Tetracycline resistance determinants: mechanisms of action, regulation of expression, genetic mobility, and distribution

Antimicrobial Resistance in Livestock: A Serious Threat to Public Health

Antimicrobial resistance represents an alarming public health problem; its importance is related to the significant clinical implications (increased morbidity, mortality, disease duration, development of comorbidities, and epidemics), as well as its economic effects on the healthcare sector. In fact, therapeutic options are severely limited by the advent and spread of germs resistant to many antibiotics. The situation worldwide is worrying, especially in light of the prevalence of Gram-negative bacteria-Klebsiella pneumoniae and Acinetobacter baumannii-which are frequently isolated in hospital environments and, more specifically, in intensive care units. The problem is compounded by the ineffective treatment of infections by patients who often self-prescribe therapy. Resistant bacteria also show resistance to the latest generation antibiotics, such as carbapenems. In fact, superbacteria, grouped under the acronym extended-spectrum betalactamase (ESBL), are becoming common. Antibiotic resistance is also found in the livestock sector, with serious repercussions on animal production. In general, this phenomenon affects all members of the biosphere and can only be addressed by adopting a holistic "One Health" approach. In this literature overview, a stock is taken of what has been learned about antibiotic resistance, and suggestions are proposed to stem its advance.

Extending the Potency and Lifespan of Antibiotics: Inhibitors of Gram-Negative Bacterial Efflux Pumps

Efflux is a natural process found in all prokaryotic and eukaryotic cells that removes a diverse range of substrates from inside to outside. Many antibiotics are substrates of bacterial efflux pumps, and modifications to the structure or overexpression of efflux pumps are an important resistance mechanism utilized by many multidrug-resistant bacteria. Therefore, chemical inhibition of bacterial efflux to revitalize existing antibiotics has been considered a promising approach for antimicrobial chemotherapy over two decades, and various strategies have been employed. In this review, we provide an overview of bacterial multidrug resistance (MDR) efflux pumps, of which the resistance nodulation division (RND) efflux pumps are considered the most clinically relevant in Gram-negative bacteria, and describe over 50 efflux inhibitors that target such systems. Although numerous efflux inhibitors have been identified to date, none have progressed into clinical use because of formulation, toxicity, and pharmacokinetic issues or a narrow spectrum of inhibition. For these reasons, the development of efflux inhibitors has been considered a difficult and complex area of research, and few active preclinical studies on efflux inhibitors are in progress. However, recently developed tools, including but not limited to computational tools including molecular docking models, offer hope that further research on efflux inhibitors can be a platform for research and development of new bacterial efflux inhibitors.

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.

Plasmid-free cheater cells commonly evolve during laboratory growth

It has been nearly a century since the isolation and use of penicillin, heralding the discovery of a wide range of different antibiotics. In addition to clinical applications, such antibiotics have been essential laboratory tools, allowing for selection and maintenance of laboratory plasmids that encode cognate resistance genes. However, antibiotic resistance mechanisms can additionally function as public goods. For example, extracellular beta-lactamases produced by resistant cells that subsequently degrade penicillin and related antibiotics allow neighboring plasmid-free susceptible bacteria to survive antibiotic treatment. How such cooperative mechanisms impact selection of plasmids during experiments in laboratory conditions is poorly understood. Here, we show in multiple bacterial species that the use of plasmid-encoded beta-lactamases leads to significant curing of plasmids in surface-grown bacteria. Furthermore, such curing was also evident for aminoglycoside phosphotransferase and tetracycline antiporter resistance mechanisms. Alternatively, antibiotic selection in liquid growth led to more robust plasmid maintenance, although plasmid loss was still observed. The net outcome of such plasmid loss is the generation of a heterogenous population of plasmid-containing and plasmid-free cells, leading to experimental confounds that are not widely appreciated.IMPORTANCEPlasmids are routinely used in microbiology as readouts of cell biology or tools to manipulate cell function. Central to these studies is the assumption that all cells in an experiment contain the plasmid. Plasmid maintenance in a host cell typically depends on a plasmid-encoded antibiotic resistance marker, which provides a selective advantage when the plasmid-containing cell is grown in the presence of antibiotic. Here, we find that growth of plasmid-containing bacteria on a surface and to a lesser extent in liquid culture in the presence of three distinct antibiotic families leads to the evolution of a significant number of plasmid-free cells, which rely on the resistance mechanisms of the plasmid-containing cells. This process generates a heterogenous population of plasmid-free and plasmid-containing bacteria, an outcome which could confound further experimentation.

Unraveling the diversity and dissemination dynamics of antimicrobial resistance genes in Enterobacteriaceae plasmids across diverse ecosystems

AIM

The objective of this study was to investigate the antimicrobial resistance genes (ARGs) in plasmids of Enterobacteriaceae from soil, sewage, and feces of food-producing animals and humans.

METHODS AND RESULTS

The plasmid sequences were obtained from the NCBI database. For the identification of ARG, comprehensive antibiotic resistance database (CARD), and ResFinder were used. Gene conservation and evolution were investigated using DnaSP v.6. The transfer potential of the plasmids was evaluated using oriTfinder and a MOB-based phylogenetic tree was reconstructed using Fastree. We identified a total of 1064 ARGs in all plasmids analyzed, conferring resistance to 15 groups of antibiotics, mostly aminoglycosides, beta-lactams, and sulfonamides. The greatest number of ARGs per plasmid was found in enterobacteria from chicken feces. Plasmids from Escherichia coli carrying multiple ARGs were found in all ecosystems. Some of the most abundant genes were shared among all ecosystems, including aph(6)-Id, aph(3'')-Ib, tet(A), and sul2. A high level of sequence conservation was found among these genes, and tet(A) and sul2 are under positive selective pressure. Approximately 62% of the plasmids carrying at least one ARG were potentially transferable. Phylogenetic analysis indicated a potential co-evolution of Enterobacteriaceae plasmids in nature.

CONCLUSION

The high abundance of Enterobacteriaceae plasmids from diverse ecosystems carrying ARGs reveals their widespread distribution and importance.

Study of Antimicrobial Resistance (AMR) in Shigella spp. in India

Antimicrobial agents are essential in reducing illness and mortality brought on by infectious diseases in both humans and animals. However, the therapeutic effect of antibiotics has diminished due to an increase in antimicrobial drug resistance (AMR). This article provides a retrospective analysis of AMR in Shigella infections in India, showing a rise in resistance that has contributed to a global burden. Shigella spp. are widespread and the second-leading cause of diarrheal death in people of all ages. The frequency and mortality rates of Shigella infections are decreased by antibiotic treatment. However, the growth of broad-spectrum antibiotic resistance is making it more difficult to treat many illnesses. Reduced cell permeability, efflux pumps, and the presence of enzymes that break down antibiotics are the causes of resistance. AMR is a multifaceted and cross-sectoral problem that affects humans, animals, food, and the environment. As a result, there is a growing need for new therapeutic approaches, and ongoing surveillance of Shigella spp. infections which should definitely be improved for disease prevention and management. This review emphasizes on the epidemiological data of India, and antimicrobial resistance in Shigella spp.

Combination techniques towards novel drug delivery systems manufacturing: 3D PCL scaffolds enriched with tetracycline-loaded PVP nanoparticles

Drug delivery systems based on synthetic and natural polymers offer a new approach with a capacity to control the release of bio-active agents within time. In this work, we present different designs of Polycaprolactone (PCL) 3D scaffolds containing Polyvinylpyrrolidone (PVP) nanoparticles that can store a hydrophilic drug. The drug delivery system, combined of PCL and PVP polymers fabricated by additive manufacturing, aims for a solution for longer and more stabled drug delivery carrier. The drug, planned to be released to the targeted area, is sprayed with the electrospray method inside PVP nanoparticles on the different layers of the fabricated PCL scaffolds 3D printing. This makes obtaining a layered and porous scaffold and drug-loaded nanoparticles within this structure easier. Obtained PCL scaffolds containing Tetracyclines (Tet) loaded PVP nanoparticles showed that drug encapsulation into the interlayer extended the release time and exhibited a controlled release profile for days. Moreover, produced scaffolds have good biocompatibility and no harmful effects. The combination of 3D scaffolds and drug-loaded nanoparticles aims to develop new functional scaffolds by targeting more efficient and longer-lasting drug delivery.

