Resistance Genes Research Articles

Association of the tomato co-chaperone gene Sldnaj harboring a promoter deletion with susceptibility to Tomato spotted wilt virus (TSWV)

Abstract Tomato spotted wilt virus (TSWV) poses a significant threat as a devastating pathogen to the global production and quality of tomato (Solanum lycopersicum). Mining novel resistance genes within the tomato germplasm is an effective and environmentally friendly approach to combat TSWV. In this study, we investigated the mechanisms underlying high TSWV resistance in a specific tomato line after experimental inoculation, despite not possessing any known TSWV resistance genes. The candidate causal genes of disease resistance traits were finely mapped by constructing different genetic populations and performing bulk segregant analysis sequencing. This approach identified SlDnaJ (Solyc10g081220) as a key locus potentially regulating TSWV resistance. We determined a structural variant of SlDnaJ (designated Sldnaj) containing a 61-bp promoter sequence deletion that was specifically present in the germplasm of the susceptible M82 tomato plant lines. Sldnaj-knockout transgenic plants were significantly more resistant to TSWV than wild-type plants. Up-regulated expression of Sldnaj affected the salicylic acid/jasmonic acid signaling pathway, which induced and promoted the systemic infection of TSWV in M82 susceptible plants. In summary, this study identified a new candidate TSWV susceptibility gene with a natural deletion variation in tomato. These findings provide insights into the molecular mechanism underlying pathogen resistance while offering a target for breeding strategies of tomato with TSWV resistance.

A novel broad-spectrum bacteriophage cocktail against methicillin-resistant Staphylococcus aureus: Isolation, characterization, and therapeutic potential in a mastitis mouse model

Bovine mastitis is a considerable challenge within the dairy industry, causing significant financial losses and threatening public health. The increased occurrence of methicillin-resistant Staphylococcus aureus (MRSA) has provoked difficulties in managing bovine mastitis. Bacteriophage therapy presents a novel treatment strategy to combat MRSA infections, emerging as a possible substitute for antibiotics. This study evaluated the therapeutic potency of a novel bacteriophage cocktail against MRSA mastitis. Two new bacteriophages (vB_SauR_SW21 and vB_SauR_SW25) with potent lytic activity against MRSA were isolated and characterized. The one-step growth curve displayed a rapid latent period (20–35 min) and substantial burst size (418 and 316 PFU/ cell). In silico analyses have confirmed the absence of antimicrobial resistance or virulence factor-encoding genes within their genomes. According to the results, combining these phages augmented their host range and virulence. The phage cocktail significantly reduced bacterial burden in a BALB/c mastitis model, demonstrating efficacy comparable to antibiotic treatment. Moreover, its administration led to decreased concentrations of IL-1β and TNF-α compared to the negative control group. The bacteriophage cocktail (SW21-SW25) exhibits a promising profile for therapeutic applications and may represent a novel substitute to antibiotics for managing MRSA bovine mastitis.

Resistome and plasmidome genomic features of mcr-1.1-harboring E. coli: a One Health approach.

This study evaluated the phenotypic and genotypic traits of mcr-1.1-harboring Escherichia coli isolates from chickens, pigs, humans, and farm environments. The resistome and the mobile genetic elements associated with the spread of mcr-1.1 in Southern Brazil were also characterized. The 22 mcr-1.1-harboring E. coli isolates from different origins were selected for antimicrobial susceptibility testing and whole genome sequencing for characterization of the resistome, plasmids, and STs. All isolates presented several resistance genes and harbored the mcr-1.1 gene in a highly similar IncX4 plasmid. Furthermore, the mcr-1.1 gene co-occurred with the mcr-3.12 gene in a multidrug-resistant isolate from the farm environment. These findings demonstrate that the mcr-1.1 gene in E. coli isolates from Brazil is spreading mainly by horizontal transfer of the IncX4 plasmid. The co-occurrence of mcr-1.1 and mcr-3.12 highlights pig farming as an important reservoir of colistin resistance.

Unraveling Effects of miRNAs Associated with APR Leaf Rust Resistance Genes in Hybrid Forms of Common Wheat (Triticum aestivum L.)

