Abstract
Bacteriophages are abundant in human biomes and therefore in human clinical samples. Although this is usually not considered, they might interfere with the recovery of bacterial pathogens at two levels: 1) by propagating in the enrichment cultures used to isolate the infectious agent, causing the lysis of the bacterial host and 2) by the detection of bacterial genes inside the phage capsids that mislead the presence of the bacterial pathogen. To unravel these interferences, human samples (n = 271) were analyzed and infectious phages were observed in 11% of blood culture, 28% of serum, 45% of ascitic fluid, 14% of cerebrospinal fluid and 23% of urine samples. The genetic content of phage particles from a pool of urine and ascitic fluid samples corresponded to bacteriophages infecting different bacterial genera. In addition, many bacterial genes packaged in the phage capsids, including antibiotic resistance genes and 16S rRNA genes, were detected in the viromes. Phage interference can be minimized applying a simple procedure that reduced the content of phages up to 3 logs while maintaining the bacterial load. This method reduced the detection of phage genes avoiding the interference with molecular detection of bacteria and reduced the phage propagation in the cultures, enhancing the recovery of bacteria up to 6 logs.
Highlights
Bacteriophages are abundant in human biomes and in human clinical samples
This interference can be envisaged at two levels: 1) phages may propagate in enriched liquid culture media by infecting bacteria and causing their lysis during the process; and 2) phages can transport bacterial DNA, including virulence genes such as toxins16, antibiotic resistance genes (ARG)11,17,18 or bacterial 16S rRNA genes18
Confirmation of the phage particles obtained from samples showing positive lysis on E. coli was conducted by Transmission Electron Microscopy (TEM)
Summary
Bacteriophages are abundant in human biomes and in human clinical samples This is usually not considered, they might interfere with the recovery of bacterial pathogens at two levels: 1) by propagating in the enrichment cultures used to isolate the infectious agent, causing the lysis of the bacterial host and 2) by the detection of bacterial genes inside the phage capsids that mislead the presence of the bacterial pathogen. The existence of phages in human biomes presupposes their presence in human samples and their contamination of laboratory cultures initiated from these samples15 This interference can be envisaged at two levels: 1) phages may propagate in enriched liquid culture media (used to enhance analytical sensitivity and selectively propagate the pathogen) by infecting bacteria (the pathogen targeted for isolation) and causing their lysis during the process; and 2) phages can transport bacterial DNA, including virulence genes such as toxins, antibiotic resistance genes (ARG) or bacterial 16S rRNA genes.
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