Possibility of transfer and activation of 'silent' tetracycline resistance genes among Enterococcus faecalis under high-pressure processing

In this study, the tetracycline resistance of Enterococcus faecalis strains isolated from food was determined and molecular analyses of the resistance background were performed by determining the frequency of selected tetracycline resistance genes. In addition, the effect of high-pressure stress (400 and 500 MPa) on the expression of selected genes encoding tetracycline resistance was determined, as well as changes in the frequency of transfer of these genes in isolates showing sensitivity to tetracyclines. In our study, we observed an increase in the expression of genes encoding tetracyclines, especially the tet(L) gene, mainly under 400 MPa pressure. The study confirmed the possibility of transferring genes encoding tetracyclines such as tet(M), tet(L), tet(K), tet(W) and tet(O) by horizontal gene transfer in both control strains and exposed to high-pressure. Exposure of the strains to 400 MPa pressure had a greater effect on the possibility of gene transfer and expression than the application of a higher-pressure. To our knowledge, this study for the first time determined the effect of high-pressure stress on the expression of selected genes encoding tetracycline resistance, as well as the possibility and changes in the frequency of transfer of these genes in Enterococcus faecalis isolates showing sensitivity to tetracyclines and possessing silent genes. Due to the observed possibility of increased expression of some of the genes encoding tetracycline resistance and the possibility of their spread by horizontal gene transfer to other microorganisms in the food environment, under the influence of high-pressure processing in strains phenotypically susceptible to this antibiotic, it becomes necessary to monitor this ability in isolates derived from foods.

One Health-based management for sustainably mitigating tetracycline-resistant Aeromonas hydrophila-induced health risk

Aeromonas hydrophila has ability to spread tetracycline resistance (tetR) under stresses of oxytetracycline (OTC), one of the most important antibiotics in aquaculture industry. Even though environmental reservoir of Aeromonas allows it to be at interfaces across One Health components, a robust modelling framework for rigorously assessing health risks is currently lacking. We proposed a One Health-based approach and leveraged recent advances in quantitative microbial risk assessment appraised by available dataset to interpret interactions at the human-animal-environment interfaces in various exposure scenarios. The dose-response models were constructed considering the effects on mortality for aquaculture species and tetR genes transfer for humans. A scenario-specific risk assessment on pond species-associated A. hydrophila infection and human gut-associated tetR genes transfer was examined. Risk-based control strategies were involved to test their effectiveness. We showed that farmed shrimp exposed to tetracycline-resistant A. hydrophila in OTC-contaminated water experienced higher infection risk (relative risk: 1.25-1.34). The tetR genes transfer risk for farmers in shrimp ponds (∼2 × 10-4) and swimmers in coastal areas (∼4 × 10-6) during autumn exceeded acceptable risk (10-6). This cautionary finding underscores the importance of accounting for monitoring, assessing, and mitigating occupational health hazards among workers in shrimp farming sectors within future One Health-based strategies for managing water infection risks. We recommend that OTC emission rate together with A. hydrophila concentration should be reduced by up to 70-99% to protect human, farmed shrimp, and environmental health. Our predictive framework can be adopted for other systems and be used as a "risk detector" for assessing tetR-related health risks that invoke potential risk management on addressing sustainable mitigation on offsetting residual OTC emission and tetR genes spread in a species-human-environmental health system.

Novel tetracycline resistance gene tet(65) located on a multi-resistance Corynebacterium plasmid

BACKGROUND

Corynebacterium (C.) sp. 22KM0430 related to C. oculi and isolated from a dog exhibited resistance to tetracycline, and its WGS analysis revealed a putative resistance gene on a 35 562-bp plasmid also harbouring the MLSB resistance gene erm(X).

OBJECTIVES

To characterize the novel tetracycline resistance gene tet(65) and demonstrate its functionality by expression in C. glutamicum and Escherichia coli and plasmid curing of the host strain.

METHODS

tet(65) was cloned with and without its repressor tetR(65) and expressed in C. glutamicum DSM20300 and E. coli DH5α. Plasmid was cured by non-selective passages. Minimal inhibitory concentrations (MICs) of tetracyclines were determined according to CLSI guidelines. Association of tet(65) with efflux was shown by the addition of reserpine to MIC assays. Phylogenetic position and transmembrane structure of Tet(65) were analysed using MEGA11 and DeepTMHMM.

RESULTS

Tet(65) shows 73% amino acid identity with the closest related Tet(Z), contains 12 transmembrane domains and is structurally related to the Major Facilitator Superfamily. The tetracycline MICs decreased in the plasmid-cured strain and increased when tet(65) was expressed in C. glutamicum and in E. coli. The MICs of tetracycline decreased in the presence of reserpine indicating that tet(65) functions as an efflux pump. A GenBank search also identified tet(65) in C. diphtheriae and Brevibacterium (B.) casei and B. luteolum.

CONCLUSIONS

A novel tetracycline efflux gene tet(65) was identified in a C. oculi related species and was also present in the human pathogen C. diphtheriae and in Brevibacterium species indicating broader potential for dissemination.

Priority establishment of soil bacteria in rhizosphere limited the spread of tetracycline resistance genes from pig manure to soil-plant systems based on synthetic communities approach

The spread of antibiotic resistance genes (ARGs) in agroecosystems through the application of animal manure is a global threat to human and environmental health. However, the adaptability and colonization ability of animal manure-derived bacteria determine the spread pathways of ARG in agroecosystems, which have rarely been studied. Here, we performed an invasion experiment by creating a synthetic communities (SynCom) with ten isolates from pig manure and followed its assembly during gnotobiotic cultivation of a soil-Arabidopsis thaliana (A. thaliana) system. We found that Firmicutes in the SynCom were efficiently filtered out in the rhizosphere, thereby limiting the entry of tetracycline resistance genes (TRGs) into the plant. However, Proteobacteria and Actinobacteria in the SynCom were able to establish in all compartments of the soil-plant system thereby spreading TRGs from manure to soil and plant. The presence of native soil bacteria prevented the establishment of manure-borne bacteria and effectively reduced the spread of TRGs. Achromobacter mucicolens and Pantoea septica were the main vectors for the entry of tetA into plants. Furthermore, doxycycline stress promoted the horizontal gene transfer (HGT) of the conjugative resistance plasmid RP4 within the SynCom in A. thaliana by upregulating the expression of HGT-related mRNAs. Therefore, this study provides evidence for the dissemination pathways of ARGs in agricultural systems through the invasion of manure-derived bacteria and HGT by conjugative resistance plasmids and demonstrates that the priority establishment of soil bacteria in the rhizosphere limited the spread of TRGs from pig manure to soil-plant systems.

Description of a Case of Helicobacter pylori Infection with In Vitro Resistance to Tetracycline: An Exceptional Event with No Consequences?

Resistance in Helicobacter pylori to tetracycline is rare. We describe the case of an H. pylori strain with a high level of resistance to tetracycline (minimum inhibitory concentration = 12 mg/L). However, despite tetracycline resistance, bismuth quadritherapy was effective. Analysis of the patient's antibiotic treatment history over the previous 25 years revealed repeated 3-month courses of tetracycline for the treatment of acne, suggesting in vivo selection pressure responsible for the emergence of the triple mutation (AGA→TTC) in 16S rDNA associated with tetracycline resistance. This is a rare event but one worth monitoring, especially in view of the widespread use of bismuth quadritherapy for probabilistic treatment in countries where it is available.

GWAS and comparative genomics reveal candidate antibiotic resistance genes in the avian pathogen Gallibacterium anatis for six widespread antibiotics

Gallibacterium anatis is a Gram-negative bacterium found in the respiratory and genital tracts of various animals, primarily poultry. Its association with septicemia and high mortality in poultry, along with the rise in multidrug-resistant strains, has amplified concerns. Recent research uncovered significant variability in antibiotic resistance profiles among G. anatis isolates from different Austrian flocks, and even between different organs within the same bird. In response, in the present study 60 of these isolates were sequenced and a combination of comparative genomics and genome-wide association study (GWAS) analysis was applied to understand the genetic variability of G. anatis across flocks and organs and to identify genes related to antibiotic resistance. The results showed that each flock harbored one or two strains of G. anatis with only a few strains shared between flocks, demonstrating a great variability among flocks. We identified genes associated with resistance to nalidixic acid, trimethoprim, cefoxitin, tetracycline, ampicillin and sulfamethoxazole. Our findings revealed that G. anatis may develop antibiotic resistance through two mechanisms: single-nucleotide mutations and the presence of specific genes that confer resistance. Unexpectedly, some tetracycline-resistant isolates lacked all known tetracycline-associated genes, suggesting the involvement of novel mechanisms of tetracycline resistance that require additional exploration. Furthermore, our functional annotation of resistance genes highlighted the citric acid cycle pathway as a potential key modulator of antibiotic resistance in G. anatis. In summary, this study describes the first application of GWAS analysis to G. anatis and provides new insights into the acquisition of multidrug resistance in this important avian pathogen.

