Genetic diversity of Streptococcus pneumoniae in Tunisia.

OBJECTIVES: This study aimed to explore the genetic diversity of Streptococcus pneumoniae isolates in a Tunisian pneumology hospital. METHODS: A total of 141 S. pneumoniae strains isolated between 2009-2016 in the microbiology laboratory at A. Mami Hospital of Pneumology were investigated. Antimicrobial susceptibility testing was performed the disk diffusion method. MICs of penicillin G, amoxicillin and cefotaxime were determined by Etest. Serotyping was inferred from the results of multiplex PCR targeting 40 serotypes. Sequence types (STs) were determined by multilocus sequence typing (MLST). RESULTS: Among the 141 S. pneumoniae isolates, 98 (69.5%) were resistant to erythromycin. Evaluation of ß-lactam susceptibility showed that 90 strains (63.8%) were non-susceptible to penicillin, whereas 48 (34.0%) had decreased susceptibility to amoxicillin and 21 (14.9%) to cefotaxime. Twenty-five serotypes were detected, and 10 isolates were classified as non-typeable. Vaccine coverage was 56.7%, 60.3% and 75.2% for pneumococcal conjugate vaccine 7 (PCV7), PCV10 and PCV13, respectively. Overall, 73 STs were identified, including 23 described for the first time. The most frequent STs were ST179 (n = 17), ST3772 (n = 14), ST2918 (n = 10) and ST4003 (n = 5), related to serotypes 19F, 19A, 14 and 23F, respectively. Moreover, 110 strains were classified within 45 STs. Three international antimicrobial-resistant clones were found, including Denmark14-ST230 (n = 22), Spain9V-ST156 (n = 22) and Portugal19F-ST177 (n = 20). CONCLUSION: This study emphasises the clonal and international dissemination of antimicrobial-resistant S. pneumoniae clones. Significant differences in genetic variation were documented by MLST within the various serotypes identified.

Is sequencing better than phenotypic tests for the detection of pyrazinamide resistance?

SETTING: Phenotypic tests used to detect pyrazinamide (PZA) resistance are slow and have a high rate of false resistance. OBJECTIVE: To evaluate the accuracy of pncA sequencing for the detection of PZA resistance in Mycobacterium tuberculosis strains isolated in Tunisia. DESIGN: A total of 82 isolates, 41 resistant and 41 susceptible to PZA on BACTEC™ MGIT™ 960, were sequenced for pncA. Whole genome sequencing was performed for strains that were phenotypically resistant and had wild-type pncA in addition to MGIT retesting with a modified protocol. RESULTS: Twenty-three strains resistant to PZA with negative pyrazinamidase (PZase) activity harboured a mutation in the promoter or coding region of pncA. However, 18 strains resistant to PZA did not present any mutation. Repeat MGIT 960 showed that 16 of 18 M. tuberculosis isolates were falsely resistant to PZA. Compared with MGIT, PZase activity assay and pncA sequencing both presented a sensitivity of 92.0% (95%CI 73.9-99.0) and a specificity of respectively 96.5% (positive predictive value [PPV] 92.0%, negative predictive value [NPV] 96.5%) and 100.0% (PPV 100.0%, NPV 96.6%). CONCLUSION: The standard MGIT assay showed a high rate of false resistance to PZA, and the PZase activity assay is slow. pncA sequencing could therefore represent a rapid, accurate, alternative test to detect PZA resistance.

Duffy blood group system genotyping in an urban Tunisian population.

BACKGROUND: The Duffy blood group system, besides its relevance in transfusion medicine, is of major interest for population genetics. In fact, the Duffy molecule is the only red cell receptor for Plasmodium vivax, thus the fixation of FY*silent allele in western south-Saharan Africa resulted in the absence of this type of malaria in that area (for a review see Kwiatowski, Am J Hum Genet 77:171-192, 2005). For the Duffy functional role see, for example, Daniels (Vox Sanguinis 93:331-340, 2007). METHODS: Duffy blood group distribution in 115 unrelated Tunisians was determined using the polymerase chain reaction with sequence specific primer (PCR-SSP) method detecting the five allelic versions of the FY gene. The red cell antigenic FY phenotype, for each donor, was deduced through DNA analysis. The blood samples of the positive FY*X alleles were investigated by serological methods, mainly the fixation-elution technique. RESULTS: The following allele frequencies were found (after having excluded FY*X, which had frequency of 0.0174): FY*1 = 0.291 (expressed 0.260; silent 0.031); FY*2 = 0.709 (expressed 0.427; silent 0.282). The most surprising result in this work is the detection of the FY*1 silent allele, usually quite rare, in four samples (1.74%). For FY*2 silent, the predominant allele in Africans, genotyping results showed a prevalence of 29.57%. The FY locus was in Hardy-Weinberg equilibrium in the present sample. CONCLUSION: When compared with European and African data, Tunisian samples demonstrated the presence of the common signs of these two ancestries (FY*2 and FY*X for the first population; and FY*2 silent for the last one). These data confirm the mixed roots of this urban Tunisian population already suggested by numerous studies on other haematological markers.

Prevalence of C282Y and H63D mutations in the haemochromatosis (HFE) gene in Tunisian population.

The studies of the HFE mutations: H63D and C282Y in North African populations have revealed the extreme rarity or even the absence of the C282Y mutation. We have examined 1140 chromosomes (570 Tunisian people) for the presence of the two HFE mutations by PCR-RFLP analysis. We have found that the allele frequencies are, respectively, 15.17% (+/-2.1%) for the H63D and 0.09% (+/-0.17%) for the C282Y. These results are consistent with the worldwide spread of the H63D mutation and the north European restriction of the C282Y. This study will be completed by determining whether homozygote trait for H63D and associated risk factors (beta thalassémia) can lead to iron overload in Tunisia.

[ABO system polymorphism in the Tunisian population]. / Polymorphisme du système ABO dans la population tunisienne.

A survey carried out on 18820 Tunisian blood donors enabled us to evaluate the distribution of ABO blood group in Tunisia. The genic frequencies in ABO system were as follows: A(0,192), B(0,122), O(0,686).