Resistance Cassette Research Articles

Creating a Genetic Toolbox for the Carbon-Fixing, Nitrogen-Fixing and Dehalogenating Bacterium Xanthobacter autotrophicus.

Xanthobacter autotrophicus is a metabolically flexible microorganism with two key features: (1) The organism has adapted to grow on a wide variety of carbon sources including CO2, methanol, formate, propylene, haloalkanes and haloacids; and (2) X. autotrophicus was the first chemoautotroph identified that could also simultaneously fix N2, meaning the organism can utilize CO2, N2, and H2 for growth. This metabolic flexibility has enabled use of X. autotrophicus for gas fixation, the creation of fertilizers and foods from gases, and the dehalogenation of environmental contaminants. Despite the wide variety of applications that have already been demonstrated for this organism, there are few genetic tools available to explore and exploit its metabolism. Here, we report a genetic toolbox for use in X. autotrophicus. We first identified suitable origins of replication and quantified their copy number, and identified antibiotic resistance cassettes that could be used as selectable markers. We then tested several constitutive and inducible promoters and terminators and quantified their promoter strengths and termination efficiencies. Finally, we demonstrated that gene expression tools remain effective under both autotrophic and dehalogenative metabolic conditions to show that these tools can be used in the environments that make X. autotrophicus unique. Our extensive characterization of these tools in X. autotrophicus will enable genetic and metabolic engineering to optimize production of fertilizers and foods from gases, and enable bioremediation of halogenated environmental contaminants.

The expression of integron arrays is shaped by the translation rate of cassettes

Integrons are key elements in the rise and spread of multidrug resistance in Gram-negative bacteria. These genetic platforms capture cassettes containing promoterless genes and stockpile them in arrays of variable length. In the current integron model, expression of cassettes is granted by the Pc promoter in the platform and is assumed to decrease as a function of its distance. Here we explored this model using a large collection of 136 antibiotic resistance cassettes and show the effect of distance is in fact negligible. Instead, cassettes have a strong impact in the expression of downstream genes because their translation rate affects the stability of the whole polycistronic mRNA molecule. Hence, cassettes with reduced translation rates decrease the expression and resistance phenotype of cassettes downstream. Our data puts forward an integron model in which expression is contingent on the translation of cassettes upstream, rather than on the distance to the Pc.

An Enhanced Retroviral Vector for Efficient Genetic Manipulation and Selection in Mammalian Cells.

Introducing genetic material into hard-to-transfect mammalian cell lines and primary cells is often best achieved through retroviral infection. An ideal retroviral vector should offer a compact, selectable, and screenable marker while maximizing transgene delivery capacity. However, a previously published retroviral vector featuring an EGFP/Puromycin fusion protein failed to meet these criteria in our experiments. We encountered issues such as low infection efficiency, weak EGFP fluorescence, and selection against infected cells. To address these shortcomings, we developed a novel retroviral vector based on the Moloney murine leukemia virus. This vector includes a compact bifunctional EGFP and Puromycin resistance cassette connected by a 2A peptide. Our extensively tested vector demonstrated superior EGFP expression, efficient Puromycin selection, and no growth penalty in infected cells compared with the earlier design. These benefits were consistent across multiple mammalian cell types, underscoring the versatility of our vector. In summary, our enhanced retroviral vector offers a robust solution for efficient infection, reliable detection, and effective selection in mammalian cells. Its improved performance and compact design make it an ideal choice for a wide range of applications involving precise genetic manipulation and characterization in cell-based studies.

Expanding the genetic toolbox for the obligate human pathogen Streptococcus pyogenes.