Tigecycline Sensitivity Reduction in Escherichia coli Due to Widely Distributed tet(A) Variants

Despite scattered studies that have reported mutations in the tet(A) gene potentially linked to tigecycline resistance in clinical pathogens, the detailed function and epidemiology of these tet(A) variants remains limited. In this study, we analyzed 64 Escherichia coli isolates derived from MacConkey plates supplemented with tigecycline (2 μg/mL) and identified five distinct tet(A) variants that account for reduced sensitivity to tigecycline. In contrast to varied tigecycline MICs (0.25 to 16 μg/mL) of the 64 tet(A)-variant-positive E. coli isolates, gene function analysis confirmed that the five tet(A) variants exhibited a similar capacity to reduce tigecycline sensitivity in DH5α carrying pUC19. Among the observed seven non-synonymous mutations, the V55M mutation was unequivocally validated for its positive role in conferring tigecycline resistance. Interestingly, the variability in tigecycline MICs among the E. coli strains did not correlate with tet(A) gene expression. Instead, a statistically significant reduction in intracellular tigecycline concentrations was noted in strains displaying higher MICs. Genomic analysis of 30 representative E. coli isolates revealed that tet(A) variants predominantly resided on plasmids (n = 14) and circular intermediates (n = 13). Within China, analysis of a well-characterized E. coli collection isolated from pigs and chickens in 2018 revealed the presence of eight tet(A) variants in 103 (4.2%, 95% CI: 3.4-5.0%) isolates across 13 out of 17 tested Chinese provinces or municipalities. Globally, BLASTN analysis identified 21 tet(A) variants in approximately 20.19% (49,423/244,764) of E. coli genomes in the Pathogen Detection database. These mutant tet(A) genes have been widely disseminated among E. coli isolates from humans, food animals, and the environment sectors, exhibiting a growing trend in tet(A) variants over five decades. Our findings underscore the urgency of addressing tigecycline resistance and the underestimated role of tet(A) mutations in this context.

Effect of dry cow therapy on antimicrobial resistance of mastitis pathogens post-calving

The aim of this study was to evaluate the effect of dry cow therapy (DCT) on the antimicrobial resistance (AMR) profile of mastitis pathogens post-calving. A repository of isolates based on a DCT trial was utilized for the current study. A stratified random survey sample of cows from the trial were identified within the strata of season, herd, and trial treatment resulting in 382 cows. All isolates from the 382 cows were selected for the current study, which identified 566 isolates from milk samples collected at dry off (S1), post-calving (S2), and at the first clinical mastitis event up to 150 days in milk (S3). The AMR profiles were determined using broth microdilution method. Less than 10% of the coagulase-negative Staphylococcus species (CNS) isolates (n = 421) were resistant to tetracycline, ceftiofur, penicillin/novobiocin or erythromycin, while higher proportions of resistance to sulfadimethoxine (72%) and penicillin (28%) were observed. All Staphylococcus aureus (S. aureus) isolates (n = 4) were susceptible to all tested AMD except sulfadimethoxine, to which all isolates were resistant. Similarly, all Streptococcus spp. (n = 37) were susceptible to penicillin, penicillin/novobiocin, and ampicillin while resistant to tetracycline (17%). All coliforms (n = 21) were susceptible to ceftiofur, but resistance was recorded for sulfadimethoxine (70%), cephalothin (56%), and tetracycline (43%). The increased resistance percent from S1 to S2 was observed in CNS isolates from AMD-treated cows, with the highest increase recorded for penicillin (12.2%). Parametric survival interval regression models were used to explore the association between antimicrobial drug (AMD) therapy at dry off and the AMR phenotype post-calving. The accelerated failure-time metric was adopted to minimum inhibitory concentration measurements to permit interpretation of model exponentiated coefficients. Models for cows with CNS isolated at both S1 and S2 showed increased resistance against cephalothin, oxacillin, and ceftiofur in cows that received DCT from the same drug class, or a class with a shared resistance mechanism. In contrast, resistance of CNS isolates to tetracycline were associated with any AMD therapy at dry off. Resistance of CNS isolates to Penicillin decreased in CNS isolates in cows that received any AMD therapy at dry off compared to those that didn't. The study provided evidence that dry-cow IMM AMD was associated with AMR post-calving.

A local-scale One Health genomic surveillance of Clostridioides difficile demonstrates highly related strains from humans, canines, and the environment

Although infections caused by Clostridioides difficile have historically been attributed to hospital acquisition, growing evidence supports the role of community acquisition in C. difficile infection (CDI). Symptoms of CDI can range from mild, self-resolving diarrhoea to toxic megacolon, pseudomembranous colitis, and death. In this study, we sampled C. difficile from clinical, environmental, and canine reservoirs in Flagstaff, Arizona, USA, to understand the distribution and transmission of the pathogen in a One Health framework; Flagstaff is a medium-sized, geographically isolated city with a single hospital system, making it an ideal site to characterize genomic overlap between sequenced C. difficile isolates across reservoirs. An analysis of 562 genomes from Flagstaff isolates identified 65 sequence types (STs), with eight STs being found across all three reservoirs and another nine found across two reservoirs. A screen of toxin genes in the pathogenicity locus identified nine STs where all isolates lost the toxin genes needed for CDI manifestation (tcdB, tcdA), demonstrating the widespread distribution of non-toxigenic C. difficile (NTCD) isolates in all three reservoirs; 15 NTCD genomes were sequenced from symptomatic, clinical samples, including two from mixed infections that contained both tcdB+ and tcdB- isolates. A comparative single nucleotide polymorphism (SNP) analysis of clinically derived isolates identified 78 genomes falling within clusters separated by ≤2 SNPs, indicating that ~19 % of clinical isolates are associated with potential healthcare-associated transmission clusters; only symptomatic cases were sampled in this study, and we did not sample asymptomatic transmission. Using this same SNP threshold, we identified genomic overlap between canine and soil isolates, as well as putative transmission between environmental and human reservoirs. The core genome of isolates sequenced in this study plus a representative set of public C. difficile genomes (n=136), was 2690 coding region sequences, which constitutes ~70 % of an individual C. difficile genome; this number is significantly higher than has been published in some other studies, suggesting that genome data quality is important in understanding the minimal number of genes needed by C. difficile. This study demonstrates the close genomic overlap among isolates sampled across reservoirs, which was facilitated by maximizing the genomic search space used for comprehensive identification of potential transmission events. Understanding the distribution of toxigenic and non-toxigenic C. difficile across reservoirs has implications for surveillance sampling strategies, characterizing routes of infections, and implementing mitigation measures to limit human infection.

Plasmid-free cheater cells commonly evolve during laboratory growth

It has been nearly a century since the isolation and use of penicillin, heralding the discovery of a wide range of different antibiotics. In addition to clinical applications, such antibiotics have been essential laboratory tools, allowing for selection and maintenance of laboratory plasmids that encode cognate resistance genes. However, antibiotic resistance mechanisms can additionally function as public goods. For example, secretion of beta-lactamase from resistant cells, and subsequent degradation of nearby penicillin and related antibiotics, allows neighboring plasmid-free susceptible bacteria to survive antibiotic treatment. How such cooperative mechanisms impact selection of plasmids during experiments in laboratory conditions is poorly understood. Here, we show that the use of plasmid-encoded beta-lactamases leads to significant curing of plasmids in surface grown bacteria. Furthermore, such curing was also evident for aminoglycoside phosphotransferase and tetracycline antiporter resistance mechanisms. Alternatively, antibiotic selection in liquid growth led to more robust plasmid maintenance, although plasmid loss still occurred. The net outcome of such plasmid loss is the generation of a heterogenous population of plasmid-containing and plasmid-free cells, leading to experimental confounds that are not widely appreciated.

Phenotypic and Genotypic Characteristics of Antimicrobial Resistance in Citrobacter freundii Isolated from Domestic Ducks (Anas platyrhynchos domesticus) in Bangladesh

Antimicrobial resistance (AMR) in Citrobacter freundii poses a serious challenge as this species is one of the sources of nosocomial infection and causes diarrheal infections in humans. Ducks could be the potential source of multidrug-resistant (MDR) C. freundii; however, AMR profiles in C. freundii from non-human sources in Bangladesh have remained elusive. This study aimed to detect C. freundii in domestic ducks (Anas platyrhynchos domesticus) in Bangladesh and to determine their phenotypic and genotypic antibiotic susceptibility patterns. A total of 150 cloacal swabs of diseased domestic ducks were screened using culturing, staining, biochemical, polymerase chain reaction (PCR), and matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) to detect C. freundii. Phenotypic and genotypic antibiotic susceptibility patterns were done by the disk diffusion method and PCR, respectively. In total, 16.67% (25/150) of the samples were positive for C. freundii. C. freundii isolates showed a range of 20% to 96% resistance to cefotaxime, gentamicin, levofloxacin, ciprofloxacin, cotrimoxazole, tetracycline, ampicillin, and cephalexin. More than 60% of the isolates were phenotypically MDR, and the index of multiple antibiotic resistance ranged from 0.07 to 0.79. Genes encoding resistance to beta-lactams [bla_TEM-1-88% (22/25), bla_CMY-2-56% (14/25), bla_CMY-9-8% (2/25), and bla_CTX-M-14-20% (5/25)], sulfonamides [sul1-52% (13/25), sul2-24% (6/25)], tetracyclines [tetA-32% (8/25) and tetB-4% (1/25)], aminoglycosides [aacC4-16% (4/25)], and fluoroquinolones [qnrA-4% (1/25), qnrB-12% (3/25), and qnrS-4% (1/25)] were detected in the isolated C. freundii. To the best of our knowledge, this is the first study in Bangladesh to detect MDR C. freundii with their associated resistance genes from duck samples. We suggest addressing the burden of diseases in ducks and humans and associated AMR issues using the One Health approach.