The fungus Puccinia triticina Eriks (Pt) is the cause of leaf rust, one of the most damaging diseases, which significantly reduces common wheat yields. In Pt-resistant adult plants, an APR-type resistance is observed, which protects the plant against multiple pathogen races and is distinguished by its persistence under production conditions. With a more complete understanding of the molecular mechanisms underlying the function of APR genes, it will be possible to develop new strategies for resistance breeding in wheat. Currently, mainly APR genes, such as Lr34, Lr46, and Lr67, are principally involved in resistance breeding as they confer durable resistance to multiple fungal races occurring under different climatic and environmental conditions. However, the mechanisms underlying the defence against pathogens mediated by APR genes remain largely unknown. Our research aimed to shed light on the molecular mechanisms related to resistance genes and miRNAs expression, underlying APR resistance to leaf rust caused by Pt. Furthermore, the present study aimed to identify and functionally characterize the investigated miRNAs and their target genes in wheat in response to leaf rust inoculation. The plant material included hybrid forms of wheat from the F2 and BC1F1 generations, obtained by crossing the resistance cultivar Glenlea (CItr 17272) with agriculturally important Polish wheat cultivars. Biotic stress was induced in adult plants via inoculation with Pt fungal spores under controlled conditions. The RT-qPCR method was used to analyze the expression profiles of selected APR genes at five time points (0, 6, 12, 24, and 48 hpi). The results presented here demonstrate the differential expression of APR genes and miRNAs at stages of leaf rust development at selected timepoints after inoculation. We analyzed the expression of three leaf rust resistance genes, using different genetic backgrounds in F2 and BC1F1 segregation materials, in leaf tissues after Pt infection. Our goal was to investigate potential differences resulting from the genetic background found in different generations of hybrid forms of the same parental forms. Gene ontology analysis predicted 190 target genes for tae-miR5384-3p and 167 target genes for tae-miR9653b. Our findings revealed distinct expression profiles for genes, with the highest expression levels observed mainly at 6, 24, and 48 hpi. The candidate gene Lr46-Glu2 displayed an upregulation, suggesting its potential involvement in the immune response against Pt infection.

Pathogenic potential of ornithogenic <i>Escherichia coli</i> strains detected in the Earth's polar regions

Introduction. Pathogenic strains of Escherichia coli are an important object of surveillance within the One Health concept in the wild, agriculture and human society. Migratory bird colonies and high latitude avian colonies may be points of active intraspecies and interspecies contact between different animal species, accompanied by the spread of pathogens. At the same time, the phylogeography of E. coli in relation to the presence of natural foci of colibacillosis in polar regions remains virtually unstudied. The aim of this study was to assess the pathogenic potential of E. coli strains from the polar regions of the Earth, based on the analysis of the genomes of these bacteria from typical ornithogenic ecosystems of the Arctic and Antarctic. Materials and methods. The study used collections of E. coli isolated from ornithogenic biological material during expeditions to high latitude areas of the Arctic (archipelagos of Novaya Zemlya, Franz Josef Land, Svalbard) and Antarctic (Haswell Archipelago). 16 cultures associated with avian E. coli (12 polar and 4 temperate strains) were selected for genome-wide sequencing using BGI technology. The annotation of the genomes focused on the identification of genes for pathogenicity factors and antimicrobial resistance, as well as the identification of strains belonging to individual genetic lineages using the cgMLST method. Results. The annotation of the genomes allowed their assignment to different sequence types in the multilocus sequencing typing and genome-wide sequencing typing schemes. The analysis of the geographical distribution of the sequence types of polar E. coli strains determined by the cgMLST method showed their global representation in geographically distant regions of the planet. For example, cgST 133718 was observed in Antarctica (strain 17_1myr) and in the UK, and sequence 11903, to which strain 32-1 from the northernmost point of Novaya Zemlya belonged, was previously identified in the USA. All strains studied were characterized by the presence of extensive virulence. Among the pathogenicity factors identified were haemolysins A, E, F, siderophores, including the yersiniabactin gene cluster, a number of adhesion, colonization and invasion factors, as well as the thermostable enterotoxin EAST-1 and genes that characterize enteroaggregative strains of E. coli (the virulence regulator gene eilA and enteroaggregative protein (air)). One of the Arctic strains (33-1) had determinants of antibiotic resistance, in particular the extended-spectrum beta-lactamase gene TEM-1b and the Tn1721 transposon, including tetracycline resistance genes (tetA-TetR), were detected in its genome. Conclusion. The results of the study indicate the circulation of E. coli strains with strong pathogenic potential in high-latitude Arctic and Antarctic ornithogenic ecosystems. The analysis of genomic data indicates the presence of geographically widespread genetic lineages in these regions, which justifies the importance of monitoring epidemic clones of E. coli, along with monitoring for other pathogens, in bird colonies in high-latitude areas.

