Study of the prevalence of antibiotic-resistant bacterial strains of clinical origin in the region of Sétif and molecular characterization of their resistance

Abstract

Antibiotic resistance (AR) is among the leading global health concerns to date. In our study, 402 strains were collected from 7 medical diagnostic laboratories and 3 government hospitals in Sétif region over three years (2021-2023). First, the identification of 326 clinical community samples and 76 hospitalized samples, isolated from different specimens, was carried out using microbiological and biochemical tests and confirmed by API gallery. This analysis identified 10 species belonging to Gram negative bacteria (GNB) and 3 species belonging to Gram positive bacteria (GPB). E. coli was the predominant pathogen among GNB (50%) while S.aureus was the most common GPB (7.7%). The majority of these strains were found in urine samples from adult patients. Antibiotic susceptibility tests and MICs were performed according to CA-SFM recommendations. A significant proportion of the identified strains exhibited high resistance rates against first-line antibiotics commonly used in the treatment of various bacterial infections including penicillins and cephalosporins, but a substantial resistance was recorded against imipenem in E. coli (49.8%) and Proteus species (32.1%).Similarly, tobramycin and gentamycin exhibited limited effectiveness against P. aeruginosa, Enterobacter spp., (20% to100%) and all GPB. MDR strains represented 56% of all tested isolates, followed by XDR (26.1%). Amikacin was the most effective antibiotic. Among K. pneumoniae isolates, 66.6% were classified as hypervirulent K. pneumoniae (hvKp) based on the string test. In S. aureus species, 61.3% were methicillin-resistant S. aureus (MRSA), while 9.7% exhibited the constitutive macrolide-lincosamide-streptogramin B (CMLSB) phenotype, and 16.1% displayed the inducible MLSB (IMLSB) phenotype, as determined by the D-test. Different virulence factors were tested in our pathogenic strains. Biofilm formation was assessed in microtiter plates using crystal violet dye, while hemolysin, protease, lecithinase, and lipase enzyme production were determined using plates containing human blood, skimmed milk, and egg yolk, respectively. Overall, 88.1% of strains were biofilm producers, with the majority (64.9%) exhibiting a weak ability to produce biofilms. XDR strains exhibited the highest percentage of strong biofilm producers (47.6%). Hemolysin production was found in 55.5% of strains, followed by protease production 47.3% and lecithinase and lipase activities (23.1% and 10%). A phenotypic search for the production of extended-spectrum β-lactamases and AmpC was conducted, 32.6% presented ESBL phenotype and 12.7% were positive AmpC,furthermore, molecular characterization of β-lactamase genes and quinolone genes with Multiplex PCR was used for phenotypic confirmation. blaTEM was the emergence ESBL-type gene (53.8%), followed by blaSHV (15.9%), while blaCMY II was the most frequent AmpC detected gene (10.4%) followed by blaDHA (7.1%). All these genes and other virulence genes were carried by plasmids with size ranged from approximately 1.5 to ˃10 kb profiling by PCR method. 26.7% of E. coli strains harbored at least one qnr gene. The most frequent was qnrB (78.3%), followed by qnrD (26.1%). Clermont et al. PCR was used for the detection of phylogenetic groups of urinary imipenem-resistant E. coli. Of 86 clinical imipenem resistant E.coli isolates, the B2 group (48.9%) was the most prevalent phylogroup, followed by groups E (22.1%), unknown (12.8%), A (8.1%), and B1 (4.7%), and Clade I, D, Clade I, or Clade II (1.2%).