Carbapenem- and colistin-resistant Enterobacterales in intensive care unit patients in Mediterranean countries, 2019.

Introduction: The colonization of patients by carbapenemase-producing Enterobacterales (CPE) has been associated with heightened mortality, especially in vulnerable individuals within intensive care units (ICUs). Our study aimed to comprehensively assess CPE prevalence among ICU patients across the Mediterranean region pre-COVID-19, conducting a multicenter prevalence study in the first quarter of 2019. Methods: We collected clinical data and rectal or fecal samples from 256 ICU patients for CPE testing. Additionally, we performed whole-genome sequencing on 40 representative CPE strains to document their molecular characteristics. Results: Among the 256 patients, CPE was detected in 73 samples (28.5%), with prevalence varying from 3.3 to 69.0% across participating centers. We observed 13 colistin-resistant CPE strains, affecting three ICUs. Genetic analysis revealed highly diverse E. coli and K. pneumoniae strains, predominantly from international high-risk clones. Notably, blaOXA-48 and blaNDM-1 were the most prevalent carbapenemase genes. Molecular typing uncovered potential patient clusters in six centers. Significantly, longer hospital stays were associated with increased CPE carriage (p < 0.001). Nine centers across Morocco, Tunisia, Egypt, and Lebanon voluntarily participated. Discussion: Our study provides CPE prevalence in Mediterranean ICUs and reaffirms established CPE presence in this setting but also provides updates on the molecular diversity of CPE strains. These findings highlight the imperative of reinforcing infection control measures in the participating ICUs to curtail escalated mortality rates, and of strictly applying isolation measures around patients originating from the Mediterranean region when transferred to other healthcare institutions.

Genomic Surveillance of SARS-CoV-2: Data Analysis and Assessment of Tunisian Strategy from January 2021 to February 2022.

Due to the emergence of the SARS-CoV-2 B.1.1.7 (Alpha) variant in the UK in 2020 and its risk of increased transmission, the Ministry of Health in Tunisia implemented a sequencing surveillance strategy for SARS-CoV-2. The aim of this study was to analyze SARS-CoV-2 genomic surveillance data in Tunisia (January 2021-February 2022) and to assess the implementation of the sequencing strategy for SARS-CoV-2 in accordance with national recommendations and the guidance for SARS-CoV-2 genomic surveillance for public health goals. A descriptive study of all sequenced RT-PCR samples sequenced (January 2021-February2022). An internal audit was also done to assess the compliance against standards covering national recommendations and the Guidance for SARS-CoV-2 genomic surveillance for public health goals. A total of 12 simple or composite requirements related to the following areas were included in the audit standards: sampling (one requirements); data collection/analysis (six requirements); partnership (one requirement); and ethical considerations (one requirement). A total of 4819 samples were sent to laboratories and 4278 samples were sequenced. A total of 3648 samples were classified. Positive variants of concern (VOC) samples were 80.92%, differentiated as follows: Alpha, 40.24%; Beta, 0.24%; Gamma, 0.03%; Delta, 45.26%; and Omicron, 14.19%. Three principal phases of VOCs per ISO-week were shown: Alpha 3/2021-25/2021; Delta 26/2021-2/2022; and Omicron 3/2022-6/2022. Levels of compliance were identified; from a total of 12 requirements, 7 were considered as "not met", 4 as "partially met", and 1 as "fully met" but including not totally achieved objectives. In conclusion, the internal audit of the national SARS-CoV-2 sequencing strategy revealed an overall "not met" level of compliance. The results offered a trigger to collaborate with all stakeholders to develop a surveillance strategy for early detection and response to outbreaks caused by VOCs.

Global Antimicrobial Resistance and Use Surveillance System on the African continent: Early implementation 2017-2019.

