Enrichment of antibiotic resistance genes within bacteriophage populations in saliva samples from individuals undergoing oral antibiotic treatments

Abstract

Spread of antibiotic resistance is a significant challenge for our modern health care system, and even more so in developing countries with higher prevalence of both infections and resistant bacteria. Faulty usage of antibiotics has been pinpointed as a driving factor in spread of resistant bacteria through selective pressure. However, horizontal gene transfer mediated through bacteriophages may also play an important role in this spread. In a cohort of Tanzanian patients suffering from bacterial infections, we demonstrate significant differences in the oral microbial diversity between infected and non-infected individuals, as well as before and after oral antibiotics treatment. Further, the resistome carried both by bacteria and bacteriophages vary significantly, with bla _CTX-M1 resistance genes being mobilized and enriched within phage populations. This may impact how we consider spread of resistance in a biological context, as well in terms of treatment regimes.

Keywords: Bacteriophage; antibiotic resistance; antibiotic treatment; microbiota; saliva.

Figure 1

Individuals with ongoing infection have altered prokaryotic compositions in the saliva. The prokaryotic composition from the cellular fraction of individuals undergoing oral antibiotic treatment was compared with a control group. The main identified genus among bacteria (A) are reported, together with alpha (B) and beta (C) diversity. A heat map summarizing the findings can also be visualized in (D).

Figure 2

Individuals with ongoing infection have altered eukaryotic compositions in the saliva. The eukaryotic composition from the cellular fraction of individuals undergoing oral antibiotic treatment was compared with a control group. The main identified genus among eukaryotes (A) are reported, together with alpha (B) and beta (C) diversity. A heat map summarizing the findings can also be visualized in (D).

Figure 3

Individuals with ongoing infection have altered fungal compositions in the saliva. The fungal composition from the cellular fraction of individuals undergoing oral antibiotic treatment was compared with a control group. The main identified genus among fungi (A) are reported, together with alpha (B) and beta (C) diversity. A heat map summarizing the findings can also be visualized in (D).

Figure 4

Bacteriophage genetic diversity is linked to patient health status. Bacteriophage DNA was isolated from saliva from patients or controls, and the microbiome and mycobiome determined through 16S and 18S amplicon sequencing. The main identified genus among bacteria (A) are reported, together with alpha (B) and beta (C) diversity of bacteria and. A heat map summarizing the findings can also be visualized in (D).

Figure 5

Prevalence of resistance genes is dependent on infection and gender. tetA was quantified by ddPCR, and abundance compared between patients (Infect+) and controls (Infect−) change over time in bacterial (A) and phage fraction (B). Effect on antibiotic usage on tetA prevalence in bacterial and phage fractions was also evaluated (C), as well as if gender affected prevalence (D). The y-axis represents relative number of gene copies in the sample.

Figure 6

Resistance genes are differently associated with bacterial and bacteriophage populations. tetA (A), bla_CTX-M1 (B), qnrS1 (C), and bla_OXA-48 (D) were quantified by ddPCR for both the bacterial and bacteriophage population. The y-axis represents relative number of gene copies in the sample.