Genetic diversity and characteristics of high-level tigecycline resistance Tet(X) in Acinetobacter species

Abstract

Background The recent emergence and dissemination of high-level mobile tigecycline resistance Tet(X) challenge the clinical effectiveness of tigecycline, one of the last-resort therapeutic options for complicated infections caused by multidrug-resistant Gram-negative and Gram-positive pathogens. Although tet(X) has been found in various bacterial species, less is known about phylogeographic distribution and phenotypic variance of different genetic variants. Methods Herein, we conducted a multiregional whole-genome sequencing study of tet(X)-positive Acinetobacter isolates from human, animal, and their surrounding environmental sources in China. The molecular and enzymatic features of tet(X) variants were characterized by clonal expression, microbial degradation, reverse transcription, and gene transfer experiments, while the tet(X) genetic diversity and molecular evolution were explored by comparative genomic and Bayesian evolutionary analyses. Results We identified 193 tet(X)-positive isolates from 3846 samples, with the prevalence ranging from 2.3 to 25.3% in nine provinces in China. The tet(X) was broadly distributed in 12 Acinetobacter species, including six novel species firstly described here. Besides tet(X3) (n = 188) and tet(X4) (n = 5), two tet(X5) variants, tet(X5.2) (n = 36) and tet(X5.3) (n = 4), were also found together with tet(X3) or tet(X4) but without additive effects on tetracyclines. These tet(X)-positive Acinetobacter spp. isolates exhibited 100% resistance rates to tigecycline and tetracycline, as well as high minimum inhibitory concentrations to eravacycline (2–8 μg/mL) and omadacycline (8–16 μg/mL). Genetic analysis revealed that different tet(X) variants shared an analogous ISCR2-mediated transposon structure. The molecular evolutionary analysis indicated that Tet(X) variants likely shared the same common ancestor with the chromosomal monooxygenases that are found in environmental Flavobacteriaceae bacteria, but sequence divergence suggested separation ~ 9900 years ago (7887 BC), presumably associated with the mobilization of tet(X)-like genes through horizontal transfer. Conclusions Four tet(X) variants were identified in this study, and they were widely distributed in multiple Acinetobacter spp. strains from various ecological niches across China. Our research also highlighted the crucial role of ISCR2 in mobilizing tet(X)-like genes between different Acinetobacter species and explored the evolutionary history of Tet(X)-like monooxygenases. Further studies are needed to evaluate the clinical impact of these mobile tigecycline resistance genes.

Feasibility of predicting allele specific expression from DNA sequencing using machine learning

“…A number of obstacles must be addressed before such models can be translated into practical tools, including performing clinical validation and providing implementation guidelines. Nevertheless, we are convinced that ASE predictors would perfectly complement existing in silico tools that infer all kinds of information from DNA variation, for example, tools that predict splicing 48 , evolutionary pressure 49 or estimate pathogenicity 35 . Such tools are already an established part of diagnostic variant interpretation 50 .…”

Acquisition and Spread of Antimicrobial Resistance: A tet(X) Case Study

“…Unfortunately, however, during the past two years there have been an explosive number of publications showing that the worst-case scenario with the extensive dissemination of tet (X) into pathogenic microbiota is actively taking place, especially in China [ 15 , 16 , 17 , 18 ]. Current epidemiological data indicate that the variants of tet (X), tet (X3)/(X4)/(X5/X6/X14), can be detected in various ecological compartments in China, including humans and animals (mainly pigs, chickens, and ducks) [ 11 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 ]. According to a recent epidemiological analysis [ 18 ], the highest occurrence of Tet X-producing isolates has been recorded in China—42, followed by Sierra Leone—5, USA—4, Hungary—3, the Americas—1, the Czech Republic—1, France—1, and Japan—1.…”

“…Previous phylogenetic analyses suggested that the FMO-encoding genes from the group of environmental bacteria belonging to the Flavobacteriaceae family are most likely to be the origin of the tet (X) genes [ 18 , 19 ]. Indeed, the vast diversity of genes encoding tetracycline-inactivating monooxygenases resides within the species belonging to the Cytophaga, Fusobacterium, and Bacteroides (CFB) group bacteria (alternative naming—Bacteroidetes phylum, consisting of Bacteroidia, Flavobacteriia and Sphingobacteriia classes) ( Figure 1 and Figure 2 ).…”

“…With the exception of the prototype tet (X/X2), genetic context surrounding other tet (X) genes is almost uniformly associated with IS CR2 or IS 26 , occasionally in combination [ 15 , 16 , 17 , 18 , 19 , 23 , 24 , 28 , 47 ]. Sometimes, IS CR2 is called IS Vsa3 [ 48 ]; here, IS CR2 will be used for the sake of consistency.…”

“…Regrettably, however, the worst-case scenario has taken place during the past decade. Several tet (X) variants that are located on plasmids and confer high level resistance to the next-generation tetracyclines, tigecycline, eravacycline and omadacycline, can be found in human and animal isolates of Acinetobacter species, including A. baumannii [ 15 , 19 , 22 , 28 ]. Acquisition and dissemination of these tet (X) variants was mediated via IS CR2 and IS 26 transposition into a variety of conjugative and mobilizable plasmids belonging to different incompatibility groups.…”