Double illegitimate recombination events integrate DNA segments through two different mechanisms during natural transformation of Acinetobacter baylyi

Assessment of genetically modified maize MON 95275 (application GMFF-2022-5890)

Genetically modified maize MON 95275 was developed to confer protection to certain coleopteran species. These properties were achieved by introducing the mpp75Aa1.1, vpb4Da2 and DvSnf7 expression cassettes. The molecular characterisation data and bioinformatic analyses reveal similarity to known toxins, which was further assessed. None of the identified differences in the agronomic/phenotypic and compositional characteristics tested between maize MON 95275 and its conventional counterpart needs further assessment. The GMO Panel does not identify safety concerns regarding the toxicity and allergenicity of the Mpp75Aa1.1 and Vpb4Da2 proteins and the DvSnf7 dsRNA and derived siRNAs as expressed in maize MON 95275 and finds no evidence that the genetic modification would change the overall allergenicity of maize MON 95275. In the context of this application, the consumption of food and feed from maize MON 95275 does not represent a nutritional concern in humans and animals. The GMO Panel concludes that maize MON 95275 is as safe as the conventional counterpart and non-GM maize varieties tested, and no post-market monitoring of food/feed is considered necessary. In the case of accidental release of maize MON 95275 material into the environment, this would not raise environmental safety concerns. The post-market environmental monitoring plan and reporting intervals are in line with the intended uses of maize MON 95275. The GMO Panel concludes that maize MON 95275 is as safe as its conventional counterpart and the tested non-GM maize varieties with respect to potential effects on human and animal health and the environment.

Assessment of genetically modified maize DP910521 (application GMFF-2021-2473)

Genetically modified (GM) maize DP910521 was developed to confer resistance against certain lepidopteran insect pests as well as tolerance to glufosinate herbicide; these properties were achieved by introducing the mo-pat, pmi and cry1B.34 expression cassettes. The molecular characterisation data and bioinformatic analyses did not identify issues requiring food/feed safety assessment. None of the identified differences in the agronomic/phenotypic and compositional characteristics tested between maize DP910521 and its conventional counterpart needs further assessment except for the levels of iron in grain, which do not raise safety and nutritional concerns. The GMO Panel does not identify safety concerns regarding the toxicity and allergenicity of the Cry1B.34, PAT and PMI proteins as expressed in maize DP910521. The GMO panel finds no evidence that the genetic modification impacts the overall safety of maize DP910521. In the context of this application, the consumption of food and feed from maize DP910521 does not represent a nutritional concern in humans and animals. The GMO Panel concludes that maize DP910521 is as safe as its conventional counterpart and non-GM maize varieties tested, and no post-market monitoring of food/feed is considered necessary. In the case of accidental release of maize DP910521 material into the environment, this would not raise environmental safety concerns. The post-market environmental monitoring plan and reporting intervals are in line with the intended uses of maize DP910521. The GMO Panel concludes that maize DP910521 is as safe as its conventional counterpart and the tested non-GM maize varieties with respect to potential effects on human and animal health and the environment.

Assessment of genetically modified maize MON 94804 (application GMFF-2022-10651)

Genetically modified (GM) maize MON 94804 was developed to achieve a reduction in plant height by introducing the GA20ox_SUP suppression cassette. The molecular characterisation and bioinformatic analyses do not identify issues requiring food/feed safety assessment. None of the agronomic/phenotypic and compositional differences identified between maize MON 94804 and its conventional counterpart needs further assessment, except for ear height, plant height and levels of carbohydrates in forage, which do not raise safety or nutritional concerns. The Panel on Genetically Modified Organisms (GMO Panel) does not identify safety concerns regarding the toxicity and allergenicity of the GA20ox_SUP precursor-miRNA and derived mature miRNA as expressed in maize MON 94804 and finds no evidence that the genetic modification would change the overall allergenicity of maize MON 94804. In the context of this application, the consumption of food and feed from maize MON 94804 does not represent a nutritional concern in humans and animals. The GMO Panel concludes that maize MON 94804 is as safe as the conventional counterpart and non-GM maize varieties tested, and no post-market monitoring of food/feed is considered necessary. In the case of accidental release of viable maize MON 94804 grains into the environment, this would not raise environmental safety concerns. The post-market environmental monitoring plan and reporting intervals are in line with the intended uses of maize MON 94804. The GMO Panel concludes that maize MON 94804 is as safe as its conventional counterpart and the tested non-GM maize varieties with respect to potential effects on human and animal health and the environment.

Assessment of genetically modified maize DP202216 for food and feed uses, under Regulation (EC) No 1829/2003 (application EFSA-GMO-NL-2019-159)

Genetically modified maize DP202216 was developed to confer tolerance to glufosinate-ammonium-containing herbicides and to provide an opportunity for yield enhancement under field conditions. These properties were achieved by introducing the mo-pat and zmm28 expression cassettes. The molecular characterisation data and bioinformatic analyses do not identify issues requiring food/feed safety assessment. None of the identified differences in the agronomic/phenotypic and compositional characteristics tested between maize DP202216 and its comparator needs further assessment, except for the levels of stearic acid (C18:0), which do not raise nutritional and safety concerns. The GMO Panel does not identify safety concerns regarding the toxicity and allergenicity of the PAT and ZMM28 proteins as expressed in maize DP202216, and finds no evidence that the genetic modification would change the overall allergenicity of maize DP202216. In the context of this application, the consumption of food and feed from maize DP202216 does not represent a nutritional concern in humans and animals. The GMO Panel concludes that maize DP202216 is as safe as the comparator and non-GM reference varieties tested, and no post-market monitoring of food/feed is considered necessary. In the case of accidental release of viable maize DP202216 grains into the environment, this would not raise environmental safety concerns. The post-market environmental monitoring plan and reporting intervals are in line with the intended uses of maize DP202216. The GMO Panel concludes that maize DP202216 is as safe as its comparator and the tested non-GM reference varieties with respect to potential effects on human and animal health and the environment.