Genetic tools form the basis for the study of molecular mechanisms. Despite many recent advances in the field of genetic engineering in bacteria, genetic toolsets remain scarce for non-model organisms, such as the obligatory human pathogen Streptococcus pyogenes. To overcome this limitation and enable the straightforward investigation of gene functions in S. pyogenes, we have developed a comprehensive genetic toolset. By adapting and combining different tools previously applied in other Gram-positive bacteria, we have created new replicative and integrative plasmids for gene expression and genetic manipulation, constitutive and inducible promoters as well as fluorescence reporters for S. pyogenes. The new replicative plasmids feature low- and high-copy replicons combined with different resistance cassettes and a standardized multiple cloning site for rapid cloning procedures. We designed site-specific integrative plasmids and verified their integration by nanopore sequencing. To minimize the effect of plasmid integration on bacterial physiology, we screened publicly available RNA-sequencing datasets for transcriptionally silent sites. We validated this approach by designing the integrative plasmid pSpy0K6 targeting the transcriptionally silent gene SPy_1078. Analysis of the activity of different constitutive promoters indicated a wide variety of strengths, with the lactococcal promoter P 23 showing the strongest activity and the synthetic promoter P xylS2 showing the weakest activity. Further, we assessed the functionality of three inducible regulatory elements including a zinc- and an IPTG-inducible promoter as well as an erythromycin-inducible riboswitch that showed low-to-no background expression and high inducibility. Additionally, we demonstrated the applicability of two codon-optimized fluorescent proteins, mNeongreen and mKate2, as reporters in S. pyogenes. We therefore adapted the chemically defined medium called RPMI4Spy that showed reduced autofluorescence and enabled efficient signal detection in plate reader assays and fluorescence microscopy. Finally, we developed a plasmid-based system for genome engineering in S. pyogenes featuring the counterselection marker pheS*, which enabled the scarless deletion of the sagB gene. This new toolbox simplifies previously laborious genetic manipulation procedures and lays the foundation for new methodologies to study gene functions in S. pyogenes, leading to a better understanding of its virulence mechanisms and physiology.

Three concurrent mechanisms generate gene copy number variation and transient antibiotic heteroresistance

Heteroresistance is a medically relevant phenotype where small antibiotic-resistant subpopulations coexist within predominantly susceptible bacterial populations. Heteroresistance reduces treatment efficacy across diverse bacterial species and antibiotic classes, yet its genetic and physiological mechanisms remain poorly understood. Here, we investigated a multi-resistant Klebsiella pneumoniae isolate and identified three primary drivers of gene dosage-dependent heteroresistance for several antibiotic classes: tandem amplification, increased plasmid copy number, and transposition of resistance genes onto cryptic plasmids. All three mechanisms imposed fitness costs and were genetically unstable, leading to fast reversion to susceptibility in the absence of antibiotics. We used a mouse gut colonization model to show that heteroresistance due to elevated resistance-gene dosage can result in antibiotic treatment failures. Importantly, we observed that the three mechanisms are prevalent among Escherichia coli bloodstream isolates. Our findings underscore the necessity for treatment strategies that address the complex interplay between plasmids, resistance cassettes, and transposons in bacterial populations.

Molecular Characterization of Resistance and Virulence Factors of Trueperella pyogenes Isolated from Clinical Bovine Mastitis Cases in China.

The present study was designed to investigate the resistance determinants and virulence factors of 45 Trueperella pyogenes isolates from clinical bovine mastitis in Hexi Corridor of Gansu, China. Minimum inhibitory concentrations (MICs) was tested by E-test method. Gene of antimicrobial resistance, virulence integrase and integron gene cassettes were determined by PCR and DNA sequencing. The T. pyogenes isolates exhibited high resistance to streptomycin (88.9%) and tetracycline (64.4%), followed by erythromycin (15.6%) and gentamicin (13.3%). Resistance to streptomycin was most commonly encoded by aadA9 (88.9%); and to tetracycline, by tetW (64.4%). Importantly, all streptomycin-resistant isolates carried aadA9 alone or in combination with aadA1, aadA11 and strA-strB. Similarly, all tetracycline-resistant isolates harbored tetW alone or in combination with tetA33. Meanwhile, ermX was detected in 13.3% isolates, only one erythromycin-resistant isolate was not identified for this gene. Moreover, all T. pyogenes isolates carried class 1 integrons, and 17.8% of them contained gene cassettes, including arrays aadA1-aadB (4.4%), aad A24-dfrA1-ORF1 (2.2%) and aadA1 (2.2%). Furthermore, all tested isolates harbored virulent genes plo and fimA, followed by fimC (88.9%), fimE (86.6%) nanP (75.6%), nanH (40.0%), cbpA (35.6%) and fimG (6.7%). To our knowledge, this is the first report of integron gene cassettes of T. pyogenes isolates from bovine mastitis cases in China. These findings are useful for developing the prevention and the virulence factors of T. pyogenes could be promising candidates for vaccine antigens for bovine mastitis caused by T. pyogenes in China.

Insertion of a neomycin selection cassette in the Amigo1 locus alters gene expression in the olfactory epithelium leading to region-specific defects in olfactory receptor neuron development.

