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Molecular Analysis of Cryptococcus spp. Reveals Species Diversity and Multilocus Sequence Typing Heterogeneity among People Living with HIV in Kinshasa
Zono, Bive; SACHELI, Rosalie; Situakibanza, Hippolyte et al.
2021In Journal of Fungi, 7 (916), p. 42-43
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Keywords :
Cryptococcus spp.; species diversity; ITS sequencing; MALDI-TOF MS; Multilocus sequence typing; cryptococcosis; people living with HIV; neuromeningeal; Kinshasa; DRC
Abstract :
[en] Objectives: In the Democratic Republic of Congo (DRC), the neuromeningeal cryptococcosis (NMC) hospital prevalence varies between 8.8 and 11% with a death rate of about 50%. However, the Cryptococcus isolates circulating are poorly and formerly described. We describe the molecular characterization of Cryptococcus spp. isolated from people living with HIV (PLWHIV), and the association between NMC severity factors and the Cryptococcus multilocus sequence typing (MLST) profiles. Materials & Methods: Cerebral spinal fluid (CSF) was collected from PLWHIV with neuromeningeal syndrome hospitalized in three Kinshasa public hospitals from 1 February 2019 to 29 February 2020, and cultured on Sabouraud dextrose agar + chloramphenicol medium afterwards. Serotyping PCR, internal transcribed spacer (ITS) sequencing, and MLST from next-generation sequencing (NGS) data were performed to genotype the Cryptococcus isolates. Raw NGS data were processed and the loci alleles were manually extracted using Geneious software. NMC severity factors such as hypoglycorrhachia (<50 mg/dL), raised CSF opening pressure (>30 cm water), and the patient pejorative outcome were compared to the Cryptococcus sequence type (ST)-MLST profile which was identified, using Pearson chi-square test or Fisher exact test. Results: Out of 29 isolates included in the present study, 23 (79.3%; 95% IC: 65.5–93.1) have been identified as serotype A using serotyping PCR, while 6 (20.7%; 95% IC: 6.9–34.5) had unidentifiable profile. Moreover, all the 29 isolates have been characterized by ITS sequencing as follow: Cryptococcus neoformans var. grubii (23 of 29 isolates, 79.3%), Cryptococcus curvatus (5 of 29, 17.2%), and Cryptococcus laurentii (1 of 29, 3.5%). Apart from this highlighted species diversity, C. neoformans var. grubii isolates were all identified as molecular type VNI using the MLST ISHAM scheme, with seven different STs including ST93 (14 out of 23, 60.9%), ST53 (1 out of 23, 4.3%), ST31 (1 out of 23, 4.3%), ST5 (1 out of 23, 4.3%), ST4 (1 out of 23, 4.3%), ST69 (1 out 23, 4.3%), and one novel ST not yet reported worldwide (2 out of 23, 8.6%). Furthermore, two isolates (8.6%) showed a mixed molecular profile (under investigation). Phylogenetic analysis carried out by the unweighted pair group method with arithmetic mean algorithm (UPGMA) of concatenated gene sequences from the seven MLST loci indicated that the main ST isolated in this study is very close to the only isolate previously reported from the DRC. The others are distant from it, even more so for ST69. All the STs identified in the present study have been isolated in the neighbouring countries of the DRC except for ST53, which has only been reported in Southeast Asia. Among NMC severity factors, only the patient pejorative outcome was associated with the minority STs infections (87.5%, p = 0.02) (ST53, ST31, ST5, ST4, STA, ST69). Conclusions: Molecular analysis of Cryptococcus spp. isolates showed wide species diversity, and ST-MLST heterogenicity within the only one molecular type identified. The existence of the STs isolated in this study in the DRC neighbouring countries suggests probable close-to-home spread. Furthermore, infections due to minority STs were associated with a pejorative outcome than those due to ST93.
Research center :
CIRM - Centre Interdisciplinaire de Recherche sur le Médicament - ULiège
Disciplines :
Laboratory medicine & medical technology
Immunology & infectious disease
Author, co-author :
Zono, Bive  ;  Université de Liège - ULiège > Doct. sc. bioméd. & pharma. (paysage)
SACHELI, Rosalie  ;  Centre Hospitalier Universitaire de Liège - CHU > Unilab > Laboratoire CNR
Situakibanza, Hippolyte;  Université de Kinshasa > Médecine interne/médecine tropicale > Maladies infectieuses
Kabututu, Pius;  Université de Kinshasa > Sciences de base > Biologie moléculaire
Mbula, Marcel;  Université de Kinshasa > Médecine interne/médecine tropicale > maladies infectieuses
Muendele, Gaultier;  Centre hospitalier mère et enfant de ngaba > Médecine interne > Unité de prise en charge VIH
BOREUX, Raphaël ;  Centre Hospitalier Universitaire de Liège - CHU > Unilab > Laboratoire biologie moléculaire
Landu, Nicole;  Centre médical et évangélique révérend Luyindu > Médecine interne > Unité de prise en charge VIH
Mudogo, Célestin;  Université de Kinshasa > Sciences de base > Biologie moléculaire
M'buze, Pierre-Robert;  Centre hospitalier roi baudouin 1er > Médecine interne > Unité de prise en charge VIH
Moutschen, Michel  ;  Université de Liège - ULiège > Département des sciences cliniques > Immunopath. - Maladies infect. et médec. interne gén.
Mvumbi, Georges;  Université de Kinshasa > Sciences de base > Biologie moléculaire
Hayette, Marie-Pierre ;  Université de Liège - ULiège > Département des sciences biomédicales et précliniques > Bact., mycologie, parasitologie, virologie, microbio.
More authors (3 more) Less
Language :
English
Title :
Molecular Analysis of Cryptococcus spp. Reveals Species Diversity and Multilocus Sequence Typing Heterogeneity among People Living with HIV in Kinshasa
Alternative titles :
[fr] L'analyse moléculaire de Cryptococcus spp. révèle une diversité d'espèces et une hétérogénéité du typage des séquences multilocus chez les personnes vivant avec le VIH à Kinshasa
Publication date :
28 October 2021
Event name :
10th Trends in Medical Mycology (TIMM)
Event organizer :
European Confederation of Medical Mycology (ECMM)
Event place :
Aberdeen AB21 9FX, United Kingdom
Event date :
8-11 October 2021
Audience :
International
Journal title :
Journal of Fungi
eISSN :
2309-608X
Publisher :
MDPI AG, Switzerland
Special issue title :
Conference Report:10th Trends in Medical Mycology Held on 8 to 11 October 2021, Aberdeen, Scotland, Organized by the European Confederation of Medical Mycology (ECMM)
Volume :
7
Issue :
916
Pages :
42-43
Peer reviewed :
Peer Reviewed verified by ORBi
Name of the research project :
Cryptococcose chez les personnes vivant avec le VIH à Kinshasa (RDC) : Etude épidémiologique et moléculaire
Funders :
ARES - Académie de Recherche et d'Enseignement Supérieur [BE]
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since 06 January 2022

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