Pentachlorophenol affects doxycycline and tetracycline resistance genes in soil by altering microbial structure

Tetracycline antibiotics play a vital role in animal husbandry, primarily employed to uphold the health of livestock and poultry. Consequently, when manure is reintegrated into farmland, tetracycline antibiotics can persist in the soil. Simultaneously, to ensure optimal crop production, organochlorine pesticides (OCPs) are frequently applied to farmland. The coexistence of tetracycline antibiotics and OCPs in soil may lead to an increased risk of transmission of tetracycline resistance genes (TRGs). Nevertheless, the precise mechanism underlying the effects of OCPs on tetracycline antibiotics and TRGs remains elusive. In this study, we aimed to investigate the effects of OCPs on soil tetracycline antibiotics and TRGs using different concentrations of doxycycline (DOX) and pentachlorophenol (PCP). The findings indicate that PCP and DOX mutually impede their degradation in soil. Furthermore, our investigation identifies Sphingomonas and Bacillus as potential pivotal microorganisms influencing the reciprocal inhibition of PCP and DOX. Additionally, it is observed that the concurrent presence of PCP and DOX could impede each other's degradation by elevating soil conductivity. Furthermore, we observed that a high concentration of PCP (10.7 mg/kg) reduced the content of efflux pump tetA, ribosome protective protein tetM, tetQ, and passivating enzyme tetX. In contrast, a low PCP concentration (6.4 mg/kg) only reduced the content of ribosome protective protein tetQ. This suggests that PCP may reduce the relative abundance of TRGs by altering the soil microbial community structure and inhibiting the potential host bacteria of TRGs. These findings have significant implications in understanding the combined pollution of veterinary antibiotics and OCPs. By shedding light on the interactions between these compounds and their impact on microbial communities, this study provides a theoretical basis for developing strategies to manage and mitigate their environmental impact, and may give some information regarding the sustainable use of antibiotics and pesticides to ensure the long-term health and productivity of agricultural systems.

The distribution profiles of tetracycline resistance genes in rice: Comparisons using four genotypes

The potential transmission of antibiotic resistance genes (ARGs) from the rhizosphere to plants and humans poses a significant concern. This study aims to investigate the distribution of tetracycline resistance genes (TRGs) in rice using four genotypes and identify the primary source of TRGs in grains. Quantitative polymerase chain reaction (qPCR) was employed to determine the abundance of seven TRGs and intI1 in four rice varieties and three partitions during the jointing and heading stages, respectively. The analysis of the bacterial community was conducted to elucidate the underlying mechanism of the profiles of TRGs. It was observed that tetZ was predominantly present in the rhizosphere and endoroot, whereas tetX became dominant in grains. The relative abundances of TRGs and intI1 exhibited significant variations across both the variety and partition. However, no significant differences were observed in grains, where the abundances of TRGs were several orders of magnitude lower compared to those in the rhizosphere. Nevertheless, the potential risk of the dissemination of TRGs to humans, particularly those carried by potential pathogens in grains, warrants attention. The increased likelihood of TRGs accumulation in the rhizosphere and endoroot of hybrid rice varieties, as opposed to japonica varieties, may be attributed to the heightened metabolic activities of their roots. The significant associations observed between intI1 and TRGs, coupled with the substantial alterations in potential hosts for intI1 across various treatments, indicate that intI1-mediated horizontal gene transfer plays a role in the diverse range of bacterial hosts for TRGs. The study also revealed that rhizosphere bacteria during the jointing stage serve as the primary contributors of TRGs in grains through the endoroot junction. The findings indicate that Japonica rice varieties exhibit superior control over TRGs compared to hybrid varieties, emphasizing the need for early interventions throughout the entire growth period of rice.

A highly selective and sensitive electrochemical sensor for tetracycline resistant genes detection based on the non-covalent interaction of graphene oxide and nucleobase

Antibiotic resistance genes (ARGs) are causing worldwide environmental problems, however, the traditional analytical methods and test equipment for them are time-consuming and expensive. The electrochemical sensor using the non-covalent bond between graphene oxide (GO) and single-stranded tet (ss-tet) was established for specific tetracycline resistance genes (tet, composed of ss-tet and complementary ss-tet (ss-tet') in water) detection, which preparation time was only 35 min and far less than most reported sensors based on covalent bond. As the result of the detection for tet, the developed sensor not only had the low detection limit of 50.0 pM (8.1 × 102 copies·mL-1), the short detection time within 42 min, but also had satisfactory stability, excellent reproducibility, and highly selectivity (RSD < 4.43 %). Besides, it also had acceptable accuracy comparing to the real-time quantitative polymerase chain reaction (RT-qPCR) and PCR array in tet detection. Noticeably, it also had been successfully applied to tetA detection in different water samples. In brief, the prepared non-covalent bond sensor is simple, rapid, and suitable for highly selective and sensitive detection of the ARGs in actual water.

Prevalence and genetic basis of tetracycline resistance in Vibrioparahaemolyticus isolates recovered from food products in Shenzhen, China during 2013 to 2021

Understanding tetracycline resistance in Vibrio parahaemolyticus from food products is crucial for effective control measures against this foodborne pathogen. This study aimed to investigate the prevalence, evolution routes, and mechanism of transmission of tetracycline resistance in Vibrio parahaemolyticus isolates collected from food products in Shenzhen, China. A total of 2342 non-duplicate Vibrio parahaemolyticus were isolated from 3509 food samples during the period 2013-2021. Among these 2342 Vibrio parahaemolyticus strains, 530 (21.37 %) were resistant to tetracycline. These tetracycline-resistant Vibrio parahaemolyticus strains were mainly isolated from shrimp samples, with the highest resistance rate (46.9 %) observed in 2019. Phylogenetic and genomic analyses of 387 isolates carrying the tet genes revealed that five different types of tet genes (tet(34), tet(A), tet(B), tet(M), and tet(E)) were present. The tet(A) gene was the most common (65 % of isolates), while tet(E) and tet(M) genes were only detected in specific years. Although tet(A) is the most commonly detected gene, it only encodes resistance in a low percentage of strains (47/129). On the other hand, the resistance rate is highest in isolates carrying tet(B) (41/55). Interestingly, V. parahaemolyticus carrying the tet genes were not necessarily tetracycline-resistant, and vice versa. A total of six different types of plasmids and two transposable units were found to carry the tet genes. V. parahaemolyticus strains that harbored these plasmids were often resistant to multiple antibiotics, indicating that horizontal transfer of antibiotic resistance genes is common among V. parahaemolyticus strains. Our findings suggest a high prevalence of tetracycline resistance in Vibrio parahaemolyticus strains recovered from food products in Shenzhen, China. These results provide valuable insight into the evolution and transmission of tetracycline resistance in foodborne Vibrio parahaemolyticus isolates and highlight the need for effective control measures to prevent the spread of antibiotic resistance.

Tetracycline resistance in Listeria monocytogenes and L. innocua from wild black bears (Ursus americanus) in the United States is mediated by novel transposable elements

IMPORTANCE

Listeria monocytogenes causes severe foodborne illness and is the only human pathogen in the genus Listeria. Previous surveys of AMR in Listeria focused on clinical sources and food or food processing environments, with AMR in strains from wildlife and other natural ecosystems remaining under-explored. We analyzed 185 sequenced strains from wild black bears (Ursus americanus) from the United States, including 158 and 27 L. monocytogenes and L. innocua, respectively. Tetracycline resistance was the most prevalent resistance trait. In L. monocytogenes, it was encountered exclusively in serotype 4b strains with the novel Tn916-like element Tn916.1039. In contrast, three distinct, novel tetracycline resistance elements (Tn5801.UAM, Tn5801.551, and Tn6000.205) were identified in L. innocua. Interestingly, Tn5801.551 was identical to elements in L. monocytogenes from a major foodborne outbreak in the United States in 2011. The findings suggest the importance of wildlife and non-pathogenic Listeria species as reservoir for resistance elements in Listeria.

Mechanism of antibiotic resistance development in an activated sludge system under tetracycline pressure

The mechanism of antibiotic resistance (AR) development in an activated sludge system under tetracycline (TC) pressure was discussed and analyzed. According to the variation of macro-factors, including TC, COD, TN, TP, NH3-N, pH, heavy metals, and reactor settings, the tet genes respond accordingly. Consequently, the enrichment sites of tet genes form an invisible AR selection zone, where AR microorganisms thrive, gather, reproduce, and spread. The efflux pump genes tetA and tetB prefer anaerobic environment, while ribosome protective protein genes tetM, tetO, tetQ, tetT, and tetW were more concentrated in aerobic situations. As a corresponding micro-effect, different types of tet genes selected the corresponding dominant bacteria such as Thauera and Arthrobacter, suggesting the intrinsic relationship between tet genes and potential hosts. In summary, the macro-response and micro-effect of tet genes constitute an interactive mechanism with tet genes as the core, which is the crucial cause for the continuous development of AR. This study provides an executable strategy to control the development of AR in actual wastewater treatment plants from the perspective of macro-factors and micro-effects.