Assessment of genetically modified maize DP23211 for food and feed uses, under Regulation (EC) No 1829/2003 (application EFSA-GMO-NL-2019-163)

Genetically modified maize DP23211 was developed to confer control of certain coleopteran pests and tolerance to glufosinate-containing herbicide. These properties were achieved by introducing the pmi, mo-pat, ipd072Aa and DvSSJ1 expression cassettes. The molecular characterisation data and bioinformatic analyses do not identify issues requiring food/feed safety assessment. None of the identified differences in the agronomic/phenotypic and compositional characteristics tested between maize DP23211 and its conventional counterpart needs further assessment, except for those in levels of histidine, phenylalanine, magnesium, phosphorus and folic acid in grain, which do not raise safety and nutritional concerns. The GMO Panel does not identify safety concerns regarding the toxicity and allergenicity of the IPD072Aa, PAT and PMI proteins and the DvSSJ1 dsRNA and derived siRNAs newly expressed in maize DP23211, and finds no evidence that the genetic modification impacts the overall safety of maize DP23211. In the context of this application, the consumption of food and feed from maize DP23211 does not represent a nutritional concern in humans and animals. Therefore, no post-market monitoring of food/feed is considered necessary. In the case of accidental release of viable maize DP23211 grains into the environment, this would not raise environmental safety concerns. The post-market environmental monitoring plan and reporting intervals are in line with the intended uses of maize DP23211. The GMO Panel concludes that maize DP23211 is as safe as its conventional counterpart and the tested non-GM reference varieties with respect to potential effects on human and animal health and the environment.

Assessment of genetically modified maize DP915635 for food and feed uses, under regulation (EC) No 1829/2003 (application EFSA-GMO-NL-2020-172)

Genetically modified maize DP915635 was developed to confer tolerance to glufosinate herbicide and resistance to corn rootworm pests. These properties were achieved by introducing the ipd079Ea, mo-pat and pmi expression cassettes. The molecular characterisation data and bioinformatic analyses do not identify issues requiring food/feed safety assessment. None of the identified differences in the agronomic/phenotypic and compositional characteristics tested between maize DP915635 and its conventional counterpart needs further assessment, except for the levels of crude protein in forage, which does not raise nutritional and safety concerns. The GMO Panel does not identify safety concerns regarding the toxicity and allergenicity of the IPD079Ea, PAT and PMI proteins expressed in maize DP915635. The GMO Panel finds no evidence that the genetic modification impacts the overall safety of maize DP915635. In the context of this application, the consumption of food and feed from maize DP915635 does not represent a nutritional concern in humans and animals. The GMO Panel concludes that maize DP915635 is as safe as the conventional counterpart and non-GM maize varieties tested, and no post-market monitoring of food/feed is considered necessary. In the case of accidental release of viable maize DP915635 grains into the environment, this would not raise environmental safety concerns. The post market environmental monitoring plan and reporting intervals are in line with the intended uses of maize DP915635. The GMO Panel concludes that maize DP915635 is as safe as its conventional counterpart and the tested non-GM maize varieties with respect to potential effects on human and animal health and the environment.

Assessment of genetically modified cotton COT102 for food and feed uses, under Regulation (EC) No 1829/2003 (application EFSA-GMO-DE-2017-141)

Genetically modified cotton COT102 was developed to confer resistance against several lepidopteran species. The molecular characterisation data and bioinformatic analyses do not identify issues requiring food/feed safety assessment. None of the differences in the agronomic-phenotypic and compositional characteristics between cotton COT102 and its non-GM comparator needs further assessment, except for levels of acid detergent fibre, which do not raise safety or nutritional concerns. The GMO Panel does not identify safety concerns regarding the toxicity and allergenicity of the Vip3Aa19 and APH4 proteins as expressed in cotton COT102 and finds no evidence that the genetic modification would change the overall allergenicity of cotton COT102. In the context of this application, the consumption of food and feed from cotton COT102 does not represent a nutritional concern for humans and animals. The GMO Panel concludes that cotton COT102 is as safe as the non-GM comparator and non-GM cotton varieties tested, and no post-market monitoring of food/feed is considered necessary. In the case of accidental release of viable cotton COT102 seeds into the environment, this would not raise environmental safety concerns. The post-market environmental monitoring plan and reporting intervals are in line with the intended uses of cotton COT102. The GMO Panel concludes that cotton COT102 is as safe as its non-GM comparator and the tested non-GM cotton varieties with respect to potential effects on human and animal health and the environment.

Assessment of genetically modified maize MON 87419 for food and feed uses, under Regulation (EC) No 1829/2003 (application EFSA-GMO-NL-2017-140)

Genetically modified maize MON 87419 was developed to confer tolerance to dicamba- and glufosinate-based herbicides. These properties were achieved by introducing the dmo and pat expression cassettes. The molecular characterisation data and bioinformatic analyses do not identify issues requiring food/feed safety assessment. None of the identified differences in the agronomic/phenotypic and compositional characteristics tested between maize MON 87419 and its conventional counterpart needed further assessment, except for the levels of arginine and protein in grains which did not raise safety and nutritional concerns. The GMO Panel does not identify safety concerns regarding the toxicity and allergenicity of the dicamba mono-oxygenase (DMO) and phosphinothricin N-acetyltransferase (PAT) proteins as expressed in maize MON 87419. The GMO Panel finds no evidence that the genetic modification impacts the overall safety of maize MON 87419. In the context of this application, the consumption of food and feed from maize MON 87419 does not represent a nutritional concern in humans and animals. The GMO Panel concludes that maize MON 87419 is as safe as the conventional counterpart and non-GM maize varieties tested, and no post-market monitoring of food/feed is considered necessary. In the case of accidental release of viable maize MON 87419 grains into the environment, this would not raise environmental safety concerns. The post-market environmental monitoring plan and reporting intervals are in line with the intended uses of maize MON 87419. The GMO Panel concludes that maize MON 87419 is as safe as its conventional counterpart and the tested non-GM maize varieties with respect to potential effects on human and animal health and the environment.

