Phenotypic and molecular characterization of resistance to macrolides and Lincosamides in Corynebacterium striatum clinical strains isolated from Tunisia

Objectives: In this study we investigated the susceptibility profiles against macrolides and lincosamides of 85 C. striatum strains isolated at a clinical centre in Sousse (Tunisia). Methods: The strains were identified by the routine biochemical assays and then confirmed by Vitek-Maldi-Tof-MS. MIC?s of erythromycin and clindamycin were determined using the microdilution method. The detection of erm(X), erm(B), msr(A), mph(A) and mef(A-E) resistance genes was performed by PCR. The strains were typed by PFGE using XbaI. Results: Sixty-nine (81.17%) strains were resistant to erythromycin, 58 (67.44%) strains were resistant to clindamycin. There was a high correlation between the resistance to erythromycin and clindamycin and the presence of erm(X) gene in 85.50% and 89.65% respectively. The erm(B) gene was detected in 21(24.70%) strains whereas, no others genes were detected in our strains collection. By PFGE, the 85 strains belonged to 18 different clones. Conclusion: erm(X) is implicated in macrolide resistance for almost all the Corynebacterium strains analyzed in our study. Other resistance genes like erm(B) must also be implicated in this resistance, although its presence seems to be unusual in previously reported studies

In vitro Antibacterial Effects of Salvia sclarea, Eucalyptus Globulus and Eugenia Caryophyllata Essential oils Against Multidrug Resistant Corynebacterium spp Clinical Isolates

Objectives: Multidrug resistant Corynebacterium species are increasingly reported as the ethiological agent of various clinical infections. Thus, the purpose of this research was to evaluate the in vitro antimicrobial activity of three essential oils Salvia sclarea, Eucalyptus globulus and Eugenia caryophyllata against Corynebacterium species. Methods: Twenty-four multidrug resistant strains including C. striatum, C. amycolatum, C. urealyticum, C. aurimucosum, C. imitans, and C. jeikeium were used in the study. Inhibition diameter zone, minimum inhibitory concentration and minimum bactericide concentration of these oils were determined using agar disc diffusion method and microdilution method. Tigecycline was used as positive control. Results: Our study showed that Eugenia caryophyllata had the best activity. Eucalyptus globulus extract exhibited a moderate activity and Salvia sclarea was inactive against all the species tested. We found that C. amycolatum was more resistant to the essential oils than other species. On the other hand, tigecycline was effective on the majority of the strains (37.5%), but his action was lower than Eugenia caryophyllata oil. Conclusion: These results support the use of clove oil as a natural alternative to treat infections caused by multidrug resistant corynebacteria

Correlation between superficial and intra-operative specimens in diabetic foot infections: results of a cross-sectional Tunisian study

Objective: To determine the correlation between superficial, and intra-operative specimens in diabetic foot infections (DFIs). Methods: We conducted a cross-sectional study in patients with DFIs hospitalized in a Tunisian teaching hospital. Superficial specimens were collected for all patients, and intra-operative specimens were collected in operated patients. The specimens were processed using standard microbiology techniques. Antimicrobial susceptibility testing was carried out according to the protocol established by the European Committee on Anti-microbial Susceptibility Testing. Intra-operative and superficial specimens were considered correlated if they isolated the same microorganism(s), or if they were both negative. Results: One hundred twelve patients, 81 males and 31 females, mean age 56 years, were included. Superficial samples were positive in 77% of cases, and isolated 126 microorganisms. Among the positive samples, 71% were monomicrobial. The most frequently isolated microorganisms were Enterobacteriaceae (53%), followed by streptococci (21%) and Staphylococcus aureus (17%). Nine microorganisms (7%) were multi-drug resistant. Intra-operative samples were positive in 93% of cases. Superficial specimens were correlated to intra-operative specimens in 67% of cases. Initial antibiotic therapy was appropriate in 70% of cases. The lower-extremity amputation and the mortality rates were 41% and 1%, respectively. Conclusion: In our study, DFIs were most frequently caused by Enterobacteriaceae and superficial specimens were correlated to intra-operative specimens in only two thirds of cases. Clinicians should emphasize on the systematic practice of intraoperative specimens in all patients with DFIs treated surgically, while well-performed superficial specimens could be useful for prescribing appropriate antibiotic therapy in other patients