During development of the nervous system, neurons connect to one another in a precisely organized manner. Sensory systems provide a good example of this organization, whereby the composition of the outside world is represented in the brain by neuronal maps. Establishing correct patterns of neural circuitry is crucial, as inaccurate map formation can lead to severe disruptions in sensory processing. In rodents, olfactory stimuli modulate a wide variety of behaviors essential for survival. The formation of the olfactory glomerular map is dependent on molecular cues that guide olfactory receptor neuron axons to broad regions of the olfactory bulb and on cell adhesion molecules that promote axonal sorting into specific synaptic units in this structure. Here, we demonstrate that the cell adhesion molecule Amigo1 is expressed in a subpopulation of olfactory receptor neurons, and we investigate its role in the precise targeting of olfactory receptor neuron axons to the olfactory bulb using a genetic loss-of-function approach in mice. While ablation of Amigo1 did not lead to alterations in olfactory sensory neuron axonal targeting, our experiments revealed that the presence of a neomycin resistance selection cassette in the Amigo1 locus can lead to off-target effects that are not due to loss of Amigo1 expression, including unexpected altered gene expression in olfactory receptor neurons and reduced glomerular size in the ventral region of the olfactory bulb. Our results demonstrate that insertion of a neomycin selection cassette into the mouse genome can have specific deleterious effects on the development of the olfactory system and highlight the importance of removing antibiotic resistance cassettes from genetic loss-of-function mouse models when studying olfactory system development.

Optical Mapping: Detecting Genomic Resistance Cassettes in MRSA.

Methicillin-resistant Staphylococcus aureus (MRSA) is a multidrug-resistant bacterium with a global presence in healthcare facilities as well as community settings. The resistance of MRSA to beta-lactam antibiotics can be attributed to a mobile genetic element called the staphylococcal cassette chromosome mec (SCCmec), ranging from 23 to 68 kilobase pairs in length. The mec gene complex contained in SCCmec allows MRSA to survive in the presence of penicillin and other beta-lactam antibiotics. We demonstrate that optical mapping (OM) is able to identify the bacterium as S. aureus, followed by an investigation of the presence of kilobase pair range SCCmec elements by examining the associated OM-generated barcode patterns. By employing OM as an alternative to traditional DNA sequencing, we showcase its potential for the detection of complex genetic elements such as SCCmec in MRSA. This approach holds promise for enhancing our understanding of antibiotic resistance mechanisms and facilitating the development of targeted interventions against MRSA infections.

Multireceptor phage cocktail against Salmonella enterica to circumvent phage resistance.

Non-Typhoidal Salmonella (NTS) is one of the most common food-borne pathogens worldwide, with poultry products being the major vehicle for pathogenesis in humans. The use of bacteriophage (phage) cocktails has recently emerged as a novel approach to enhancing food safety. Here, a multireceptor Salmonella phage cocktail of five phages was developed and characterized. The cocktail targets four receptors: O-antigen, BtuB, OmpC, and rough Salmonella strains. Structural analysis indicated that all five phages belong to unique families or subfamilies. Genome analysis of four of the phages showed they were devoid of known virulence or antimicrobial resistance factors, indicating enhanced safety. The phage cocktail broad antimicrobial spectrum against Salmonella, significantly inhibiting the growth of all 66 strains from 20 serovars tested in vitro. The average bacteriophage insensitive mutant (BIM) frequency against the cocktail was 6.22 × 10-6 in S. Enteritidis, significantly lower than that of each of the individual phages. The phage cocktail reduced the load of Salmonella in inoculated chicken skin by 3.5 log10 CFU/cm2 after 48 h at 25°C and 15°C, and 2.5 log10 CFU/cm2 at 4°C. A genome-wide transduction assay was used to investigate the transduction efficiency of the selected phage in the cocktail. Only one of the four phages tested could transduce the kanamycin resistance cassette at a low frequency comparable to that of phage P22. Overall, the results support the potential of cocktails of phage that each target different host receptors to achieve complementary infection and reduce the emergence of phage resistance during biocontrol applications.