Assessment of genetically modified Maize MON 87429 for food and feed uses, under Regulation (EC) No 1829/2003 (application EFSA-GMO-NL-2019-161)

Maize MON 87429 was developed to confer tolerance to dicamba, glufosinate, quizalofop and 2,4-D herbicides. The molecular characterisation data and bioinformatic analyses do not identify issues requiring food/feed safety assessment. None of the identified differences in the agronomic/phenotypic and compositional characteristics tested between maize MON 87429 and its conventional counterpart needs further assessment, except for the levels of phytic acid in grains, which do not raise nutritional and safety concerns. The GMO Panel does not identify safety concerns regarding the toxicity and allergenicity of the DMO, PAT, FT_T and CP4 EPSPS proteins as expressed in maize MON 87429. The GMO Panel finds no evidence that the genetic modification impacts the overall safety of maize MON 87429. In the context of this application, the consumption of food and feed from maize MON 87429 does not represent a nutritional concern in humans and animals. The GMO Panel concludes that maize MON 87429 is as safe as the conventional counterpart and non-GM maize reference varieties tested, and no post-market monitoring of food/feed is considered necessary. In the case of accidental release of viable maize MON 87429 grains into the environment, this would not raise environmental safety concerns. The post-market environmental monitoring plan and reporting intervals are in line with the intended uses of maize MON 87429. The GMO Panel concludes that maize MON 87429, as described in this application, is as safe as its conventional counterpart and the tested non-GM maize reference varieties with respect to potential effects on human and animal health and the environment.

Assessment of genetically modified maize MON 95379 for food and feed uses, under Regulation (EC) No 1829/2003 (application EFSA-GMO-NL-2020-170)

Genetically modified maize MON 95379 was developed to confer insect protection against certain lepidopteran species. These properties were achieved by introducing the cry1B.868 and cry1Da_7 expression cassettes. The molecular characterisation data and bioinformatic analyses do not identify issues requiring food/feed safety assessment. None of the identified differences in the agronomic/phenotypic and compositional characteristics tested between maize MON 95379 and its conventional counterpart needs further assessment. The GMO Panel does not identify safety concerns regarding the toxicity and allergenicity of the Cry1B.868 and Cry1Da_7 proteins as expressed in maize MON 95379. The GMO Panel finds no evidence that the genetic modification impacts the overall safety of maize MON 95379. In the context of this application, the consumption of food and feed from maize MON 95379 does not represent a nutritional concern in humans and animals. Therefore, no post-market monitoring of food/feed is considered necessary. In the case of accidental release of viable maize MON 95379 grains into the environment, this would not raise environmental safety concerns. The post-market environmental monitoring plan and reporting intervals are in line with the intended uses of maize MON 95379. The GMO Panel concludes that maize MON 95379 is as safe as its conventional counterpart and the tested non-GM maize varieties with respect to potential effects on human and animal health and the environment.

Horizontal gene transfer from genetically modified plants - Regulatory considerations

Gene technology regulators receive applications seeking permission for the environmental release of genetically modified (GM) plants, many of which possess beneficial traits such as improved production, enhanced nutrition and resistance to drought, pests and diseases. The regulators must assess the risks to human and animal health and to the environment from releasing these GM plants. One such consideration, of many, is the likelihood and potential consequence of the introduced or modified DNA being transferred to other organisms, including people. While such gene transfer is most likely to occur to sexually compatible relatives (vertical gene transfer), horizontal gene transfer (HGT), which is the acquisition of genetic material that has not been inherited from a parent, is also a possibility considered during these assessments. Advances in HGT detection, aided by next generation sequencing, have demonstrated that HGT occurrence may have been previously underestimated. In this review, we provide updated evidence on the likelihood, factors and the barriers for the introduced or modified DNA in GM plants to be horizontally transferred into a variety of recipients. We present the legislation and frameworks the Australian Gene Technology Regulator adheres to with respect to the consideration of risks posed by HGT. Such a perspective may generally be applicable to regulators in other jurisdictions as well as to commercial and research organisations who develop GM plants.

Repeat sequences limit the effectiveness of lateral gene transfer and favored the evolution of meiotic sex in early eukaryotes

The transition from prokaryotic lateral gene transfer to eukaryotic meiotic sex is poorly understood. Phylogenetic evidence suggests that it was tightly linked to eukaryogenesis, which involved an unprecedented rise in both genome size and the density of genetic repeats. Expansion of genome size raised the severity of Muller's ratchet, while limiting the effectiveness of lateral gene transfer (LGT) at purging deleterious mutations. In principle, an increase in recombination length combined with higher rates of LGT could solve this problem. Here, we show using a computational model that this solution fails in the presence of genetic repeats prevalent in early eukaryotes. The model demonstrates that dispersed repeat sequences allow ectopic recombination, which leads to the loss of genetic information and curtails the capacity of LGT to prevent mutation accumulation. Increasing recombination length in the presence of repeat sequences exacerbates the problem. Mutational decay can only be resisted with homology along extended sequences of DNA. We conclude that the transition to homologous pairing along linear chromosomes was a key innovation in meiotic sex, which was instrumental in the expansion of eukaryotic genomes and morphological complexity.

