Genomic surveillance of SARS-CoV-2 in North Africa: 4 years of GISAID data sharing

Objectives

This study aimed to construct geographically, temporally, and epidemiologically representative data sets for SARS-CoV-2 in North Africa, focusing on Variants of Concern (VOCs), Variants of Interest (VOIs), and Variants Under Monitoring (VUMs).

Methods

SARS-CoV-2 genomic sequences and metadata from the EpiCoV database via the Global Initiative on Sharing All Influenza Data platform were analyzed. Data analysis included cases, deaths, demographics, patient status, sequencing technologies, and variant analysis.

Results

A comprehensive analysis of 10,783 viral genomic sequences from six North African countries revealed notable insights. SARS-CoV-2 sampling methods lack standardization, with a majority of countries lacking clear strategies. Over 59% of analyzed genomes lack essential clinical and demographic metadata, including patient age, sex, underlying health conditions, and clinical outcomes, which are essential for comprehensive genomic analysis and epidemiological studies, as submitted to the Global Initiative on Sharing All Influenza Data. Morocco reported the highest number of confirmed COVID-19 cases (1,272,490), whereas Tunisia leads in reported deaths (29,341), emphasizing regional variations in the pandemic's impact. The GRA clade emerged as predominant in North African countries. The lineage analysis showcased a diversity of 190 lineages in Egypt, 26 in Libya, 121 in Tunisia, 90 in Algeria, 146 in Morocco, and 10 in Mauritania. The temporal dynamics of SARS-CoV-2 variants revealed distinct waves driven by different variants.

Conclusions

This study contributes valuable insights into the genomic landscape of SARS-CoV-2 in North Africa, highlighting the importance of genomic surveillance in understanding viral dynamics and informing public health strategies.

Tunisian Multicenter Study on the Prevalence of Colistin Resistance in Clinical Isolates of Gram Negative Bacilli: Emergence of Escherichia coli Harbouring the mcr-1 Gene

Background: Actually, no data on the prevalence of plasmid colistin resistance in Tunisia are available among clinical bacteria. Objectives: This study aimed to investigate the current epidemiology of colistin resistance and the spread of the mcr gene in clinical Gram-negative bacteria (GNB) isolated from six Tunisian university hospitals. Methods: A total of 836 GNB strains were inoculated on COL-R agar plates with selective screening agar for the isolation of GNB resistant to colistin. For the selected isolates, mcr genes, beta-lactamases associated-resistance genes and molecular characterisation were screened by PCRs and sequencing. Results: Colistin-resistance was detected in 5.02% (42/836) of the isolates and colistin-resistant isolates harboured an ESBL (bla_CTX-M-15) and/or a carbapenemase (bla_OXA-48, bla_VIM) encoding gene in 45.2% of the cases. The mcr-1 gene was detected in four E. coli isolates (0.59%) causing urinary tract infections and all these isolates also contained the bla_TEM-1 gene. The bla_CTX-M-15 gene was detected in three isolates that also carried the IncY and IncFIB replicons. The genetic environment surrounding the mcr-carrying plasmid indicated the presence of pap-2 gene upstream mcr-1 resistance marker with unusual missing of ISApl1 insertion sequence. The Conclusions: This study reports the first description of the mcr-1 gene among clinical E. coli isolates in Tunisia and provides an incentive to conduct routine colistin susceptibility testing in GNB clinical isolates.

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 bla_GES-5 and bla_VIM-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.

Prognostic Value of High-sensitivity Troponin I in Patients with Septic Shock: A Prospective Observational Study

BACKGROUND

Myocardial dysfunction is one of the mechanisms involved in the pathophysiology of septic shock. The role of troponin as a surrogate of myocardial injury in septic shock is still debated. The aim of this study was to assess the prognostic value of high-sensitivity cardiac troponin I (hs-cTnI) assay in predicting 28-day mortality in patients with septic shock.

