sequence analysis to identify molds by using the GenBank database. 89% of isolates were identified by phenotypic methods. PCR- sequencing allowed the fungal identification in all cases. The concordance between molecular and morphological identification was obtained for 33 cases (40.2%). In 36 cases (43.9%), the molecular study gave the exact species identification. PCR sequencing allowed as revising mycological identification for 13 fungi strains (15.9%). The concordance of identification at species level by phenotypic method and by sequence analysis was obtained for 28% of clinical samples and for 59% of environmental samples. The phylogenetic tree for the ITS sequences showed six different clusters that are composed of isolates belonging to the same genus or species. PCR sequencing has been shown to be useful for the detection of the presence of fungal DNA in both environmental and clinical samples. It is rapid and more sensitive for the identification of medically important fungi.
DOI: 10.1016/j.retram.2019.04.001
PubMed: 30975553
Affiliations:
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Le document en format XML
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Trabelsi</name><affiliation wicri:level="1"><nlm:affiliation>Laboratory of Parasitology-Mycology, Habib Bourguiba Hospital, Sfax, Tunisia.</nlm:affiliation><country xml:lang="fr">Tunisie</country><wicri:regionArea>Laboratory of Parasitology-Mycology, Habib Bourguiba Hospital, Sfax</wicri:regionArea><wicri:noRegion>Sfax</wicri:noRegion></affiliation></author><author><name sortKey="Neji, S" sort="Neji, S" uniqKey="Neji S" first="S" last="Neji">S. Neji</name><affiliation wicri:level="1"><nlm:affiliation>Laboratory of Parasitology-Mycology, Habib Bourguiba Hospital, Sfax, Tunisia.</nlm:affiliation><country xml:lang="fr">Tunisie</country><wicri:regionArea>Laboratory of Parasitology-Mycology, Habib Bourguiba Hospital, Sfax</wicri:regionArea><wicri:noRegion>Sfax</wicri:noRegion></affiliation></author><author><name sortKey="Hadrich, I" sort="Hadrich, I" uniqKey="Hadrich I" first="I" last="Hadrich">I. Hadrich</name><affiliation wicri:level="1"><nlm:affiliation>Laboratory of Parasitology-Mycology, Habib Bourguiba Hospital, Sfax, Tunisia.</nlm:affiliation><country xml:lang="fr">Tunisie</country><wicri:regionArea>Laboratory of Parasitology-Mycology, Habib Bourguiba Hospital, Sfax</wicri:regionArea><wicri:noRegion>Sfax</wicri:noRegion></affiliation></author><author><name sortKey="Khemakhem, N" sort="Khemakhem, N" uniqKey="Khemakhem N" first="N" last="Khemakhem">N. Khemakhem</name><affiliation wicri:level="1"><nlm:affiliation>Laboratory of Parasitology-Mycology, Habib Bourguiba Hospital, Sfax, Tunisia.</nlm:affiliation><country xml:lang="fr">Tunisie</country><wicri:regionArea>Laboratory of Parasitology-Mycology, Habib Bourguiba Hospital, Sfax</wicri:regionArea><wicri:noRegion>Sfax</wicri:noRegion></affiliation></author><author><name sortKey="Sellami, H" sort="Sellami, H" uniqKey="Sellami H" first="H" last="Sellami">H. Sellami</name><affiliation wicri:level="1"><nlm:affiliation>Laboratory of Parasitology-Mycology, Habib Bourguiba Hospital, Sfax, Tunisia.</nlm:affiliation><country xml:lang="fr">Tunisie</country><wicri:regionArea>Laboratory of Parasitology-Mycology, Habib Bourguiba Hospital, Sfax</wicri:regionArea><wicri:noRegion>Sfax</wicri:noRegion></affiliation></author><author><name sortKey="Makni, F" sort="Makni, F" uniqKey="Makni F" first="F" last="Makni">F. Makni</name><affiliation wicri:level="1"><nlm:affiliation>Laboratory of Parasitology-Mycology, Habib Bourguiba Hospital, Sfax, Tunisia.</nlm:affiliation><country xml:lang="fr">Tunisie</country><wicri:regionArea>Laboratory of Parasitology-Mycology, Habib Bourguiba Hospital, Sfax</wicri:regionArea><wicri:noRegion>Sfax</wicri:noRegion></affiliation></author><author><name sortKey="Ayadi, A" sort="Ayadi, A" uniqKey="Ayadi A" first="A" last="Ayadi">A. Ayadi</name><affiliation wicri:level="1"><nlm:affiliation>Laboratory of Parasitology-Mycology, Habib Bourguiba Hospital, Sfax, Tunisia. Electronic address: ali.ayadi@rns.tn.