Molecular analysis of HBV genotypes and subgenotypes in the Central-East region of Tunisia

<p>Abstract</p> <p>Background</p> <p>In Tunisia, country of intermediate endemicity for Hepatitis B virus (HBV) infection, most molecular studies on the virus have been carried out in the North of the country and little is known about other regions. The aim of this study was to determine HBV genotype and subgenotypes in Central-East Tunisia. A total of 217 HBs antigen positive patients were enrolled and determination of genotype was investigated in 130 patients with detectable HBV DNA. HBV genotyping methods were: PCR-RFLP on the pre-S region, a PCR using type-specific primers in the S region (TSP-PCR) and partial sequencing in the pre-S region.</p> <p>Results</p> <p>Three genotypes (D, B and A) were detected by the PCR-RFLP method and two (D and A) with the TSP-PCR method, the concordance between the two methods was 93%. Sequencing and phylogenetic analysis of 32 strains, retrieved the same genotype (D and A) for samples with concordant results and genotype D for samples with discordant results. The sequences of discordant genotypes had a restriction site in the pre-S gene which led to erroneous result by the PCR-RFLP method. Thus, prevalence of genotype D and A was 96% and 4%, respectively. Phylogenetic analysis showed the predominance of two subgenotypes D1 (55%) and D7 (41%). Only one strain clustered with D3 subgenotype (3%).</p> <p>Conclusions</p> <p>Predominance of subgenotype D7 appears to occur in northern regions of Africa with transition to subgenotype D1 in the East of the continent. HBV genetic variability may lead to wrong results in rapid genotyping methods and sequence analysis is needed to clarify atypical results.</p

Perceived risk of infection and death from COVID-19 among community members of low- and middle-income countries: A cross-sectional study [version 1; peer review: awaiting peer review]

Background: Risk perceptions of coronavirus disease 2019 (COVID-19) are considered important as they impact community health behaviors. The aim of this study was to determine the perceived risk of infection and death due to COVID-19 and to assess the factors associated with such risk perceptions among community members in low- and middle-income countries (LMICs) in Africa, Asia, and South America. Methods: An online cross-sectional study was conducted in 10 LMICs in Africa, Asia, and South America from February to May 2021. A questionnaire was utilized to assess the perceived risk of infection and death from COVID-19 and its plausible determinants. A logistic regression model was used to identify the factors associated with such risk perceptions. Results: A total of 1,646 responses were included in the analysis of the perceived risk of becoming infected and dying from COVID-19. Our data suggested that 36.4% of participants had a high perceived risk of COVID-19 infection, while only 22.4% had a perceived risk of dying from COVID-19. Being a woman, working in healthcare-related sectors, contracting pulmonary disease, knowing people in the immediate social environment who are or have been infected with COVID-19, as well as seeing or reading about individuals infected with COVID-19 on social media or TV were all associated with a higher perceived risk of becoming infected with COVID-19. In addition, being a woman, elderly, having heart disease and pulmonary disease, knowing people in the immediate social environment who are or have been infected with COVID-19, and seeing or reading about individuals infected with COVID-19 on social media or TV had a higher perceived risk of dying from COVID-19. Conclusions: The perceived risk of infection and death due to COVID-19 are relatively low among respondents; this suggests the need to conduct health campaigns to disseminate knowledge and information on the ongoing pandemic

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Evaluation of Three Carbapenemase-Phenotypic Detection Methods and Emergence of Diverse VIM and GES Variants among <i>Pseudomonas aeruginosa</i> Isolates in Tunisia

