Identification and Characterization of Bacterial Pathogens Causing Bloodstream Infections by DNA Microarray

Abstract

Bloodstream infections are potentially life-threatening and require rapid identification and antibiotic susceptibility testing of the causative pathogen in order to facilitate specific antimicrobial therapy. We developed a prototype DNA microarray for the identification and characterization of three important bacteremia-causing species: Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa. The array consisted of 120 species-specific gene probes 200 to 800 bp in length that were amplified from recombinant plasmids. These probes represented genes encoding housekeeping proteins, virulence factors, and antibiotic resistance determinants. Evaluation with 42 clinical isolates, 3 reference strains, and 13 positive blood cultures revealed that the DNA microarray was highly specific in identifying S. aureus, E. coli, and P. aeruginosa strains and in discriminating them from closely related gram-positive and gram-negative bacterial strains also known to be etiological agents of bacteremia. We found a nearly perfect correlation between phenotypic antibiotic resistance determined by conventional susceptibility testing and genotypic antibiotic resistance by hybridization to the S. aureus resistance gene probes mecA (oxacillin-methicillin resistance), aacA-aphD (gentamicin resistance), ermA (erythromycin resistance), and blaZ (penicillin resistance) and the E. coli resistance gene probes bla TEM-106 (penicillin resistance) and aacC2 (aminoglycoside resistance). Furthermore, antibiotic resistance and virulence gene probes permitted genotypic discrimination within a species. This novel DNA microarray demonstrates the feasibility of simultaneously identifying and characterizing bacteria in blood cultures without prior amplification of target DNA or preidentification of the pathogen.

Rapid Identification of Bacterial Species with Bacterial DNA Microarray in Cirrhotic Patients with Spontaneous Bacterial Peritonitis

“…1). Hybridization of bacterial DNA to these 4 probes generates a signal, and that signal is used to identify a species of bacteria based on previously described criteria for bacterial identification (13 Hy b r i d i z a t i o n o f b a c t e r i a l DNA t o t h e s e 4 p r o b e s g e n e r a t e s a s i g n a l , a n d t h a t s i g n a l i s u s e d t o i d e n t i f y a s p e c i e s o f b a c t e r i a . Ma t c h i n g f o r t h e s e 3 v a r i a b l e r e g i o n s i s n e c e s s a r y t o d e t e c t t h e c o r r e c t s p e c i (Fig.…”

“…It appears that 16S rRNA gene sequencing is a more accurate and objective method than conventional phenotypic identification (9,10). The microarray technique has been assessed for bacterial identification in blood of septic patients (12,13). In this study, we compared the usefulness of the 16S rRNA-based DNA microarray with the conventional culture method in terms of detection and identification of bacteria.…”

Characterization of Coagulase-Negative Staphylococci Isolated from Hospitalized Patients in Narayana Medical College and Hospital Nellore, A.P. South India

“…Many of nosocomial infections are associated with microorganisms that are resistant to antibiotics and can easily spread by hospital environment and personnel. Monitoring of antimicrobial susceptibility can aid to clinicians for prescript appropriate antibiotics and prevent the development of drug resistance (Cleven et al, 2006). Effective treatment of patients with UTI and blood stream infections associated with CNS commonly relays on the identification of the type of organisms and the selection of an effective antibiotic agent to the organism in question.…”

Comparison between two PCR‐based bacterial identification methods through artificial neural network data analysis

“…Molecular diagnosis is playing an increasingly important role in the rapid detection and identification of pathogenic organisms in clinical samples (2). The genetic variation of ribosomal genes in bacteria offers an alternative target for bacterial detection and identification.…”