</nlm:affiliation><country xml:lang="fr">Tunisie</country><wicri:regionArea>Laboratory of Parasitology-Mycology, Habib Bourguiba Hospital, Sfax</wicri:regionArea><wicri:noRegion>Sfax</wicri:noRegion></affiliation></author></analytic><series><title level="j">Current research in translational medicine</title><idno type="eISSN">2452-3186</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Adolescent (MeSH)</term><term>Adult (MeSH)</term><term>Aged (MeSH)</term><term>Child (MeSH)</term><term>Child, Preschool (MeSH)</term><term>DNA, Fungal (genetics)</term><term>DNA, Fungal (isolation & purification)</term><term>DNA, Ribosomal Spacer (analysis)</term><term>DNA, Ribosomal Spacer (physiology)</term><term>Databases, Nucleic Acid (MeSH)</term><term>Female (MeSH)</term><term>Fungi (genetics)</term><term>Fungi (isolation & purification)</term><term>Humans (MeSH)</term><term>Infant (MeSH)</term><term>Male (MeSH)</term><term>Middle Aged (MeSH)</term><term>Mycological Typing Techniques (methods)</term><term>Mycoses (diagnosis)</term><term>Mycoses (epidemiology)</term><term>Mycoses (microbiology)</term><term>Phylogeny (MeSH)</term><term>Polymerase Chain Reaction (methods)</term><term>Sequence Analysis, DNA (methods)</term><term>Tunisia (epidemiology)</term><term>Young Adult (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN fongique (génétique)</term><term>ADN fongique (isolement et purification)</term><term>Adolescent (MeSH)</term><term>Adulte (MeSH)</term><term>Adulte d'âge moyen (MeSH)</term><term>Analyse de séquence d'ADN (méthodes)</term><term>Bases de données d'acides nucléiques (MeSH)</term><term>Champignons (génétique)</term><term>Champignons (isolement et purification)</term><term>Enfant (MeSH)</term><term>Enfant d'âge préscolaire (MeSH)</term><term>Espaceur de l'ADN ribosomique (analyse)</term><term>Espaceur de l'ADN ribosomique (physiologie)</term><term>Femelle (MeSH)</term><term>Humains (MeSH)</term><term>Jeune adulte (MeSH)</term><term>Mycoses (diagnostic)</term><term>Mycoses (microbiologie)</term><term>Mycoses (épidémiologie)</term><term>Mâle (MeSH)</term><term>Nourrisson (MeSH)</term><term>Phylogenèse (MeSH)</term><term>Réaction de polymérisation en chaîne (méthodes)</term><term>Sujet âgé (MeSH)</term><term>Techniques de typage mycologique (méthodes)</term><term>Tunisie (épidémiologie)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="analysis" xml:lang="en"><term>DNA, Ribosomal Spacer</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA, Fungal</term></keywords><keywords scheme="MESH" type="chemical" qualifier="isolation & purification" xml:lang="en"><term>DNA, Fungal</term></keywords><keywords scheme="MESH" type="chemical" qualifier="physiology" xml:lang="en"><term>DNA, Ribosomal Spacer</term></keywords><keywords scheme="MESH" type="geographic" qualifier="epidemiology" xml:lang="en"><term>Tunisia</term></keywords><keywords scheme="MESH" qualifier="analyse" xml:lang="fr"><term>Espaceur de l'ADN ribosomique</term></keywords><keywords scheme="MESH" qualifier="diagnosis" xml:lang="en"><term>Mycoses</term></keywords><keywords scheme="MESH" qualifier="diagnostic" xml:lang="fr"><term>Mycoses</term></keywords><keywords scheme="MESH" qualifier="epidemiology" xml:lang="en"><term>Mycoses</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Fungi</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN fongique</term><term>Champignons</term></keywords><keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>Fungi</term></keywords><keywords scheme="MESH" qualifier="isolement et purification" xml:lang="fr"><term>ADN fongique</term><term>Champignons</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Mycological Typing Techniques</term><term>Polymerase Chain