Biological Characteristics and Whole-Genome Analysis of a Porcine E. coli Phage

(1) Background: In recent years, the increasing emergence of multidrug-resistant pathogens in pig farms has begun to pose a severe threat to animal welfare and, by extension, public health. In this study, we aimed to explore the biological characteristics and genomic features of bacteriophages that are capable of lysing porcine multidrug-resistant E. coli, which was isolated from sewage. In doing so, we provided a reference for phage therapies that can be used to treat multidrug-resistant strains. (2) Method: Using the multidrug-resistant E. coli isolate sq-1 as the host bacterium, bacteriophages were isolated and purified from fecal samples using a double-layer agar plate method. The morphology was observed using a transmission electron microscope, and its host range, optimal multiplicity of infection (MOI), one-step growth curve, thermal stability, acid–base tolerance, and in vitro antibacterial ability were tested. Genomic features were analyzed using whole-genome sequencing. (3) Results: A lytic phage named vB_EcoS_Psq-1 (abbreviated as Psq-1) was successfully isolated. Electron microscopy revealed that Psq-1 belongs to the family of long-tailed phages, possessing clear and transparent plaques of approximately 1 mm in diameter. Psq-1 only lyses the host bacterium and does not affect other E. coli strains or other species of bacteria. The optimal MOI for phage Psq-1 was 0.1, with a latent period of 25 min, an exponential growth period of 25 min, and a lysis yield of 44.21 PFU/cell. Its activity remains stable at temperatures between 40 °C and 60 °C and from pH 4.0 to pH 13.0. Psq-1 exhibited a significant inhibitory effect on E. coli in liquid culture medium. The nucleic acid type of phage Psq-1 was dsDNA, with a total genome length of 44,183 bp and a GC content of 52.16%. No known resistance, lysogenic, or virulence-related genes were detected. The whole genome contains 55 open reading frames (ORFs). (4) Conclusions: This study isolated a bacteriophage that is capable of lysing multidrug-resistant E. coli. Characterized by a narrow E. coli lysis range, a long latent period, limited lytic ability, and stable biological properties, this bacteriophage can serve as a reference isolate for E. coli phages and can provide biological materials and data to support research on bacteriophages that are effective against multidrug-resistant porcine E. coli.

Cryo-EM structure and evolutionary history of the conjugation surface exclusion protein TraT

Conjugation plays a major role in dissemination of antimicrobial resistance genes. Following transfer of IncF-like plasmids, recipients become refractory to a second wave of conjugation with the same plasmid via entry (TraS) and surface (TraT) exclusion mechanisms. Here, we show that TraT from the pKpQIL and F plasmids (TraTpKpQIL and TraTF) exhibits plasmid surface exclusion specificity. The cryo-EM structures of TraTpKpQIL and TraTF reveal that they oligomerise into decameric champagne bottle cork-like structures, which are anchored to the outer membrane via a diacylglycerol and palmitic acid modified α-helical barrel domain. Unexpectedly, we identify chromosomal TraT homologues from multiple Gram-negative phyla which form numerous divergent lineages in a phylogenetic tree of TraT sequences. Plasmid-associated TraT sequences are found in multiple distinct lineages, including two separate clades incorporating TraT from Enterobacteriaceae IncF/F-like and Legionellaceae F-like plasmids. These findings suggest that different plasmid backbones have acquired and co-opted TraT on independent occasions.

