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. 2019 Aug 30:12:2703-2710.
doi: 10.2147/IDR.S213958. eCollection 2019.

Rapid diagnosis of neonatal sepsis by PCR for detection of 16S rRNA gene, while blood culture and PCR results were similar in E.coli-predominant EOS cases

Mostafa I El-Amir  1 , Mohamed Ali El-Feky  1   2 , Doaa A Abo Elwafa  1 , Eman Ahmed Abd-Elmawgood  3
Affiliations

Rapid diagnosis of neonatal sepsis by PCR for detection of 16S rRNA gene, while blood culture and PCR results were similar in E.coli-predominant EOS cases

Mostafa I El-Amir et al. Infect Drug Resist. .

Abstract

Purpose: To determine the bacteriological pattern and antibiotic susceptibility of bacterial isolates causing neonatal sepsis in Qena University Hospitals and compare polymerase chain reaction (PCR) and blood culture results in a trial for rapid diagnosis.

Patients and methods: Blood samples from 75 clinically suspected cases of neonatal sepsis were subjected to identification of bacteria and determination of their antibiotic sensitivity through blood culture, and rapid detection of 16S rRNA and the uidA gene (to confirm the presence of E. coli) by PCR from extracted bacterial DNA.

Results: Most patients were preterm (64%) and low birth weight (LBW) (68%). In total, 42.7% presented with early onset sepsis (EOS). LBW was significantly associated with EOS (P-value=0.03). Although the blood culture and PCR results were similar in EOS, the PCR results were significantly higher than those of blood culture in detecting bacteria (85.3% vs 68%, respectively, P-value=0.001). Blood culture showed 100% specificity. The most common pathogen was E. coli (86.2%) in EOS and Staphylococcus spp. (45.5%) in late-onset sepsis (LOS) (P-value=0.001 and 0.02, respectively). The most effective antibiotics against Gram-negative bacteria were ofloxacin, ciprofloxacin, imipenem, and amikacin, while vancomycin, oxacillin, and imipenem were the most effective antibiotics against Gram-positive bacteria.

Conclusion: EOS was mainly caused by E. coli, while LOS was mainly caused by Staphylococcus spp. The 16S rRNA PCR showed higher sensitivity with rapid and accurate diagnosis. Blood culture is the most suitable method for antimicrobial sensitivity testing.

Keywords: 16S rRNA; EOS; LOS; blood culture; neonatal sepsis.

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Conflict of interest statement

The authors report no conflicts of interest in this work.

Figures

Figure 1
Figure 1
Gel electrophoresis showing bands of the PCR product of the 16S rRNA gene. Lane 1 shows a 100 bp DNA ladder from 100 to 3000 bp. (A) Lanes 2–8 show the amplified PCR product at 380 bp. (B) Negative samples were detected in lanes 3 and 5. Samples in lane 3 of the causative microbe were Candida spp., while samples in lane 5 were negative for PCR.
Figure 2
Figure 2
E. coli isolates were confirmed by the presence of the uidA gene, which shows a 212 bp band in gel electrophoresis.
See this image and copyright information in PMC

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