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

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 Pseudomonas aeruginosa 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

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

Characterization of <i>Escherichia</i> <i>coli</i> Cefotaxime-Resistance in Al-Ahsa, KSA: Predominance of CTX-15 and First Report of <i>bla_CMY-42</i> Gene

We determined an antibiotic resistance mechanism in the eastern region, KSA, and the genetic factor clonal relatedness within Gram-negative bacteria. During our retrospective study, a total number of 29 E. coli ESBL producer strains were isolated for patients visiting King Fahad Hospital, Al-Ahsa, KSA. The bla genes were detected via PCR and identified via sequencing. Associated plasmid-mediated quinolone resistance genes, as well as int1 and int2 genes, were also studied. Phylogenetic groups, the ST131 clone, virulence factors, and PFGE were also checked. The blaCTX-M-9 (3.7%), blaCTX-M-27 (22.2%), and blaCTX-M-15 (77.8%) genes were identified; however, the blaCMY-42 (7.4%) gene was recorded for the first time in KSA. The qnrS1 gene was found in 44.4% of strains, and among them, 50% concomitantly harbored the aac(6′)Ib-cr. The int1 gene was detected in 25.9% strains; nonetheless, the int2 gene was found in 7.4% of isolates. The strains belonged mainly to the B2 and D phylogroups. PFGE showed unrelated patterns. Some isolates belonged to the pandemic clone ST131. We describe a large dissemination of antibiotic resistance to third-generation cephalosporins in the eastern region, KSA, with the occurrence of the blaCMY-42 gene. The clone ST131 seems to be the principal contributor for blaCTX-M-15 gene spread

Chemical composition, antioxidant and allelopathic activities of essential oils and crude extracts of Cupressus arizonica Greene

Chemical composition, antioxidant, and allelopathic activities of extract from leaves and cones of Tunisian Cupressus arizonica were evaluated. The values of essential oils (EO) yields were 0.18% for leaves and 1.07% for cones. Following GC/MS analysis of C. arizonica leaves and cones, the major compounds identified in leaves EO were umbellulone (19.4%) and α-pinene (10.75%) while the EO of the cones was characterized by its richness with α-pinene (81.3%). In comparison with different extracts, the highest total antioxidant capacity was registered with ethanolic extracts of leaves followed by that of cones. However, the antioxidant activity was stronger with ethanolic extract of leaves than that of cones using both DPPH or ABTS in free radical scavenging activity assays. Results of allelopathic activity showed that the germination reduction depends on the nature of extract and their concentration level. All extracts of C. arizonica decreased the germination of Sinapis arvensis compared to the control. The EO from leaves and cones had the greatest reduction on germination and the strongest growth inhibition followed by the ethanolic extract then the aqueous extract. Results of this study can lead to identification of new phytotoxic compounds in extracts of C. arizonica useful in controlling weeds.La composition chimique, les activités antioxydantes et allélopathiques de l’extrait de feuilles et de cônes de Cupressus arizonica de Tunisie ont été évaluées. Les valeurs des rendements en huiles essentielles (HE) étaient de 0,18 % pour les feuilles et de 1,07 % pour les cônes. Grâce à l’analyse par GC/MS des feuilles et des cônes de C. arizonica, les principaux composés identifiés dans l’HE des feuilles étaient l’umbellulone (19,4 %) et l’α-pinène (10,75 %) tandis que l’HE des cônes était caractérisée par sa richesse en α-pinène (81,3 %). Par rapport à différents extraits, la capacité antioxydante totale la plus élevée a été enregistrée avec les extraits éthanoliques des feuilles, suivie par celle des cônes. Cependant, l’activité antioxydante était plus forte avec l’extrait éthanolique des feuilles que celle des cônes en utilisant DPPH ou ABTS dans les deux tests d’activité de piégeage des radicaux libres. Les résultats de l’activité allélopathique ont montré que la réduction de la germination dépend de la nature des extraits et de leurs niveaux de concentration. Tous les extraits de C. arizonica étaient capables de diminuer la germination de Sinapis arvensis par rapport au témoin. Les HE des feuilles et des cônes avaient un impact plus important sur la réduction de la germination et l’inhibition de la croissance, suivi par l’extrait éthanolique puis par l’extrait aqueux. Les résultats de cette étude peuvent conduire à identifier de nouveaux composés phytotoxiques dans des extraits de C. arizonica utiles pour la lutte contre les mauvaises herbes