Whole genome sequencing and phylogenetic classification of Tunisian SARS-CoV-2 strains from patients of the Military Hospital in Tunis.

In the present work, two complete genome sequences of SARS-CoV-2 were obtained from nasal swab samples of Tunisian SARS-CoV-2 PCR-positive patients using nanopore sequencing. The virus genomes of two of the patients examined, a Tunisian soldier returning from a mission in Morocco and a member of another Tunisian family, showed significant differences in analyses of the total genome and single nucleotide polymorphisms (SNPs). Phylogenetic relationships with known SARS-CoV-2 genomes in the African region, some European and Middle Eastern countries and initial epidemiological conclusions indicate that the introduction of SARS-CoV-2 into Tunisia from two independent sources was travel-related.

SARS-CoV-2 infection virological diagnosis.

SARS-CoV-2 infection has to be confirmed by virological diagnosis. Multiple diagnostic tests are available without enough perspective on their reliability. Therefore, it is important to choose the most suitable test according to its sensitivity and specificity but also to the stage of the disease. Currently, the RT-PCR detection of the viral genome in respiratory samples is the most reliable test to confirm the diagnosis of an acute SARS-CoV-2 infection. It has to be done in Class II biological safety laboratory. However, it may lack sensitivity, particularly in the advanced phase of infection, and depends closely on the samples' quality. Rapid PCR by cartridge system reduces response times but is not suitable for laboratories with high throughput of requests. Detection of virus antigens on respiratory samples is a quick and easy to use technique; however it has not good specificity and sensitivity and cannot be used for diagnosis and patient management. The detection of specific antibodies against SARS-CoV-2 is better used for epidemiological analyses. Research should be encouraged to overcome the limits of the currently available diagnostic tests.

Screening for Carbapenemases in Ertapenem-Resistant Enterobacteriaceae Collected at a Tunisian Hospital Between 2014 and 2018.

BACKGROUND: Carbapenem-resistance is frequently detected in Enterobacteriaceae isolated from patients in Tunisia. The study was performed to identify frequent carbapenemases in Tunisian isolates. METHODS: Between May 2014 and January 2018, 197 ertapenem-resistant Enterobacteriaceae were isolated at the microbiological department of the Military Hospital of Tunis. The strains were phenotypically characterized and then subjected to in-house polymerase chain reaction (PCR) targeting the carbapenemase genes blaIMP, blaVIM, blaNDM, blaSPM, blaAIM, blaDIM,blaGIM, blaSIM, blaKPC, blaBIC , and blaOXA-48. RESULTS: The assessed 197 ertapenem-resistant Enterobacteriaceae from Tunis comprised 170 Klebsiella pneumoniae, 19 Enterobacter cloacae, 6 Escherichia coli, 1 Citrobacter sedlakii, and 1 Enterobacter asburiae. Thereby, 55 out of 197 isolates (27.9%) were from blood cultures, suggesting a systemic disease. The carbapenemase gene blaOXA-48 quantitatively dominated by far with 153 detections, followed by blaNDM with 14 detections, which were distributed about the whole study interval. In contrast, blaBIC and blaVIM were only infrequently identified in 5 and 3 cases, respectively, while the other carbapenamases were not observed. CONCLUSIONS: The carbapenemase gene blaOXA-48 was identified in the vast majority of ertapenem-resistant Tunisian Enterobacteriaceae while all other assessed carbapenemases were much less abundant. In a quantitatively relevant minority of isolates, the applied PCR-based screening approach did not identify any carbapenemases.

Nosocomial urinary tract infections caused by extended-spectrum beta-lactamase uropathogens: Prevalence, pathogens, risk factors, and strategies for infection control.

