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

Abstract

Antibiotic resistance is increasing among pathogens, and the human microbiome contains a reservoir of antibiotic resistance genes. Acidaminococcus intestini is the first Negativicute bacterium (Gram-negative Firmicute) shown to be resistant to beta-lactam antibiotics. Resistance is conferred by the aci1 gene, but its evolutionary history and prevalence remain obscure. We discovered that ACI-1 proteins are phylogenetically distinct from beta-lactamases of Gram-positive Firmicutes and that aci1 occurs in bacteria scattered across the Negativicute clade, suggesting lateral gene transfer. In the reference A. intestini RyC-MR95 genome, we found transposons residing within a tailed prophage context are likely vehicles for aci1's mobility. We found aci1 in 56 (4.4%) of 1,267 human gut metagenomes, mostly hosted within A. intestini, and, where could be determined, mostly within a consistent mobile element constellation. These samples are from Europe, China and the USA, showing that aci1 is distributed globally. We found that for most Negativicute assemblies with aci1, the prophage observed in A. instestini is absent, but in all cases aci1 is flanked by varying transposons. The chimeric mobile elements we identify here likely have a complex evolutionary history and potentially provide multiple complementary mechanisms for antibiotic resistance gene transfer both within and between cells.

Comparative genomics groups phages of Negativicutes and classical Firmicutes despite different Gram‐staining properties

“…It is, however, also possible that a predicted prophage lacks a virome counterpart, which suggests a prophage remnant that is not any longer active in producing an extracellular phage or a phage simply not present in the examined sample. The virome sequences confirmed the previously described prophages 1 and 2 in A. intestini (Rands et al ., ) and prophage 4 we predicted here (Supporting Information Fig. S2A).…”

“…Although we do identify antibiotic resistance genes within prophage contexts, potentially of public health interest, we note that these are actually rare (only three separate examples). Furthermore, these examples are based on only limited bioinformatic evidence: aci1, which we described previously (Rands et al, 2018), is still a credible ARG whose function was demonstrated experimentally by other researchers (Galán et al, 2000).…”

“…Therefore, during evolutionary history Firmicute phages had to adapt to a different membrane boundary constellation, assuming vertical phage-bacteria co-evolution. An alternative is that Negativicute phages were acquired horizontally from Proteobacteria, plausible given the shared outer cell structure of their bacterial hosts, and possible environmentally as both bacterial groups share an ecological niche in human microbiomes, particularly in the human gut (Rands et al, 2018).…”

“…Conversely, we might find Negativicute phages are grouped with phages from Proteobacteria, 'attracted' by the similar cell surface structure, as lipopolysaccharides and outer membrane proteins are the primary point of contact for phages in the infection process. These hypotheses have not been tested as sequence data on phages from gram-negative Firmicutes is currently limited to a few incomplete Negativicute phage sequences reconstituted from human and mouse virome projects (Pride et al, 2012;Kim and Bae, 2016), some predicted but uncharacterized prophages (Roux et al, 2015), and two possibly defective lambdoid prophages (Rands et al, 2018).…”

Comparative genomics groups phages of Negativicutes and classical Firmicutes despite different Gram-staining properties

“…Therefore, during evolutionary history Firmicute phages had to adapt to a different membrane boundary, assuming vertical phage-bacteria co-evolution. An alternative is that 75 Negativicute phages were acquired horizontally from Proteobacteria, plausible given the shared outer cell structure of their bacterial hosts, and possible environmentally since both bacterial groups share an ecological niche in human microbiomes, particularly in the human gut (Rands et al, 2018). 80 We used the unusual relationship between Negativicutes and classical Gram-Positive Firmicutes to investigate phage-bacteria co-evolution.…”