Prevalence of Resistant Enterobacterales, in Particular ESBL-Producing Escherichia coli in Hospital Wastewater Discharged into the Environment: Study of the Abidjan District, Côte d’Ivoire

Aims: Hospital effluent constitutes a reservoir for antibiotic-resistant bacteria. In particular, Gram-negative bacteria carrying several antibiotic resistance genes. This study was to evaluate the prevalence of antibiotic-resistant Enterobacterales and ESBL Escherichia coli in hospital effluents. Methodology: In total, 112 wastewater samples from 4 hospital sites were collected and examined during 2020 at the Pasteur Institute of Côte d’ivoire. Enumeration of total Enterobacterales was carried out on McConkey agar. McConkey agar was supplemented with 4 mg/l ceftazidime to detect resistant Enterobacterales. Antibiotic-resistant Escherichia coli were identified using MALDI-TOF MS. The production of ESBL was investigated by synergy tests on Mueller-Hinton agar. Results: The results indicate a prevalence of resistant Enterobacterales varied between 4.6% and 2.6% with an average of 3.9%. A proportion of 69.2% of resistant Enterobacterales were strains of Escherichia coli. ESBL Escherichia coli represented a rate of 32.7% among resistant Enterobacterales. A rate of 47.3% of resistant Escherichia coli strains produced an ESBL. It appears from this study that the phenomenon of multi-resistance is undoubtedly present in bacteria isolated from hospital effluents, because the Enterobacterales isolated from these waters are mainly strains of ESBL-producing Escherichia coli. Conclusion: Resistant Enterobacterales and particularly ESBL-producing Escherichia coli present in hospital effluents released without treatment into the environment are likely to cause public health problems. These bacteria should be considered environmental pollutants.

Re-Examination Characterization and Screening of Stripe Rust Resistance Gene of Wheat TaPR1 Gene Family Based on the Transcriptome in Xinchun 32

Pathogenesis-related protein-1 (PR1) encodes a water-soluble protein produced in plants after pathogen infection or abiotic stimulation. It plays a crucial role in plant-induced resistance by attacking pathogens, degrading cell wall macromolecules and pathogen toxins, and inhibiting the binding of viral coat proteins to plant receptor molecules. Compared to model plants, the mechanism of action of PR1 in wheat remains underexplored. In this study, the recently published wheat genome database (IWGSC RefSeq V2.1) was used to identify 83 genes in the TaPR1 gene family. Compared to previous work, the duplicate genes were removed and we corrected misannotated genes. Fourteen TaPR1 genes involved in the wheat–Pst interaction were identified based on RNA sequencing from Xinchun 32. The expression patterns of eight genes were validated using qRT-PCR, and the results showed that PR1 was highly expressed following Puccinia striiformis f. sp. tritici (Pst) infection. This study enhances previous research on wheat PR1, contributing to a more comprehensive understanding of the TaPR1 gene family and providing a reference for the screening of more broad-spectrum and high-resistance wheat populations.

Isolation and Characterization of Colistin-Resistant Enterobacteriaceae from Foods in Two Italian Regions in the South of Italy

The emergence of colistin-resistant Enterobacteriaceae in food products is a growing concern due to the potential transfer of resistance to human pathogens. This study aimed to assess the prevalence of colistin-resistant Enterobacteriaceae in raw and ready-to-eat food samples collected from two regions of Italy (Apulia and Basilicata) and to evaluate their resistance phenotypes and genetic characteristics. A total of 1000 food samples were screened, with a prevalence of 4.4% of colistin-resistant Enterobacteriaceae. The majority of the isolates belonged to Enterobacter spp. (60%), followed by Moellerella wisconsensis, Atlantibacter hermannii, Klebsiella pneumoniae, and Escherichia coli, among others. Genomic sequencing and antimicrobial susceptibility testing revealed high levels of resistance to β-lactams, with most isolates exhibiting multidrug resistance (MDR). Notably, seven isolates harbored mcr genes (mcr-1, mcr-9, and mcr-10). Additionally, in four of them were predicted the IncHI2 plasmids, known to facilitate the spread of colistin resistance. Furthermore, 56 antimicrobial resistance genes were identified, suggesting the genetic mechanisms underlying resistance to several antibiotic classes. Virulence gene analysis showed that E. coli and other isolates carried genes linked to pathogenicity, increasing the potential risk to public health. This study emphasizes the role of food as a potential reservoir for colistin-resistant bacteria and the importance of monitoring the spread of AMR genes in foodborne pathogens.

