Worldwide Prevalence of Class 2 Integrases outside the Clinical Setting Is Associated with Human Impact

Abstract

An intI-targeted PCR assay was optimized to evaluate the frequency of partial class 2-like integrases relative to putative, environmental IntI elements in clone libraries generated from 17 samples that included various terrestrial, marine, and deep-sea habitats with different exposures to human influence. We identified 169 unique IntI phylotypes (<98% amino acid identity) relative to themselves and with respect to those previously described. Among these, six variants showed an undescribed, extended, IntI-specific additional domain. A connection between human influence and the dominance of IntI-2-like variants was also observed. IntI phylotypes 80 to 99% identical to class 2 integrases comprised ϳ70 to 100% (n ‫؍‬ 65 to 87) of the IntI elements detected in samples with a high input of fecal waste, whereas IntI2-like sequences were undetected in undisturbed settings and poorly represented (1 to 10%; n ‫؍‬ 40 to 79) in environments with moderate or no recent fecal or anthropogenic impact. Eleven partial IntI2-like sequences lacking the signature ochre 179 codon were found among samples of biosolids and agricultural soil supplemented with swine manure, indicating a wider distribution of potentially functional IntI2 variants than previously reported. To evaluate IntI2 distribution patterns beyond the usual hosts, namely, the Enterobacteriaceae, we coupled PCR assays targeted at intI and 16S rRNA loci to G؉C fractionation of total DNA extracted from manured cropland. IntI2-like sequences and 16S rRNA phylotypes related to Firmicutes (Clostridium and Bacillus) and Bacteroidetes (Chitinophaga and Sphingobacterium) dominated a low-G؉C fraction (ϳ40 to 45%), suggesting that these groups could be important IntI2 hosts in manured soil. Moreover, G؉G fractionation uncovered an additional set of 36 novel IntI phylotypes (<98% amino acid identity) undetected in bulk DNA and revealed the prevalence of potentially functional IntI2 variants in the low-G؉C fraction.

Novel integrons and gene cassettes from a Cascadian submarine gas-hydrate-bearing core

“…A large fraction of current integrase phylotypes was rooted with those from other deep‐sea habitats. Twelve phylotypes, constituting cluster 1, were rooted with integrases from metagenomic DNA of deep Arctic sediment (Rodrı′guez‐Minguela et al ., ). The phylotypes 5ACas.GasHyd and 6BCas.GasHyd, 14‐, 18, and 32Cas.IntI were located in the clusters of the deep marine integrases from Tokyo Bay and hydrothermal vents, respectively (Elsaied et al ., , ).…”

“…Integrons from marine microorganisms, called marine integrons, like integrons in pathogenic bacteria, consist of an integrase gene, intI , which encodes a site‐specific recombinase, IntI (Stokes & Hall, ). intI genes of marine integrons have been recovered as part of PCR fragments of sizes ranging from 485 bp to 1269 bp, and these contained most of the IntI catalytic domains (Elsaied et al ., , ; Rodrı′guez‐Minguela et al ., ). The attachment site, attI , is the integron‐associated recombination site, where the gene cassettes are captured by integrons (Collis et al ., ).…”

“…Potential P c sequences have been identified, by sequence analysis, in 42 marine integrons (Elsaied et al ., ). Marine integrons are highly diverse, based on phylogenetic analysis of the intI genes (Argos et al ., ; Rodrı′guez‐Minguela et al ., ). Class 1 integrons have also been recovered from marine environments (Gillings et al ., ).…”

Prevalence of Class 1, 2, and 3 Integrons and Biofilm Formation in Pseudomonas aeruginosa and Acinetobacter baumannii among ICU and non-ICU Patients

“…In the Class 1 integrons, the 3′ conserved segment includes three open reading frames (ORFs)-qacEΔ1, a deletion derivative of the antiseptic resistance gene qacE; the sul1 sulfonamide resistance gene; and ORF5, of unknown function or int genes, as in Tn402 (10,11). More than 80 different gene cassettes of Class 1 integrons have been described and shown to confer resistance to a wide range of antibiotics such as β-lactams, fluoroquinolones, aminoglycosides, chloramphenicol, trimethoprim, streptothricin, rifampin, erythromycin, fosfomycin, lincomycin, and antiseptics, and disinfectants (12). The second class of integrons (Class 2) was found in transposon Tn7 and its derivatives, and its 3′ conserved segment containing five tns genes involved in the movements of the transposon, which have been reported most often in isolates within the Enterobacteriaceae family (13).…”

Oral Spirochetes Implicated in Dental Diseases Are Widespread in Normal Human Subjects and Carry Extremely Diverse Integron Gene Cassettes

“…PCR with degenerate primers targeting the conserved regions of attC sites has recovered novel integrase genes and hundreds of diverse gene cassettes from various environments, including soil, sediment, biomass, and water habitats (24,33,38). Rowe-Magnus et al employed a three-plasmid genetic strategy to recover integron genes, using the integrase to bind integron attC sites (34).…”