Assessment of genetically modified oilseed rape MON 94100 for food and feed uses, under regulation (EC) No 1829/2003 (application EFSA-GMO-NL-2020-169)

Oilseed rape MON 94100 was developed to confer tolerance to dicamba herbicide. The molecular characterisation data and bioinformatic analyses do not identify issues requiring food/feed safety assessment. None of the identified differences in the agronomic/phenotypic and compositional characteristics tested between oilseed rape MON 94100 and its conventional counterpart needs further assessment, except for the levels of carbohydrates, calcium and ADF in seeds, which do not raise nutritional and safety concerns. The GMO Panel does not identify safety concerns regarding the toxicity and allergenicity of the dicamba mono-oxygenase (DMO) protein as expressed in oilseed rape MON 94100. The GMO Panel finds no evidence that the genetic modification impacts the overall safety of oilseed rape MON 94100. In the context of this application, the consumption of food and feed from oilseed rape MON 94100 does not represent a nutritional concern in humans and animals. The GMO Panel concludes that oilseed rape MON 94100 is as safe as the conventional counterpart and non-GM oilseed rape reference varieties tested, and no post-market monitoring of food/feed is considered necessary. In the case of accidental release of viable oilseed rape MON 94100 seeds into the environment, this would not raise environmental safety concerns. The post-market environmental monitoring plan and reporting intervals are in line with the intended uses of oilseed rape MON 94100. The GMO Panel concludes that oilseed rape MON 94100 is as safe as its conventional counterpart and the tested non-GM oilseed rape reference varieties with respect to potential effects on human and animal health and the environment.

Natural Transformation in Acinetobacter baumannii W068: A Genetic Analysis Reveals the Involvements of the CRP, XcpV, XcpW, TsaP, and TonB2

Acinetobacter baumannii is a serious threat to public health, and there is increasing attention to the development of antibiotic resistance in this bacterium. Natural transformation is a major horizontal gene transfer mechanism that can lead to antibiotic resistance. To better understand the mechanism of natural transformation in A. baumannii, we selected a clinical isolate that was transformable but had no visible extracellular type IV pili (T4P) filaments and then examined the effects of multiple single-gene knockouts on natural plasmid transformation. Among 33 candidate genes, 28 knockout mutants had severely or completely impaired transformability. Some of these genes had established roles in T4P biogenesis; DNA transfer across the outer membrane, periplasm, or inner membrane; and protection of intracellular single-stranded DNA (ssDNA). Other genes had no previously reported roles in natural transformation of A. baumannii, including competence activator cAMP receptor protein (CRP), a periplasmic protein that may function in T4P assembly (TonB₂), a T4P secretin-associated protein (TsaP), and two type II secretion system (T2SS) minor pseudopilus assembly prime complex competent proteins (XcpV and XcpW). The deletion of the T2SS assembly platform protein X had no effect on transformation, and the minor pseudopilins were capable of initiating major pilin assembly. Thus, we speculate that XcpV and XcpW may function in DNA uptake with major pilin assembly, a non-T2SS-dependent mechanism and that a competence pseudopilus similar to T4P constituted the central part of the DNA uptake complex. These results may help guide future research on the alarming increase of antibiotic resistance in this pathogen.

Antimicrobial resistance acquisition via natural transformation: context is everything

Natural transformation is a process where bacterial cells actively take up free DNA from the environment and recombine it into their genome or reconvert it into extra-chromosomal genetic elements. Although this mechanism is known to mediate the uptake of antibiotic resistance determinants in a range of human pathogens, its importance in the spread of antimicrobial resistance is not always appreciated. This review highlights the context in which transformation takes place: in diverse microbiomes, in interaction with other forms of horizontal gene transfer and in increasingly polluted environments. This examination of the abiotic and biotic drivers of transformation reveals that it could be more important in the dissemination of resistance genes than is often recognised.

Assessment of genetically modified cotton GHB811 for food and feed uses, under Regulation (EC) No 1829/2003 (application EFSA-GMO-ES-2018-154)

Cotton GHB811 was developed to confer tolerance to glyphosate and HPPD inhibitor herbicides. The molecular characterisation data and bioinformatic analyses do not identify issues requiring food/feed safety assessment. None of the identified differences in the agronomic/phenotypic and compositional characteristics tested between cotton GHB811 and its conventional counterpart needs further assessment, except for % lint, lint length and dihydrosterculic acid, which do not raise nutritional and safety concerns. The GMO Panel does not identify safety concerns regarding the toxicity and allergenicity of the 2mEPSPS and HPPD W336 proteins as expressed in cotton GHB811 and finds no evidence that the genetic modification would change the overall allergenicity of cotton GHB811. In the context of this application, the consumption of food and feed from cotton GHB811 does not represent a nutritional concern in humans and animals. The GMO Panel concludes that cotton GHB811 is as safe as the conventional counterpart and non-GM cotton reference varieties tested, and no post-market monitoring of food/feed is considered necessary. In the case of accidental release of viable cotton GHB811 seeds into the environment, this would not raise environmental safety concerns. The post-market environmental monitoring plan and reporting intervals are in line with the intended uses of cotton GHB811. The GMO Panel concludes that cotton GHB811 is as safe as its conventional counterpart and the tested non-GM cotton reference varieties with respect to potential effects on human and animal health and the environment.

Assessment of genetically modified oilseed rape 73496 for food and feed uses, under Regulation (EC) No 1829/2003 (application EFSA-GMO-NL-2012-109)

Oilseed rape 73496 was developed to confer tolerance to the herbicidal active substance glyphosate through the expression of the glyphosate acetyltransferase protein GAT4621. The molecular characterisation data and bioinformatic analyses identify no issues requiring food/feed safety assessment. None of the identified differences between oilseed rape 73496 and its conventional counterpart in the agronomic/phenotypic endpoints tested needs further assessment. Differences identified in seed composition of oilseed rape 73496 as compared to its conventional counterpart raise no safety and nutritional concerns in the context of the scope of this application. No safety concerns are identified regarding toxicity and allergenicity of the GAT4621 protein as expressed in oilseed rape 73496. No evidence is found that the genetic modification would change the overall allergenicity of oilseed rape 73496. Based on the outcome of the comparative and nutritional assessments, the consumption of oilseed rape 73496 does not represent any nutritional concern, in the context of the scope of this application. The implementation of a post-market monitoring plan is recommended to confirm the predicted consumption data and to verify that the conditions of use are those considered during the pre-market risk assessment. In the case of accidental release of viable oilseed rape 73496 seeds into the environment, oilseed rape 73496 would not raise environmental safety concerns. The post-market environmental monitoring plan and reporting intervals are in line with the intended uses of oilseed rape 73496. The GMO Panel concludes that oilseed rape 73496, as described in this application, is as safe as its conventional counterpart and the non-genetically modified oilseed rape reference varieties tested with respect to potential effects on human and animal health and the environment.