Class 1 and 2 integrons and antibiotic resistance profile in Salmonella spp. from San Cristobal River, Laguna, Philippines

ABSTRACT Infection with multidrug resistant bacteria is a significant public health concern. Bacteria culture of water samples (n=120) collected in San Cristobal River, Philippines, showed that half (n=60) were positive for Salmonella spp. Screening of all isolates (n=179) for susceptibility to antibiotics showed that most (76.4%; n=113) were positive for class 1 integrons, of which one isolate was also positive for the class 2 integron. The presence of class 1 integrons was associated with resistance to antibiotics (p<0.05). Sequencing of class 1 integron variable regions (VRs) differeciated 11 gene cassettes: dfrA1 or dfrA17; aadA1 or aadA2; blaCTX-M-2 or bla-OXA-1; SmdAB; CmlA1 and aaC 3-Id. However, sequencing of class 2 integron VR differenciated estX, sat2, and aadA1. These results provide insights into evolutionary changes within bacterial multidrug resistant cassettes, more accurately to estimate heath risk associated with the river water.

POMBOX: A Fission Yeast Cloning Toolkit for Molecular and Synthetic Biology.

The fission yeast Schizosaccharomyces pombe is a popular model organism in molecular biology and cell physiology. With its ease of genetic manipulation and growth, supported by in-depth functional annotations in the PomBase database and genome-wide metabolic models,S. pombe is an attractive option for synthetic biology applications. However,S. pombe currently lacks modular tools for generating genetic circuits with more than 1 transcriptional unit. We developed a toolkit to address this gap. Adapted from the MoClo-YTK plasmid kit for Saccharomyces cerevisiae and using the same modular cloning grammar, our POMBOX toolkit is designed to facilitate fast, efficient, and modular construction of genetic circuits inS. pombe. It allows for interoperability when working with DNA sequences that are functional in bothS. cerevisiae and S. pombe (e.g., protein tags, antibiotic resistance cassettes, and coding sequences). Moreover, POMBOX enables the modular assembly of multigene pathways and increases the possible pathway length from 6 to 12 transcriptional units. We also adapted the stable integration vector homology arms to Golden Gate assembly and tested the genomic integration success rates depending on different sequence sizes, from 4 to 24 kb. We included 14 S. pombe promoters that we characterized using two fluorescent proteins, in both minimally defined (EMM2─Edinburgh minimal media) and complex (YES─yeast extract with supplements) media. Then, we examined the efficacy of 6 S. cerevisiae and 6 synthetic terminators in S. pombe. Finally, we used the POMBOX kit for a synthetic biology application in metabolic engineering and expressed plant enzymes in S. pombe to produce specialized metabolite precursors, namely, methylxanthine, amorpha-4,11-diene, and cinnamic acid from the purine, mevalonate, and aromatic amino acid pathways.

An expanded toolkit of drug resistance cassettes for Candida glabrata, Candida auris, and Candida albicans leads to new insights into the ergosterol pathway.

The increasing problem of drug resistance and emerging pathogens is an urgent global health problem that necessitates the development and expansion of tools for studying fungal drug resistance and pathogenesis. Prior studies in Candida glabrata, Candida auris, and Candida albicans have been mainly limited to the use of NatMX/SAT1 and HphMX/CaHyg for genetic manipulation in prototrophic strains and clinical isolates. In this study, we demonstrated that NatMX/SAT1, HphMX, KanMX, and/or BleMX drug resistance cassettes when coupled with a CRISPR-ribonucleoprotein (RNP)-based system can be efficiently utilized for deleting or modifying genes in the ergosterol pathway of C. glabrata, C. auris, and C. albicans. Moreover, the utility of these tools has provided new insights into ERG genes and their relationship to azole resistance in Candida. Overall, we have expanded the toolkit for Candida pathogens to increase the versatility of genetically modifying complex pathways involved in drug resistance and pathogenesis.

A Genome Scale CRISPR Screen Identifies Novel Genes That Regulate Erythropoietin Production

