Carbapenem triggers dissemination of chromosomally integrated carbapenemase genes via conjugative plasmids in Escherichia coli.

Epidemiological surveys have shown that carbapenem resistance is mainly transmitted across species by carbapenemase genes located on conjugative plasmids. As chromosomal integration of carbapenemase genes has rarely been identified, only a few studies have investigated their advantages to the carbapenem-resistant bacterial community. Here, we confirmed the increased stability of blaIMP-6 on a chromosome-integrated plasmid in an Escherichia coli isolate compared with that on original plasmids in the absence of antibiotic pressure. Although plasmids carrying carbapenemase genes are supposedly lost in successive generations, we found that the complete plasmid backbone was retained in bacterial cells even after the occasional loss of their antibiotic-resistance cassettes. This backbone structure has been observed worldwide to carry various antimicrobial resistance genes. Although the chromosomally integrated plasmid carrying blaIMP-6 could not be transmitted by conjugation, we found that meropenem treatment for 1 wk allowed the plasmid to be released from the chromosome and spread among E. coli strains that were susceptible to meropenem. The copy number of blaIMP-6 on the plasmid was amplified eight times, resulting in enhanced resistance. Although the carbapenemase producers that carry chromosomal carbapenemase genes comprised of small subpopulations, they functioned as stable, long-term reservoirs of carbapenem resistance that could be disseminated via plasmids with amplified resistance upon meropenem stimulation. Although plasmids occasionally lose their resistance cassettes as a scaffold for the acquisition of another resistance gene, chromosomal integration may contribute to the effective sharing of carbapenem resistance within a population, complicating the development of a strategy to avoid the dissemination of antimicrobial resistance. IMPORTANCE Although carbapenem antibiotics are the last resort for combating multidrug-resistant organisms, global dissemination of carbapenem-resistant Enterobacteriaceae (CRE) threatens public health. Carbapenemases, which are enzymes responsible for carbapenem resistance, are mainly encoded by genes on plasmids that can be transmitted across bacterial species. Owing to the rarity of chromosomally encoded carbapenemase genes, studies investigating their properties in bacterial communities are lacking. In our study, we revealed the stability of carbapenemase genes on chromosomes compared with those on plasmids, which can be lost through the loss of antimicrobial resistance cassettes despite robust retention of plasmid backbones. Following exposure to meropenem, the carbapenemase gene integrated into the chromosome was released as a plasmid, restarting the dissemination of enhanced carbapenem resistance through amplified copy numbers of carbapenemase genes. Chromosomally encoded carbapenemase genes may function as a reservoir of resistance genes within the bacterial community and challenge infection control against CRE dissemination.

A Single Residue within the MCR-1 Protein Confers Anticipatory Resilience.

The envelope stress response (ESR) of Gram-negative enteric bacteria senses fluctuations in nutrient availability and environmental changes to avert damage and promote survival. It has a protective role toward antimicrobials, but direct interactions between ESR components and antibiotic resistance genes have not been demonstrated. Here, we report interactions between a central regulator of ESR viz., the two-component signal transduction system CpxRA (conjugative pilus expression), and the recently described mobile colistin resistance protein (MCR-1). Purified MCR-1 is specifically cleaved within its highly conserved periplasmic bridge element, which links its N-terminal transmembrane domain with the C-terminal active-site periplasmic domain, by the CpxRA-regulated serine endoprotease DegP. Recombinant strains harboring cleavage site mutations in MCR-1 are either protease resistant or degradation susceptible, with widely differing consequences for colistin resistance. Transfer of the gene encoding a degradation-susceptible mutant to strains that lack either DegP or its regulator CpxRA restores expression and colistin resistance. MCR-1 production in Escherichia coli imposes growth restriction in strains lacking either DegP or CpxRA, effects that are reversed by transactive expression of DegP. Excipient allosteric activation of the DegP protease specifically inhibits growth of isolates carrying mcr-1 plasmids. As CpxRA directly senses acidification, growth of strains at moderately low pH dramatically increases both MCR-1-dependent phosphoethanolamine (PEA) modification of lipid A and colistin resistance levels. Strains expressing MCR-1 are also more resistant to antimicrobial peptides and bile acids. Thus, a single residue external to its active site induces ESR activity to confer resilience in MCR-1-expressing strains to commonly encountered environmental stimuli, such as changes in acidity and antimicrobial peptides. Targeted activation of the nonessential protease DegP can lead to the elimination of transferable colistin resistance in Gram-negative bacteria. IMPORTANCE The global presence of transferable mcr genes in a wide range of Gram-negative bacteria from clinical, veterinary, food, and aquaculture environments is disconcerting. Its success as a transmissible resistance factor remains enigmatic, because its expression imposes fitness costs and imparts only moderate levels of colistin resistance. Here, we show that MCR-1 triggers regulatory components of the envelope stress response, a system that senses fluctuations in nutrient availability and environmental changes, to promote bacterial survival in low pH environments. We identify a single residue within a highly conserved structural element of mcr-1 distal to its catalytic site that modulates resistance activity and triggers the ESR. Using mutational analysis, quantitative lipid A profiling and biochemical assays, we determined that growth in low pH environments dramatically increases colistin resistance levels and promotes resistance to bile acids and antimicrobial peptides. We exploited these findings to develop a targeted approach that eliminates mcr-1 and its plasmid carriers.