Comparative metagenomics reveals poultry and swine farming are hotspots for multidrug and tetracycline resistance

Antibiotic misuse in livestock is a major threat to human health, as bacteria are quickly developing resistance to them. We performed a comparative analysis of 25 faecal metagenomes from swine, poultry, cattle, and humans to investigate their resistance profiles. Our analysis revealed that all genes conferring resistance to antibiotic classes assessed except tetracyclines were more prevalent in poultry manure than in the remaining species. We detected clinically relevant antibiotic resistance genes, such as mcr-1 which confers resistance to polymyxins. Among them, extended-spectrum β-lactamase blaCTX-M genes were particularly abundant in all species. Poultry manure was identified as a hotspot for multidrug resistance, which may compromise medical treatment options. Urgent actions in the livestock industry are imperative to hamper the emergence and spread of antibiotic resistance.

Tea polyphenols and catechins postpone evolution of antibiotic resistance genes and alter microbial community under stress of tetracycline

Relying on the high mobility of water flow, the dissemination of antibiotic resistance genes (ARGs) in the water tends to be exacerbated and enlarged. It caused negative impacts on a wider scope of the environment. The ARGs dissemination monitoring and the methods efficiently reducing their concentration in water became the focus of interest. Green chemicals with antibacterial effects such as tea polyphenols (TPs) and catechins (CA) have been considered as auxiliary disinfectants for ARGs removal in the water environment. However, the antibacterial performance of TPs and CA under the stress of external antibiotics still lacks sufficient research. The results show that more operational taxonomic units can be observed in water samples with TPs and CA than in those without the ingredients under pressure of tetracycline. An unexpected increase along with the increase of ARGs concentrations and the diversity of microbial communities under the low-concentration TPs or CA (1 mg/L). Besides, under the stress of tetracycline, the inhibition of TPs was detected to be strengthened for increase of inti1 and tetC but weakened towards for the increase of tetA. Whilst CA substantially diminished abundances of tetC and tetA under tetracycline pressure. This research demonstrated that TPs and CA are able to assuage development of ARGs under the pressure of antibiotic in water system.

Tetracycline Resistance Genes in the Traditional Swedish Sour Herring surströmming as Revealed Using qPCR

Antibiotic resistance (AR) represents a global concern for human health. To the best of the authors' knowledge, no study addressing AR in surströmming, a traditional Swedish fermented herring, has been performed to date. The aim of the present research was to study the prevalence of tet(O), tet(S), tet(W), tet(K), and tet(M) genes encoding for resistance to tetracycline using quantitative PCR (qPCR) applied to ready-to-eat surströmming samples collected from three producers located in Sweden. The tet(M) gene was found in all the analyzed samples, and it was also the most abundant among the tested tet genes; moreover, tet(O) was the least frequently detected gene. As a general trend, all the analyzed samples showed a high occurrence of the target genes, with slight variations among the producers. A principal component analysis did not reveal any separation among the samples or producers. All the collected data allowed for a drawing of a first picture of the occurrence of tetracycline resistance genes in ready-to-eat surströmming samples. Since no differences among the samples manufactured by the different producers were observed, it is likely that the detected genes were homogeneously spread among the microbial species shared by the herrings used as raw materials. Moreover, it can be hypothesized that the presence of the detected genes was also the result of a selective pressure of the natural marine environment on the herrings' gut microbiota and, hence, on the pro-technological microorganisms responsible for the fermentation of surströmming. However, the contribution of the manufacturers to the contamination of the processed herrings cannot be excluded.

The enhanced degradation behavior of oxytetracycline by black soldier fly larvae with tetracycline resistance genes in the larval gut: Kinetic process and mechanism

Black soldier fly larvae (larvae) can digest organic wastes and degrade contaminants such as oxytetracycline (OTC). However, compared to the kinetic processes and enhanced mechanisms used in the traditional microbial degradation of OTC, those employed by larvae are largely uncharacterized. To obtain further details, a combined analysis of larval development, larval nutritional values (crude protein, crude fat and the composition of fatty acids) and the expression of tetracycline resistance genes (TRGs) in the larval gut was performed for the degradation of OTC added to substrates and for oxytetracycline bacterial residue (OBR). When the larvae were exposed to the substrates, the degradation processes were enhanced significantly (P < 0.01), with a 4.74-7.86-fold decrease in the degradation half-life (day^-1) and a 3.34-5.74-fold increase in the final degradation efficiencies. This result was attributed to the abundant TRGs (with a detection rate of 35.90%∼52.14%) in the larval gut. The TRGs presented the resistance mechanisms of cellular protection and efflux pumps, which ensured that the larvae could tolerate elevated OTC concentrations. Investigation of the TRGs indicated that enzymatic inactivation enhanced OTC degradation by larvae. These findings demonstrate that the larval degradation of antibiotic contaminants is an efficient method based on abundant TRGs in the larval gut, even though OTC degradation results in OBR. In addition, a more optimized system for higher reductions in antibiotic levels and the expansion of larval bioremediation to other fields is necessary.

[Seasonal variation of distribution and removal of high-risk tetracycline resistance genes in constructed wetland.]

Livestock wastewater is an important reservoir of antibiotic resistance genes (ARGs), with high environmental risks. We investigated the seasonal variations of distribution and removal of swine wastewater originated high-risk tetracycline resistance genes (TRGs) in horizontal subsurface flow constructed wetlands. The effects of exogenous addition of tetracycline (TC) and copper ion (Cu²⁺) on the abundance of TRGs in effluent with single and combined pollution of antibiotic and heavy metal were studied. The results showed that all the three high-risk TRGs (tetM, tetO and tetW) were detected in swine wastewater. Wetlands could effectively reduce the ARGs, with the absolute abundance of TRGs in effluent being decreased by 1.1-2.4 and 1.7-2.9 orders of magnitude in summer and winter compared with the influent, respectively. The abundance of TRGs in wetland soils showed the characte-ristics that the outflow side was lower than the inflow side, the non-rhizosphere area was lower than the rhizosphere area, and lower in winter than in summer. In summer and winter, single and combined pollution of TC and Cu²⁺ in swine wastewater would increase the abundance of TRGs in effluent compared with that in the control. The constructed wetland is suitable for controlling the environmental diffusion of ARGs in livestock wastewater.

Profiles of tetracycline resistance genes in paddy soils with three different organic fertilizer applications

The rapid expansion of organic rice cultivation areas have been accompanied by increased application of organic fertilizers. The high prevalence of soil antibiotic resistance caused by organic fertilizer application poses a severe threat to the agricultural and soil ecosystems. To date, research efforts and understanding of the effects and mechanism of action of the various organic fertilizers on antibiotic resistance in paddy soils remain poorly investigated. Tetracycline resistance genes (TRGs, including tetB, tetC, tetL, tetZ, tetM, tetO, tetT, and tetX), class 1 integron-integrase gene (intI1) and bacterial communities were characterized using quantitative-PCR and Illumina MiSeq sequencing, in paddy soils exposed to inorganic fertilizer (NPK), animal-derived organic fertilizer (AOF, composted swine and/or chicken manure), plant-derived organic fertilizer (POF, rapeseed cake and/or astragalus) and commercial organic fertilizer (COF, composted of animal manure mix with crop residues) applications. Compared with NPK, AOF applications significantly increased the relative abundance of TRGs, which was predominantly expressed in the increase of the relative abundance of tetC, tetM, tetO, tetT, and tetX, while POF and COF had no significant effect on the relative abundance of TRGs. Principal coordinate analysis revealed that AOF and POF significantly altered bacterial communities in paddy soils relative to NPK, while COF had no significant change of bacterial communities. Variation partitioning analysis indicated that soil physicochemical properties were the decisive factors for the changes of TRGs in organic paddy fields. Furthermore, redundancy analysis and the Mantel test showed that TRG profiles in AOF applied paddy soils were strongly influenced by electrical conductivity (EC). Total nitrogen (TN) and organic matter (OM) affected the distribution of TRGs in COF and POF applied paddy soils through a different mechanism. This study provides insights into the impacts of different types of organic fertilizer on the profiles of TRGs in paddy soils.