Erythropoietin (EPO) is a plasma glycoprotein that binds bone marrow erythroid progenitors, stimulating their proliferation and differentiation. EPO is secreted into the circulation by hepatocytes and specialized kidney peritubular fibroblasts, which contribute ~20% and ~80% of the total plasma EPO level, respectively. EPO production is induced during hypoxia, due to enhanced stability of the transcription factor hypoxia-inducible factor (HIF). However, increased HIF activity results in enhanced expression of angiogenesis and oncogenesis promoting genes, raising concerns about clinical strategies that promote EPO production via increasing HIF levels. To define novel regulators of EPO production, we developed a genome-wide functional screen that provides a quantifiable and selectable readout of EPO production. In order to perform such a screen, we generated a reporter HEP3B cell line with homozygous insertion of coding sequences for p2A and eGFP at the endogenous EPO locus. This HEP3B EPO-p2A-eGFP (HEG) cell line expresses equivalent levels of EPO and eGFP proteins, both translated from the same mRNA molecule. Treatment of HEG cells with the HIF stabilizing molecule DMOG results in increased EPO expression, which is abolished by deletion of the hypoxia-responsive-element in the EPO locus. These findings demonstrate the utility of this reporter cell line to study the regulation of EPO production. To identify novel genes that regulate EPO production, we mutagenized the HEG cell line with the GeCKO-v2 CRISPR/Cas9 knock-out library, which delivers a puromycin resistance cassette, SpCas9, and a pooled collection of 123,411 single guide RNAs (sgRNAs) that include 6 independent sgRNAs targeting every human gene. Transduction was performed at a low multiplicity of infection (MOI ~0.3), so that most infected cells receive 1 sgRNA to delete 1 gene only. Puromycin selection was applied from days 1-4 post-transduction and cells were subsequently recovered for 8 days. Cells were then treated with DMOG for 24 hours or left untreated. Cells with increased (top ~10%) or decreased (bottom ~10%) eGFP fluorescence were isolated. This screen was done in biological triplicates. Genes for which sgRNAs are enriched/depleted in eGFP high versus eGFP low DMOG-treated cells likely impact EPO expression independently of the HIF pathway. In contrast, genes for which sgRNAs are enriched/depleted in eGFP high versus eGFP low untreated cells may impact EPO expression in either a HIF dependent or independent manner. As expected, sgRNAs targeting VHL were found to be among the most significantly enriched sgRNAs in eGFP-high versus eGFP-low cells under no treatment conditions. Also as anticipated, sgRNAs targeting genes known to promote EPO production ( HNF4A, WT1, RXRA, and CREBBP) were enriched in eGFP-low versus eGFP-high cells under either DMOG-treated or untreated conditions. To refine our findings, we generated a custom library targeting the top 1,200 candidate regulators of EPO production nominated by the genome-scale screen. Using this library, we performed a secondary CRISPR screen (in biological triplicates) as above. Owning to the 10-fold smaller size of the custom library, the secondary screen was performed with average coverage of &amp;gt;150x throughout the entire screen (including the sorted cell populations). Indeed, the statistical confidence obtained with the secondary screen was superior than that achieved in the genome scale screen. Using a false discovery rate (FDR) cutoff of 1%, gene-level analysis identified 100 and 79 candidate genes whose targeting was associated with increased or decreased EPO production respectively, under either untreated or DMOG-treated conditions. A high degree of concordance was observed for regulators of EPO expression between both screens, performed with and without DMOG treatment. To identify genes that regulate EPO production independent of HIF, we evaluated several of the top genes for which sgRNAs were enriched in eGFP high vs. eGFP low cells treated with DMOG. Using 3 independent sgRNAs targeting each of these candidates, we found 2 genes ( ZNF574 and RBM18), that when deleted, result in increased EPO mRNA, even following DMOG treatment. Additional validation experiments as well as studies aimed to define the role of these 2 genes in the regulation of EPO production are ongoing.