Assessment of genetically modified soybean GMB151 for food and feed uses, under Regulation (EC) No 1829/2003 (application EFSA-GMO-NL-2018-153)

Soybean GMB151 was developed to confer tolerance to 4-hydroxyphenylpyruvate dioxygenase (HPPD) inhibitor herbicides and resistance to nematodes. The molecular characterisation data and bioinformatic analyses do not identify issues requiring food/feed safety assessment. None of the identified differences in the agronomic/phenotypic and compositional characteristics tested between soybean GMB151 and its conventional counterpart needs further assessment, except for palmitic acid and heptadecenoic acid in seeds and carbohydrate and crude protein in forage, which does not raise nutritional and safety concerns. The GMO Panel does not identify safety concerns regarding the toxicity and allergenicity of the HPPD-4 and Cry14Ab-1 proteins as expressed in soybean GMB151, and finds no evidence that the genetic modification would change the overall allergenicity of soybean GMB151. In the context of this application, the consumption of food and feed from soybean GMB151 does not represent a nutritional concern in humans and animals. The GMO Panel concludes that soybean GMB151 is as safe as the conventional counterpart and non-GM soybean reference varieties tested, and no post-market monitoring of food/feed is considered necessary. In the case of accidental release of viable soybean GMB151 seeds into the environment, this would not raise environmental safety concerns. The post-market environmental monitoring plan and reporting intervals are in line with the intended uses of soybean GMB151. The GMO Panel concludes that soybean GMB151 is as safe as its conventional counterpart and the tested non-GM soybean reference varieties with respect to potential effects on human and animal health and the environment.

Tn1 transposition in the course of natural transformation enables horizontal antibiotic resistance spread in Acinetobacter baylyi

Transposons are genetic elements that change their intracellular genomic position by transposition and are spread horizontally between bacteria when located on plasmids. It was recently discovered that transposition from fully heterologous DNA also occurs in the course of natural transformation. Here, we characterize the molecular details and constraints of this process using the replicative transposon Tn1 and the naturally competent bacterium Acinetobacter baylyi. We find that chromosomal insertion of Tn1 by transposition occurs at low but detectable frequencies and preferably around the A. baylyi terminus of replication. We show that Tn1 transposition is facilitated by transient expression of the transposase and resolvase encoded by the donor DNA. RecA protein is essential for the formation of a circular, double-stranded cytoplasmic intermediate from incoming donor DNA, and RecO is beneficial but not essential in this process. Absence of the recipient RecBCD nuclease stabilizes the double-stranded intermediate. Based on these results, we suggest a mechanistic model for transposition during natural transformation.

Microevolution in the major outer membrane protein OmpA of Acinetobacter baumannii

Acinetobacter baumannii is nowadays a relevant nosocomial pathogen characterized by multidrug resistance (MDR) and concomitant difficulties to treat infections. OmpA is the most abundant A. baumannii outer membrane (OM) protein, and is involved in virulence, host-cell recognition, biofilm formation, regulation of OM stability, permeability and antibiotic resistance. OmpA members are two-domain proteins with an N-terminal eight-stranded β-barrel domain with four external loops (ELs) interacting with the environment, and a C-terminal periplasmic domain binding non-covalently to the peptidoglycan. Here, we combined data from genome sequencing, phylogenetic and multilocus sequence analyses from 975 strains/isolates of the Acinetobacter calcoaceticus/Acinetobacter baumannii complex (ACB), 946 from A. baumannii, to explore ompA microevolutionary divergence. Five major ompA variant groups were identified (V1 to V5) in A. baumannii, encompassing 52 different alleles coding for 23 different proteins. Polymorphisms were concentrated in five regions corresponding to the four ELs and the C-terminal end, and provided evidence for intra-genic recombination. ompA variants were not randomly distributed across the A. baumannii phylogeny, with the most frequent V1(lct)a1 allele found in most clonal complex 2 (CC2) strains and the second most frequent V2(lct)a1 allele in the majority of CC1 strains. Evidence was found for assortative exchanges of ompA alleles not only between separate A. baumannii lineages, but also different ACB species. The overall results have implications for A. baumannii evolution, epidemiology, virulence and vaccine design.

Assessment of genetically modified maize MZIR098 for food and feed uses, under Regulation (EC) No 1829/2003 (application EFSA-GMO-DE-2017-142)

Maize MZIR098 was developed to confer tolerance to glufosinate-ammonium-containing herbicides and resistance to certain coleopteran pests. The molecular characterisation data and bioinformatic analyses do not identify issues requiring food/feed safety assessment. None of the identified differences in the agronomic/phenotypic and compositional characteristics tested between maize MZIR098 and its conventional counterpart needs further assessment, except for neutral detergent fibre (NDF) in grains, which does not raise nutritional and safety concerns. The GMO Panel does not identify safety concerns regarding the toxicity and allergenicity of the eCry3.1Ab, mCry3A and PAT proteins as expressed in maize MZIR098, and finds no evidence that the genetic modification would change the overall allergenicity of maize MZIR098. In the context of this application, the consumption of food and feed from maize MZIR098 does not represent a nutritional concern in humans and animals. The GMO Panel concludes that maize MZIR098 is as safe as the conventional counterpart and non-GM maize reference varieties tested, and no post-market monitoring of food/feed is considered necessary. In the case of accidental release of viable maize MZIR098 grains into the environment, maize MZIR098 would not raise environmental safety concerns. The post-market environmental monitoring plan and reporting intervals are in line with the intended uses of maize MZIR098. In conclusion, the GMO Panel considers that maize MZIR098, as described in this application, is as safe as its conventional counterpart and the non-GM maize reference varieties tested with respect to potential effects on human and animal health and the environment.

