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. 2022 Oct 19:12:955481.
doi: 10.3389/fcimb.2022.955481. eCollection 2022.

NGS in the clinical microbiology settings

Milena Pitashny  1   2 , Balqees Kadry  1 , Raya Shalaginov  2 , Liat Gazit  2 , Yaniv Zohar  3 , Moran Szwarcwort  2 , Yoav Stabholz  4 , Mical Paul  4
Affiliations

NGS in the clinical microbiology settings

Milena Pitashny et al. Front Cell Infect Microbiol. .

Abstract

We hypothesized that targeted NGS sequencing might have an advantage over Sanger sequencing, especially in polymicrobial infections. The study included 55 specimens from 51 patients. We compared targeted NGS to Sanger sequencing in clinical samples submitted for Sanger sequencing. The overall concordance rate was 58% (32/55) for NGS vs. Sanger. NGS identified 9 polymicrobial and 2 monomicrobial infections among 19 Sanger-negative samples and 8 polymicrobial infections in 11 samples where a 16S gene was identified by gel electrophoresis, but could not be mapped to an identified pathogen by Sanger. We estimated that NGS could have contributed to patient management in 6/18 evaluated patients and thus has an advantage over Sanger sequencing in certain polymicrobial infections.

Keywords: 16s; NGS; clinical microbiology; next generation sequencing; polymicrobial; polymicrobial infections.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Concordance between Sanger sequencing and NGS in a scheme. Sanger negative are those samples that did not give any signal on PCR gels. "Sanger unidentified" are those samples that presented a band in agarose gels, but on Sanger sequencing it was not possible to define a unique organism against public databases.
Figure 2
Figure 2
Effect of NGS findings on patient management. In 8/22 samples the result obtained with NGS contributed to diagnosis (also congruent when there were repeated samples from the same patient). In 6/18 patients, treatment could have been changed to a more appropriate one had NGS results been available at the time of diagnosis.
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