Impact of antibiotic withdrawal and starvation conditions on plasmid elimination and consequent loss of resistance.

OBJECTIVE: To assess resistance-loss due to plasmid elimination under experimental conditions, including withdrawal of antibiotics and administration of starvation conditions. METHODS: The experimental study was conducted at the Department of Pathology, King Edward Medical University, Lahore, Pakistan, from July to December 2019. A single sensitive clinical isolate of escherichia coli, showing resistance towards ampicillin was collected and separately sub-cultured in three different culture broths: tryptic soya broth, minimal broth and control broth for a period of one month under standard laboratory conditions. Minimum inhibitory concentrations of the strains were calculated after every seven days to check antibiotic susceptibility. RESULTS: Minimum inhibitory concentrations of the initial escherichia coli strain measured on Day 1 was 6mg/mL and it became sensitive after continual sub-culturing in the absence of antibiotics in 21 days. Due to starvation conditions, the bacterial strain exhibited sensitivity to an even lower antibiotic concentration of 1.5mg/mL on the 28th day. Bacterial growth inhibition zones determined by disc diffusion method using an ampicillin disc of 10µg/mL showed no zone of inhibition. CONCLUSIONS: Provision of starvation conditions and withdrawal of antibiotic allowed the escherichia coli strain to exhibit gradual loss of resistance over a period of time.

Antibiotic resistance genes attenuated with salt accumulation in saline soil.

Salt accumulation on the surface of the soil layer driven by the strong evaporation is a natural phenomenon that usually happens in the dry season, particularly on the coastal lands reclaimed from tidal flats. However, the influence of salt accumulation on the distribution profile of antibiotic resistance genes (ARGs) and mobile gene elements (MGEs) remains unclear. In this study, we sampled a wild saline soil where the salt accumulation was frequently observed to investigate the vertical distribution profiles of ARGs and MGEs. The results showed that an increasing gradient of ARGs and MGEs was observed from the top to deep layer with the decreasing of electrical conductivity (EC1:5 values) indicating the salt-influenced attenuation of ARGs in the saline soil. The competing test suggested that the attenuation of ARGs in response to salinity gradient was attributable to the elimination of the ARG-harboring plasmids, due to the reduction of the relative fitness of plasmid-harboring strains. Additionally, the network analyses showed that the attenuation of ARGs might be associated with decreased abundance of Actinobacteria. Overall, this study identifies that salinity as an abiotic stress could re-shape the distribution of ARGs, which may influence the dissemination of ARGs in the environment.

Construction of an easy-to-use CRISPR-Cas9 system by patching a newly designed EXIT circuit.

BACKGROUND: Plasmid-borne genetic editing tools, including the widely used CRISPR-Cas9 system, have greatly facilitated bacterial programming to obtain novel functionalities. However, the lack of effective post-editing plasmid elimination methods impedes follow-up genetic manipulation or application. Conventional strategies including exposure to physical and chemical treatments, or exploiting temperature-sensitive replication origins have several drawbacks (e.g., they are limited for efficiency and are time-consuming). Therefore, the demand is apparent for easy and rapid elimination of the tool plasmids from their bacterial hosts after genetic manipulation. RESULTS: To bridge this gap, we designed a novel EXIT circuit with the homing endonuclease, which can be exploited for rapid and efficient elimination of various plasmids with diverse replication origins. As a proof of concept, we validated the EXIT circuit in Escherichia coli by harnessing homing endonuclease I-SceI and its cleavage site. When integrated into multiple plasmids with different origins, the EXIT circuit allowed them to be eliminated from the host cells, simultaneously. By combining the widely used plasmid-borne CRISPR-Cas9 system and the EXIT circuit, we constructed an easy-to-use CRISPR-Cas9 system that eliminated the Cas9- and the single-guide RNA (sgRNA)-encoding plasmids in one-step. Within 3 days, we successfully constructed an atrazine-degrading E. coli strain, thus further demonstrating the advantage of this new CRISPR-Cas9 system for bacterial genome editing. CONCLUSIONS: Our novel EXIT circuit, which exploits the homing endonuclease I-SceI, enables plasmid(s) with different replication origins to be eliminated from their host cells rapidly and efficiently. We also developed an easy-to-use CRISPR-Cas9 system with the EXIT circuit, and this new system can be widely applied to bacterial genome editing.