Background: Antimicrobial resistance (AMR) is becoming a critical public health issue globally. The World Health Organization launched the Global Antimicrobial Resistance and Use Surveillance System (GLASS) to support the strengthening of the AMR evidence base. Objective: The article describes the evolution of national AMR surveillance systems and AMR data reporting of countries in the African continent between 2017 and 2019, and the constraints, perceived impact and value of the participation in GLASS. Methods: Data on implementation of national surveillance systems and AMR rates were submitted to GLASS between 2017 and 2019 and summarised though descriptive statistics. The information on constraints and perceived impact and value in GLASS participation was collected though a set of questionnaires. Results: Between 2017 and 2019, Egypt, Ethiopia, Madagascar, Malawi, Mali, Mozambique, Nigeria, South Africa, Sudan, Tunisia, Uganda and Zambia submitted data to GLASS. The main constraints listed are linked to scarce laboratory capacity and capability, limited staffing, budget issues, and data management. Moreover, while the data are not yet nationally representative, high resistance rates were reported to commonly-used antibiotics, as the emerging resistance to last treatment options. Conclusion: Despite the limitations, more and more countries in the African continent are working towards reaching a status that will enable them to report AMR data in a complete and systematic manner. Future improvements involve the expansion of routine surveillance capacity for several countries and the implementation of surveys that allow to effectively define the magnitude of AMR in the continent.

First Description of Various Bacteria Resistant to Heavy Metals and Antibiotics Isolated from Polluted Sites in Tunisia.

Environmental bacteria belonging to various families were isolated from polluted water collected from ten different sites in Tunisia. Sites were chosen near industrial and urban areas known for their high degree of pollution. The aim of this study was to investigate cross-resistance between heavy metals (HM), i.e., silver, mercury and copper (Ag, Hg, and Cu), and antibiotics. In an initial screening, 80 isolates were selected on ampicillin, and 39 isolates, retained for further analysis, could grow on a Tris-buffered mineral medium with gluconate as carbon source. Isolates were identified based on their 16S rRNA gene sequence. Results showed the prevalence of antibiotic resistance genes, especially all isolates harbored the bla TEM gene. Some of them (15.38%) harbored bla SHV. Moreover, several were even ESBLs and MBLs-producers, which can threaten the human health. On the other hand, 92.30%, 56.41%, and 51.28% of the isolates harbored the heavy metals resistance genes silE, cusA, and merA, respectively. These genes confer resistance to silver, copper, and mercury. A cross-resistance between antibiotics and heavy metals was detected in 97.43% of our isolates.

High genotypic diversity of Rhinoviruses obtained from Tunisian children with severe acute respiratory infection.

INTRODUCTION: Rhinoviruses (HRV) are among the leading causes of Severe Acute Respiratory Infection (SARI). Their burden and genetic diversity vary from one region to another and little is known in Northern African regions. This study describes epidemiological patterns and genotypic diversity of HRV in SARI cases during a two and half year's study, in Northern Tunisia. METHODOLOGY: A total of 271 SARI cases, admitted into the Pediatric Intensive Care Unit of Bechir Hamza Children's Hospital in Tunis, were collected between September 2015 and December 2017. The investigation concerned 104 samples positive for HRV and/or HEV (Human Enterovirus) obtained among these cases. Specific HRV and HEV detections were assessed by real-time PCRs. The HRV molecular typing was based on the VP4-VP2 genomic region analyses. RESULTS: Among the viral SARI cases, 33.5% and 12.3% were positive for HRV and HEV respectively. Molecular investigations showed high prevalence of HRV-A (63.3%) followed by HRV-C (30.6%) and HRV-B (6.1%) and high genotypic diversity with 27 types. HRV cases were mostly detected in toddlers younger than 6 months. A total of 16 cases (28%) were found with bacterial and/or viral co-infection. HRV-C infection and HRV-A with bacterial co-infection were associated with complicated infection. Some of the detected types showed a continuous circulation or turnover during an extended period. HRV-A101 and HRV-C45 were the most frequently detected types. CONCLUSIONS: This study revealed, for the first time, the high HRV diversity in Tunisia, a North-African region. Specific phylogenetic investigations may help to evaluate their diversity and to trace their spread and epidemiological origin.