The Dual Roles of Nano Zero-Valent Iron and Zinc Oxide in Antibiotics Resistance Genes (ARGs) SPREAD in Sediment

Nanoparticles (NPs) are widely used and ubiquitous in the environment, but the consequences of their release into the environment on antibiotics resistance genes (ARGs), microbial abundance, and community, are largely unknown. Therefore, this study examined the effect of nano zero-valent iron (nZVI) and zinc oxide (nZnO) on tetracycline resistance genes (tet-ARGs) and class 1 integron (intI1) in sediment under laboratory incubation. The coexistence of NPs and tetracycline (TC) on tet-ARGs/intI1 was also investigated. It was found that nZVI and nZnO promoted tet-ARGs/intI1 abundance in sediment without TC but reduced the inducing effect of TC on tet-ARGs/intI1 in sediment overlaid with TC solution. Without TC, nZVI, intI1, and the bacterial community could directly promote tet-ARGs spread in nZVI sediment, while intI1 and bacterial abundance were the most directly important reasons for tet-ARGs spread in nZnO sediment. With TC, nZVI and bacterial community could reduce tet-ARGs abundance in nZVI sediment, while nZnO and bacterial community could directly promote tet-ARGs in nZnO sediment. Finally, these findings provided valuable information for understanding the role of NPs in promoting and reducing ARGs in the environment.

The Impact of Lateral Gene Transfer in Chlamydia

Lateral gene transfer (LGT) facilitates many processes in bacterial ecology and pathogenesis, especially regarding pathogen evolution and the spread of antibiotic resistance across species. The obligate intracellular chlamydiae, which cause a range of diseases in humans and animals, were historically thought to be highly deficient in this process. However, research over the past few decades has demonstrated that this was not the case. The first reports of homologous recombination in the Chlamydiaceae family were published in the early 1990s. Later, the advent of whole-genome sequencing uncovered clear evidence for LGT in the evolution of the Chlamydiaceae, although the acquisition of tetracycline resistance in Chlamydia (C.) suis is the only recent instance of interphylum LGT. In contrast, genome and in vitro studies have shown that intraspecies DNA exchange occurs frequently and can even cross species barriers between closely related chlamydiae, such as between C. trachomatis, C. muridarum, and C. suis. Additionally, whole-genome analysis led to the identification of various DNA repair and recombination systems in C. trachomatis, but the exact machinery of DNA uptake and homologous recombination in the chlamydiae has yet to be fully elucidated. Here, we reviewed the current state of knowledge concerning LGT in Chlamydia by focusing on the effect of homologous recombination on the chlamydial genome, the recombination machinery, and its potential as a genetic tool for Chlamydia.

Effects of different oxygen conditions on pollutants removal and the abundances of tetracycline resistance genes in activated sludge systems

The individual and combined effects of tetracycline (TC) and divalent copper (Cu²⁺) on the performance of activated sludge systems and the abundances of tetracycline resistance genes (TRGs) in activated sludge, under both aerobic and anaerobic conditions, were studied. Activated sludge systems received TC (0.2 mg L^-1) and Cu²⁺ (5 mg L^-1) separately or jointly under either aerobic or anaerobic conditions. The addition of TC did not affect the performance of activated sludge systems and the addition of Cu²⁺ and mixed TC/Cu²⁺ inhibited biological phosphorus removal. The TC removal efficiencies in systems under aerobic and anaerobic conditions were 98.4%-99.7% and 96.8%-99.9%, respectively, and Cu²⁺ promoted TC removal in activated sludge systems. The TC degradation product was 4-epitetracycline (ETC) in activated sludge systems under both aerobic and anaerobic conditions. The total relative abundances of TRGs (tetA, tetC, tetE, tetM, tetO, tetW, tetX and tetB(P)) in activated sludge showed opposite development trends under the two oxygen conditions and aerobic condition was beneficial to the attenuation of high-risk TRGs. The results of this study might improve evaluation of the combined effects of antibiotics and heavy metals on wastewater biological treatment systems.

Comprehensive Genomic Investigation of Tigecycline Resistance Gene tet(X4)-Bearing Strains Expanding among Different Settings

The emergence of plasmid-mediated tigecycline resistance genes has attracted a great deal of attention globally. Currently, no comprehensive in-depth genomic epidemiology study of tet(X4)-bearing pathogens present of pork origin as the One Health approach has been performed. Herein, 139 fresh pork samples were collected from multiple regions in China and 58 tet(X4)-positive strains were identified. The tet(X4) gene mainly distributed in Escherichia coli (n = 55). Besides, 4 novel tet(X4)-positive bacterial species Klebsiella pneumoniae (n = 2), Klebsiella quasipneumoniae (n = 1), Citrobacter braakii (n = 1) and Citrobacter freundii (n = 1) were first characterized here. Four different core tet(X4)-bearing genetic environments and five types of tet(X4)-bearing tandem duplications were discovered among 58 strains. The results of the phylogenetic tree showed that there was some correlation between E. coli strains from pork, human, pig farms, and slaughterhouses. A total of seven types of plasmid replicons were found in tet(X4)-positive plasmids, among which multireplicon plasmids were observed. Notably, two tet(X4)-positive fusion plasmids pCSZ11R (IncX1-IncFIA-IncFIB-IncFIC) and pCSX5G-tetX4 (IncX1-IncFII-IncFIA) were formed by IS26 in the hot spot. Besides, six samples were identified to harbor two different tet(X4)-bearing strains. More interestingly, the absolute quantitative results showed that the expression levels of tet(X4) between different strains with different tet(X4) copies were approximate. In this study, the genetic environment of tet(X4)-positive plasmids containing different plasmid replicons was analyzed to provide a basis for the further development of effective control measures. It is also highlighted that animal-borne tet(X4)-bearing pathogens incur a transmission risk to consumed food. Therefore, there is an urgent need for large-scale monitoring as well as the development of effective control measures. IMPORTANCE Tigecycline was considered the last-line drug against serious infections caused by multidrug-resistant Gram-negative bacteria. However, the plasmid-mediated tigecycline resistance gene tet(X) has been widely reported in different sources of Enterobacterales and Acinetobacter in China. China is one of the largest pig-producing nations in the world, and in-depth investigation of gene in pork is vital to figure out the fundamental dissemination of these genes and set up a reasonable control framework. In this study, we conducted an in-depth and systematic analysis of the diversity of tet(X4)-positive plasmids and the genetic environment of tet(X4) contained in pork samples from multiple regions of China, providing a basis for further development of effective control measures. It is also highlighted that animal-borne tet(X4)-bearing pathogens incur a transmission risk to consumed food. Therefore, there is an urgent need for large-scale monitoring as well as the development of effective control measures.

Zero valent iron improved methane production and specifically reduced aminoglycoside and tetracycline resistance genes in anaerobic digestion

It is unadvisable to discuss the antibiotic resistance genes (ARGs) reduction in anaerobic digestion (AD) system neglecting its main purpose-methane production. The methane production improvement coupling with antibiotic resistance genes (ARGs) reduction in anaerobic digestion (AD) by zero valent iron (ZVI) were simultaneously investigated. Whether the role of ZVI on the ARGs fate was random or specific was clarified through the high-throughput qPCR (HT-qPCR). Results indicated that ZVI improved methane production and ARGs reduction by 23.9% and 25.0%, respectively. The improved methane production was associated with chemical reaction and variances of microbial community caused by ZVI, where DIET between Petrimonas, Clostridium and Syntrophomonas, Methanosarcina was established along with ACAS being enriched. ZVI specifically, not randomly, facilitated the reduction of aminoglycoside resistance genes of antibiotic inactivation and tetracycline resistance genes of ribosomal protection proteins. The specifical reduction could be attributed to enzyme activity inhibition and intracellular ionic disturbance caused by higher amounts of ZVI, although most of ARGs fate could be well explained by microbial community which contributed the most to ARGs dynamics as a whole. ZVI-based AD was a promising way for the improvement of methane production coupling ARGs reduction.

Abiotic mechanism changing tetracycline resistance in root mucus layer of floating plant: The role of antibiotic-exudate complexation

Antibiotic contamination and antibiotic resistance have caused growing concerns in different aquatic environments. This work investigated the complexation between tetracycline chloride (TCH) and the molecular weight (MW)-fractionated root exudates - the key abiotic mechanism impacting antibiotic fate and antibiotic resistance in rhizosphere. Results show that the affinity of TCH to the high MW exudates (≥10 kDa) facilitated the TCH deposition on roots and meanwhile reinforced the expression of certain tetracycline resistance genes (i.e. tetA) and the growth of tetracycline resistant bacteria. The interaction between TCH and the lower MW exudates (<10 kDa) completely inhibited the bacteria growth even below the minimum inhibitory concentration of TCH. In microcosms, the abiotic interaction between TCH and root exudates made effects along with biotic processes. Persistent TCH stimulation (≥50 µg/L, 7 d) induced the change of tet gene abundance and bacteria phyla composition though the mediation of root exudates made the rhizosphere less sensitive to the TCH stress. Summarily, the affinity of antibiotics to root exudates varied with MWs, which was closely related to (i) the antibiotic fate in the root mucus layer, (ii) the bacteria inhibition capacity of antibiotics, and (iii) the antibiotic resistance and bacterial community.