Assessment of genetically modified oilseed rape MS11 for food and feed uses, import and processing, under Regulation (EC) No 1829/2003 (application EFSA-GMO-BE-2016-138)

Oilseed rape MS11 has been developed to confer male sterility and tolerance to glufosinate-ammonium-containing herbicides. Based on the information provided in the application and in line with the scope of application EFSA-GMO-BE-2016-138, the genetically modified organism (GMO) Panel concludes that the molecular characterisation data and bioinformatic analyses do not identify issues requiring food/feed safety assessment. None of the identified differences in the agronomic/phenotypic characteristics tested between oilseed rape MS11 and its conventional counterpart needs further assessment. No conclusions can be drawn for the compositional analysis due to the lack of an appropriate compositional data set. No toxicological or allergenicity concerns are identified for the Barnase, Barstar and PAT/bar proteins expressed in oilseed rape MS11. Owing to the incompleteness of the compositional analysis, the toxicological, allergenicity and nutritional assessment of oilseed rape MS11 cannot be completed. In the case of accidental release of viable oilseed rape MS11 seeds into the environment, oilseed rape MS11 would not raise environmental safety concerns. The post-market environmental monitoring plan and reporting intervals are in line with the scope of the application. Since oilseed rape MS11 is designed to be used only for the production of hybrid seed, it is not expected to be commercialised as a stand-alone product for food/feed uses. Thus, seeds harvested from oilseed rape MS11 are not expected to enter the food/feed chain, except accidentally. In this context, the GMO Panel notes that, oilseed rape MS11 would not pose risk to humans and animals, while the scale of environmental exposure will be substantially reduced compared to a stand-alone product.

Assessment of genetically modified soybean SYHT0H2 for food and feed uses, import and processing, under Regulation (EC) No 1829/2003 (application EFSA-GMO-DE-2012-111)

The scope of application EFSA-GMO-DE-2012-111 is for food and feed uses, import and processing of genetically modified (GM) soybean SYHT0H2 in the European Union. Soybean SYHT0H2 was developed to confer tolerance to the herbicidal active substances mesotrione and other p-hydroxyphenylpyruvate dioxygenase (HPPD)-inhibiting herbicides and glufosinate ammonium. The molecular characterisation data and bioinformatic analyses do not identify issues except for sequence similarity of AvHPPD-03 to bacterial haemolysins that was considered in food/feed safety assessment. The outcome of the comparative analysis (agronomic/phenotypic and compositional characteristics) did not need further assessment except for the changes in seed levels of α-tocopherol and γ-tocopherol that were assessed for food and feed relevance. The GMO Panel does not identify toxicological and allergenicity concerns for the AvHPPD-03 and PAT proteins expressed in soybean SYHT0H2 and finds no evidence that the genetic modification would change the overall allergenicity of soybean SYHT0H2. The nutritional impact of food/feed from soybean SYHT0H2 is expected to be the same as that of food/feed from the conventional counterpart and commercial non-GM soybean reference varieties. The GMO Panel concludes that soybean SYHT0H2 is as safe as and nutritionally equivalent to the conventional counterpart and the tested non-GM soybean reference varieties, and no post-market monitoring of food/feed is considered necessary. In the case of accidental release of viable soybean SYHT0H2 grains into the environment, soybean SYHT0H2 would not raise environmental safety concerns. The post-market environmental monitoring plan and reporting intervals are in line with the intended uses of soybean SYHT0H2. In conclusion, the GMO Panel considers that soybean SYHT0H2, as described in this application, is as safe as its conventional counterpart and the tested non-GM soybean reference varieties with respect to potential effects on human and animal health and the environment.

Assessment of genetically modified soybean MON 87751 for food and feed uses under Regulation (EC) No 1829/2003 (application EFSA-GMO-NL-2014-121)

Soybean MON 87751 was developed through Agrobacterium tumefaciens-mediated transformation to provide protection certain specific lepidopteran pests by the expression of the Cry1A.105 and Cry2Ab2 proteins derived from Bacillus thuringiensis. The molecular characterisation data and bioinformatic analyses did not identify issues requiring assessment for food and feed safety. None of the compositional, agronomic and phenotypic differences identified between soybean MON 87751 and the conventional counterpart required further assessment. The GMO Panel did not identify safety concerns regarding the toxicity and allergenicity of the Cry1A.105 and Cry2Ab2 proteins as expressed in soybean MON 87751, and found no evidence that the genetic modification might significantly change the overall allergenicity of soybean MON 87751. The nutritional impact of soybean MON 87751-derived food and feed is expected to be the same as those derived from the conventional counterpart and non-GM commercial reference varieties. The GMO Panel concludes that soybean MON 87751, as described in this application, is nutritionally equivalent to and as safe as the conventional counterpart and the non-GM soybean reference varieties tested, and no post-market monitoring of food and feed is considered necessary. In the case of accidental release of viable soybean MON 87751 seeds into the environment, soybean MON 87751 would not raise environmental safety concerns. The post-market environmental monitoring plan and reporting intervals are in line with the intended uses of soybean MON 87751. In conclusion, soybean MON 87751, as described in this application, is as safe as its conventional counterpart and the tested non-GM soybean reference varieties with respect to potential effects on human and animal health and the environment.