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.

Genetic Diversity of HIV-1 in Tunisia.

In this study, the genetic diversity of HIV-1 in Tunisia was analyzed. For this, 193 samples were collected in different regions of Tunisia between 2012 and 2015. A protease and reverse transcriptase fragment were amplified and sequenced. Phylogenetic analyses were performed through maximum likelihood and recombination was analyzed by bootscanning. Six HIV-1 subtypes (B, A1, G, D, C, and F2), 5 circulating recombinant forms (CRF02_AG, CRF25_cpx, CRF43_02G, CRF06_cpx, and CRF19_cpx), and 11 unique recombinant forms were identified. Subtype B (46.4%) and CRF02_AG (39.4%) were the predominant genetic forms. A group of 44 CRF02_AG sequences formed a distinct Tunisian cluster, which also included four viruses from western Europe. Nine viruses were closely related to isolates collected in other African or in European countries. In conclusion, a high HIV-1 genetic diversity is observed in Tunisia and the local spread of CRF02_AG is first documented in this country.

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.

[Peritonitis in pediatric patients receiving peritoneal dialysis]. / Péritonite infectieuse sur cathéter de dialyse péritonéale chez l'enfant.

BACKGROUND: Peritonitis on catheter of dialysis represents the most frequent complication of the peritoneal dialysis (PD) in the pediatric population. It remains a significant cause of morbidity and mortality. In this study, we investigated the risk factors for peritonitis in children. METHODS: In this study, we retrospectively collected the records of 85 patients who were treated with PD within the past ten years in the service of pediatrics of the University Hospital Charles-Nicolle of Tunis. RESULTS: Peritonitis rate was 0.75 episode per patient-year. Notably, peritonitis caused by Gram-positive organisms were more common. Analysis of infection risk revealed three significant independent factors: the poor weight (P=0.0045), the non-automated PD (P=0.02) and the short delay from catheter insertion to starting PD (P=0.02). The early onset peritonitis was significantly associated with frequent peritonitis episodes (P=0.0008). The mean duration between the first and second episode of peritonitis was significantly shorter than between PD commencement and the first episode of peritonitis. We revealed a significant association between Gram-negative peritonitis and the presence of ureterostomy (0.018) and between Gram-positive peritonitis and the presence of exit-site and tunnel infections (0.02). Transition to permanent hemodialysis was needed in many children but no death occurred in patients with peritonitis. CONCLUSION: Considering the important incidence of peritonitis in our patients, it is imperative to establish a targeted primary prevention. Nutritional care must be provided to children to avoid poor weight. The automated dialysis has to be the modality of choice.

[Antibiotic resistance among E. coli isolates from urinary tract infections (1999-2000): a multicenter study]. / Sensibilite aux antibiotiques des souches urinaires d'E. coli (1999-2000): resultats d'une étude multicentrique.

E. coli is the most frequently isolate species in community as well as in nosocomial acquired urinary tract infections (UTI). Trimethoprim-sulfamethoxazole (TMP-SMX), is commonly used as empiric treatment for managing uncomplicated UTI whereas the rate of resistance to amoxicilline is increasing. A multicentric retrospective study was conducted from January 1st 1999 to December 31st 2000 to evaluate the prevalence of E. coli isolates from UTI and to guide empiric therapies. Among 6994 urinary isolates, 62.6% were resistant to amoxicilline, this rate fell to 33.6% when amoxicilline was associated to clavulanic acide, 2.7% were producing extended spectrum b-lactamases (BLSE), higher than reported in France and USA. 37.3% were resistant to TMP-SMX. The high prevalence of antimicrobial resistance among UTI E. coli isolates emphasizes the necessity to review the empiric therapies. Fluoroquinolones can be considered as an alternative therapy according to their excellent tissue penetration and their wide spectrum of activity.