The CDK-Inhibitor p27 Kip1 Regulates Fetal Hemoglobin Expression

γ-globin upregulation has been shown to be beneficial for individuals with Sickle Cell Disease, leading to improvement in morbidity and mortality rates. Intriguingly, small molecules that modulate the cell cycle have been observed to impact γ-globin expression in erythroid cells, though a causal relationship has not been definitively established. Understanding the connection between cell cycle dynamics/regulation and γ-globin production may shed light into a novel molecular mechanism by which γ-globin expression is regulated, with potential therapeutic implications for Sickle Cell Disease. To evaluate if cell cycle speed correlates with γ-globin expression, we labeled HUDEP-2 cells (which express beta-globin) with carboxyfluorescein diacetate succinimidyl ester (CFSE) at different days of differentiation. With each cell division, CFSE dye intensity is expected to be reduced by half; therefore, faster cycling cells retain less CFSE than slower cycling cells. Forty-eight hours post-CFSE labeling, HUDEP-2 cells were analyzed for γ-globin expression by intracellular flow cytometry at days 2, 4, 6, and 8 of differentiation. Starting at Day 6 of differentiation, the slowest cycling (Top 5% CFSE) HUDEP-2 cells exhibited &amp;gt;2-fold increase in γ-globin expressing cells (F-cells) compared to the fastest cycling (bottom 5% CFSE) cells. Notably, these results were confirmed in erythroid cells differentiated from primary human CD34+ hematopoietic stem and progenitor cells (HSPCs), therefore ruling out the possibility that the above findings were an artifact of the immortalized HUDEP-2 cell line. The correlation between slow cell cycling speed and increased γ-globin expression prompted us to genetically perturb the cell cycle machinery and define the impact of these genetic perturbations on γ-globin expression. Using CRISPR activation (CRISPRa), we increased the expression of 8 Cyclin Dependent Kinase Inhibitors (CDKN2A, CDKN2B, CDKN2C, CDKN2D, CDKN1A, CDKN1B, CDKN1C and CDKN3) in HUDEP-2 cells. To do so, we first generated a HUDEP-2-MPH cell line that stably expresses the transcriptional activator complex MPH (MS2-P65-HSF1). We then transduced this cell line with a virus that expresses one of 3 sgRNAs targeting each of the 8 CDKIs, a VP64 activation domain fused to catalytically dead Cas9 (dCas9-VP64), and a blasticidin resistance cassette. We found that activation of CDKN1b (P27 Kip1) in particular, resulted in increased F-cell percentage. Indeed, compared to cells transduced with control sgRNAs, HUDEP-2-MPH cells transduced with a CDKN1B-targeting sgRNA (resulting in a 2-fold higher CDKN1B mRNA level; p= 0.006) exhibited an increased proportion of F-cells, from a baseline of ~6% up to ~20% (p= 0.024). Increased CDKN1B expression resulted in a ~14-fold increase in γ-globin mRNA levels (p= 0.026), associated with a mild reduction in beta-globin mRNA level and a reduction in BCL11A mRNA level to ~65% of normal. These results suggest that the increased γ-globin expression resulting from CDKN1B overexpression may result, at least in part, from reduced BCL11A expression (which we are currently validating). To rule out an off-target effect of the CDKN1B targeting sgRNA, we overexpressed CDKN1B in HUDEP-2 cells, using a cDNA expression construct, and found comparable results as observed with CDKN1B CRISPRa. We next overexpressed CDKN1B cDNA in erythroid cells differentiated from CD34+ HSPCs. In early preliminary results, increased CDKN1B expression in the latter cells resulted in increased γ-globin expression, both at the mRNA and protein level, validating the HUDEP-2 data. Additional studies are ongoing to define the role of CDKN1B in the regulation of γ-globin expression, and to define the impact of CDKN1B overexpression on erythroid differentiation. In summary, our preliminary studies have uncovered a link between cell cycle regulation and γ-globin production. These findings may lay the foundation for the development of new therapeutic strategies for Sickle Cell Disease.

Identifying Novel Regulators of γ-Globin Expression Using a Genome-Scale CRISPR Activation Screen

