Molecular Subtyping and Gene Expression Analysis of Drug Resistant Invasive Non-Typhoidal Salmonella

Abstract

Invasive Non-Typhoidal Salmonella infections have become widespread in sub-Saharan Africa. Predominant hyper-virulent clone S. Typhimurium ST313 is found to be associated with bloodstream invasion and multidrug resistance. Despite its importance, limited information is available on the circulating genotypes causing invasive non-typhoidal salmonellosis in Ghana. A total of fifty-one NTS isolates from pediatric blood samples was used for this study. The resistance profiles of isolates were assessed against 8 classes of antibiotics by disc diffusion method followed by PCR detection of resistance markers. Molecular detection of the presence of a virulence associated gene, st313-td, was used as plausive test to select isolates for Multi-Locus Sequence Typing (MLST) analysis. Additionally, the mechanism of ciprofloxacin resistance was explored by monitoring changes in expression levels of important targeted genes including gyrA, acrA, ydhJ, emrD, and soxR under drug pressure using reverse transcription quantitative PCR. Antibiotic susceptibility testing results showed all isolates were completely susceptible to imipenem, ceftriaxone and ceftazidime. In most cases, multidrug resistance (including reduced susceptibility to fluoroquinolones) were frequently recorded among S. Typhimurium isolates (63%, n=32/51). On the contrary, nine out of ten S. Dublin and the five unknown serovars were susceptible to all antibiotics used for screening. The virulence gene st313-td was detected in only 27% (n=14/51) isolates. Eight (8) other isolates showing varying resistance phenotypes were selected in addition to the 14 positive isolates for typing and analyses by MLST. Out of twenty-two (22) selected isolates, 82% (n=18), 4% (n=1) and 14% (n=3) were S. Typhimurium ST313, S. Typhimurium ST19, and S. Dublin ST 10 respectively. Most importantly, it was observed that about 83% (n=15/18) of S. Typhimurium ST313 clones were multidrug resistant (MDR).

Likewise, ten selected isolates for PCR analyses tested positive for the resistance markers; CatA1 (30%), StrA (90%), BlaTem (50%), TetA (30%) & TetB (10%), Sul1 (80%) & Sul2 (100%) and aadA (70%). The normalized transformed mRNA transcript levels showed significant variations in gene expression of gyrA, acrA, ydhJ, emrD and soxR among susceptible, intermediate and laboratory induced resistant isolates. Further, sequence data analysis detected a single nucleotide polymorphism at position 324 resulting in a mutation (Phe → Asp) in the gyr A of clinical intermediate isolate, although there were no significant mutations in acrA, ydhJ, emrD and soxR genes among the three test isolates. From the results, high frequencies of multidrug resistant invasive NTS pathogens carrying plasmid-borne resistance gene markers were found. Also, reduced susceptibility to fluoroquinolones and cephalosporin were observed which calls for increased surveillance and management of antimicrobial resistance to guide treatment. Detection of a SNP in gyrA gene and variations in mRNA levels suggest possible genetic and transcriptional regulation mechanisms employed by Salmonella pathogen to withstand drug stress. Therefore, further investigations are required to understand these mechanisms which will assist in developing alternative therapeutic interventions.