MATERIALS AND METHODS

Prospective study including 75 patients with septic shock admitted to a medico-surgical ICU from January to December 2017. Patients under the age of 18 years, known pregnancy and patients in post-cardiac arrest were excluded. Clinical and demographic data including age, gender, comorbidities, SAPS II and SOFA scores were collected. Hs-cTnI was measured soon after admission and 12, 24, 48 and 72 after. Receiver operating characteristic (ROC) analysis was performed to identify the most useful troponin I cut-off level for the prediction of 28-day mortality. A p <0.05 was considered significant.

RESULTS

Seventy-five (M/F = 53/22) patients with septic shock were included in the study. The median SOFA and SAPS II scores were 10 and 42, respectively. The median duration of mechanical ventilation was 8 days and the median length of ICU stay was 11 days. The 28-day mortality was 54.6%. We found a high prevalence (47%) of elevated hs-cTnI in patients with septic shock. Median hs-cTnI on admission in the whole group was 36 ng/L. The 28-day mortality was found to be related to age (p <0.001), SAPS II score (p = 0.001), mean arterial pressure (p = 0.038), lactate (p <0.001) and glomerular filtration rate (p <0.001).Hs-cTnI levels were significantly higher in non-survival group than survival one at all time points: H12 (p = 0.006), H24 (p = 0.003), H48 (p = 0.005) and H72 (p=0.001). In multivariate analysis, hs-cTnI at H72 was independently associated with 28-day mortality.

CONCLUSION

Hs-cTnI elevation at 72 hours was associated with 28-day mortality in septic shock patients.

HOW TO CITE THIS ARTICLE

Jendoubi A, Jerbi S, Maamar E, Abbess A, Samoud Z, Kanzari L, et al. Prognostic Value of High-Sensitivity Troponin I in Patients with Septic Shock: A Prospective Observational Study. Indian J Crit Care Med 2019;23(7):320-325.

First report of extensively-drug-resistant Proteus mirabilis isolate carrying plasmid-mediated blaNDM-1 in a Tunisian intensive care unit

Emergence of the New Delhi metallo-β-lactamase (NDM-1), an Ambler class B metallo-β-lactamase able to hydrolyse all β-lactams except monobactams, constitutes a critical and increasingly important medical issue. The acquisition of bla_NDM-1 is of particular concern for Proteus mirabilis, which is intrinsically resistant to tetracycline, tigecycline and colistin, as this will make clinical treatment extremely difficult. To the authors' knowledge, this is the first report of the bla_NDM-1 gene in an extensively-drug-resistant P. mirabilis clinical isolate carrying plasmid-mediated resistance to carbapenems (bla_NDM-1), cephalosporins (bla_CMY-4), aminoglycosides (aph3 VIa and aph3 Ia) and fluoroquinolones (qnrA6).

Epidemiological profile and antibiotic resistance of Pseudomonas aeruginosa isolates in burn and Traumatology center in Tunisia over a three-year period

BACKGROUND

Pseudomonas aeruginosa is a known opportunistic pathogen frequently causing serious infections in burned patients.

AIM

To analyze the epidemiological profile of Pseudomonas aeruginosa isolated in a Tunisian burn unit.

METHODS

During a 3-year period (from 01 July 2008 to 30 June 2011), 544 non repetitive strains of P. aeruginosa were isolated from burn patients. Susceptibility to antibiotics was assessed according to CA-SFM guidelines. Serotypes were identified by slide agglutination test using P.aeruginosa O antisera (Biorad). Producing carbapenemase was analyzed for 202 imipenem resistant isolates by EDTAtest. Susceptibility testing data were stored in a laboratory data base using whonet 5.3 software.

RESULTS

The most frequent sites of isolation were cutaneous infections and blood cultures (83.4%). The percentages of resistant isolates were as follows: ceftazidime: 34%; imipenem: 37.1%, ciprofloxacin: 27.1% and amikacin: 29.6%. The most prevalent serotypes were: 011(51%), 06(17%), 03 (8%), 04(12%), 012(5%). Among the 202 imipenem resistant strains, 58% expressed a metallocarbapenemase. All theses strains were resistant to all tested antibiotics except colistin and belonged to the serotype O11.

CONCLUSION

The dissemination of carbapenemases strains must be contained by implementation of timely identification, strict isolation methods and better hygienic procedures.