Scientific Opinion on an application by Dow AgroSciences LLC (EFSA-GMO-NL-2011-91) for the placing on the market of genetically modified herbicide-tolerant soybean DAS-68416-4 for food and feed uses, import and processing under Regulation (EC) No 1829/2003

Soybean DAS-68416-4 was developed by Agrobacterium tumefaciens-mediated transformation to express the aryloxyalkanoate dioxygenase-12 (AAD-12) protein, conferring tolerance to 2,4-dichlorophenoxyacetic acid (2,4-D) and other related phenoxy herbicides, and the phosphinothricin acetyltransferase (PAT) protein, conferring tolerance to glufosinate ammonium-based herbicides. The molecular characterisation data and bioinformatics analyses did not identify issues requiring further assessment for food/feed safety. The agronomic and phenotypic characteristics tested revealed no relevant differences between soybean DAS-68416-4 and its conventional counterpart, except for 'days to 50% flowering'. The compositional analysis identified no differences requiring further assessment, except for an increase (up to 36%) in lectin activity in soybean DAS-68416-4. Such increase is unlikely to raise additional concerns for food/feed safety and nutrition for soybean DAS-68416-4 as compared to its conventional counterpart and the non-GM reference varieties. There were no concerns regarding the potential toxicity and allergenicity of the two newly expressed proteins, and no evidence that the genetic modification might significantly change the overall allergenicity of soybean DAS-68416-4. Soybean DAS-68416-4 is as nutritious as its conventional counterpart and the non-GM reference varieties. There are no indications of an increased likelihood of establishment and spread of occasional feral soybean DAS-68416-4 plants, unless these are exposed to the intended herbicides. The likelihood of environmental effects resulting from the accidental release of viable seeds from soybean DAS-68416-4 into the environment is therefore very low. The post-market environmental monitoring plan and reporting intervals are in line with the intended uses of soybean DAS-68416-4. The GMO Panel concludes that the information available addresses the scientific comments of the Member States and that soybean DAS-68416-4, as described in this application, is as safe as its conventional counterpart and the tested non-GM reference varieties with respect to potential effects on human and animal health and the environment in the context of the scope of this application.

Assessment of the potential integration of the DNA plasmid vaccine CLYNAV into the salmon genome

The European Commission mandated EFSA to review a new data package provided by the company Elanco, for the possible integration/non‐integration of the DNA plasmid vaccine CLYNAV into the genome of Atlantic salmon (Salmo salar) and to indicate whether EFSA agrees with the conclusions drawn by Elanco. The vaccine is injected into fish to confer protection against pancreas disease caused by the salmonid alphavirus. The majority of the experimental data provided by the company was for muscle tissue close to the injection site and for gonadal tissue. EFSA considers that the long persistence of DNA plasmid in muscle tissue close to the injection site and the potential heritability of an integration event in gonad cells support the focus of the assessment on both these tissues. The experimental data did not provide scientifically robust evidence for a true integration event. The company overall concluded that the likelihood of integration is negligible, based on considerations in the context of the company's environmental risk assessment, but did not provide a quantitative value for the rate of integration linked to the term ‘negligible’. It is therefore not possible to evaluate this statement specifically with regard to integration rates. EFSA notes that knowledge about homologous and non‐homologous integration predicts that integration could occur with certain frequency. Therefore, EFSA has constructed worst‐case scenarios leading to upper estimates for possible integration rates of the DNA plasmid vaccine into the Atlantic salmon genome. EFSA concludes that, based on the worst‐case scenarios described here and taking into account additional factors decreasing the likelihood of integration, the actual integration rate is likely to be orders of magnitude lower than the upper estimated integration rate calculated in the context of the worst‐case scenarios. With the available evidence, the actual integration rate cannot be estimated with more precision.

Substitutions of short heterologous DNA segments of intragenomic or extragenomic origins produce clustered genomic polymorphisms

In a screen for unexplained mutation events we identified a previously unrecognized mechanism generating clustered DNA polymorphisms such as microindels and cumulative SNPs. The mechanism, short-patch double illegitimate recombination (SPDIR), facilitates short single-stranded DNA molecules to invade and replace genomic DNA through two joint illegitimate recombination events. SPDIR is controlled by key components of the cellular genome maintenance machinery in the gram-negative bacterium Acinetobacter baylyi. The source DNA is primarily intragenomic but can also be acquired through horizontal gene transfer. The DNA replacements are nonreciprocal and locus independent. Bioinformatic approaches reveal occurrence of SPDIR events in the gram-positive human pathogen Streptococcus pneumoniae and in the human genome.

Region 4 of Rhizobium etli Primary Sigma Factor (SigA) Confers Transcriptional Laxity in Escherichia coli

Sigma factors are RNA polymerase subunits engaged in promoter recognition and DNA strand separation during transcription initiation in bacteria. Primary sigma factors are responsible for the expression of housekeeping genes and are essential for survival. RpoD, the primary sigma factor of Escherichia coli, a γ-proteobacteria, recognizes consensus promoter sequences highly similar to those of some α-proteobacteria species. Despite this resemblance, RpoD is unable to sustain transcription from most of the α-proteobacterial promoters tested so far. In contrast, we have found that SigA, the primary sigma factor of Rhizobium etli, an α-proteobacteria, is able to transcribe E. coli promoters, although it exhibits only 48% identity (98% coverage) to RpoD. We have called this the transcriptional laxity phenomenon. Here, we show that SigA partially complements the thermo-sensitive deficiency of RpoD285 from E. coli strain UQ285 and that the SigA region σ4 is responsible for this phenotype. Sixteen out of 74 residues (21.6%) within region σ4 are variable between RpoD and SigA. Mutating these residues significantly improves SigA ability to complement E. coli UQ285. Only six of these residues fall into positions already known to interact with promoter DNA and to comprise a helix-turn-helix motif. The remaining variable positions are located on previously unexplored sites inside region σ4, specifically into the first two α-helices of the region. Neither of the variable positions confined to these helices seem to interact directly with promoter sequence; instead, we adduce that these residues participate allosterically by contributing to correct region folding and/or positioning of the HTH motif. We propose that transcriptional laxity is a mechanism for ensuring transcription in spite of naturally occurring mutations from endogenous promoters and/or horizontally transferred DNA sequences, allowing survival and fast environmental adaptation of α-proteobacteria.