INTRODUCTION: Our goal was to investigate the prevalence and antibiogram pattern of extended spectrum beta-lactamase (ESBL) production among uropathogens using isolates from urine samples collected at the Department of Urology in the Sahloul Hospital, Tunisia We also aimed to identify the risk factors for nosocomial urinary tract infections (UTIs) in patients who underwent transurethral resection of the prostate (TURP) and the measures for infection control. METHODS: Laboratory records of a five-year period from January 2004 to December 2008 were submitted for retrospective analysis to determine the incidence of ESBL infections. A total of 276 isolates were collected. A case-control study involving comparisons between two groups of patients who underwent TURP was performed to determine the risk factors for ESBL infection. Group 1, designated case subjects, included 51 patients with nosocomial UTI after TURP. Group 2, designated control subjects, consisted of 58 randomly selected patients who underwent TURP without nosocomial UTI in the same period. Factors suspected to be implicated in the emergence of ESBL infection were compared between the two groups in order to identify risk factors for infection. A univariate regression analysis was performed, followed by a multivariate one. RESULTS: The annual prevalence of ESBL infection ranged from 1.3-2.5%. After performing univariate and multivariate regression analysis, the main risk factors for ESBL infections were identified as: use of antibiotics the year preceding the admission, duration of catheter use, and bladder washout (p=0.012, p=0.019, and p<0.001. CONCLUSIONS: Urologists have to perform a good hemostasis, especially in endoscopic resections, in order to avoid bladder irrigation and bladder washout and to reduce the time of bladder catheterization, which is a strong risk factor of nosocomial UTIs.

Successful treatment of a Carbapenem-resistant Klebsiella pneumoniae carrying bla OXA-48 , bla VIM-2 , bla CMY-2 and bla SHV- with high dose combination of imipenem and amikacin.

We describe a case of 58-year-old man with septic shock due to Carbapenem-resistant Klebsiella pneumoniae (CR-Kp) bloodstream infections (BSI) who was successfully treated with a high dose association of amikacin and imipenem combined with continuous venovenous hemodiafiltration (CVVHDF). A Klebsiella pneumoniae (Kp) was isolated from the catheter culture and from two blood samples, drawn from the catheter before removal and from a peripheral vein. The Kp was intermediate to Amikacin (MIC = 16 µg/ml) and was resistant to all other antibiotics including Imipenem (MIC = 4 µg/ml), Colistin (MIC = 16 µg/ml) and Tigecycline (MIC = 4 µg/ml) according to the Clinical and Laboratory Standards Institute (CLSI) published in 2011. PCR amplification and sequencing verified the presence of blaOXA-48, blaVIM-2, blaCMY-2 and blaSHV-1 genes. Amikacin was given at a dose of 30 mg/kg (2.5 g) in a 30 min infusion and the dose of imipenem was increased to 1 g every 6 h despite patient's altered renal function (Creatinine Clearance = 25 ml/min). To avoid amikacin nephrotoxicity and to allow the use of high doses of imipenem, continuous venovenous hemodiafiltration (CVVHDF) (blood flow, 200 ml/h; dialysate, 1000 ml/h; ultrafiltrate, 2000 ml/h) was initiated 1 h after the start of the amikacin infusion and continued thereafter. The patient improved hemodynamically and norepinephrine was stopped five days after antibiotherapy adaptation.

Performance of a new rapid test for the detection of hepatitis B surface antigen in various patient populations.

BACKGROUND: Rapid diagnostic tests (RDT) have been developed for the detection of hepatitis B surface antigen (HBsAg). They represent a promising alternative to enzyme immunoassays and a powerful tool for large-scale screening and diagnosis of HBV infection, especially in regions without easy access to serological and molecular testing. OBJECTIVES: The aims of the present study were to evaluate the characteristics and clinical performance of a new CE-marked HBsAg RDT, DRW-HBsAg v2.0 assay (Diagnostics for the Real World™, Ltd., USA), in various patient populations, including those chronically infected with HBV, patients with severe acute hepatitis of unknown origin and pregnant women with unknown HBV serological status at delivery. RESULTS: The lower limit of detection of the assay, evaluated in 21 clinical samples, ranged from 0.30 ± 0.07 to 0.97 ± 0.26 international units/mL (using Abbott Architect as a reference), depending on the HBV genotype. The assay tested positive in 100% of patients with chronic hepatitis B, 96.3% of HBsAg-positive acute hepatitis patients, and 95.2% of HBsAg-positive pregnant women. Its specificity was 98.8% in HBsAg-negative patients, 98.7% in HBsAg-negative patients with acute hepatitis of unknown origin and 97.8% in HBsAg-negative pregnant women. Amino acid substitutions in the HBsAg major hydrophilic region did not affect HBsAg detection by DRW-HBsAg v2.0. CONCLUSIONS: The new DRW-HBsAg v2.0 assay is a simple, rapid, easy-to-run and highly sensitive assay that can be used in both high- and low-risk populations for the diagnosis of HBsAg carriage. It appears to be a promising new tool for large-scale screening and diagnosis of HBV infection.