Chlamydia suis and tetracycline resistance genes un Italian wild boar (Sus scrofa)

The aim of this study was to investigate the occurrence of Chlamydia suis and tetracycline resistance determinants in conjunctival swabs of Italian wild boars, by PCR. Extracted DNA collected from 50 wild boars from Northern and Central Italy was examined by molecular methods. One sample (2%) from the Central Italy was positive for C. suis. Fragments of tetR(C) and tetR(C)-tet(C) resistance determinants were amplified from the same sample. Further molecular investigations suggested the attribution of these tetracycline resistance determinants to C. suis, such as the truncation oftetR(C) and absence of a intact invasion (inv)-like region. While tetracycline-resistant C. suis is very common in domestic pigs, its occurrence has not been reported in wild boar before. Wild boar might acquire tetracycline resistance determinants through direct or indirect contact with domestic pigs.

Significant effect of pH on tetracycline resistance genes reduction during sludge thermal hydrolysis treatment

Thermal hydrolysis (TH) treatment has been verified to effectively reduce antibiotic resistance genes (ARGs) in waste activated sludge. This study focused on the effect of TH parameters on ARGs reduction, and the optimal conditions basing on tetracycline (tet) resistance genes reduction rate in sludge phase were pH 3, temperature 160 °C and reaction time 2 h. The pH was found to play a critical role in tet genes reduction behavior. Additionally, the tet genes distributions in TH supernatant are considered as well because genes will release from solid to liquid phase as sludge cell breaking. The lowest genes content in TH supernatant was also observed at pH 3. Further investigation revealed that contents of DNA and organics released from sludge phase to liquid phase under pH 3 were less than that in neutral and alkaline condition; moreover, the organics in TH supernatant was found to protect DNA. Therefore, under the acidic condition, the genes had less releasing from the sludge phase and the DNA protection effect of organics was weaker, resulting in the lowest tet genes content in TH supernatant. Moreover, bacterial community structure after TH was closely related with the ARGs content. The bacterial on phylum and genus level showed various responses to TH pH values. Although the Firmicutes phylum and Escherichia-Shigella genus exhibited the stronger resistance and had higher accumulation in TH acidic condition, more possible total tet genes hosts were destroyed in acidic condition, causing less ARGs remaining in the sludge phase under pH 3.

Synergistic impacts of Cu2+ on simultaneous removal of tetracycline and tetracycline resistance genes by PSF/TPU/UiO forward osmosis membrane

Cu²⁺, tetracycline (TC), and corresponding tetracycline resistance genes (TRGs) are common micropollutants in aquaculture wastewater, which have great impact on environment and human health. In this study, we developed a thin-film nanocomposite (TFN) forward osmosis (FO) membrane with an electrospinning thermoplastic polyurethane/polysulfone (PSF/TPU) substrate and a UiO-66-NH₂ particle interlayer modified active layer. The effects of Cu²⁺ concentration on the synergetic removal of TC and TRGs (e.g., tetA/M/X/O/C, int1, and 16 S rRNA gene) were analyzed to determine the role of Cu²⁺ in FO process. The rejection mechanism was also analyzed in depth. Results demonstrated that the rejection of TC and Cu²⁺ was 99.53% and 97.99%. The rejection of TRGs exceeded 90% (specifically, over 99% for tetC) at a Cu²⁺ concentration of 500 μg/L when 0.5 M (NH₄)₂HPO₄ was used as draw solution. Complexation reaction between Cu²⁺ and TC, electrostatic interaction, and the adsorption of Cu²⁺ on membrane surface were the main contributing factors for the high rejection efficiencies. Altogether, the as-prepared FO membrane holds great potential for simultaneously removing heavy metals, antibiotics, and resistance genes in real wastewater.

Complete Genome Sequencing of Acinetobacter baumannii AC1633 and Acinetobacter nosocomialis AC1530 Unveils a Large Multidrug-Resistant Plasmid Encoding the NDM-1 and OXA-58 Carbapenemases

Carbapenem-resistant Acinetobacter spp. are considered priority drug-resistant human-pathogenic bacteria. The genomes of two carbapenem-resistant Acinetobacter spp. clinical isolates obtained from the same tertiary hospital in Terengganu, Malaysia, namely, A. baumannii AC1633 and A. nosocomialis AC1530, were sequenced. Both isolates were found to harbor the carbapenemase genes blaNDM-1 and blaOXA-58 in a large (ca. 170 kb) plasmid designated pAC1633-1 and pAC1530, respectively, that also encodes genes that confer resistance to aminoglycosides, sulfonamides, and macrolides. The two plasmids were almost identical except for the insertion of ISAba11 and an IS4 family element in pAC1633-1, and ISAba11 along with relBE toxin-antitoxin genes flanked by inversely orientated pdif (XerC/XerD) recombination sites in pAC1530. The blaNDM-1 gene was encoded in a Tn125 composite transposon structure flanked by ISAba125, whereas blaOXA-58 was flanked by ISAba11 and ISAba3 downstream and a partial ISAba3 element upstream within a pdif module. The presence of conjugative genes in plasmids pAC1633-1/pAC1530 and their discovery in two distinct species of Acinetobacter from the same hospital are suggestive of conjugative transfer, but mating experiments failed to demonstrate transmissibility under standard laboratory conditions. Comparative sequence analysis strongly inferred that pAC1633-1/pAC1530 was derived from two separate plasmids in an IS1006-mediated recombination or transposition event. A. baumannii AC1633 also harbored three other plasmids designated pAC1633-2, pAC1633-3, and pAC1633-4. Both pAC1633-3 and pAC1633-4 are cryptic plasmids, whereas pAC1633-2 is a 12,651-bp plasmid of the GR8/GR23 Rep3-superfamily group that encodes the tetA(39) tetracycline resistance determinant in a pdif module.IMPORTANCE Bacteria of the genus Acinetobacter are important hospital-acquired pathogens, with carbapenem-resistant A. baumannii listed by the World Health Organization as the one of the top priority pathogens. Whole-genome sequencing of carbapenem-resistant A. baumannii AC1633 and A. nosocomialis AC1530, which were isolated from the main tertiary hospital in Terengganu, Malaysia, led to the discovery of a large, ca. 170-kb plasmid that harbored genes encoding the New Delhi metallo-β-lactamase-1 (NDM-1) and OXA-58 carbapenemases alongside genes that conferred resistance to aminoglycosides, macrolides, and sulfonamides. The plasmid was a patchwork of multiple mobile genetic elements and comparative sequence analysis indicated that it may have been derived from two separate plasmids through an IS1006-mediated recombination or transposition event. The presence of such a potentially transmissible plasmid encoding resistance to multiple antimicrobials warrants vigilance, as its spread to susceptible strains would lead to increasing incidences of antimicrobial resistance.

A fast and robust iterative genome-editing method based on a Rock-Paper-Scissors strategy

The production of optimized strains of a specific phenotype requires the construction and testing of a large number of genome modifications and combinations thereof. Most bacterial iterative genome-editing methods include essential steps to eliminate selection markers, or to cure plasmids. Additionally, the presence of escapers leads to time-consuming separate single clone picking and subsequent cultivation steps. Herein, we report a genome-editing method based on a Rock-Paper-Scissors (RPS) strategy. Each of three constructed sgRNA plasmids can cure, or be cured by, the other two plasmids in the system; plasmids from a previous round of editing can be cured while the current round of editing takes place. Due to the enhanced curing efficiency and embedded double check mechanism, separate steps for plasmid curing or confirmation are not necessary, and only two times of cultivation are needed per genome-editing round. This method was successfully demonstrated in Escherichia coli and Klebsiella pneumoniae with both gene deletions and replacements. To the best of our knowledge, this is the fastest and most robust iterative genome-editing method, with the least times of cultivation decreasing the possibilities of spontaneous genome mutations.

Harnessing efficient multiplex PCR methods to detect the expanding Tet(X) family of tigecycline resistance genes

A growing number of tet(X)-type tigecycline resistance determinants [tet(X1) to tet(X5)] constitutes an expanding family of tetracycline-inactivating enzymes, posing a potential risk to global public health. Here, we report the development of an efficient multiplex PCR method to detect the family of tet(X) variants. This method is successfully applied in the screen and validation of tet(X) genes in the field and clinic bacterial samples. In addition, we found that the formerly proposed tet(X1) is a premature truncated version by the inappropriate annotation, and fixed this error. Overall, it might be the first genetic tool for the detection of different Tet(X) members.