Involvement of aph(3')-IIa in the formation of mosaic aminoglycoside resistance genes in natural environments

Intragenic recombination leading to mosaic gene formation is known to alter resistance profiles for particular genes and bacterial species. Few studies have examined to what extent aminoglycoside resistance genes undergo intragenic recombination. We screened the GenBank database for mosaic gene formation in homologs of the aph(3')-IIa (nptII) gene. APH(3')-IIa inactivates important aminoglycoside antibiotics. The gene is widely used as a selectable marker in biotechnology and enters the environment via laboratory discharges and the release of transgenic organisms. Such releases may provide opportunities for recombination in competent environmental bacteria. The retrieved GenBank sequences were grouped in three datasets comprising river water samples, duck pathogens and full-length variants from various bacterial genomes and plasmids. Analysis for recombination in these datasets was performed with the Recombination Detection Program (RDP4), and the Genetic Algorithm for Recombination Detection (GARD). From a total of 89 homologous sequences, 83% showed 99-100% sequence identity with aph(3')-IIa originally described as part of transposon Tn5. Fifty one were unique sequence variants eligible for recombination analysis. Only a single recombination event was identified with high confidence and indicated the involvement of aph(3')-IIa in the formation of a mosaic gene located on a plasmid of environmental origin in the multi-resistant isolate Pseudomonas aeruginosa PA96. The available data suggest that aph(3')-IIa is not an archetypical mosaic gene as the divergence between the described sequence variants and the number of detectable recombination events is low. This is in contrast to the numerous mosaic alleles reported for certain penicillin or tetracycline resistance determinants.

Horizontal gene transfer can rescue prokaryotes from Muller's ratchet: benefit of DNA from dead cells and population subdivision

Horizontal gene transfer (HGT) is a major factor in the evolution of prokaryotes. An intriguing question is whether HGT is maintained during evolution of prokaryotes owing to its adaptive value or is a byproduct of selection driven by other factors such as consumption of extracellular DNA (eDNA) as a nutrient. One hypothesis posits that HGT can restore genes inactivated by mutations and thereby prevent stochastic, irreversible deterioration of genomes in finite populations known as Muller’s ratchet. To examine this hypothesis, we developed a population genetic model of prokaryotes undergoing HGT via homologous recombination. Analysis of this model indicates that HGT can prevent the operation of Muller’s ratchet even when the source of transferred genes is eDNA that comes from dead cells and on average carries more deleterious mutations than the DNA of recipient live cells. Moreover, if HGT is sufficiently frequent and eDNA diffusion sufficiently rapid, a subdivided population is shown to be more resistant to Muller’s ratchet than an undivided population of an equal overall size. Thus, to maintain genomic information in the face of Muller’s ratchet, it is more advantageous to partition individuals into multiple subpopulations and let them “cross-reference” each other’s genetic information through HGT than to collect all individuals in one population and thereby maximize the efficacy of natural selection. Taken together, the results suggest that HGT could be an important condition for the long-term maintenance of genomic information in prokaryotes through the prevention of Muller’s ratchet.

Natural competence and the evolution of DNA uptake specificity

Many bacteria are naturally competent, able to actively transport environmental DNA fragments across their cell envelope and into their cytoplasm. Because incoming DNA fragments can recombine with and replace homologous segments of the chromosome, competence provides cells with a potent mechanism of horizontal gene transfer as well as access to the nutrients in extracellular DNA. This review starts with an introductory overview of competence and continues with a detailed consideration of the DNA uptake specificity of competent proteobacteria in the Pasteurellaceae and Neisseriaceae. Species in these distantly related families exhibit strong preferences for genomic DNA from close relatives, a self-specificity arising from the combined effects of biases in the uptake machinery and genomic overrepresentation of the sequences this machinery prefers. Other competent species tested lack obvious uptake bias or uptake sequences, suggesting that strong convergent evolutionary forces have acted on these two families. Recent results show that uptake sequences have multiple "dialects," with clades within each family preferring distinct sequence variants and having corresponding variants enriched in their genomes. Although the genomic consensus uptake sequences are 12 and 29 to 34 bp, uptake assays have found that only central cores of 3 to 4 bp, conserved across dialects, are crucial for uptake. The other bases, which differ between dialects, make weaker individual contributions but have important cooperative interactions. Together, these results make predictions about the mechanism of DNA uptake across the outer membrane, supporting a model for the evolutionary accumulation and stability of uptake sequences and suggesting that uptake biases may be more widespread than currently thought.

Molecular epidemiological study of clinical Acinetobacter baumannii isolates: phenotype switching of antibiotic resistance

BACKGROUND

The presence of clinical Acinetobacter baumannii (A. baumannii) isolates with differing antibiotic resistance phenotypes in the same patient causes difficulties and confusion in treatment. This phenomenon may be caused by reasons such as cross-infection from neighboring patients that switches to different A. baumannii strain, natural mutation of A. baumannii, inducing of different antibiotic resistance genes expression or acquisition of genes conferring resistance from another source. To elucidate this question, clinical A. baumannii strains, isolated from the same individual patients, showed antibiotic resistance phenotypes switching during the same hospitalization period, were attentively collected for further analysis. Molecular approaches for phylogenetic analysis, including pulsed field gel electrophoresis, multilocus sequence typing, and short tandem repeat analysis, were employed for the chronological studies.

FINDINGS

Our results showed that antibiotic resistance phenotype switching could have occurred as a result through both cross-infection and natural mutation roots. Our results also suggest that rapid phenotype switching between paired isolates could occur during one single course of antibiotic treatment.

CONCLUSIONS

Though cross infection caused antibiotic resistance phenotype switching does occur, natural mutation of A. baumannii isolates is particularly cautious for antibiotic treatment.