Antibacterial and NDM-1 Plasmid Elimination Effects of Radix Scutellariae Baicalensis on Acinetobacter calcoaceticus / 中国药学杂志

OBJECTIVE: To explore the bacteriostasis and plasmid elimination activities of different extracted parts of traditional Chinese medicine Radix Scutellariae Baicalensis on NDM-1 Acinetobacter calcoaceticus. METHODS: Thein vitro antibacterial effect of the extracts from Radix Scutellariae Baicalensis was studied. Inhibition zone and minimum inhibitory concentration(MIC) of the alcohol extract and water decoction were examined by using MH agar plates and microdilution susceptibility testing. The growth curve of the NDM-1 Acinetobacter calcoaceticus was tested after being incubated with alcohol extract and water decoction at sub-MIC. At three time points after incubation with different extracts at sub-MIC, photocopy dish method was used to screen plasmid-cured strains of NDM-1 Acinetobacter calcoaceticus. The plasmid-elimination rates and phenotypic changes were compared. RESULTS: Both the alcohol extract and water decoction of Radix Scutellariae Baicalensis inhibited the growth of NDM-1 Acinetobacter calcoaceticus. The MICs were 1.56 mg·mL-1 for the alcohol extract and 6.25 mg·mL-1 for the water decoction. The growth curve showed that the antibacterial effect of the alcohol extract was more obvious. Both the alcohol extract and water decoction of Radix Scutellariae Baicalensis had some degrees of plasmid elimination effect. The plasmid-elimination rates in the alcohol extract group were higher than those in the water decoction group. The plasmid-elimination rates were 61.27% for the alcohol extract and 49.78% for the water decoction, respectively. CONCLUSION: Radix Scutellariae Baicalensis can inhibit the growth of NDM-1Acinetobacter calcoaceticus and eliminate the drug-resistant plasmid effectively and has the potential to be used to control the spread of pan-drug resistant Acinetobacter strains or be an adjuvant treatment method for clinical infections. Its alcohol extract has better effect.

Enhanced plasmid loss in bacterial populations exposed to the antimicrobial compound irgasan delivered from interpenetrating polymer network silicone hydrogels.

The spread of antimicrobial resistance, usually mediated by horizontal transfer of plasmids, limits the options of treating bacterial infections and thereby poses a crucial human health problem. The disturbance of plasmid stability within bacterial species in clinical environments serves as a novel strategy to reduce the development and dissemination of antibiotic resistance. We tested the ability of irgasan to destabilize plasmids from Escherichia coli K-12 cells when added directly into liquid growth medium at concentrations below levels of marked bacterial growth inhibition, or when released into liquid growth medium from irgasan-impregnated Interpenetrating Polymer Network (IPN) silicone hydrogel objects, a novel technology developed as drug-delivery platform. IPN-mediated irgasan-release was indirectly monitored as the extent of plasmid loss from bacterial cells during a 24-hour period or during repeated exposure to new irgasan-loaded IPN devices every 24h for a total of 10days. The cells were genetically modified so that plasmid loss could be quantified by applying a combination of fluorescence-based reporter gene technology and flow cytometry. When exposing bacterial cells to the irgasan-impregnated IPNs for 24h, we observed a modest (2.8-4.7%), but significant (P<0.05), plasmid loss as well as an inhibition of bacterial growth, both gradually increasing with increasing impregnation concentration. Repeated exposure to irgasan-impregnated IPNs drastically increased the plasmid loss of up to 83%, but cells adapted over time, which indicated the limitations of this specific drug for future medical applications. This study, however, illustrates the ability of IPNs to release an impregnated compound into a liquid suspension to induce a significant biological impact on growing bacterial cells.

Construction of a food-grade cell surface display system for Lactobacillus casei.

In this study, a food-grade cell surface display host/vector system for Lactobacillus casei was constructed. The food-grade host L. casei Q-5 was a lactose-deficient derivative of L. casei ATCC 334 obtained by plasmid elimination. The food-grade cell surface display vector was constructed based on safe DNA elements from lactic acid bacteria containing the following: pSH71 replicon from Lactococcus lactis, lactose metabolism genes from L. casei ATCC 334 as complementation markers, and surface layer protein gene from Lactobacillus acidophilus ATCC 4356 for cell surface display. The feasibility of the new host/vector system was verified by the expression of green fluorescent protein (GFP) on L. casei. Laser scanning confocal microscopy and immunofluorescence analysis using anti-GFP antibody confirmed that GFP was anchored on the surface of the recombinant cells. The stability of recombinant L. casei cells in artificial gastrointestinal conditions was verified, which is beneficial for oral vaccination applications. These results indicate that the food-grade host/vector system can be an excellent antigen delivery vehicle in oral vaccine construction.

Indigenous plasmids of Bacillus megaterium WSH-002 involved in mutualism with Ketogulonicigenium vulgare WSH-001.

In the two-step vitamin C fermentation process, the precursor 2-keto-l-gulonic acid (2-KLG) was synthesized using a mixed culture of Ketogulonicigenium vulgare WSH-001 and Bacillus megaterium WSH-002, which contained three plasmids, pBME1, pBME2 and pBME3. The cell growth of B. megaterium was not affected by the elimination of these plasmids. However, elimination of pBME2 and pBME3 significantly affected l-sorbose uptake and 2-KLG production. Sequence analysis of the plasmids showed that many of the pBME2 and pBME3 genes were of unknown function or could not be assigned to a specific metabolic pathway. The current work showed that the indigenous plasmids pBME2 and pBME3 of B. megaterium WSH-002 involved in mutualism with K. vulgare WSH-001. The results provided a promising new route to further demonstrate the mutualism process between the two bacteria.