Comprehensive screening of genomic and metagenomic data reveals a large diversity of tetracycline resistance genes

Tetracyclines are broad-spectrum antibiotics used to prevent or treat a variety of bacterial infections. Resistance is often mediated through mobile resistance genes, which encode one of the three main mechanisms: active efflux, ribosomal target protection or enzymatic degradation. In the last few decades, a large number of new tetracycline-resistance genes have been discovered in clinical settings. These genes are hypothesized to originate from environmental and commensal bacteria, but the diversity of tetracycline-resistance determinants that have not yet been mobilized into pathogens is unknown. In this study, we aimed to characterize the potential tetracycline resistome by screening genomic and metagenomic data for novel resistance genes. By using probabilistic models, we predicted 1254 unique putative tetracycline resistance genes, representing 195 gene families (<70 % amino acid sequence identity), whereof 164 families had not been described previously. Out of 17 predicted genes selected for experimental verification, 7 induced a resistance phenotype in an Escherichia coli host. Several of the predicted genes were located on mobile genetic elements or in regions that indicated mobility, suggesting that they easily can be shared between bacteria. Furthermore, phylogenetic analysis indicated several events of horizontal gene transfer between bacterial phyla. Our results also suggested that acquired efflux pumps originate from proteobacterial species, while ribosomal protection genes have been mobilized from Firmicutes and Actinobacteria. This study significantly expands the knowledge of known and putatively novel tetracycline resistance genes, their mobility and evolutionary history. The study also provides insights into the unknown resistome and genes that may be encountered in clinical settings in the future.

Plasmid mediated penicillin and tetracycline resistance among Neisseria gonorrhoeae isolates from Kenya

BACKGROUND

Treatment of gonorrhea is complicated by the development of antimicrobial resistance in Neisseria gonorrhoeae (GC) to the antibiotics recommended for treatment. Knowledge on types of plasmids and the antibiotic resistance genes they harbor is useful in monitoring the emergence and spread of bacterial antibiotic resistance. In Kenya, studies on gonococcal antimicrobial resistance are few and data on plasmid mediated drug resistance is limited. The present study characterizes plasmid mediated resistance in N. gonorrhoeae isolates recovered from Kenya between 2013 and 2018.

METHODS

DNA was extracted from 36 sub-cultured GC isolates exhibiting varying drug resistance profiles. Whole genome sequencing was done on Illumina MiSeq platform and reads assembled de-novo using CLC Genomics Workbench. Genome annotation was performed using Rapid Annotation Subsystem Technology. Comparisons in identified antimicrobial resistance determinants were done using Bioedit sequence alignment editor.

RESULTS

Twenty-four (66.7%) isolates had both β-lactamase (TEM) and TetM encoding plasmids. 8.3% of the isolates lacked both TEM and TetM plasmids and had intermediate to susceptible penicillin and tetracycline MICs. Twenty-six (72%) isolates harbored TEM encoding plasmids. 25 of the TEM plasmids were of African type while one was an Asian type. Of the 36 isolates, 31 (86.1%) had TetM encoding plasmids, 30 of which harbored American TetM, whereas 1 carried a Dutch TetM. All analyzed isolates had non-mosaic penA alleles. All the isolates expressing TetM were tetracycline resistant (MIC> 1 mg/L) and had increased doxycycline MICs (up to 96 mg/L). All the isolates had S10 ribosomal protein V57M amino acid substitution associated with tetracycline resistance. No relation was observed between PenB and MtrR alterations and penicillin and tetracycline MICs.

CONCLUSION

High-level gonococcal penicillin and tetracycline resistance in the sampled Kenyan regions was found to be mediated by plasmid borne blaTEM and tetM genes. While the African TEM plasmid, TEM1 and American TetM are the dominant genotypes, Asian TEM plasmid, a new TEM239 and Dutch TetM have emerged in the regions.

Tetracycline resistance in Moraxella catarrhalis clinical strains isolated in Poland

Moraxella catarrhalis is considered an important, exclusively human respiratory tract pathogen which, along with Streptococcus pneumoniae and Haemophilus influenzae, is classified as one of the most frequent bacterial etiological factors causing upper respiratory tract infections. In this manuscript, we report the existence of five tetracycline-resistant M. catarrhalis strains with confirmed presence of tetracycline resistance tetB gene. The strains were isolated from children under the age of three with signs of upper respiratory tract infections. Our research also investigated the occurrence of virulence genes in these strains and involved the analysis of drug resistance to five antibiotic groups. It is the first description of clinical strains with confirmed presence of drug resistance tetB genes isolated in Europe.

Escherichia coli as a carrier of tetracyclines and penicillins resistance in wild pheasant (Phasianus colchicus)

Wild animals like pheasant seem to be a good source of information about human activities. Therefore, the wild pheasants and relative stable appendix microcenosis were selected for antibiotic resistance testing. Penicillin resistance by MALDI-TOF Mass Spectrometry and tetracyclines resistance by genetic methods using specific primers were tested. Differences between tetracycline and penicillin resistance were detected. Results showed high prevalence of resistant Escherichia coli isolated from wild pheasant appendix. E. coli isolated from wild pheasant appendix carried plasmids for penicillins and tetracyclines resistance where they were responsible for enzymatic degradation of penicillin and carried genes for regulating efflux pumps for tetracyclines. Results showed that tetracyclines and penicillins resistance is widespread between wild pheasants with a carrier as Escherichia coli isolated from relative stable microcenosis of appendix.

Spread of chloramphenicol and tetracycline resistance genes by plasmid mobilization in agricultural soil

Spread of antibiotic resistance genes (ARGs) poses a worldwide threat to public health and food safety. However, ARG spread by plasmid mobilization, a broad host range transfer system, in agricultural soil has received little attention. Here, we investigated the spread of chloramphenicol resistance gene (CRG) and tetracycline resistance gene (TRG) in agricultural soil by mobilization of pSUP106 under different conditions, including different concentrations of nutrients, temperatures, soil depths, rhizosphere soils, and soil types. The number of resistant bacteria isolated in non-sterilized soil from the experiments was approximately 10⁴ to 10⁷ per gram of soil, belonging to 5-10 species from four genera, including nonpathogen, opportunistic pathogen, pathogen bacteria, and gram-positive and gram-negative bacteria, depending on the experiment conditions. In sterilized soil, higher levels of nutrients and higher temperatures promoted plasmid mobilization and ARG expression. Topsoil and deep soil might not support the spread of antibiotic resistance, while ARG dissemination by plasmid mobilization was better supported by maize rhizosphere and loam soils. All these factors might change bacterial growth and the activity of bacteria and lead to the above influence. Introduction of only the donor and helper, or the donor alone also resulted in the transfer of ARGs and large numbers of antibiotic resistant bacteria (ARB), indicating that some indigenous bacteria contain the elements necessary for plasmid mobilization. Our results showed that plasmid mobilization facilitated dissemination of ARGs and ARB in soil, which led to the disturbance of indigenous bacterial communities. It is important to clear ARG dissemination routes and inhibit the spread of ARGs.

Co-occurrence of Plasmid-Mediated Tigecycline and Carbapenem Resistance in Acinetobacter spp. from Waterfowls and Their Neighboring Environment

Tigecycline serves as one of the antibiotics of last resort to treat multidrug-resistant (including carbapenem-resistant) pathogens. However, the recently emerged plasmid-mediated tigecycline resistance mechanism, Tet(X), challenges the clinical efficacy of this class of antibiotics. In this study, we detected 180 tet(X)-harboring Acinetobacter isolates (8.9%, n = 180) from 2,018 samples collected from avian farms and adjacent environments in China. Eighteen tet(X)-harboring isolates (10.0%) were found to cocarry the carbapenemase gene blaNDM-1, mostly from waterfowl samples (94.4%, 17/18). Interestingly, among six Acinetobacter strains, tet(X) and blaNDM-1 were found to colocalize on the same plasmids. Moreover, whole-genome sequencing (WGS) revealed a novel orthologue of tet(X) in the six isolates coharboring tet(X) and blaNDM-1 Inverse PCR suggested that the two tet(X) genes form a single transposable unit and may be cotransferred. Sequence comparison between six tet(X)- and blaNDM-1-coharboring plasmids showed that they shared a highly homologous plasmid backbone even though they were isolated from different Acinetobacter species (three from Acinetobacter indicus, two from Acinetobacter schindleri, and one from Acinetobacter lwoffii) from various sources and from different geological regions, suggesting the horizontal genetic transfer of a common tet(X)- and blaNDM-1-coharboring plasmid among Acinetobacter species in China. Emergence and spread of such plasmids and strains are of great clinical concern, and measures must be implemented to avoid their dissemination.