The Plasmidomic Landscape of Clinical Methicillin-Resistant Staphylococcus aureus Isolates from Malaysia

Methicillin-resistant Staphylococcus aureus (MRSA) is a priority nosocomial pathogen with plasmids playing a crucial role in its genetic adaptability, particularly in the acquisition and spread of antimicrobial resistance. In this study, the genome sequences of 79 MSRA clinical isolates from Terengganu, Malaysia, (obtained between 2016 and 2020) along with an additional 15 Malaysian MRSA genomes from GenBank were analyzed for their plasmid content. The majority (90%, 85/94) of the Malaysian MRSA isolates harbored 1-4 plasmids each. In total, 189 plasmid sequences were identified ranging in size from 2.3 kb to ca. 58 kb, spanning all seven distinctive plasmid replication initiator (replicase) types. Resistance genes (either to antimicrobials, heavy metals, and/or biocides) were found in 74% (140/189) of these plasmids. Small plasmids (<5 kb) were predominant (63.5%, 120/189) with a RepL replicase plasmid harboring the ermC gene that confers resistance to macrolides, lincosamides, and streptogramin B (MLS_B) identified in 63 MRSA isolates. A low carriage of conjugative plasmids was observed (n = 2), but the majority (64.5%, 122/189) of the non-conjugative plasmids have mobilizable potential. The results obtained enabled us to gain a rare view of the plasmidomic landscape of Malaysian MRSA isolates and reinforces their importance in the evolution of this pathogen.

In vitro activity of tetracycline analogs against multidrug-resistant and extensive drug resistance clinical isolates of Mycobacterium tuberculosis

BACKGROUND

Multidrug-resistant tuberculosis (MDR-TB) has become a big threaten to global health. The current strategy for treatment of MDR-TB and extensive drug resistant tuberculosis (XDR-TB) is with low efficacy and high side effect. While new drug is fundamental for cure MDR-TB, repurposing the Food and Drug Administration (FDA)-approved drugs represents an alternative soluation with less cost.

METHODS

The activity of 8 tetracycline-class antibiotics against mycobacterium tuberculosis (M.tb) were determined by Minimum Inhibitory Concentration (MIC) in vitro. A transposon M.smeg libraries was generated by using the Harm phage and then used to isolate the conditional growth mutants in doxycycline containing plate. Eleven mutants were isolated and genomic DNAs were extracted using the cetyltrimethyl ammonium bromide (CTAB) method and analyzed by whole genome sequencing.

RESULTS

We found that three of eight drugs efficiently inhibited mycobacteria growth under the peak plasma concentration in the human body. Further tests showed these three tetracycline analogs (demeclocycline, doxycycline and methacycline) had antimicrobial activity against seven clinical isolates, including MDR and XDR strains. Among them, Doxycycline had the lowest MICs in all mycobacteria strains tested in this study. By using a transposon library, we identify the insertion of transposon in two genes, porin and MshA, associatewith the resistant to doxycycline.

CONCLUSIONS

Our findings show that tetracycline analogs such as doxycycline, has bactericidal activity against not only drug sensitive M.tb, but also clinical MDR and XDR strains, provided proof of concept to repurpose doxycycline to fight MDR-TB and XDR-TB. Further investigations are warranted to clarify the underlying mechanism and optimize the strategy in combination with other anti-TB drugs.

Comparison of antimicrobial resistant Escherichia coli isolated from Irish commercial pig farms with and without zinc oxide and antimicrobial usage

BACKGROUND

The prophylactic use of antimicrobials and zinc oxide (ZnO) in pig production was prohibited by the European Union in 2022 due to potential associations between antimicrobial and heavy metal usage with antimicrobial resistance (AMR) and concerns regarding environmental pollution. However, the effects of their usage on the bacterial AMR profiles on commercial pig farms are still not fully understood and previous studies examining the effect of ZnO have reported contrasting findings. The objective of this study was to examine the effects of antimicrobial and ZnO usage on AMR on commercial pig farms. Faecal and environmental samples were taken on 10 Irish commercial farms, of which 5 farms regularly used ZnO and antimicrobials (amoxicillin or sulphadiazine-trimethoprim) for the prevention of disease. The other 5 farms did not use ZnO or any other form of prophylaxis. Escherichia coli numbers were quantified from all samples using non-supplemented and supplemented Tryptone Bile X-glucuronide agar.

RESULTS

In total 351 isolates were phenotypically analysed, and the genomes of 44 AmpC/ESBL-producing E. coli isolates from 4 farms were characterised using whole-genome sequencing. Phenotypic analysis suggested higher numbers of multi-drug resistant (MDR) E. coli isolates on farms using prophylaxis. Furthermore, farms using prophylaxis were associated with higher numbers of isolates resistant to apramycin, trimethoprim, tetracycline, streptomycin, and chloramphenicol, while resistance to ciprofloxacin was more associated with farms not using any prophylaxis. Thirty-four of the 44 AmpC/ESBL-producing E. coli strains harboured the bla_CTX-M-1 resistance gene and were multi drug resistant (MDR). Moreover, network analysis of plasmids and analysis of integrons showed that antimicrobial and biocide resistance genes were frequently co-located on mobile genetic elements, indicating the possibility for co-selection during antimicrobial or biocide usage as a contributor to AMR occurrence and persistence on farms.

CONCLUSIONS

The results of this study showed evidence that antimicrobial and ZnO treatment of pigs post-weaning can favour the selection and development of AMR and MDR E. coli. Co-location of resistance genes on mobile genetic elements was observed. This study demonstrated the usefulness of phenotypic and genotypic detection of antimicrobial resistance by combining sequencing and microbiological methods.

Disrupting the ArcA Regulatory Network Amplifies the Fitness Cost of Tetracycline Resistance in Escherichia coli

There is an urgent need for strategies to discover secondary drugs to prevent or disrupt antimicrobial resistance (AMR), which is causing >700,000 deaths annually. Here, we demonstrate that tetracycline-resistant (Tet^R) Escherichia coli undergoes global transcriptional and metabolic remodeling, including downregulation of tricarboxylic acid cycle and disruption of redox homeostasis, to support consumption of the proton motive force for tetracycline efflux. Using a pooled genome-wide library of single-gene deletion strains, at least 308 genes, including four transcriptional regulators identified by our network analysis, were confirmed as essential for restoring the fitness of Tet^R E. coli during treatment with tetracycline. Targeted knockout of ArcA, identified by network analysis as a master regulator of this new compensatory physiological state, significantly compromised fitness of Tet^R E. coli during tetracycline treatment. A drug, sertraline, which generated a similar metabolome profile as the arcA knockout strain, also resensitized Tet^R E. coli to tetracycline. We discovered that the potentiating effect of sertraline was eliminated upon knocking out arcA, demonstrating that the mechanism of potential synergy was through action of sertraline on the tetracycline-induced ArcA network in the Tet^R strain. Our findings demonstrate that therapies that target mechanistic drivers of compensatory physiological states could resensitize AMR pathogens to lost antibiotics. IMPORTANCE Antimicrobial resistance (AMR) is projected to be the cause of >10 million deaths annually by 2050. While efforts to find new potent antibiotics are effective, they are expensive and outpaced by the rate at which new resistant strains emerge. There is desperate need for a rational approach to accelerate the discovery of drugs and drug combinations that effectively clear AMR pathogens and even prevent the emergence of new resistant strains. Using tetracycline-resistant (Tet^R) Escherichia coli, we demonstrate that gaining resistance is accompanied by loss of fitness, which is restored by compensatory physiological changes. We demonstrate that transcriptional regulators of the compensatory physiologic state are promising drug targets because their disruption increases the susceptibility of Tet^R E. coli to tetracycline. Thus, we describe a generalizable systems biology approach to identify new vulnerabilities within AMR strains to rationally accelerate the discovery of therapeutics that extend the life span of existing antibiotics.

