Whole Genome Sequencing and Molecular Epidemiology of Clinical Isolates of Staphylococcus aureus from Algeria.

Staphylococcus aureus is an important pathogen responsible for various healthcare- and community-acquired infections. In this study, whole genome sequencing (WGS) was used to genotype S. aureus clinical isolates from two hospitals in Algeria and to characterize their genetic determinants of antimicrobial resistance. Seventeen S. aureus isolates were included in this study. WGS, single-nucleotide polymorphism (SNP)-based phylogenetic analysis, in silico multilocus sequence typing (MLST), spa and staphylococcal cassette chromosome mec (SCCmec) typing and in silico antimicrobial resistance profiling were performed. Phenotypic antibiotic susceptibility testing was performed using the Vitek 2 system and the disk diffusion method. The isolates were separated into sequence types (STs), with ST80 being predominant; five clonal complexes (CCs); four spa types (t044, t127, t368, t386); and two SCCmec types (IVc and IVa). Whole genome analysis revealed the presence of the resistance genes mecA, blaZ, ermC, fusB, fusC, tetK, aph(3')-IIIa and aad(6) and mutations conferring resistance in the genes parC and fusA. The rate of multidrug resistance (MDR) was 64%. This work provides a high-resolution characterization of methicillin-resistant S. aureus (MRSA) and methicillin-susceptible S. aureus (MSSA) isolates and emphasizes the importance of continuous surveillance to monitor the spread of S. aureus in healthcare settings in the country.

Bayesian spatio-temporal analysis of the incidence of lung cancer in the North West of Algeria, 2014-2020.

Lung cancer is the most common type of cancer worldwide. This study assessed the spatio-temporal variations of the incidence rate of lung cancer between 2014 and 2020 in Chlef, a province in the North West of Algeria. Case data recoded by municipality, sex and age were collected from the oncology department in a local hospital. A hierarchical Bayesian spatial model, adjusted by urbanization level, with zero inflated Poisson distribution was used to study the variation of lung cancer incidence. A total of 250 lung cancer cases were registered during the study period, with a crude incidence rate of 4.12 per 100,000 inhabitants. The results of the model showed that residents in urban municipalities had a significantly higher risk of lung cancer than those in rural municipalities: incidence ratio rate (IRR) = 2.83 (95% CI: 1.91 - 4.31) and 1.80 (95% CI: 1.02 - 3.16) for men and women, respectively. In addition, the estimated incidence rate by the model for both sexes in the Chlef province indicated that only three urban municipalities had a higher incidence rate of lung cancer than the average of the province. The results of our study suggest that the risk factors for lung cancer in the North West of Algeria were mainly related to the level of urbanization. Our findings provide important information to guide the health authorities in designing measures for the surveillance and control of lung cancer.

Molecular epidemiology and antimicrobial resistance patterns of Clostridioides difficile isolates in Algerian hospitals.

INTRODUCTION: Clostridioides difficile is a major pathogen responsible for hospital-associated diarrhoea. This study investigated the molecular epidemiology and antibiotic resistance of C. difficile isolates in five Algerian hospitals. METHODOLOGY: Between 2016 and 2019, faecal specimens were collected from in-patients and were cultured for C. difficile. Isolates were characterised by toxin genes detection, Polymerase Chain Reaction (PCR)-ribotyping, Multilocus Sequence Typing (MLST), antimicrobial susceptibility testing against a panel of antibiotics, and screened for antimicrobial resistance genes. RESULTS: Out of 300 patient stools tested, 18 (6%) were positive for C. difficile by culture, and were found to belong to 11 different ribotypes (RT) and 12 sequence types (ST): RT 085/ST39, FR 248/ST259, FR 111/ST48, RT 017/ST37, RT 014/ST2, RT 014/ST14, FR 247/new ST, RT 005/ST6, RT 029/ST16, RT 039/ST26, RT 056/ST34 and RT 446/ST58. MLST analysis assigned the isolates to two clades, 1 and 4. Clade 4 was more homogeneous, as it mainly included non-toxigenic isolates. Three toxin gene profiles were detected, two toxigenic, A+B+CDT- (33.3%) and A-B+CDT- (11%); and one non-toxigenic, A-B-CDT- (55.5%). All C. difficile isolates were susceptible to metronidazole, vancomycin and moxifloxacin. CONCLUSIONS: Overall prevalence of C. difficile in our healthcare settings was 6%. Antibiotic resistance rates ranged from 72.2% (clindamycin) to 16.6% (tetracycline). This study highlighted a relatively high genetic diversity in term of ribotypes, sequence types, toxin and antibiotic resistance patterns, in the C. difficile isolates. Further larger studies are needed to assess the true extent of C. difficile infections in Algeria.

First molecular characterisation and PCR ribotyping of Clostridium difficile strains isolated in two Algerian Hospitals.

INTRODUCTION: Clostridium difficile is the major etiological agent of nosocomial antibiotics associated diarrhoea. C. difficile infection is associated with considerable morbidity and mortality among hospitalized patients worldwide. Despite its known importance, there is no study on this important pathogen in Algeria. METHODOLOGY: In this prospective study, undertaken between 2013 and 2015, faecal specimens were collected from 159 hospitalized patients with antibiotic-associated diarrhoea in two tertiary health care hospitals in Chlef, Algeria. Faecal samples were cultured on CLO plates Agar with cefoxitin, cycloserine antibiotics and sodium taurocholate. C. difficile suspected colonies were analysed by multiplex PCR for the detection of the toxin genes. C. difficile isolates were analysed by PCR ribotyping and multi-locus tandem repeat analysis. Antimicrobial susceptibility was determined by the E-test method, according to the Clinical and Laboratory Standards Institute protocol. RESULTS: C. difficile was cultured from 11 of 159 stool specimen (6.9%). Seven strains were toxigenic, mainly represented by the 020 and 014 PCR ribotypes and four non toxigenic belong to PCR ribotype 084. All 11 isolates were susceptible to both vancomycin and metronidazole and resistant to ciprofloxacin. CONCLUSIONS: This study, which reported for the first time C. difficile ribotypes circulating in Algerian health care facilities, could paves the way for further more comprehensive studies on this important pathogen, and could be useful to the local health authorities to implement a surveillance program of C. difficile in Algeria.