Importance of OsRac1 in Signalling of Pigm-1 Mediated Resistance to Rice Blast Disease

In rice, leucine-rich repeat nucleotide-binding site (NLR) proteins are pivotal immune receptors in combating Magnaporthe oryzae-triggered rice blast. However, the precise molecular mechanism underlying how NLR proteins regulate downstream signalling remains elusive due to the lack of knowledge regarding their direct downstream targets. The NLR protein Pigm-1 was cloned from Shuangkang 77009 in our laboratory. This study shows that the nucleotide-binding site (NBS) domain of Pigm-1 facilitates its binding to and activation of OsRac1 while the coiled-coil (CC) domain enables its binding to and activation of RAI1, ultimately inducing cell death. At the same time, after knocking out OsRac1 in the background of Shuangkang 77009 containing Pigm-1, two knockout lines showed susceptibility to rice blast. This study reveals OsRac1, a GTPase, as a signalling molecule involved in Pigm-1-mediated blast resistance, suggesting its potential as a common downstream effector of rice NLR proteins. Additionally, a transcriptional activator, RAI1, acts as an essential Pigm-1 interactor for blast resistance. Furthermore, a novel material 9311(Pigm-1) was prepared by using two-line restorer line 9311 as receptor and Shuangkang 77009 as donor with molecular marker-assisted technology, which improved blast resistance and yield. This research demonstrates that molecular marker-assisted selection technology enhances both resistance and yield in the crucial two-line restorer 9311(Pigm-1). This study offers crucial insights into how Pigm-1 protein activates downstream molecules and serves as a valuable reference for the molecular breeding of rice blast resistance genes, particularly Pigm-1.

Effect of Fecal Microbiota Transplant on Antibiotic Resistance Genes Among Patients with Chronic Pouchitis.

Pouchitis is common among patients with ulcerative colitis (UC) who have had colectomy with ileal pouch-anal anastomosis. Antibiotics are first-line therapy for pouch inflammation, increasing the potential for gut colonization with multi-drug resistant organisms (MDRO). Fecal microbial transplant (FMT) is being studied in the treatment of pouchitis and in the eradication of MDRO. Prior work using aerobic antibiotic culture disks suggests that some patients with chronic pouchitis may regain fluoroquinolone sensitivity after FMT. However, gut MDRO include anaerobic, fastidious organisms that are difficult to culture using traditional methods. We aimed to assess whether FMT reduced the abundance of antibiotic resistance genes (ARG) or affected resistome diversity, evenness, or richness in patients with chronic pouchitis. We collected clinical characteristics regarding infections and antibiotic exposures for 18 patients who had previously been enrolled in an observational study investigating FMT as a treatment for pouchitis. Twenty-six pre- and post-FMT stool samples were analyzed using FLASH (Finding Low Abundance Sequences by Hybridization), a CRISPR/Cas9-based shotgun metagenomic sequence enrichment technique that detects acquired and chromosomal bacterial ARGs. Wilcoxon rank sum tests were used to assess differences in clinical characteristics, ARG counts, resistome diversity and ARG richness, pre- and post-FMT. All 13 of the patients with sufficient stool samples for analysis had recently received antibiotics for pouchitis prior to a single endoscopic FMT. Fecal microbiomes of all patients had evidence of multi-drug resistance genes and ESBL resistance genes at baseline; 62% encoded fluoroquinolone resistance genes. A numerical decrease in overall ARG counts was noted post-FMT, but no statistically significant differences were noted (P = 0.19). Richness and diversity were not significantly altered. Three patients developed infections during the 5-year follow-up period, none of which were associated with MDRO. Antibiotic resistance genes are prevalent among antibiotic-exposed patients with chronic pouchitis. FMT led to a numerical decrease, but no statistically significant change in ARG, nor were there significant changes in the diversity, richness, or evenness of ARGs. Further investigations to improve FMT engraftment and to optimize FMT delivery in patients with inflammatory pouch disorders are warranted.

