Novel “Superspreader” Bacteriophages Promote Horizontal Gene Transfer by Transformation

Abstract

Bacteriophages infect an estimated 1023 to 1025 bacterial cells each second, many of which carry physiologically relevant plasmids (e.g., those encoding antibiotic resistance). However, even though phage-plasmid interactions occur on a massive scale and have potentially significant evolutionary, ecological, and biomedical implications, plasmid fate upon phage infection and lysis has not been investigated to date. Here we show that a subset of the natural lytic phage population, which we dub “superspreaders,” releases substantial amounts of intact, transformable plasmid DNA upon lysis, thereby promoting horizontal gene transfer by transformation. Two novel Escherichia coli phage superspreaders, SUSP1 and SUSP2, liberated four evolutionarily distinct plasmids with equal efficiency, including two close relatives of prominent antibiotic resistance vectors in natural environments. SUSP2 also mediated the extensive lateral transfer of antibiotic resistance in unbiased communities of soil bacteria from Maryland and Wyoming. Furthermore, the addition of SUSP2 to cocultures of kanamycin-resistant E. coli and kanamycin-sensitive Bacillus sp. bacteria resulted in roughly 1,000-fold more kanamycin-resistant Bacillus sp. bacteria than arose in phage-free controls. Unlike many other lytic phages, neither SUSP1 nor SUSP2 encodes homologs to known hydrolytic endonucleases, suggesting a simple potential mechanism underlying the superspreading phenotype. Consistent with this model, the deletion of endonuclease IV and the nucleoid-disrupting protein ndd from coliphage T4, a phage known to extensively degrade chromosomal DNA, significantly increased its ability to promote plasmid transformation. Taken together, our results suggest that phage superspreaders may play key roles in microbial evolution and ecology but should be avoided in phage therapy and other medical applications.

ACI‐1 beta‐lactamase is widespread across human gut microbiomes in Negativicutes due to transposons harboured by tailed prophages

“…Numerous different mobile elements types have been implicated in spreading ARGs within pathogens, most frequently plasmids and transposons (Davies and Davies, 2010;Ruppé et al, 2015). Interestingly, although phages may package ARGs in their capsids via generalized transduction (Balcazar, 2014;Brown-Jaque et al, 2015), there are only a few clear-cut examples (Schuch and Fischetti, 2006;Keen et al, 2017) of ARGs encoded within sequenced genomes from isolated phages (Kleinheinz et al, 2014;Enault et al, 2017). By contrast, phages have long been known to encode important bacterial toxins and virulence factors (Brüssow et al, 2004), such as the Shiga, cholera, diphtheria, and botulinum toxins (Uchida et al, 1971;Eklund et al, 1972;Waldor and Mekalanos, 1996;Rohde et al, 2011).…”

Strategies for Editing Virulent Staphylococcal Phages Using CRISPR-Cas10

“…While optimal for antimicrobial applications, 15,16 virulent staphylococcal phages also carry an inherent risk of eliciting detrimental side-effects—over half their genes have unknown functions, 11 and their molecular interactions with the bacterial host remain poorly understood. As examples of such side-effects, virulent phages have the potential to facilitate horizontal gene transfer, 17,18 promote biofilm formation, 19 and/or elicit unanticipated immune responses. 20 These issues are compounded by the need to use cocktails of diverse phages for antimicrobial applications to curb the emergence of phage-resistant pathogens.…”

No genome is an island: toward a 21st century agenda for evolution

“…The overwhelmingly abundant bacteriophage particles are major reservoirs of environmental DNA, and they can disaggregate to liberate their DNA cargos, which can be taken up by unrelated competent bacteria, archaea, yeast, and perhaps other types of eukaryotic cells . The ability of so‐called “superspreader” phages to release encapsidated Escherichia coli DNA for uptake by unrelated Streptococcus pneumoniae bacteria has recently been reported . Moreover, phages have been shown to pose a public health threat by serving as environmental reservoirs for antibiotic resistance DNA determinants, particularly in soils associated with intensive agriculture …”

“…gg The ability of so-called "superspreader" phages to release encapsidated Escherichia coli DNA for uptake by unrelated Streptococcus pneumoniae bacteria has recently been reported. 94 Moreover, phages have been shown to pose a public health threat by serving as environmental reservoirs for antibiotic resistance DNA determinants, particularly in soils associated with intensive agriculture. 95…”