β-hemoglobinopathies are the most common monogenic disorders worldwide, and are defined based on whether patients have quantitative (β-thalassemia) or qualitative (Sickle Cell Disease (SCD)) defects in β-globin synthesis. Unfortunately, there are limited treatment options for β-hemoglobinopathies, and the majority of patients continue to develop life-threatening complications from their diseases. An alternative β-like subunit, γ-globin, has been shown to inhibit pathogenic hemoglobin polymerization in SCD and to functionally replace β-globin in β-thalassemia. The discovery of novel strategies to upregulate γ-globin expression may lead to effective therapies for β-hemoglobinopathies. To identify novel regulators of γ-globin expression, we performed a genome-wide pooled CRISPR activation (CRISPRa) screen, using the Synergistic Activation Mediator (SAM) system. The screen was performed in the HUDEP-2 cell line, which expresses adult β-globin. We generated a clonal HUDEP-2-MPH cell line, which stably expresses the transcriptional activator complex MPH (MS2-P65-HSF1). This cell line was transduced with a viral library that delivers a VP64 activation domain fused to a catalytically dead Cas9 (dCas9-VP64), a blasticidin resistance cassette, and one of 3 unique sgRNAs targeting virtually every coding gene in the human genome (the library consists of 70,290 sgRNAs). At day 8 of erythroid differentiation, the top and bottom 10% γ-expressing cells were sorted, and integrated sgRNAs were sequenced using NextGen sequencing. As expected, sgRNAs targeting BCL11A and ZBTB7A (known negative regulators of γ-globin) were enriched in the bottom 10% γ-expressing cells, while sgRNAs targeting HIF1A (known positive regulator of γ-globin) were enriched in the top 10% γ-expressing cells. Notably, this screen identified several novel candidate positive regulators of γ-globin expression, including the transcriptional repressor Hypermethylated in Cancer 1 (HIC1). In preliminary validation studies, we used 2 independent sgRNAs to activate HIC1 in HUDEP-2-MPH cells and measured the percentage of γ-globin expressing cells (F-cells) by flow cytometry. Compared to cells transduced with control sgRNAs, increased HIC1 transcription (&amp;gt;200-fold) resulted in a profound increase in the proportion of F-cells, from a baseline of ~6% up to ~76%. Similarly, HIC1 overexpression in HUDEP-2 cells resulted in a ~13-fold increase in γ-globin mRNA levels and reduction in BCL11A mRNA level to ~30% of normal. These results suggest that the increased γ-globin expression resulting from HIC1 overexpression may result, at least in part, from reduced BCL11A levels (which we are currently validating). Recently, increased expression of HIC2, a paralogous protein for HIC1, was reported to result in increased γ-globin expression. To exclude the possibility that HIC1 targeting sgRNAs may also target HIC2, we measured the HIC2 mRNA level in HUDEP-2 cells targeted with sgRNAs aimed at increasing HIC1 expression. HIC2 mRNA was not increased in the latter cells. We next overexpressed HIC1 cDNA in erythroid cells differentiated from primary human CD34+ hematopoietic stem and progenitor cells (HSPCs). In early preliminary results, we found that HIC1 overexpression resulted in increased γ-globin expression, validating the HUDEP-2 data. Additional studies are ongoing to define the role of HIC1 in the regulation of γ-globin expression, and to define the impact of HIC1 overexpression on erythroid differentiation. In summary, our screen uncovered HIC1, and other potential novel regulators of γ-globin expression, which we are currently validating. These findings may result in future therapeutic approaches for β-hemoglobinopathies.

Altering under-represented DNA sequences elevates bacterial transformation efficiency.

Manipulating the genomes of bacteria is critical to many fields. Such manipulations are made by genetic engineering, which often requires new pieces of DNA to be added to the genome. Bacteria have robust systems for identifying and degrading new DNA, some of which rely on restriction enzymes. These enzymes cut DNA at specific sequences. We identified a set of DNA sequences that are missing normally from a bacterium's genome, more than would be expected by chance. Eliminating these sequences from a new piece of DNA allowed it to be incorporated into the bacterial genome at a higher frequency than new DNA containing the sequences. Removing such sequences appears to allow the new DNA to fly under the bacterial radar in "stealth" mode. This transformation improvement approach is straightforward to apply and likely broadly applicable.

Profile and resistance levels of 136 integron resistance genes

Integrons have played a major role in the rise and spread of multidrug resistance in Gram-negative pathogens and are nowadays commonplace among clinical isolates. These platforms capture, stockpile, and modulate the expression of more than 170 antimicrobial resistance cassettes (ARCs) against most clinically-relevant antibiotics. Despite their importance, our knowledge on their profile and resistance levels is patchy, because data is scattered in the literature, often reported in different genetic backgrounds and sometimes extrapolated from sequence similarity alone. Here we have generated a collection of 136 ARCs against 8 antibiotic families and disinfectants. Cassettes are cloned in a vector designed to mimic the genetic environment of a class 1 integron, and transformed in Escherichia coli. We have measured the minimal inhibitory concentration (MIC) to the most relevant molecules from each antibiotic family. With more than 500 MIC values, we provide an exhaustive and comparable quantitation of resistance conferred by ARCs. Our data confirm known resistance trends and profiles while revealing important differences among closely related genes. We have also detected genes that do not confer the expected resistance, to the point of challenging the role of the whole family of qac genes in resistance against disinfectants. Our work provides a detailed characterization of integron resistance genes at-a-glance.

An expanded CRISPR-Cas9-assisted recombineering toolkit for engineering genetically intractable Pseudomonas aeruginosa isolates.

