Detection of a Novel, and Likely Ancestral, Tn916-Like Element from a Human Saliva Metagenomic Library

Abstract

Tn916 is a conjugative transposon (CTn) and the first reported and most well characterised of the Tn916/Tn1545 family of CTns. Tn916-like elements have a characteristic modular structure and different members of this family have been identified based on similarities and variations in these modules. In addition to carrying genes encoding proteins required for their conjugation, Tn916-like elements also carry accessory, antimicrobial resistance genes; most commonly the tetracycline resistance gene, tet(M). Our study aimed to identify and characterise tetracycline resistance genes from the human saliva metagenome using a functional metagenomic approach. We identified a tetracycline-resistant clone, TT31, the sequencing of which revealed it to encode both tet(M) and tet(L). Comparison of the TT31 sequence with the accessory, regulation, and recombination modules of other Tn916-like elements indicated that a partial Tn916-like element encoding a truncated orf9 was cloned in TT31. Analysis indicated that a previous insertion within the truncated orf9 created the full length orf9 found in most Tn916-like transposons; demonstrating that orf9 is, in fact, the result of a gene fusion event. Thus, we hypothesise that the Tn916-like element cloned in TT31 likely represents an ancestral Tn916.

ResFinderFG v2.0: a database of antibiotic resistance genes obtained by functional metagenomics

“…ResFinderFG v2.0 includes more ARGs coming from human-associated samples [12][13][14][15][16][17][18][19][20][21][22] . For example, characterization of the gut resistome with functional metagenomics showed that its ARGs were not well described in ARG databases 14 .…”

“…This technique is based on phenotypic detection by expressing exogenous DNA in an antibiotic-susceptible host. Using functional metagenomics, ARGs sharing low amino acid identity to their closest homologue in NCBI 11 , or even not previously classified as ARGs 12 , could be detected in human [12][13][14][15][16][17][18][19][20][21][22] , animal [22][23][24][25][26][27][28][29] , wastewater [30][31][32][33][34][35][36][37] and other environmental samples 5,11, . Despite being a laborious technique, genes described by functional metagenomics are mainly absent in classical ARG databases.…”

Comparative genome analysis ofEnterococcus cecorumreveals intercontinental spread of a lineage of clinical poultry isolates

“…Note that the carriage of tet (M) and tet (L) on the same Tn916-like element is uncommon. It was first described in Streptococcus gallolyticus and proposed to benefit the host bacterium under stressful conditions (80, 81). A single clinical poultry isolate from France has the vanA operon, a gene already described in an E. cecorum strain from retail poultry in Japan (82).…”

Prevalence, diversity and transferability of the Tn916-Tn1545 family ICE in oral streptococci

“…Tn 6815 harbored two truncated copies of orf9. In spite of the absence of a complete orf9, Tn 6815 was able to form CI and excise from the genome suggesting that an alternative mechanism is regulating the excision process, as has been suggested to occur in other Tn 916 -like elements [ 23 ]. The 5,265 bp insertion downstream from the tet (M) gene resulted in an element that was 99% identical to an ICE that has been previously isolated from S. pneumonia [ 43 ].…”

“…Tn 916 , which was first isolated from Enterococcus faecalis DS16 [ 21 ], is a well-documented prototype of the Tn 916 -Tn 1545 family. It is the smallest member of the Tn 916 -Tn 1545 family and has been found in 35 different bacterial genera [ 22 , 23 ]. The wide spread of Tn 916 , is in part, attributed to the presence of integrase and excision genes, which enable the ICE to excise (cut) itself from one location and integrate itself in another location.…”