Ultrasonic coupled bioleaching pretreatment for enhancing sewage sludge dewatering: Simultaneously mitigating antibiotic resistant genes and changing microbial communities

In this study, ultrasonic as a pretreatment coupled with bioleaching was used to enhance sludge dewaterability. Changes in microbial diversity and antibiotic resistant genes (ARGs) were studied during the combined treatment process. The results show that under optimal conditions, combined ultrasonic and bioleaching treatment led to decreases in the specific resistance of filtration and bioleaching time by 7.59% and 12.5%, respectively, compared with single bioleaching process. Using high pressure filtration system, the water content of sludge cake treated by the combined treatment was decreased to 58.04%, which was 10.04% lower than bioleaching sludge. After combined treatment, the microbial diversity and the total number of bacteria in the sludge decreased significantly, which caused the decreases in the absolute abundance of sulfonamide and tetracycline ARGs by 1.56-1.58 and 0.34-1.23 log units, respectively. However, the decrease in the total bacterial biomass was greater than the decrease in the number of potential hosts carrying the tetracycline ARG, resulting in an increase in the relative abundance of tetracycline gene. Furthermore, this study proposed a mechanism of the dewatering and ARGs, involving the combined ultrasonic and bioleaching treatment: Firstly, ultrasonic cavitation causes extracellular polymeric substances (EPS) to fall off the surface of sludge; Secondly, this faster and directly makes bacteria cells affected by bio-acidification and bio-oxidation. In this case, the cells could be more easily destroyed by the combined ultrasonic and bioleaching treatment, compared with individual bioleaching treatment; As a result, stronger dewaterability and more removal rates of ARGs were achieved under the combined treatment. The economic analyses showed that the combined ultrasonic and bioleaching treatment is a more practical and economical technique for achieving deep dewatering of sludge.

Investigation of antimicrobial resistance and virulence genes of Campylobacter isolates from patients in a tertiary hospital in Edirne, Turkey

Purpose

Campylobacter is one of the most common pathogens that cause food-borne infections worldwide. The aim of this study was to determine the antimicrobial resistance rates and the presence of multiple virulence genes in Campylobacter isolates obtained from humans.

Materials and Methods

In this study, 71 Campylobacter isolates obtained from human faecal samples were used. Antimicrobial susceptibility tests were performed through the gradient strip method. The presence of virulence genes was investigated by monoplex and multiplex polymerase chain reaction.

Results

The rate of resistance of the 66 Campylobacter jejuni isolates was 12.1% for erythromycin, 40.9% for tetracycline and 68.2% for ciprofloxacin. Only one of five Campylobacter coli isolates was resistant to these three antimicrobial agents. The flaB, pldA, cdtA, cadF, cdtC and ceuE genes were found in all 66 of the C. jejuni isolates. In the C. jejuni isolates, positivity rates of 92.4% for flaA, 96.7% for cdtB, 98.5% for ciaB, 90.9% for dnaJ and 96.7% for racR were observed. The flaA, flaB, ciaB, cdtA and cdtC genes were present in all C. coli isolates.

Conclusions

It was detected that there is an increase in antimicrobial resistance of Campylobacter strains in our region, and most of the isolates harbour virulence genes.

Characterization of tetracycline effects on microbial community, antibiotic resistance genes and antibiotic resistance of Aeromonas spp. in gut of goldfish Carassius auratus Linnaeus

The gut of aquatic animals was a significant niche for dissemination of antibiotic resistance genes (ARGs) and direct response of living conditions. In this study, the gut microbiota of goldfish Carassius auratus Linnaeus was sampled at 7 days and 21 days after treatment with tetracycline at 0.285 and 2.85 μg L^-1 to investigate the influences on the microbial structure and antibiotic resistance. The proportion of tetracycline resistance bacteria was 1.02% in the control group, while increased to 23.00%, 38.43%, 62.05% in groups of high concentration for 7 days (H7), low concentration for 21 days (L21) and high concentration for 21 days (H21), respectively. Compared to the control group, the diversity of isolated Aeromonas spp. was decreased in the treatment groups and the minimal inhibitory concentration (MIC) of resistant isolates was enhanced from 32 to 256 μg mL^-1 with the treatment of tetracycline in time- and dose-dependent manners. Furthermore, the abundance of most genes was increased in treatment groups and efflux genes mainly responded to the stress of tetracycline with an average level of 1.0 × 10^-2. After treatment with tetracycline, the predominant species were changed both at phylum and genus levels. The present study explored the impact of tetracycline on gut microbiota of goldfish at environmentally realistic concentrations for the first time and our findings will provide a reference for characterizing the microbiome of fish in the natural environment.

Heterologous expression of the tetracycline resistance gene tetX to enhance degradability and safety in doxycycline degradation

Microbial remediation has the potential to inexpensively yet effectively decontaminate and restore contaminated environments, but the virulence of pathogens and risk of resistance gene transmission by microorganisms during antibiotic removal often limit its implementation. Here, a cloned tetX gene with clear evolutionary history was expressed to explore doxycycline (DOX) degradation and resistance variation during the degradation process. Phylogenetic analysis of tetX genes showed high similarity with those of pathogenic bacteria, such as Riemerella sp. and Acinetobacter sp. Successful tetX expression was performed in Escherichia coli and confirmed by SDS-PAGE and Western blot. Our results showed that 95.0 ± 1.0% of the DOX (50 mg/L) was degraded by the recombinant strain (ETD-1 with tetX) within 48 h, which was significantly higher than that for the control (38.9 ± 8.7%) and the empty plasmid bacteria (8.8 ± 5.1%) (P < 0.05). The tetX gene products in ETD-1 cell extracts also exhibited an efficient DOX degradation ability, with a degradation rate of 80.5 ± 1.2% at 168 h. Furthermore, there was no significant proliferation of the tetX resistance gene during DOX degradation (P > 0.05). The efficient and safe DOX-degrading capacity of the recombinant strain ETD-1 makes it valuable and promising for antibiotic removal in the environment.

Higher normalized concentrations of tetracycline resistance found in ballast and harbor water compared to ocean water

Although ballast water is a known vector for the global transport of microorganisms, the Ballast Water Management Convention only sets limits for indicator organisms and does not consider antibiotic resistance genes (ARGs). Herein, we examined the concentration of indicator organisms and prevalence of three ARGs (sul1, tet (M), and vanA) in a total of 53 ballast, 21 harbor, and 8 ocean samples collected in Singapore, China, South Africa, and California. E. coli was found in significantly higher concentrations in ballast samples obtained in Singapore and China compared to South Africa (Singapore, p = 0.040) and California (Singapore, p < 0.001; China, p = 0.038). Harbor samples from China had significantly higher concentrations of E. coli than Singapore (p = 0.049) and California (p = 0.001). When compared to ocean samples, there were significantly higher concentrations of normalized tet(M) in ballast samples from California (p = 0.011) and Singapore (p = 0.019) and in harbor samples from California (p = 0.018), Singapore (p = 0.010), and South Africa (p = 0.008). These findings suggest that microbial loads significantly differ among ports. Furthermore, certain ARGs are enriched in ballast and harbor waters when compared to ocean water, which suggests that ballast waters have the potential to either transport higher concentrations of certain ARGs or that ballast tank conditions may exert selective pressure for some ARGs.

Detection of Tetracycline Resistance Genes in European Hedgehogs (Erinaceus europaeus) and Crested Porcupines (Hystrix cristata)

Relatively little is known regarding the role of wildlife in the development of antibiotic resistance. Our aim was to assess the presence of the tetracycline resistance genes, tet(A), tet(B), tet(C), tet(D), tet(E), tet(G), tet(K), tet(L), tet(M), tet(O), tet(P), tet(Q), tet(S), and tet(X), in tissue samples of 14 hedgehogs (Erinaceus europaeus) and 15 crested porcupines (Hystrix cristata) using PCR assays. One or more tet genes were found in all but three hedgehogs and one crested porcupine. Of the 14 tetracycline resistance genes investigated, 13 were found in at least one sample; tet(G) was not detected. We confirmed the potential role of wild animals as bioindicators, reservoirs, or vectors of antibiotic-resistant bacteria in the environment.

Hysterical tetracycline in intensive poultry farms accountable for substantial gene resistance, health and ecological risk in Egypt- manure and fish

Although the poultry production sector plays a key role in sustaining the majority of animal protein demand in Egypt, the deleterious effects of widespread antibiotic resistance on health and environment are currently not well recognized. Litter and dropping samples from broiler and layer poultry farms as well as, tilapia samples from the Nile River and aquaculture farms were collected from Upper Egypt. Samples were extracted and examined for tetracycline residues [tetracycline (TC), chlortetracycline (CTC), oxytetracycline (OTC) and doxycycline (DC)] using HPLC. In addition, tetracycline resistance genes [tet (M), tet (W), tet (Q) and tet (G)] were screened from pooled intestinal contents collected from twelve broiler farms in Upper Egypt. The antibiotic resistance genes results revealed that tet (W) was confirmed to be expressed in all intestinal samples. In contrast, tet (Q) and tet (M) were detected only in 42% and 17% of the samples, respectively. CTC and OTC were the antimicrobial compounds with the highest concentrations in poultry litter and droppings, with concentrations of 6.05 and 2.47 μg g^-1 (CTC) and 5.9 and 1.33 μg g^-1 (OTC), respectively. However, the concentrations of DC were significantly higher than those of the other compounds in both aquaculture and Nile River tilapia. The tetracycline residue levels in aquaculture tilapia were significantly higher than those in Nile River tilapia. The hazard quotients (HQs) exceeded 1 for OTC, CTC and DC, which highlights the great risk of using broiler litter to fertilize agricultural land. Moreover, the presence of DC and CTC indicates that consumption of aquaculture tilapia poses a considerable health risk. Therefore, poultry litter or droppings containing tetracycline residues and tet resistance determinants used for aquaculture or as farmland fertilizers could be major sources of antibiotic resistance in fish, humans and environment.