Genomics of Tenacibaculum Species in British Columbia, Canada

Tenacibaculum is a genus of Gram-negative filamentous bacteria with a cosmopolitan distribution. The research describing Tenacibaculum genomes stems primarily from Norway and Chile due to their impacts on salmon aquaculture. Canadian salmon aquaculture also experiences mortality events related to the presence of Tenacibaculum spp., yet no Canadian Tenacibaculum genomes are publicly available. Ribosomal DNA sequencing of 16S and four species-specific 16S quantitative-PCR assays were used to select isolates cultured from Atlantic salmon with mouthrot in British Columbia (BC), Canada. Ten isolates representing four known and two unknown species of Tenacibaculum were selected for shotgun whole genome sequencing using the Oxford Nanopore's MinION platform. The genome assemblies achieved closed circular chromosomes for seven isolates and long contigs for the remaining three isolates. Average nucleotide identity analysis identified T. ovolyticum, T. maritimum, T. dicentrarchi, two genomovars of T. finnmarkense, and two proposed novel species T. pacificus sp. nov. type strain 18-2881-A^T and T. retecalamus sp. nov. type strain 18-3228-7B^T. Annotation in most of the isolates predicted putative virulence and antimicrobial resistance genes, most-notably toxins (i.e., hemolysins), type-IX secretion systems, and oxytetracycline resistance. Comparative analysis with the T. maritimum type-strain predicted additional toxins and numerous C-terminal secretion proteins, including an M12B family metalloprotease in the T. maritimum isolates from BC. The genomic prediction of virulence-associated genes provides important targets for studies of mouthrot disease, and the annotation of the antimicrobial resistance genes provides targets for surveillance and diagnosis in veterinary medicine.

New europium-doped carbon nanoparticles showing long-lifetime photoluminescence: Synthesis, characterization and application to the determination of tetracycline in waters

The growing appearance of antibiotic-resistant strains of microorganisms originated from the widespread use and ubiquitous presence of such drugs is a major concern in the world. The development of methodologies able to detect such substances at low concentration in real water samples is mandatory to overcome this problem. Europium(III) is known to form complexes with tetracycline (TC) with photoluminescent characteristics useful for TC determination. In the present work, we synthesized for the first time carbon nanoparticles (CN) showing delayed photoluminescence using a Europium(III) doping synthesis. The new material (PCNEu) was characterized both morphologically and spectroscopically, showing an analytical photoluminescent signal in presence of TC, arising from the ⁵D₀→⁷F₂ transition of europium, one hundred times higher than that of the europium salt alone in presence of the antibiotic. This enhancement is a consequence of the amplifying effect exerted by nanoparticle structure itself, leading to an efficient synergistic "antenna effect" in the system PCNEu - TC. The analytical signal is affected both by pH and the nature of the buffer used, and it allows the detection of tetracycline in waters with a limit of detection of 2.18 nM and recoveries between 90 and 110%. The analytical performance of the developed methodology enables having lower limits of detection than other luminescent and chemiluminescent reported methodologies.

Oral flora of domestic cats in Hong Kong: Identification of antibiotic-resistant strains

BACKGROUND

As the clinical outcome of bite-associated infection is related to the oral commensals, evaluating their composition and antibiotic susceptibility pattern can provide more information for the antibiotic treatment of wound infections and increase the awareness of the multidrug-resistant bacteria in cat oral flora.

AIMS

This study was conducted to identify the various bacterial species in the oral cavity of cats. It aimed to identify the composition of cat oral flora and antibiotic resistant bacterial stains.

MATERIALS AND METHODS

Twenty-two cats were sampled for bacterial evaluation. Matrix-assisted laser desorption/ionization time of flight mass spectrometry was used to provide rapid and reliable detection and identification of the bacterial species. Antibiotic susceptibility tests were performed in the identified isolates to determine the antibiotic susceptibility pattern and to detect the multidrug-resistant bacteria in the cat oral cavities.

RESULTS

A total of 54 isolates were identified, Pasteurella was the genus most commonly isolated from the oral cavity of cats (19/54, 35.19%), followed by Neisseria spp. (8/54, 14.81%) and Staphylococcus spp. (7/54, 12.96%). Uncommon oral flora were isolated from the samples, including Pasteurella canis, Inquilinus limosus and the Enterobacteriaceae family of Escherichia coli, Klebsiella pneumoniae and Serratia marcescens. Fourteen different multidrug-resistant bacteria were detected, including Pasteurella species (4/14), Bacillus species (2/14), Neisseria species (3/14), Escherichia species (1/14) and Staphylococcus species (4/14).

DISCUSSION AND CONCLUSIONS

This study's findings will increase the understanding of the composition of cat oral flora in Hong Kong, which can provide more evidence-based information for the prophylactic treatment of patients with cat bite infections. Moreover, the study identified and detected the antibiotic resistance pattern and multidrug-resistant bacteria in the cat oral cavity, which can help cat owners increase their awareness of maintaining regular oral hygiene for their cats to prevent the spread of pathogens from cats to humans.

Helicobacter Pylori: A Review of Current Treatment Options in Clinical Practice

BACKGROUND

When prescribing antibiotics, infection eradication rates, local resistance rates, and cost should be among the most essential considerations. Helicobacter pylori is among the most common infections worldwide, and it can lead to burdensome sequela for the patient and the healthcare system, without appropriate treatment. Due to constantly fluctuating resistance rates, regimens must be constantly assessed to ensure effectiveness.

METHODS

This was a narrative review. The sources for this review are as follows: searching on PubMed, Google Scholar, Medline, and ScienceDirect; using keywords: Helicobacter pylori, Treatment Options, Clinical Practice.

RESULTS

Multiple antibiotics are prescribed as part of the regimen to thwart high resistance rates. This can lead to unwanted adverse reactions and adherence issues, due to the amount and timing of medication administration, which also may contribute to resistance. Single-capsule combination capsules have reached the market to ease this concern, but brand-only may be problematic for patient affordability. Due to the previously mentioned factors, effectiveness and affordability must be equally considered.

CONCLUSIONS

This review will utilize guidelines to discuss current treatment options and give cost considerations to elicit the most effective regimen for the patient.

Disentangling the microbial ecological factors impacting honey bee susceptibility to Paenibacillus larvae infection

Paenibacillus larvae is a spore-forming bacterial entomopathogen and causal agent of the important honey bee larval disease, American foulbrood (AFB). Active infections by vegetative P. larvae are often deadly, highly transmissible, and incurable for colonies but, when dormant, the spore form of this pathogen can persist asymptomatically for years. Despite intensive investigation over the past century, this process has remained enigmatic. Here, we provide an up-to-date synthesis on the often overlooked microbiota factors involved in the spore-to-vegetative growth transition (corresponding with the onset of AFB disease symptoms) and offer a novel outlook on AFB pathogenesis by focusing on the 'collaborative' and 'competitive' interactions between P. larvae and other honey bee-adapted microorganisms. Furthermore, we discuss the health trade-offs associated with chronic antibiotic exposure and propose new avenues for the sustainable control of AFB via probiotic and microbiota management strategies.

Alternative strategies for Chlamydia treatment: Promising non-antibiotic approaches

Chlamydia is an obligate intracellular bacterium where most species are pathogenic and infectious, causing various infectious diseases and complications in humans and animals. Antibiotics are often recommended for the clinical treatment of chlamydial infections. However, extensive research has shown that antibiotics may not be sufficient to eliminate or inhibit infection entirely and have some potential risks, including antibiotic resistance. The impact of chlamydial infection and antibiotic misuse should not be underestimated in public health. This study explores the possibility of new therapeutic techniques, including a review of recent studies on preventing and suppressing chlamydial infection by non-antibiotic compounds.

Serious Risk of Tigecycline Resistance in Escherichia coli Isolated from Swine Manure

The emergence of the plasmid-mediated tigecycline resistance gene tetX family in pig farms has attracted worldwide attention. The use of tetracycline antibiotics in pig farms has a facilitating effect on the prevalence of the tetX family, but the relationship among its presence, expression, and resistance phenotype in resistant bacteria is unknown. In this study, the presence and expression characteristics of tetracycline resistance genes (TRGs) in 89 strains of doxycycline-resistant E. coli (DRE) isolated from pig manure samples from 20 pig farms under low concentrations of doxycycline stress (2 μg/mL) were analyzed. The detection rate of tetO was 96.63%, which is higher than those of other TRGs, such as tetA (94.38%), tetX (76.40%), tetB (73.03%), and tet(X4) (69.66%). At least three TRG types were present in DRE strains, which thus showed extensive resistance to tetracycline antibiotics, and 37% of these strains were resistant to tigecycline. In the presence of a low concentration of doxycycline, tetA played an important role, and the expression and existence ratio of TRGs indicated low expression of TRGs. Furthermore, the doxycycline resistance of DRE was jointly determined by the total absolute abundance of TRGs, and the absolute abundance of tetX and tet(X4) was significantly positively associated with tigecycline resistance in DRE (P < 0.05). Overall, DRE isolated from swine manure is an important reservoir of the tetX family, which suggests that DRE in swine manure has a high risk of tigecycline resistance, poses a potential threat to human health, and should be of public concern.

