Characterization of carbapenem resistant Acinetobacter baumannii isolated from intensive care units in two teaching hospitals from Algeria and Tunisia

Introduction: This study was conducted to identify the enzymatic mechanism of carbapenem resistance in A. baumannii isolated from intensive care units of 2 teaching hospitals (Charles Nicolle hospital of Tunis and University hospital of Annaba). Methods: Twenty seven non repetitive carbapenem-resistant A. baumannii were collected (7 strains in Algeria and 20 in Tunisia). Antibiotic susceptibility was performed by disk diffusion method. MICs were determined by agar dilution method. EDTA-disk synergy test was performed for metallo-β-lactamases (MBL) phenotypicdetection. Detection of blaOXA-23-like, blaOXA-24-like, blaOXA-51-like and blaOXA-58-like families was performed by PCR followed by sequencing. Geneticrelatedness between strains was investigated by pulsed-field gel electrophoresis (PFGE). Results: Strains were recovered especially from respiratory tract specimens (n=12) and blood (n=11). All strains were co-resistant to all β-lactams, gentamicin, amikacin and ciprofloxacin, but remainded susceptible to colistin. MBL production was negative for all isolates. blaOXA-51-like was detected in all strains and blaOXA-23-like in 23 strains. However, blaOXA-58-like and blaOXA-24-like were not found in any isolate. Six major PFGE patterns were found in the Tunisian isolates. However, the Algerian strains were clustered in one clone.Conclusion: This study shows a high distribution of blaOXA-23 in imipenem-resistant A. baumannii isolated in Tunisia and Algeria. It demonstrated the epidemic diffusion of this multidrug resistant pathogen. Thus, strengthening of prevention measures are required to control further spread of carbapenemases in the two countries.Key words: A. baumannii, Carbapenem resistance, OXA-23-like, Pulsed-field gel electrophoresi

Genetic Background of Antimicrobial Resistance in Multiantimicrobial-Resistant Escherichia Coli Isolates From Feces Of Healthy Broiler Chickens In Tunisia

Multiantimicrobial-resistant Escherichia coli isolates are a global human health problem causing increasing morbidity and mortality. Genes encoding antimicrobial resistance are mainly harbored on mobile genetic elements (MGEs) such as transposons and plasmids as well as integrons, which enhance their rapid spread. The aim of this study was to characterize 83 multiantimicrobial-resistant E. coli isolates recovered from healthy broiler chickens. Among 78 tetracycline-resistant isolates, the tetA, tetB, and tetC genes were detected in 59 (75.6%), 14 (17.9%), and one (1.2%) isolates, respectively. The sul1, sul2, and sul3 genes were detected 31 (46.2%), 16 (23.8%), and 6 (8.9%) isolates, respectively, among 67 sulfonamide-resistant isolates. The PCR-based replicon typing method showed plasmids in 29 isolates, IncFIB (19), IncI1-Iγ (17), IncF (14), IncK (14), IncFIC (10), IncP (8), IncY (3), IncHI2 (1), and IncX (1). The class 1 and 2 integrons were detected in 57 and 2 isolates, respectively; one isolate harbored both integrons. Seven and one gene cassette arrays were identified in class 1 and class 2 integrons, respectively. Our findings show that multiantimicrobial-resistant E. coli isolates from chickens serve as reservoirs of highly diverse and abundant tet and sul genes and plasmid replicons. Such isolates and MGEs pose a potential health threat to the public and animal farming

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

IntroductionThe 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.MethodsWe 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.ResultsAmong 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.DiscussionOur 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

A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa.

The progression of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in Africa has so far been heterogeneous, and the full impact is not yet well understood. In this study, we describe the genomic epidemiology using a dataset of 8746 genomes from 33 African countries and two overseas territories. We show that the epidemics in most countries were initiated by importations predominantly from Europe, which diminished after the early introduction of international travel restrictions. As the pandemic progressed, ongoing transmission in many countries and increasing mobility led to the emergence and spread within the continent of many variants of concern and interest, such as B.1.351, B.1.525, A.23.1, and C.1.1. Although distorted by low sampling numbers and blind spots, the findings highlight that Africa must not be left behind in the global pandemic response, otherwise it could become a source for new variants

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

Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

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

Successful treatment of a Carbapenem-resistant Klebsiella pneumoniae carrying blaOXA-48, blaVIM-2, blaCMY-2 and blaSHV- with high dose combination of imipenem and amikacin

AbstractWe 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=16μg/ml) and was resistant to all other antibiotics including Imipenem (MIC=4μg/ml), Colistin (MIC=16μg/ml) and Tigecycline (MIC=4μg/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 30mg/kg (2.5g) in a 30min infusion and the dose of imipenem was increased to 1g every 6h despite patient's altered renal function (Creatinine Clearance=25ml/min). To avoid amikacin nephrotoxicity and to allow the use of high doses of imipenem, continuous venovenous hemodiafiltration (CVVHDF) (blood flow, 200ml/h; dialysate, 1000ml/h; ultrafiltrate, 2000ml/h) was initiated 1h after the start of the amikacin infusion and continued thereafter.The patient improved hemodynamically and norepinephrine was stopped five days after antibiotherapy adaptation

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