Use of 16s rRNA to identify non-lactose-fermenting bacilli and molecular detection of ESBL resistance genes associated with hospital-acquired infection in Soba University Hospital, Sudan

Abstract

Background: Non-lactose-fermenting gram-negative bacilli (NLFGNB) have become significant nosocomial pathogens and often exhibit intrinsic multidrug resistance. Sequencing of 16s rRNA genes could be utilized for robust identification of NLFGNB. This study aimed to identify resistant NLFGNB associated with hospital-acquired infections using 16s rRNA sequencing and to detect the extended-spectrum β-lactamase (ESBL) genes of isolates in Soba Hospital, Khartoum State, Sudan. Methods: A prospective, cross-sectional, laboratory-based study was conducted from October 2017 to March 2018 at the Microbiology Department of Soba University Hospital. A total of 100 randomly selected NLFGNB samples were isolated from blood and urine during the time of the study. All the isolates were identified using standard biochemical tests and antimicrobial sensitivity testing, 16s rRNA gene sequencing, and bioinformatics techniques. Results: The biochemical tests revealed that, out of the 100 NLFGNB isolates, the Pseudomonas species was predominant (57 isolates), followed by gram-negative bacilli (33 isolates), Coccobacilli (9 isolates) and Coliform (1 isolate) species. Sequencing of 16s rRNA genes identified all the resistant isolates at the species level: Pseudomonas aeruginosa (26%), Acinetobacter baumannii (22%), Burkholderia cepacia (13%), Stenotrophomonas maltophilia (10%), Enterococcus species (E. faecalis, E. faecium) (10%), and other GNB (Acinetobacter variabilis, Klebsiella pneumoniae, Morganella morganii, Escherichia fergusonii, Enterobacter hormaechei and Pseudomonas stutzeri) (19%). The antimicrobial susceptibility tests indicated that 31 isolates were resistant to at least three classes of antibiotics and contain the highest level of ESBL resistance genes. Conclusions: Pseudomonas aeruginosa and Acinetobacter baumannii were the most widely recognized NLFGNB identified from hospital-acquired infections in Soba hospital. Among the NLFGNB, antimicrobial resistance and ESBL resistance genes were observed at a high frequency.