Reaction</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" qualifier="microbiologie" xml:lang="fr"><term>Mycoses</term></keywords><keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Mycoses</term></keywords><keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Réaction de polymérisation en chaîne</term><term>Techniques de typage mycologique</term></keywords><keywords scheme="MESH" qualifier="physiologie" xml:lang="fr"><term>Espaceur de l'ADN ribosomique</term></keywords><keywords scheme="MESH" qualifier="épidémiologie" xml:lang="fr"><term>Mycoses</term><term>Tunisie</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Adolescent</term><term>Adult</term><term>Aged</term><term>Child</term><term>Child, Preschool</term><term>Databases, Nucleic Acid</term><term>Female</term><term>Humans</term><term>Infant</term><term>Male</term><term>Middle Aged</term><term>Phylogeny</term><term>Young Adult</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Adolescent</term><term>Adulte</term><term>Adulte d'âge moyen</term><term>Bases de données d'acides nucléiques</term><term>Enfant</term><term>Enfant d'âge préscolaire</term><term>Femelle</term><term>Humains</term><term>Jeune adulte</term><term>Mâle</term><term>Nourrisson</term><term>Phylogenèse</term><term>Sujet âgé</term></keywords><keywords scheme="Wicri" type="geographic" xml:lang="fr"><term>Tunisie</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Fungi are morphologically and phylogenetically diverse. There identification is largely based on phenotypic methods. Thus, related species, phenotypic variants and rare species may be unidentified. So, molecular methods have been introduced for identification of pathogenic molds to overcome these problems. In this study, we report the contribution of molecular tools (PCR sequencing) to identify fungal pathogens in both clinical and environmental samples. A total of 82 mold isolates were used (50 clinical samples and 32 environmental samples). PCR and direct sequencing, targeting the internal transcribed spacer (ITS) regions, were performed. We employed comparative sequence analysis to identify molds by using the GenBank database. 89% of isolates were identified by phenotypic methods. PCR- sequencing allowed the fungal identification in all cases. The concordance between molecular and morphological identification was obtained for 33 cases (40.2%). In 36 cases (43.9%), the molecular study gave the exact species identification. PCR sequencing allowed as revising mycological identification for 13 fungi strains (15.9%). The concordance of identification at species level by phenotypic method and by sequence analysis was obtained for 28% of clinical samples and for 59% of environmental samples. The phylogenetic tree for the ITS sequences showed six different clusters that are composed of isolates belonging to the same genus or species. PCR sequencing has been shown to be useful for the detection of the presence of fungal DNA in both environmental and clinical samples. It is rapid and more sensitive for the identification of medically important fungi.</div></front></TEI><affiliations><list><country><li>Tunisie</li></country></list><tree><country name="Tunisie"><noRegion><name sortKey="Trabelsi, H" sort="Trabelsi, H" uniqKey="Trabelsi H" first="H" last="Trabelsi">H. Trabelsi</name></noRegion><name sortKey="Ayadi, A" sort="Ayadi, A" uniqKey="Ayadi A" first="A" last="Ayadi">A. Ayadi</name><name sortKey="Hadrich, I" sort="Hadrich, I" uniqKey="Hadrich I" first="I" last="Hadrich">I. Hadrich</name><name sortKey="Khemakhem, N" sort="Khemakhem, N" uniqKey="Khemakhem N" first="N" last="Khemakhem">N. Khemakhem</name><name sortKey="Makni, F" sort="Makni, F" uniqKey="Makni F" first="F" last="Makni">F. Makni</name><name sortKey="Neji, S" sort="Neji, S" uniqKey="Neji S" first="S" last="Neji">S. Neji</name><name sortKey="Sellami, H" sort="Sellami, H" uniqKey="Sellami H" first="H" last="Sellami">H. Sellami</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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