The effects of tetracycline concentrations on tetracycline resistance genes and their bacterial hosts in the gut passages of earthworms (Eisenia fetida) feeding on domestic sludge

Vermi-composting is considered to be a feasible method for reducing tetracycline resistance genes (TRGs) in the sludge. Nevertheless, the way different gut passages of earthworm might affect the fates of TRGs and whether this process is affected by tetracycline (TC) concentrations need to be further investigated. In this study, we examined the effects of TC concentrations on changes in TRGs and bacterial communities in gut passages of earthworm were determined by using quantitative PCR and Illumina high-throughput sequencing. TRGs and intI1 were mainly reduced in the hindgut under the TC concentrations ranging from 0 to 25 mg/kg, while they were enriched under higher TC stress exposure. Consequently, we suggest the TC limitation of 25 mg/kg in the domestic sludge (DS) for vermi-composting. Although the predominant genera were TC sensitive under TC stress, many bacterial hosts harboring multiple TRGs (especially those in the hindgut) should be paid further attention to. In the foregut, five genera with abundant tetracycline-resistant bacteria (TRB) were specialized taxa. Among these genera, Unclassified_Solirubrobacterales and Pirellulaceae were probably related to the digestion processes. Other unclassified taxa related to the TRGs were probably derived from the DS. Five genera with abundant TRB were shared in the gut passages, and three specialized genera in the hindgut. These genera could spread TRGs and intI1 to the environment. These results suggest that vermi-composting is a feasible approach for TRG control in the DS containing TC concentration that does not exceed 25 mg/kg. Fates of TRGs and intI1 widely differ in the gut passages, showing inevitable connections with bacterial communities.

Dynamics of oxytetracycline and resistance genes in soil under long-term intensive compost fertilization in Northern China

In the present study, we explored the dynamics of antibiotics (ciprofloxacin, norfloxacin, enrofloxacin, and oxytetracycline), tetracycline resistance genes (TRGs), and bacterial communities over 2013-2015 in soils fertilized conventionally or with two levels (82.5 and 165 t/ha) of compost for 12 years. In the soil receiving 165 t/ha of compost, only oxytetracycline was 46% higher than that in the conventionally fertilized soil. Transient enrichment of both tetM (20% to 9-fold) and tetK (25% to 67-fold) was observed in multiple instances immediately after the application of compost. The majority of genera which positively correlated with tetM or tetK were affiliated to Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes. The structural equation model analysis indicated that fertilization regimes directly affected the bacterial composition and antibiotics and had an indirect effect on the abundance of tetK and tetM via these antibiotics. In summary, this study shed light into the complex interactions between fertilization, antibiotics, and antibiotic resistance pollution in greenhouse soil.

Thermophilic anaerobic digestion reduces ARGs in excess sludge even under high oxytetracycline concentrations

The feasibility of thermophilic anaerobic digestion (AD) for the attenuation of antibiotic resistance genes (ARGs) in biomass wastes under high antibiotic concentrations remains unclear. In this study, a thermophilic completely stirred digester (55 °C) was fed with municipal excess sludge spiked with increasing concentrations of oxytetracycline (OTC) (0-1000 mg/L) over a period of 280 days. Results showed that thermophilic AD could maintain stable methane production (338.40 ± 26.26 mL/d/gVS) even at an OTC dose of 1000 mg/L with the sludge phase OTC concentration reaching around 24,000 mg/kg. More important, the abundance of resistome detected by high-throughput quantitative PCR in the substrate was reduced (p < 0.01) by 55.54%-86.27% by thermophilic AD over the whole period. Partial canonical correspondence and network analyses showed that the reduction of ARGs was achieved mainly through two ways: eliminating the original hosts of ARGs in the substrate (from 41.74% ± 2.60% in the substrate to 12.08% ± 1.02% in digested sludge), and blocking the horizontal proliferation of ARGs in the digested sludge by reducing the abundance of mobile genetic elements and restricting their horizontal exchange within a small number of thermophilic genera. This study showed that thermophilic AD is feasible for the attenuation of ARGs in biomass even containing high level of OTC.

Evolution of microbial community and drug resistance during enrichment of tetracycline-degrading bacteria

Recently, the microbial degradation of tetracycline has been widely reported. However, its potential risks in treating wastewater containing high concentrations of tetracycline have not been fully evaluated. In this study, the evolution of the microbial community and drug resistance was traced during the enrichment of tetracycline-degrading bacteria. The results showed that some minor compositions such as Shewanella, Bacillus, and Pseudomonas in the seed sludge became the predominant genera in the enrichment cultures when continuously using tetracycline as the sole carbon source, especially some possible pathogenic bacteria increased significantly in this process. The abundances of most TRGs/16S rDNA were increased after enrichment, although the relative abundance of tetA and tetL genes decreased to some extent. From the enrichment culture, 7 predominant tetracycline-degrading strains were isolated, of which TD-1 (Bacillus) and TD-5 (Shewanella) presented high degradation efficiencies (6-day degradation rate > 95%, half-life period of tetracycline ≈ 24 h). In addition, multiple TRGs, mobile genetic elements (MGEs) and even gene cassettes were found in each tetracycline-degrading isolate. The findings suggested that some risks such as the pathogenicity of isolates and the spread of ARGs should be considered when the biodegradation method is used to treat wastewater polluted with high concentrations of tetracycline.

Characterization of Erythromycin and Tetracycline Resistance Genes of Streptococcus gallolyticus Subspecies pasteurianus Strains Isolated from Patients with Septicemia and Bacteremia in Thailand

BACKGROUND

Streptococcus gallolyticus subspecies (subsp.) pasteurianus, previously known as Streptococcus bovis biotype II/2, has been described as a causative agent of endocarditis, neonatal sepsis, meningitis, bacteremia, and colorectal carcinoma in humans. The aim of this study was to characterize the erythromycin and tetracycline resistance genes of S. gallolyticus subsp. pasteurianus strains isolated from patients with septicemia and bacteremia in Thailand.

METHODS

The clinical isolates of Streptococcus gallolyticus were identified by using conventional biochemical tests, PCR, and sodA gene sequence analysis. The erythromycin and tetracycline susceptibilities were determined by disk diffusion and agar dilution methods, while the resistance genes were identified by nucleotide sequence analysis.

RESULTS

From a total of 108 blood cultures, 36 (33%) were identified as S. gallolyticus subsp. pasteurianus with the nucleotide sequence identities of partial sodA gene with the reference strains ranging from 98.1 to 100%. Of these, 25 (69.4%) contained erythromycin resistance genes and erm(B) was the most predominant gene (30.6%), followed by erm(T) (19.4%) and mef(A) (5.6%). In addition, erm(B) was also detected in combination with lnu(B) (8.3%), erm(T) and mef(A) (2.8%), and mef(A) and lnu(B) (2.8%). It was interesting to note that lnu(B) was detected for the first time in S. gallolyticus subsp. pasteurianus in this study. For tetracycline resistance genes, tet(L) and tet(M) were detected at 13.9% and 11.1%, respectively. However, tet(M) in combination with tet(L) was detected most commonly at 69.4% and with tet(L) and tet(O) at 5.6%.

CONCLUSIONS

A number of erythromycin and tetracycline resistance genes were detected in S. gallolyticus subsp. pasteurianus strains circulating in Thailand.

Persistence of elevated concentrations of PM, affiliated pharmaceuticals, and tetracycline resistance genes downwind of feedyards

Beef cattle feedyards have been identified as sources of large amounts of particulate matter (PM) which may transport affiliated chemicals including steroids, beta agonists, and antibiotics from feedyards into the environment. This study is the first to examine persistence of PM-affiliated pharmaceuticals downwind of feedyards using multiple downwind samples collected at increasing distances from feedyard boundaries (n = 5). Concentrations of antibiotics and ractopamine per gram of PM remained consistent at all downwind locations (out to 4.8 km) whereas concentrations per m³ air decreased significantly at distances between 0.1 and 0.7 km downwind, corresponding to significant decreases in mass of PM. Monensin was present in the highest concentrations of any measured pharmaceutical, with concentrations of 37 μg/g PM (376 ng/m³) air in samples collected within 0.1 km downwind of feedyards. Total copy count of tetracycline resistance genes (tetW, tetQ, tetO, tetM, tetL, and tetB) were also significantly increased in samples collected within 0.1 km downwind of feedyards (10⁶ copies) as compared to samples collected upwind (10³ copies) and farther downwind (10⁴ copies) of feedyard boundaries. These results suggest that transport of pharmaceutical-laden PM into the terrestrial environment is occurring primarily via PM deposition within 0.7 km of the feedyard, while aerial transport persists over longer distances (>4.8 km).