Growth of microbes in competitive lifestyles promotes increased ARGs in soil microbiota: insights based on genetic traits

BackgroundThe widespread selective pressure of antibiotics in the environment has led to the propagation of antibiotic resistance genes (ARGs). However, the mechanisms by which microbes balance population growth with the enrichment of ARGs remain poorly understood. To address this, we employed microcosm cultivation at different antibiotic (i.e., Oxytetracycline, OTC) stresses across the concentrations from the environmental to the clinical. Paired with shot-gun metagenomics analysis and quantification of bacterial growth, trait-based assessment of soil microbiota was applied to reveal the association between key ARG subtypes, representative bacterial taxa, and functional-gene features that drive the growth of ARGs.ResultsOur results illuminate that resistome variation is closely associated with bacterial growth. A non-monotonic change in ARG abundance and richness was observed over a concentration gradient from none to 10 mg/l. Soil microbiota exposed to intermediate OTC concentrations (i.e., 0.1 and 0.5 mg/l) showed greater increases in the total abundance of ARGs. Community compositionally, the growth of representative taxa, i.e., Pseudomonadaceae was considered to boost the increase of ARGs. It has chromosomally carried kinds of multidrug resistance genes such as mexAB-oprM and mexCD-oprJ could mediate the intrinsic resistance to OTC. Streptomycetaceae has shown a better adaptive ability than other microbes at the clinical OTC concentrations. However, it contributed less to the ARGs growth as it represents a stress-tolerant lifestyle that grows slowly and carries fewer ARGs. In terms of community genetic features, the community aggregated traits analysis further indicates the enhancement in traits of resource acquisition and growth yield is driving the increase of ARGs abundance. Moreover, optimizations in energy production and conversion, alongside a streamlining of bypass metabolic pathways, further boost the growth of ARGs in sub-inhibitory antibiotic conditions.ConclusionThe results of this study suggest that microbes with competitive lifestyles are selected under the stress of environmental sub-inhibitory concentrations of antibiotics and nutrient scarcity. They possess greater substrate utilization capacity and carry more ARGs, due to this they were faster growing and leading to a greater increase in the abundance of ARGs. This study has expanded the application of trait-based assessments in understanding the ecology of ARGs propagation. And the finding illustrated changes in soil resistome are accompanied by the lifestyle switching of the microbiome, which theoretically supports the ARGs control approach based on the principle of species competitive exclusion.4ZqjNsN9dRS1iWJDwru5hLVideo

Understanding the clinical and molecular epidemiological characteristics of carbapenem-resistant Acinetobacter baumannii infections within intensive care units of three teaching hospitals

BackgroundCarbapenem-resistant Acinetobacter baumannii (CRAB) is recognized as a common clinical conditional pathogen with blaOXA−23 gene-mediated multidrug-resistance that is a significant threat to public health safety. Timely and effective infection control measures are needed to prevent their spread.MethodsWe conducted a retrospective study of CRAB patients at three teaching hospitals from 2019 to 2022. We identified bacterial isolates, collected clinical data, and performed antimicrobial susceptibility testing. Genome characteristics of isolates were investigated by whole genome sequencing. Multilocus sequence typing and phylogenetic trees were used to assess the genetic similarity of isolates. Acquired antimicrobial resistance genes and virulence factors carried in the isolated group genome were analyzed by ResFinder, PubMLST and VFDB. Sequence alignment was used to analyze genetic environment around blaOXA−23. Phylogenetic tree was constructed to analyze the genetic relationship of isolates.ResultsA total of 92 non-repetitive CRAB isolates were collected, with sputum samples accounting for the majority (94.57%, n = 87) of samples. These were distributed into ST2, with ST2 identified to have the highest prevalence of infection, accounting for 99.99% (n = 91) of all isolates. The major resistance genes identified were blaOXA−23, blaOXA−66, blaOXA−51, and blaADC. Also, 92 CRAB strains showed high levels of resistance to common clinical antibiotics, but not minocycline. Meanwhile, most of the isolates carried virulence genes such as various ompA, csuA, csuB, csuC, csuD, abaI, abaR, lpxC, lpxA, and bmfRS. Single nucleotide polymorphism (SNP) analyses further indicated that the bacterial genome was progressively polymorphic with time. We analyzed the environment of the blaOXA−23 gene and found that CRAB accumulated in the context of prominent environmental antibiotic exposure and had longer survival times in the antibiotic environment, resulting in the tendency of bacteria to develop greater antibiotic resistance.ConclusionsWe find that CRAB is prevalent within the ICU and is progressively resistant to antibiotics over time. Enhanced clinical understanding and timely management of CRAB infections will be crucial to minimize or even eliminate the spread of CRAB within the ICU setting.