Background: Since 2012, few reports on the molecular epidemiology of Pseudomonas aeruginosa were reported in Tunisia. Objectives: This study aimed to evaluate carbapenem-resistance determinants and molecular epidemiology and to compare the carbapenemase-phenotypic detection methods of multidrug-resistant P. aeruginosa isolates. Methods: During a period of four years (2014 to 2017), all imipenem-ceftazidime-resistant P. aeruginosa isolates were retrospectively selected at the microbial laboratory of Charles Nicolle hospital of Tunis. These isolates were examined by the modified Hodge test, modified carbapenem inactivation method (mCIM), and another mCIM, called CIMTris, and their performance was evaluated using PCR analysis as the gold standard. Results: A total of 35 isolates were recovered among patients hospitalized in different units. All strains were colistin-susceptible.All carbapenem-resistant isolates showed a high-level resistance to carbapenems. CIMTris and mCIM showed 96.15% and 46.15% sensitivity and 44.44% and 100% specificity, respectively, for detecting carbapenemase production.Conclusions: CIMTris is a promising approach for detecting carbapenemase activity in P. aeruginosa and merits further testing. Moreover, this study described the first detection of GES-5- and GES-9-producing P. aeruginosa in Tunisia as well as the co-occurrence of the blaGES-5 and blaVIM-11 carbapenemase genes in one isolate. These findings are of great concern because the rapid dissemination of MDR strains represents a major therapeutic and epidemiological threat

Antimicrobial and molecular analysis of Salmonella serovar Livingstone strains isolated from humans in Tunisia and Belgium

Introduction: Salmonella Livingstone is one of the most common serotypes responsible for nosocomial outbreaks in Tunisia. In this study, 42 isolates of Salmonella Livingstone were analyzed. Most of these were isolated from humans (31 strains from Tunisia and 9 strains from Belgium) and 2 isolates came from food products (beef and pork). Methodology: All strains were characterized by antibiogram, multilocus sequence typing (MLST), and virulotyping. This last technique was carried out by simple PCR of five chromosomal genes (agfA, hin/H2, iroB, phoP/Q, and slyA) and two plasmid genes (spvA and spvC). Results: All Tunisian strains were resistant to amoxicillin, amoxicillin-clavulanic acid, ticarcillin, cefalotin, gentamicin, and kanamycin. They were also resistant to third-generation cephalosporin antibiotics (cefotaxim and ceftazidim). Belgian isolates were susceptible to all antibiotics tested. Further to MLST analyses, Tunisian strains belonged to the same sequence type, ST543. For Belgian isolates, eight strains had a ST543 profile, two strains had a ST638 profile, and one strain had a ST457 profile. Analyses of the virulence gene contents showed that strains isolated in different years and from different origins had the same virulence profile. These carried all five chromosomal genes and lacked plasmid-located virulence genes spvA and spvC. Conclusions: A combination of different typing methods showed that the majority of Belgian strains and all Tunisian strains were closely related; they belonged to the same sequence type (ST543) and had the same virulence profile, but different antibiotic resistance profiles depended on the country of origin

Biochemical characterization of Tunisian grapevine varieties

61 tunisian autochton grapevine varieties have been collected for biochemical identification. Isozymes analysis with starch gel electrophoresis technique was used to confirn or to cancel random denominations awarded to the majority of these local varieties. In our conditions, concentrated plant extracts were obtained from vigorous donnant canes newly cut off from selected mother plants during automn. These allowed us to dispose of rigorously interpretable isozyme banding patterns of GPI and PGM systems and to overcome difficulties often related to the use of PGM system. The study of GPII and PGM enzyme systems allowed us to classify the autochton accessions into 16 different groups from which 5 groups containing only 2 or 3 varieties. On the other hand, the study of AAT and peroxydase enzyme systems has shown stable and legible isozyme banding patterns allowing to discriminate between equivalent accessions such as Sakasly and Kahli (two black local vines very similar), 3 varieties of Bidh Hamem (Bidh Hamem, Bidh Hamem Rafraf and Bidh Hamem Sfax), and 2 varieties of Bezzoul Kelba Bidha (Sfax and Gabes). In addition, certain varieties having for longtime the same denominations were characterized. A case of point the 4 varieties Khalt meaning mixture (Bouchemma, Abiedh, Mdaouer and Souche 1) and the 3 varieties of Arich (Ahmar, Dressée, and Jerba) were proved to be completely different from each other. In the same way, Bezzoul Khadem has been differed from Hemri variety. The complementary use of berry colour allowed to discriminate between Saouadi, Khdhiri and Jebbi varieties and to subdivise the remainig groups into sub-groups. The study of GPI, PGM, AAT and peroxydase isozyme banding patterns in combination with berry colour has led to establish a classification of the 61 autochton varieties into 37 groups including 26 varieties definitely differentiated through the results of this biochemical study