Much of our current understanding of microbiology is based on the application of genetic engineering procedures. Since their inception (more than 30 years ago), methods based largely on allelic exchange and two-step selection processes have become a cornerstone of contemporary bacterial genetics. While these tools are established for adapted laboratory strains, they have limited applicability in clinical or environmental isolates displaying a large and unknown genetic repertoire that are recalcitrant to genetic modifications. Hence, new tools allowing genetic engineering of intractable bacteria must be developed to gain a comprehensive understanding of them in the context of their biological niche. Herein, we present a method for precise, efficient and rapid engineering of the opportunistic pathogen Pseudomonas aeruginosa. This procedure relies on recombination of short single-stranded DNA facilitated by targeted double-strand DNA breaks mediated by a synthetic Cas9 coupled with the efficient Ssr recombinase. Possible applications include introducing single-nucleotide polymorphisms, short or long deletions, and short DNA insertions using synthetic single-stranded DNA templates, drastically reducing the need of PCR and cloning steps. Our toolkit is encoded on two plasmids, harboring an array of different antibiotic resistance cassettes; hence, this approach can be successfully applied to isolates displaying natural antibiotic resistances. Overall, this toolkit substantially reduces the time required to introduce a range of genetic manipulations to a minimum of five experimental days, and enables a variety of research and biotechnological applications in both laboratory strains and difficult-to-manipulate P. aeruginosa isolates.

First Detection and Molecular Characterization of Pseudomonas aeruginosa blaNDM-1 ST308 in Greece.

The objective of the present study is to report the detection and the molecular characterization of nine blaNDM-1-positive Pseudomonas aeruginosa isolates, all of which belonged to the epidemic high-risk international clone ST308, and all were isolated from patients in a tertiary care hospital in Central Greece from May to July 2023.The isolates were characterized by whole genome sequencing to obtain multi-locus sequencing typing (MLST) and identify the blaNDM1-environment and resistome and virulence genes content. In silico MLST analysis showed that all isolates belonged to the high-risk ST308 international clone. All strains possessed 22 different genes, encoding resistance to various antimicrobial agents. Whole genome sequencing revealed that the blaNDM-1 was chromosomally located within the integrative and conjugative element ICETn43716385 and that it was part of one cassette along with two other resistance genes, floR and msrE. Two additional resistance cassettes were also found in the genome, which included the arrays of aph(6)-Id, aph(3″)-Ib, floR, sul2 and aadA10, qnrVC1, aac(3)-Id, dfrB5, aac(6')-II. Additionally, the strains possessed various virulence genes, e.g., aprA, exoU, lasA, lasB, toxA, and estA. All of the isolates shared identical genomes, which showed 98% similarity with the P. aeruginosa ST308 genome (acc. no CP020703), previously reported from Singapore. To our knowledge, this is the first report of ST308 blaNDM-1-positive P. aeruginosa isolation in Europe, which indicates the transmission dynamics of this high-risk clone.

The characterisation of antimicrobial resistant Escherichia coli from dairy calves.

Introduction. Dairy calves, particularly pre-weaned calves have been identified as a common source of multidrug resistant (MDR) Escherichia coli.Gap statement. E. coli strains isolated from dairy calves and the location of their resistance genes (plasmid or chromosomal) have not been well characterised.Aim. To characterise the phenotypic and genotypic features as well as the population structure of antimicrobial-resistant E. coli isolated from calves located on dairy farms that feed waste-milk to their replacement calves.Methodology. Recto-anal swab enrichments from 40 dairy calves (≤ 14 days old) located on four dairy farms were examined for tetracycline, streptomycin, ciprofloxacin, and third-generation cephalosporin resistant E. coli. Whole genome sequencing was performed using both short- and long-read technologies on selected antimicrobial resistant E. coli.Results. Fifty-eight percent (23/40) of calves harboured antimicrobial resistant E. coli: 43 % (17/40) harboured tetracycline resistant, and 23 % (9/40) harboured chromosomal mediated AmpC producing E. coli. Whole genome sequencing of 27 isolates revealed five sequence types, with ST88 being the dominant ST (17/27, 63 % of the sequenced isolates) followed by ST1308 (3/27, 11 %), along with the extraintestinal pathogenic E. coli lineages ST69 (3/27, 11 %), ST10 (2/27, 7 %), and ST58 (2/27, 7 %). Additionally, 16 isolates were MDR, harbouring additional resistance genes that were not tested phenotypically. Oxford Nanopore long-read sequencing technologies enabled the location of multiple resistant gene cassettes in IncF plasmids to be determined.Conclusion. Our study identified a high incidence of tetracycline and streptomycin-resistant E. coli in dairy calves, and highlighted the presence of multidrug-resistant strains, emphasising the need for further investigation into potential associations with farm management practices.