MALDI-TOF clearly outperformed the diagnosis capacities of phenotypic methods by reducing the delay of results and giving accurate identification at species level. Moreover, this approach appears to be cost-effective and should be implemented especially in resource-poor context.

Background Bacterial virulence is a key factor determining the outcome of each bacterial infection and virulent bacteria are often associated to high-risk infections. Extraintestinal pathogenic Escherichia coli (ExPEC) is the most implicated bacterium in human bacterial infections and its virulence factors are classified into five categories: adhesins, toxins, iron capture systems, protectins and invasins. Furthermore, bacterial biofilms are the main cause of hospital-acquired infections like urinary catheter-associated infections, valve endocarditis, Otitis and cystic fibrosis.Results For the sixteen virulence genes sought by standard polymerase chain reaction (PCR), all the 78 ExPECs isolates carried at least four virulence genes. Following prevalences of virulence genes were reported: adhesins genes fimH (98.7%), mrkD (98.7%), papC (46.2%), afaC (9%), sfa / focDE (1.3%); iron acquisition systems genes entB (98.7%), fepA (98.7%), ybtS (93.6%), fyuA (91%), iucA (91%), iucB (91%), iutA (34.6), iroB (6.4%), iroN (6.4%) and toxins genes hlyA (10.3%), cnf (1 & 2) (10.3%). Seventy-five out of 78 isolates (96.2%) carried at least the combination of two adhesins genes and two iron capture systems genes whereas 8 out of 78 (10.3%) harbored the combination of (adhesins genes + iron acquisition systems genes + toxins genes). Among the 78 strains studied, one hospital-acquired strain isolated from urine harbored 15 virulence genes out of 16 sought. The evaluation of biofilm-formation capacity revealed that all (29/29) hospital-acquired isolates were biofilm producers with (6/29; 20.7%) strong biofilm producers, (15/29; 51.7%) moderate biofilm producers and (8/29; 27.6%) weak biofilm producers. Isolates carrying papC had greater biofilm formation capacity than those not carrying papC (p < 0.001).Conclusions Most of our strains had moderate biofilm-formation capacity and carried an average of 9 virulence genes out of 16 sought. These eight strains carrying a combination of genes (adhesins + iron acquisition systems genes + toxins genes) may be hypervirulent isolates. Additional studies may confirm this. The deepening of this kind of study on bacterial virulence and hospital bacterial biofilms could lead to the improvement of infections investigation, prevention and therapeutic protocols.

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Extra-intestinal pathogenic Escherichia coli (ExPEC), a predominant Gram-negative bacterial pathogen, express a wide range of virulence factors and is responsible of several diseases including urinary tract infections (UTI), nosocomial pneumonia, bacteremia, and neonatal meningitis. ExPEC isolates are often multidrug resistant (MDR) and clones producing extended-spectrum beta-lactamases (ESBL) are increasingly reported all over the world.Seventy-eight clinical ExPEC strains were selected for this study. The majority was from UTIs (n=51), while the rest (n=27) was from pus, sputum, bronchial fluid and vaginal samples (non-uropathogenic ExPEC). Interestingly, 49 out of the 78 ExPEC isolates where considered as community-acquired (CA) and 29 hospital-acquired (HA) bacteria. Antibiotic susceptibility testing was performed using the Kirby-Bauer disc diffusion method. Standard polymerase chain reaction (PCR) was used to screen major ESBL genes (blaCTX-M, blaOXA-1, blaTEM, blaSHV) and blaCTX-M variants (blaCTX-M-1, blaCTX-M-9, blaCTX-M-15, blaCTX-M-25).All the ExPEC strains were resistant to ampicillin, ticarcillin, amoxicillin/clavulanic acid combination, cefalotin, cefotaxime, ceftazidime, cefepime and aztreonam, but showed a high susceptibity to fosfomycin (98.7%, n = 77), ertapenem (96.2%, n = 75), and imipenem (100%). Moreover, isolates harbored at least one ESBL gene, including blaCTX-M (98.7%), blaOXA-1 (78.2%), blaTEM (44.9%) and blaSHV (3.8%). The CTX-M variants were also found with the predominance of blaCTX-M-1 (90.9%) and blaCTX-M-15 (90.9%) followed by blaCTX-M-9 (11.7%), while blaCTX-M-25 was not detected.Despite the resistance to most of the tested antibiotics, ExPEC isolates showed fortunately a good susceptibility to fosfomycin and carbapenems. blaCTX-M (blaCTX-M1, blaCTX-M15) and blaOXA-1 seem to be E. coli major ESBL genes circulating in Senegal. No significant difference was noted when comparing prevalence of ESBL genes detected from CA and HA strains, and from UPEC and non-uropathogenic ExPEC. The high level of resistance to antimicrobials observed stresses the need of establishing an epidemiological surveillance of antimicrobial resistance in both community and hospital settings.

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