Tetracycline photolysis revisited: Overlooked day-night succession of the parent compound and metabolites in natural surface waters and associated ecotoxicity

Despite the extensive study of tetracycline photolysis in aquatic environments, the phototransformation of tetracycline and its metabolites under natural day-night succession has not been examined. In this study, we investigated tetracycline photolysis and associated ecotoxicity in two natural surface waters and one artificial ultrapure water under simulated day/night cycling over two days. Previously unrecognized and highly pH- and temperature-dependent dark interconversions of tetracycline metabolites were observed. The liquid chromatography-mass spectrometry/mass spectrometry analysis identified a range of isomerized, hydroxylated, demethylated, deaminated, and open-ring photoproducts. The hydrolysis of tetracycline, isotetracycline, and several intermediate products was proposed as the major mechanism for the observed dark transformations. Exposure studies employing Escherichia coli indicated that although the tetracycline degradation products had lower bacterial toxicities than the parent compound, increasing toxicity with irradiation time after the near-complete degradation of the parent compound in natural waters implied that product mixtures retain ecotoxicity. The dark transformations also affected the bacterial toxicity and fluorescence properties of irradiated tetracycline solutions. Overall, this study provides new insights into the photochemical behavior of tetracycline and its associated ecological risk in aquatic environments.

Antimicrobial Resistance and Its Drivers-A Review

Antimicrobial resistance (AMR) is a critical issue in health care in terms of mortality, quality of services, and financial damage. In the battle against AMR, it is crucial to recognize the impacts of all four domains, namely, mankind, livestock, agriculture, and the ecosystem. Many sociocultural and financial practices that are widespread in the world have made resistance management extremely complicated. Several pathways, including hospital effluent, agricultural waste, and wastewater treatment facilities, have been identified as potential routes for the spread of resistant bacteria and their resistance genes in soil and surrounding ecosystems. The overuse of uncontrolled antibiotics and improper treatment and recycled wastewater are among the contributors to AMR. Health-care organizations have begun to address AMR, although they are currently in the early stages. In this review, we provide a brief overview of AMR development processes, the worldwide burden and drivers of AMR, current knowledge gaps, monitoring methodologies, and global mitigation measures in the development and spread of AMR in the environment.

Biogeographical variation in antimicrobial resistance in rivers is influenced by agriculture and is spread through bacteriophages

Antibiotic resistance is currently an extensive medical challenge worldwide, with global numbers increasing steadily. Recent data have highlighted wastewater treatment plants as a reservoir of resistance genes. The impact of these findings for human health can best be summarized using a One Health concept. However, the molecular mechanisms impacting resistance spread have not been carefully evaluated. Bacterial viruses, that is bacteriophages, have recently been shown to be important mediators of bacterial resistance genes in environmental milieus and are transferrable to human pathogens. Herein, we investigated the biogeographical impact on resistance spread through river-borne bacteriophages using amplicon deep sequencing of the microbiota, absolute quantification of resistance genes using ddPCR, and phage induction capacity within wastewater. Microbial biodiversity of the rivers is significantly affected by river site, surrounding milieu and time of sampling. Furthermore, areas of land associated with agriculture had a significantly higher ability to induce bacteriophages carrying antibiotic resistance genes, indicating their impact on resistance spread. It is imperative that we continue to analyse global antibiotic resistance problem from a One Health perspective to gain novel insights into mechanisms of resistance spread.

The strategy for organic dye and antibiotic photocatalytic removal for water remediation in an example of Co-SnO2 nanoparticles

A challenging problem to create an efficient photocatalyst suitable for industrial water remediation, aiming to remove cyclic organic compounds attracts increasing attention. The current study aimed to clarify a few "dark spots" in the field, namely to find out if it is possible to make an efficient photocatalyst activated with visible light by using a simple and cheap strategy and what are the key factor impacting its efficiency. In this work, a new procedure to obtain spherical nanoparticles with the same average size but different amounts of oxygen vacancies and defects and dopant concentrations was developed. The approach based on hydrothermal treatment was suggested to obtain rod-shaped nanoparticles. The systematic study of photocatalytic behavior on the example of oxytetracycline and methylene blue degradation under visible light of widely available LED lamp was performed. Based on chemical and computational experiments the main factor affecting the process efficiency was determined.

Development and Clinical Application of a Rapid and Visual Loop-Mediated Isothermal Amplification Test for tetM gene in Clostridioides difficile Strains Cultured from Feces

OBJECTIVES

To develop a rapid and visual loop-mediated isothermal amplification (LAMP) assay targeting the tetM gene in Clostridioides difficile (C. difficile) strains cultured from feces.

METHODS

Primers were designed to recognize the tetM gene in C. difficile by LAMP, using turbidity and visual detection. The sensitivity and specificity of LAMP primers was determined. Besides, We conducted both LAMP and polymerase chain reaction (PCR) for the tcdA, tcdB, cdtA, cdtB, ermB, tetM genes in 300 toxigenic C. difficile strains cultured from feces.

RESULTS

The target DNA was amplified and visualized within 60 minutes at a temperature of 62°C. A total of 26 bacterial strains were found negative for tetM, which manifested high specificity of the primers. The detection limit of LAMP was 36.1 pg/µl, which was 100-fold more sensitive than PCR. The positive rate of tetM in toxigenic C. difficile strains cultured from feces was 93.3% by both LAMP and PCR. The proportion of toxin types in those C. difficile strains was 95.7% for A+B+CDT-, 4% for A-B+CDT-, and 0.3% for A+B+CDT+, respectively.

CONCLUSIONS

This is the first study examining tetM gene in C. difficile strains cultured from feces by LAMP. Its high specificity and sensitivity, as well as visual detection, make the new assay a powerful diagnostic tool for rapid testing.

Tetracyclines and bone: Unclear actions with potentially lasting effects

Tetracyclines are a broad-spectrum class of antibiotics that have unclear actions with potentially lasting effects on bone metabolism. Initially isolated from Streptomyces, tetracycline proved to be an effective treatment for Gram +/- infections. The emergence of resistant bacterial strains commanded the development of later generation agents, including minocycline, doxycycline, tigecycline, sarecycline, omadacycline, and eravacycline. In 1957, it was realized that tetracyclines act as bone fluorochrome labels due to their high affinity for the bone mineral matrix. Over the course of the next decade, researchers discerned that these compounds are retained in the bone matrix at high levels after the termination of antibiotic therapy. Studies during this period provided evidence that tetracyclines could disrupt prenatal and early postnatal skeletal development. Currently, tetracyclines are most commonly prescribed as a long-term systemic therapy for the treatment of acne in healthy adolescents and young adults. Surprisingly, the impact of tetracyclines on physiologic bone modeling/remodeling is largely unknown. This article provides an overview of the pharmacology of tetracycline drugs, summarizes current knowledge about the impact of these agents on skeletal development and homeostasis, and reviews prior work targeting tetracyclines' effects on bone cell physiology. The need for future research to elucidate unclear effects of tetracyclines on the skeleton is addressed, including drug retention/release mechanisms from the bone matrix, signaling mechanisms at bone cells, the impact of newer third generation tetracycline antibiotics, and the role of the gut-bone axis.

A study of the effect of reactive oxygen species induced by violet and blue light from oxytetracycline on the deactivation of Escherichia coli

Oxytetracycline (OTC), a tetracycline antibiotic, is a broad-spectrum antibacterial agent. In this investigation, liquid chromatography-mass spectrometry (LC-MS) is utilized to determine the effects of blue light (λ = 448 nm) illumination (BLIA) and violet light (λ = 403 nm) illumination (VLIA) on conformational changes in OTC at pH 7.8. The photochemical effect of OTC that is exposed to BLIA and VLIA on the deactivation of Escherichia coli (E. coli) is studied. The deactivation of E. coli has an insignificant effect on treatment with OTC alone. OTC is relatively unstable under BLIA and VLIA illumination in an alkaline solution, and OTC has been shown to inactivate E. coli by generating reactive oxygen species (ROS). Less anionic superoxide radicals (O₂^•-) are generated from OTC that is treated with BLIA than that from VLIA treatment, so OTC is more efficient in inactivating E. coli under VLIA. Inactivation of reduction rates of 0.51 and 3.65 logs in E. coli are achieved using 0.1 mM OTC under BLIA for 120 min and VLIA for 30 min, respectively, under the same illumination intensity (20 W/m²). Two photolytic products of OTC (PPOs) are produced when OTC is exposed to BLIA and VLIA, with molecular ions at m/z 447 and 431, molecular formulae C₂₁H₂₂N₂O₉ and C₂₁H₂₂N₂O₈, and masses of 446.44 and 430.44 g/mol, respectively. The results show that when exposed to VLIA, OTC exhibits enhanced inactivation of E. coli, suggesting that the photochemical treatment of OTC is a potential supplement in a hygienic process.

Sonosynthesis of nanobiotics with antimicrobial and antioxidant properties

Transforming small-molecule antibiotics into carrier-free nanoantibiotics represents an opportunity for developing new multifunctional therapeutic agents. In this study, we demonstrate that acoustic cavitation produced by high-frequency ultrasound transforms the antibiotic doxycycline into carrier-free nanobiotics. Upon sonication for 1 h at 10-15 W cm^-3, doxycycline molecules underwent hydroxylation and dimerization processes to ultimately self-assemble into nanoparticles of ∼100-200 nm in size. Micrometer sized particles can be also obtained by increasing the acoustic power to 20 W cm^-3. The nanodrugs exhibited antioxidant properties, along with antimicrobial activity against both Gram-positive (S. aureus) and Gram-negative (E. coli) bacterial strains. Our results highlight the feasibility of the ultrasound-based approach for engineering drug molecules into a nanosized formulation with controlled and multiple bio-functionalities.