[Antibiotic sensitivity of Streptococcus pneumoniae in Tunisia: results of a multicenter study (1998-1999)]. / Sensibilité aux antibiotiques de Streptococcus pneumoniae en Tunisie: résultats d'une étude multicentrique (1998-1999).

We report the results of a multicenter tunisian study, performed over a two-year period (1998-1999), to determine the susceptibility pattern of Streptococcus pneumoniae in our country. A total of 146 S. pneumoniae were collected during the study period. 76 were recovered from adults and 70 from children. 53% of isolates have decreased susceptibility to penicillin, 24% with low level resistance, and 11% with high level resistance. Amoxicillin and cefotaxime decreased susceptibility rates were: 12% (low level resistance exclusively). and 14% (10% with low level resistance and 4% with high level resistance) respectively. Strains isolated from children, showed higher resistance to b lactams than those isolated from adults. Resistance rates to other antibiotics were as follow: erythromycin 28%, choramphenicol 14%, cyclins 23%, thrimethoprim-sulfamethoxazole 28% and rifampin 1%. No vancomycin resistant strain was found. The acquire resistance rates of Streptococcus pneumoniae in Tunisia are worrying, essentially for penicillin and erythomycin. Amoxicillin and cefotaxime have conserved a good activity.

[Enterococcus faecalis: a multicenter study on antibiotic resistance]. / Enterococcus faecalis: étude multicentrique sur la résistance aux antibiotiques.

676 E. faecalis strains were listed over a period of 2 years from the Charles Nicolle hospital of Tunis (167 strains), the Habib Bourguiba hospital of Sfax (350 strains) and the National Centre of Bone marrow Transplantation of Tunis (159 strains). Antibiotic sensibility study was realized by the method of the antibiogram, E-test method and the search of penicillinase by cefinase. E. faecalis resulted essentially from services of onco-haematology (24%), external consultations (23%), surgery (18%) and medicine (15%). These strains were isolated especially from urines (54%), coprocultures (15%), bloodcultures (11%) and from pus (9%). Resistance acquired with these strains is raised for erythromycin, tetracyclin and chloramphenicol (81% to 86%), followed by high level resistance to gentamicine (37%). 0.1% of E. faecalis strains have a low level resistance to amoxicillin without production of penicillinase. No resistance to vancomycin was observed.

[Epidemiologic profile of Haemophilus influenzae infection in Tunisia]. / Profil épidémiologique des infections à H. influenzae en Tunisie.

Haemophilus influenzae, a commensal bacteria, is frequently incriminated in broncho--pulmonary surinfections and severe diseases as meningitis, pneumonia and septic arthritis, particularly in young children. A multicenter study was conducted to establish the epidemiological profile of Haemophilus influenzae diseases, to determine the rate of antibiotics resistance for guide therapeutic and preventive strategies. The identification was based on the requirements for X and V factors, and the serotype b determined by agglutination. The betalactamase production was done by nitrocefin test. Antimicrobial susceptibility testing was determined on Muller Hinton chocolate agar with isovitalex. During the two year period, (January 1998 December 1999), 192 isolates of H. Influenzae were collected, 61% were recovered from invasive infections (44 meningitis, 8 bacteremia, 2 arthritis). The serotype b was identified in 55.7% of cases, 67.3% were invasive strains. 24.5% of isolates were producing betalactamase particularly invasive serotype b strains. All isolates of H. influenzae were susceptible to cefotaxim and to ofloxacin. Resistance rates to other antibiotics were: erythromycin 56.2%, tetracyclin 10.3%, rifampin 12%, chloramphénicol 1%, cotrimoxazole 16.5%, 11.5% amikacin and 20% gentamicin. The incidence of meningitis remained frequent in our country, involving the introduction of the vaccination in official calendar. Nevertheless, the surveillance of H. influenzae invasives infections and the serotyping of isolates were necessary to evaluate the impact of the immunization.