Antibiotics Resistance in Escherichia coli Isolated from Livestock in the Emirate of Abu Dhabi, UAE, 2014–2019

Escherichia coli (E. coli) is a zoonotic pathogen that showed growing resistance to antibiotics. No descriptive analysis highlights the threat of antimicrobial-resistant (AMR) of E. coli among livestock in the United Arab Emirates (UAE). Herein, we conducted phenotypic and genotypic resistance studies on E. coli isolates from livestock samples in the Emirate of Abu Dhabi based on routine diagnosis between the periods 2014–2019. Bacterial culture and disk diffusion methods were used for bacterial isolation and phenotypic resistance analysis. Resistance mechanism was studied by PCR targeting the most commonly resistance genes: ampicillin (blaSHV, blaCMY, and blaTEM-1B), tetracyclines (tetA and tetB), co-trimoxazole [sulfamethoxazole (sul1, sul2, and sul3) + trimethoprim (dfrA1 and dfrA17)], aminoglycosides [aph(3'')-Ia, aph(6)-Id, and aac(3)-IV], and fluoroquinolones (qnrA and aac(6’)-Ib-cr). Analysis of 165 E. coli isolates showed resistant to ampicillin, tetracycline, co-trimoxazole, gentamicin, and enrofloxacin by 157/165 (95.4%), 154/165 (93.6%), 141/165 (86%), 139/165 (85%), and 135/165 (82.7%), respectively. Predominant resistance gene/s detected by PCR were blaCMY (119/160, 72%) and blaTEM-1B (154/160, 96.3%) for ampicillin; tetA (162/164, 98.8%) and tetB (112/164, 68.3%) for tetracyclines; sul2 (156/164, 95%), sul3 (138/164, 84%), and dfra17 (74/164, 44.5%) for co-trimoxazole; aph(3'')-Ia (134/164, 82.1%) and aph(6)-Id (161/164, 98.2%) for aminoglycosides; and aac(6’)-Ib-cr (61/61, 100%) for enrofloxacin. Both phenotypic and genotypic analyses revealed that all E. coli isolates were multidrug-resistant (resistance to 3, 4, and 5 antibiotics classes by 3.6%, 57.6%, and 38.8%, respectively) carrying one or more resistance gene/s for the same antibiotic. PCR profiling confirmed the presence of resistance genes corresponding to their antibiotic profile. Results of the study will highlight the knowledge based on E. coli AMR related to livestock in UAE that may call for interventions.

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.

Oxytetracycline and Streptomycin Resistance Genes in Xanthomonas arboricola pv. pruni, the Causal Agent of Bacterial Spot in Peach

Xanthomonas arboricola pv. pruni (Xap) causes bacterial spot, a major worldwide disease of Prunus species. Very few chemical management options are available for this disease and frequent applications of oxytetracycline (OTC) in the United States peach orchards have raised concerns about resistance development. During 2017-2020, 430 Xap strains were collected from ten peach orchards in South Carolina. Seven OTC-resistant (OTC R ) Xap strains were found in 2017 and 2020 from four orchards about 20-270 km apart. Interestingly, the seven strains were also resistant to streptomycin (STR). Six strains grew on media amended with ≤100 μg/mL OTC, while one strain, R1, grew on ≤250 μg/mL OTC. Genome sequence analysis of four representative OTC R strains revealed a 14-20 kb plasmid carrying tetC, tetR, and strAB in each strain. These three genes were transferable to Xanthomonas perforans via conjugation, and they were PCR confirmed in all seven OTC R Xap strains. When tetC and tetR were cloned and expressed together in a sensitive strain, the transconjugants showed resistance to ≤100 μg/mL OTC. When tetC was cloned and expressed alone in a sensitive strain, the transconjugants showed resistance to ≤250 μg/mL OTC. TetC and tetR expression was inducible by OTC in all six wild-type strains resistant to ≤100 μg/mL OTC. However, in the R1 strain resistant to ≤250 μg/mL OTC, tetR was not expressed, possibly due to the presence of Tn3 in the tetR gene, and in this case tetC was constitutively expressed. These data suggest that tetC confers OTC resistance in Xap strains, and tetR regulates the level of OTC resistance conferred by tetC. To our knowledge, this is the first report of OTC resistance in plant pathogenic xanthomonads.

Comparative analysis of antimicrobial resistance and genetic characteristics of Escherichia coli from broiler breeder farms in Korea

Broiler breeder farms could be a reservoir of Escherichia coli, disseminating antimicrobial resistance and virulence factors. We investigated the antimicrobial resistance of E. coli from nine broiler breeder farms and characterised their resistance and virulence genes. A total of 256 E. coli showed a high level of resistance to tetracycline, nalidixic acid, ampicillin, and cephalothin, followed by trimethoprim-sulfamethoxazole and chloramphenicol. The resistance to nalidixic acid, ampicillin, trimethoprim–sulfamethoxazole, and chloramphenicol showed significant differences among the farms. Among 202 β-lactam-resistant E. coli, 138 carried β-lactamase genes. The most prevalent β-lactamase gene was blaTEM-1, of which the presence differed significantly across the farms. Out of 197 tetracycline-resistant E. coli isolates, tetA and tetB were detected in 164 and 50, with significant differences among the farms. Also, 45 of 196 nalidixic acid-resistant E. coli carried qnrS while 67 of 149 trimethoprim–sulfamethoxazole-resistant E. coli carried sul2. Among the five virulence genes tested, ompT was the most prevalent, and all genes except for iutA distributed significantly different among the farms. The phenotypic and genotypic characteristics of E. coli were significantly different among the farms; therefore, management at the breeder level is required to control the vertical transmission of E. coli.

The evaluation of ESBL genes and antibiotic resistance rate in Escherichia coli strains isolated from meat and intestinal contents of turkey in Isfahan, Iran

BACKGROUND

Extended spectrum beta-lactamase (ESBL) has been described in Escherichia coli strains that have been isolated from humans and animals; it has induced a main concern with antibiotic resistance in serious bacterial infections.

AIMS

This study aimed to investigate the frequency of ESBL-producing E. coli (EPE) strains in meat and intestinal contents of turkey, and to compare the antibiotic resistance profile between EPE and non-EPE strains.

METHODS

Totally, 70 and 110 E. coli strains were isolated from turkey meat and turkey intestinal content samples, respectively. To determine EPE strains, double disc synergy test was applied by that 20 and 22 EPE strains were finally identified in meats and intestinal contents of the turkeys, respectively. Antibiotic susceptibility was exerted using disc diffusion method. Escherichia coli isolates were then characterized for virulence genes (stx-1 and stx-2) and ESBL genes (TEM, SHV, and CTX-M).

RESULTS

None of the E. coli strains harbored stx genes. The EPE strains in comparison with non-EPE strains were significantly more resistant to ciprofloxacin (47.6 vs 26.5%), tetracycline (80.9 vs 67.3%), ampicillin (47.6 vs 22.4%), penicillin (23.8 vs 10.2%), ceftazidime (57.1 vs 16.3%), ceftriaxone (38.1 vs 18.4%), and cefotaxime (47.6 vs 8.2%). The majority of EPE strains carried CTX-M gene. SHV showed the lowest frequency and it was not detected in EPE strains isolated from the intestinal contents. In this study, 75% of TEM-producing E. coli strains and 33% of SHV-producing E. coli strains were resistant to ampicillin. In addition, 41.7% of TEM-producing E. coli strains were resistant to penicillin, and 76.9% of CTX-producing E. coli were resistant to cefotaxime. Furthermore, 4.7% of EPE strains isolated from turkey meat were imipenem resistant.

CONCLUSION

The resistance to cefotaxime and imipenem in EPE strains induces a concern in growing antibiotic resistance against broad spectrum antibiotics in E. coli strains.

Gene sharing among plasmids and chromosomes reveals barriers for antibiotic resistance gene transfer

The emergence of antibiotic resistant bacteria is a major threat to modern medicine. Rapid adaptation to antibiotics is often mediated by the acquisition of plasmids carrying antibiotic resistance (ABR) genes. Nonetheless, the determinants of plasmid-mediated ABR gene transfer remain debated. Here, we show that the propensity of ABR gene transfer via plasmids is higher for accessory chromosomal ABR genes in comparison with core chromosomal ABR genes, regardless of the resistance mechanism. Analysing the pattern of ABR gene occurrence in the genomes of 2635 Enterobacteriaceae isolates, we find that 33% of the 416 ABR genes are shared between chromosomes and plasmids. Phylogenetic reconstruction of ABR genes occurring on both plasmids and chromosomes supports their evolution by lateral gene transfer. Furthermore, accessory ABR genes (encoded in less than 10% of the chromosomes) occur more abundantly in plasmids in comparison with core ABR genes (encoded in greater than or equal to 90% of the chromosomes). The pattern of ABR gene occurrence in plasmids and chromosomes is similar to that in the total Escherichia genome. Our results thus indicate that the previously recognized barriers for gene acquisition by lateral gene transfer apply also to ABR genes. We propose that the functional complexity of the underlying ABR mechanism is an important determinant of ABR gene transferability. This article is part of the theme issue 'The secret lives of microbial mobile genetic elements'.

Antimalarial Natural Products

Natural products have made a crucial and unique contribution to human health, and this is especially true in the case of malaria, where the natural products quinine and artemisinin and their derivatives and analogues, have saved millions of lives. The need for new drugs to treat malaria is still urgent, since the most dangerous malaria parasite, Plasmodium falciparum, has become resistant to quinine and most of its derivatives and is becoming resistant to artemisinin and its derivatives. This volume begins with a short history of malaria and follows this with a summary of its biology. It then traces the fascinating history of the discovery of quinine for malaria treatment and then describes quinine's biosynthesis, its mechanism of action, and its clinical use, concluding with a discussion of synthetic antimalarial agents based on quinine's structure. The volume then covers the discovery of artemisinin and its development as the source of the most effective current antimalarial drug, including summaries of its synthesis and biosynthesis, its mechanism of action, and its clinical use and resistance. A short discussion of other clinically used antimalarial natural products leads to a detailed treatment of other natural products with significant antiplasmodial activity, classified by compound type. Although the search for new antimalarial natural products from Nature's combinatorial library is challenging, it is very likely to yield new antimalarial drugs. The chapter thus ends by identifying over ten natural products with development potential as clinical antimalarial agents.

Molecular detection and antibiotyping of multi-drug resistant Enterococcus faecium from healthy broiler chickens in Bangladesh

BACKGROUND

Enterococcus faecium is a ubiquitously distributed member of the intestinal microbiota of both humans and animals. Antibiotic resistant E. faecium are a major public health concern.

OBJECTIVES

This study aimed to detect multi-drug resistant (MDR) E. faecium and their antibiotic resistance genes from broiler chickens in Bangladesh.

METHODS

A total of 100 faecal samples of healthy broilers were screened by conventional methods and polymerase chain reaction (PCR) to detect E. faecium and their resistance genes. Disk diffusion test was employed to determine antibiotic profiles.

RESULTS

By PCR, among 100 samples, 45% [95% confidence interval (CI): 35.62%-54.76%] were positive for E. faecium. Based on antibiogram, all the E. faecium isolates were found resistant to ampicillin, and frequently (93.33%-55.56%) resistant to ceftriaxone, cefotaxime, streptomycin, erythromycin, and imipenem; moderate to lower (26.67%-4.44%) resistance to tetracycline, ciprofloxacin, norfloxacin, chloramphenicol, gentamicin, and vancomycin. Interestingly, 80% (95% CI: 66.18%-89.10%) E. faecium isolates were MDR in nature. In addition, the indices of multiple antibiotic resistance (MAR) ranged from 0.08 to 0.83. By bivariate analysis, high positive significant correlations were observed between resistance profiles of erythromycin and imipenem, ciprofloxacin and norfloxacin, erythromycin and streptomycin, ceftriaxone and cefotaxime, tetracycline and chloramphenicol, and streptomycin and imipenem. Furthermore, the prevalence of resistance genes of E. faecium was 58.33% (tetA), 33.33% (tetB), 35.56% (blaTEM ), 60% (CITM), 13.33% (aadA1), and 12% (SHV).

CONCLUSIONS

To the best of our knowledge, this is the first study in Bangladesh to detect MDR and MAR E. faecium and their associated resistance genes. The detection of MDR and MAR E. faecium and their corresponding resistance genes from healthy broilers is of public health concern because of their potential to enter into the food chain.

Effects of free radicals from doxycycline hyclate and minocycline hydrochloride under blue light irradiation on the deactivation of Staphylococcus aureus, including a methicillin-resistant strain

Doxycycline hyclate (DCH) and minocycline hydrochloride (MH) are tetracycline antibiotics and broad-spectrum antimicrobial agents. The changes in DCH and MH under blue light (λ = 462 nm) irradiation in alkaline conditions (BLIA) were investigated. Deactivation caused by superoxide anion radical (O₂^•-) and deactivation from DCH and MH during photolysis on Staphylococcus aureus (S. aureus), including methicillin-resistant S. aureus (MRSA), were studied. DCH is relatively unstable compared to MH under BLIA. The level of O₂^•- generated from the MH-treated photoreaction is lower than that from DCH photolysis, and the DCH-treated photoreaction is more efficient at inactivating S. aureus and MRSA at the same radiant intensity. DCH subjected to BLIA decreased the viability of S. aureus and MRSA by 3.84 and 5.15 log, respectively. Two photolytic products of DCH (PPDs) were generated under BLIA. The mass spectra of the PPDs featured molecular ions at m/z 460.8 and 458.8. The molecular formulas of the PPDs were C₂₁H₂₂N₂O₁₀ and C₂₂H₂₄N₂O₉, and their exact masses were 462.44 and 460.44 g/mol, respectively. These results bolster the photolytic oxidation that leads to DCH-enhanced deactivation of S. aureus and MRSA. Photochemical treatment of DCH could be applied as a supplement in hygienic processes.

A brief overview of classical natural product drug synthesis and bioactivity

This manuscript briefly overviewed the total synthesis and structure–activity relationship studies of eight classical natural products, which emphasizes the important role of total synthesis in natural product-based drug development.

Resistance to Antibiotics in Thermophilic Campylobacters

Campylobacter jejuni (C. jejuni) is one of the most frequent causes of bacterial enterocolitis globally. The disease in human is usually self-limiting, but when complications arise antibiotic therapy is required at a time when resistance to antibiotics is increasing worldwide. Mechanisms of antibiotic resistance in bacteria are diverse depending on antibiotic type and usage and include: enzymatic destruction or drug inactivation; alteration of the target enzyme; alteration of cell membrane permeability; alteration of ribosome structure and alteration of the metabolic pathway(s). Resistance of Campylobacter spp. to antibiotics, especially fluoroquinolones is now a major public health problem in developed and developing countries. In this review the mechanisms of resistance to fluoroquinolones, macrolides, tetracycline, aminoglycoside and the role of integrons in resistance of Campylobacter (especially at the molecular level) are discussed, as well as the mechanisms of resistance to β-lactam antibiotics, sulphonamides and trimethoprim. Multiple drug resistance is an increasing problem for treatment of campylobacter infections and emergence of resistant strains and resistance are important One Health issues.

Comparison of antimicrobial resistance and molecular characterization of Escherichia coli isolates from layer breeder farms in Korea

In Korea, 4 big layer companies that possess one grandparent and 3 parent stocks are in charge of 100% of the layer chicken industry. In this study, we investigated the antimicrobial resistance of commensal 578 E. coli isolated from 20 flocks of 4-layer breeder farms (A, B, C, and D), moreover, compared the characteristics of their resistance and virulence genes. Isolates from farms B and D showed significantly higher resistance to the β-lactam antimicrobials (amoxicillin, ampicillin, and 1st-, 2nd-, and 3rd-generation cephalosporins). However, resistance to ciprofloxacin, nalidixic acid, and tetracycline was significantly higher in the isolates from farm A (P < 0.05). Interestingly, the isolates from farm C showed significantly lower resistance to most antimicrobials tested in this study. The isolates from farms B, C, and D showed the high multiple resistance to the 3 antimicrobial classes. Furthermore, the isolates from farm A showed the highest multiple resistance against the 5 classes. Among the 412 β-lactam-resistant isolates, 123 (29.9%) carried bla_TEM-1, but the distribution was significantly different among the farms from 17.5% to 51.4% (P < 0.05). Similarly, the most prevalent tetracycline resistance gene in the isolates from farms B, C, and D was tetA (50.0–77.0%); however, the isolates from farm A showed the highest prevalence in tetB (70.6%). The distribution of quinolone (qnrB, qnrD, and qnrS) and sulfonamide (su12)-resistant genes were also significantly different among the farms but that of chloramphenicol (catA1)- and aminoglycoside (aac [3]-II, and aac [6′]-Ib)-resistant genes possessed no significant difference among the farms. Moreover, the isolates from farm C showed significantly higher prevalence in virulence genes (iroN, ompT, hlyF, and iss) than the other 3 farms (P < 0.05). Furthermore, the phenotypic and genotypic characteristics of E. coli isolates were significantly different among the farms, and improved management protocols are required to control of horizontal and vertical transmission of avian disease, including the dissemination of resistant bacteria in breeder flocks.

Antibiotic resistance in agriculture: Perspectives on upcoming strategies to overcome upsurge in resistance

Antibiotic resistance is a massive problem rising constantly and spreading rapidly since the past decade. The major underlying mechanism responsible for this problem is an overuse or severe misuse of antibiotics. Regardless of this emerging global threat, antibiotics are still being widely used, not only for treatment of human infections, but also to a great extent in agriculture, livestock and animal husbandry. If the current scenario persists, we might enter into a post-antibiotic era where drugs might not be able to treat even the simplest of infections. This review discusses the current status of antibiotic utilization and molecular basis of antibiotic resistance mechanisms acquired by bacteria, along with the modes of transmittance of the resultant resistant genes into human pathogens through their cycling among different ecosystems. The main focus of the article is to provide an insight into the different molecular and other strategies currently being studied worldwide for their use as an alternate to antibiotics with an overall aim to overcome or minimize the global problem of antibiotic resistance.

Genetic and evolutionary characterization of the Major Facilitator Superfamily transporters of the antibacterial, Pantoea Natural Product 3

Pantoea Natural Product 3 (PNP-3) is an antibiotic produced by Pantoea agglomerans that is effective against a broad range of multi-drug resistant bacteria. PNP-3 is encoded by a unique, eight-gene biosynthetic gene cluster composed of predicted enzymes (pnp3b, pnp3e-h), a regulator (pnp3d), and two Major Facilitator Superfamily transporters (pnp3a and pnp3c). To better characterize the role of the transporters, we generated pnp3a and pnp3c mutants and evaluated PNP-3 production. Disruption of pnp3a in Pantoea results in impaired growth and loss of antibiosis, suggesting a role in PNP-3 export and resistance. In contrast, pnp3c mutants display only reduced antibiotic production/export, suggesting a minor role for Pnp3c. Expression of pnp3a in susceptible Erwinia amylovora led to increased PNP-3 tolerance, while co-expression of pnp3a and pnp3e-h resulted in the production and export of PNP-3. Comparative genomic analyses identified pnp3a in 12 other Pantoea strains, eight of which carry a complete or nearly complete PNP-3 biosynthetic cluster. The four other Pantoea strains that carry pnp3a lack most of the PNP-3 cluster; however, they are PNP-3 tolerant. These results suggest Pnp3a plays an essential role in PNP-3 export and resistance in Pantoea.

Genetic and antimicrobial resistance profiles of non-O157 Shiga toxin-producing Escherichia coli from different sources in Egypt

BACKGROUND

The Shiga toxin-producing Escherichia coli (STEC) represented a great risk to public health. In this study, 60 STEC strains recovered from broiler and duck fecal samples, cow's milk, cattle beef, human urine, and ear discharge were screened for 12 virulence genes, phenotypic and genotypic antimicrobial resistance, and multiple-locus variable-number tandem-repeat analysis (MLVA).

RESULTS

The majority of strains harbored Shiga toxin 1 (stx₁) and stx_1d, stx₂ and stx_2e, and ehxA genes, while a minority harbored stx_2c subtype and eaeA. We identified 10 stx gene combinations; most of strains 31/60 (51.7%) exhibited four copies of stx genes, namely the stx₁, stx_1d, stx₂, and stx_2e, and the strains exhibited a high range of multiple antimicrobial resistance indices. The resistance genes blaCTX-M-1 and blaTEM were detected. For the oxytetracycline resistance genes, most of strains contained tetA, tetB, tetE, and tetG while the tetC was present at low frequency. MLVA genotyping resolved 26 unique genotypes; genotype 21 was highly prevalent. The six highly discriminatory loci DI = 0.9138 are suitable for the preliminary genotyping of STEC from animals and humans.

CONCLUSIONS

The STEC isolated from animals are virulent, resistant to antimicrobials, and genetically diverse, thus demands greater attention for the potential risk to human.

Antibiogram Profile of Acinetobacterbaumannii Recovered from Selected Freshwater Resources in the Eastern Cape Province, South Africa

Acinetobacter species have been found in a variety of environments, including soil, food, plants, hospital environments and water. Acinetobacter baumannii is an opportunistic and emerging waterborne pathogen. It has been implicated in several nosocomial infections that demonstrate resistance to commonly administered antibiotics. We investigated phenotypic antibiotic resistance (PAR) and relevant antibiotic resistance genes (ARGs) in A. baumannii isolated from three freshwater resources in the Eastern Cape Province, South Africa; A. baumannii (410) was confirmed by the recA and gyrB genes of 844 suspected Acinetobacter species in the water samples. The PAR of the confirmed isolates was assessed using a panel of 11 antibiotics by the disc diffusion method, while ARGs were investigated in isolates exhibiting PAR. The A. baumannii isolates were resistant to piperacillin-tazobactam (11.2%), ceftazidime (12%), cefotaxime (18.8%), cefepime (8.8%), imipenem (2.7%), meropenem (4.15%), amikacin (2.4%), gentamicin (8.8%), tetracycline (16.8%), ciprofloxacin (11%) and trimethoprim/sulfamethoxazole (20.5%). For multidrug resistance (MDR), two isolates were resistant to all antibiotics and 28 isolates were resistant to imipenem and meropenem. Moreover, β-lactamases bla_TEM (64.4%) and bla_OXA-51 (28.70%) as well as sulphonamides sul1 (37.1%) and sul2 (49.4%) were common ARGs. Overall, PAR and ARGs had positive correlations (r) in all rivers. Detection of MDR-A. baumannii in freshwater resources could be linked to possible wastewater discharge from the nearby animal farms, indicating potential implications for public health.

Impact of Chronic Tetracycline Exposure on Human Intestinal Microbiota in a Continuous Flow Bioreactor Model

Studying potential dietary exposure to antimicrobial drug residues via meat and dairy products is essential to ensure human health and consumer safety. When studying how antimicrobial residues in food impact the development of antimicrobial drug resistance and disrupt normal bacteria community structure in the intestine, there are diverse methodological challenges to overcome. In this study, traditional cultures and molecular analysis techniques were used to determine the effects of tetracycline at chronic subinhibitory exposure levels on human intestinal microbiota using an in vitro continuous flow bioreactor. Six bioreactor culture vessels containing human fecal suspensions were maintained at 37 °C for 7 days. After a steady state was achieved, the suspensions were dosed with 0, 0.015, 0.15, 1.5, 15, or 150 µg/mL tetracycline, respectively. Exposure to 150 µg/mL tetracycline resulted in a decrease of total anaerobic bacteria from 1.9 × 10⁷ ± 0.3 × 10⁷ down to 2 × 10⁶ ± 0.8 × 10⁶ CFU/mL. Dose-dependent effects of tetracycline were noted for perturbations of tetB and tetD gene expression and changes in acetate and propionate concentrations. Although no-observed-adverse-effect concentrations differed, depending on the traditional cultures and the molecular analysis techniques used, this in vitro continuous flow bioreactor study contributes to the knowledge base regarding the impact of chronic exposure of tetracycline on human intestinal microbiota.

Antifungal Azoles as Tetracycline Resistance Modifiers in Staphylococcus aureus

Staphylococcus aureus has developed resistance to antimicrobials since their first use. The S. aureus major facilitator superfamily (MFS) efflux pump Tet(K) contributes to resistance to tetracyclines. The efflux pump diminishes antibiotic accumulation, and biofilm hampers the diffusion of antibiotics. None of the currently known compounds have been approved as efflux pump inhibitors (EPIs) for clinical use. In the current study, we screened clinically approved drugs for possible Tet(K) efflux pump inhibition. By performing in silico docking followed by in vitro checkerboard assays, we identified five azoles (the fungal ergosterol synthesis inhibitors) showing putative EPI-like potential with a fractional inhibitory concentration index of ≤0.5, indicating synergism. The functionality of the azoles was confirmed using ethidium bromide (EtBr) accumulation and efflux inhibition assays. In time-kill kinetics, the combination treatment with butoconazole engendered a marked increase in the bactericidal capacity of tetracycline. When assessing the off-target effects of the azoles, we observed no disruption of bacterial membrane permeability and polarization. Finally, the combination of azoles with tetracycline led to a significant eradication of preformed mature biofilms. This study demonstrates that azoles can be repurposed as putative Tet(K) EPIs and to reduce biofilm formation at clinically relevant concentrations. IMPORTANCE Staphylococcus aureus uses efflux pumps to transport antibiotics out of the cell and thus increases the dosage at which it endures antibiotics. Also, efflux pumps play a role in biofilm formation by the excretion of extracellular matrix molecules. One way to combat these pathogens may be to reduce the activity of efflux pumps and thereby increase pathogen sensitivity to existing antibiotics. We describe the in silico-based screen of clinically approved drugs that identified antifungal azoles inhibiting Tet(K), a pump that belongs to the major facilitator superfamily, and showed that these compounds bind to and block the activity of the Tet(K) pump. Azoles enhanced the susceptibility of tetracycline against S. aureus and its methicillin-resistant strains. The combination of azoles with tetracycline led to a significant reduction in preformed biofilms. Repurposing approved drugs may help solve the classical toxicity issues related to efflux pump inhibitors.