Making sense of sentinels: wildlife as the one health bridge for environmental antimicrobial resistance surveillance.

Antimicrobial resistance (AMR), arising from decades of imprudent anthropogenic use of antimicrobials in healthcare and agriculture, is considered one of the greatest One Health crises facing healthcare globally. Antimicrobial pollutants released from human-associated sources are intensifying resistance evolution in the environment. Due to various ecological factors, wildlife interact with these polluted ecosystems, acquiring resistant bacteria and genes. Although wildlife are recognised reservoirs and disseminators of AMR in the environment, current AMR surveillance systems still primarily focus on clinical and agricultural settings, neglecting this environmental dimension. Wildlife can serve as valuable sentinels of AMR in the environment, reflecting ecosystem health, and the effectiveness of mitigation strategies. This review explores knowledge gaps surrounding the ecological factors influencing AMR acquisition and dissemination in wildlife, and highlights limitations in current surveillance systems and policy instruments that do not sufficiently address the environmental component of AMR. We discuss the underutilised opportunity of using wildlife as sentinel species in a holistic, One Health-centred AMR surveillance system. By better integrating wildlife into systematic AMR surveillance and policy, and leveraging advances in high-throughput technologies, we can track and predict resistance evolution, assess the ecological impacts, and better understand the complex dynamics of environmental transmission of AMR across ecosystems.

Asymptomatic carriage and molecular characterization of Staphylococcus aureus in pre-clinical and clinical medical students.

Medical students are exposed to the hospital environment and patients during their studies, increasing the risk of exposure to virulent and antibiotic-resistant isolates of Staphylococcus aureus. The aim of the study is to determine the prevalence of Staphylococcus aureus among medical students who have varying levels of exposure to the hospital environment to provide valuable insights into the risk of colonization and transmission. Nasal swabs and fingerprints were obtained and cultured on a selective medium for staphylococci. The obtained isolates were confirmed as methicillin-sensitive S. aureus (MSSA) or methicillin-resistant (MRSA) using PCR. Antibiotic resistance, the presence of virulence genes including enterotoxin encoding genes, and spa typing were performed. Among pre-clinical students, MSSA was detected on the nose in 45.2% and on the fingerprints in 10.6% of the participants. Among clinical students, MSSA was detected on the nose in 42.0% and on the fingerprints in 25.4%. Only one MRSA isolate was obtained. Genes seg and sei were the most frequently detected in both student groups, with their presence in over 40% of isolates among clinical students. The eta and etb genes were mainly detected from the nose in both student groups. In pre-clinical students, S. aureus carrying eta gene occurred in 6.4% and etb in 8.5%. In clinical students, the occurrence was 5.1% for eta and 8.5% for etb. The tst gene was identified only in the nose and fingerprints of the clinical student group. The most frequently observed resistance was to clindamycin and erythromycin. In total 58 different spa types were identified. High rates of asymptomatic MSSA carriage were observed in both groups of medical students. Detected MSSA strains showed a high degree of genetic variability, with a number of them carrying the virulence and antibiotic resistance genes. Although students do not exhibit increased risk to their patient's, increased hygiene is required in asymptomatic carriage personnel. The overall prevalence of MRSA was low, with a minimal risk of spread.

Malaria prevalence, transmission potential and efficacy of artemisinin-based combination therapy in the Kenyan Central highlands: a zone previously characterized as malaria-free

BackgroundThe current study sought to re-evaluate malaria prevalence, susceptibility to artemisinin-based combination therapy (ACT), transmission patterns and the presence of malaria vectors in the Kikuyu area of the Kenyan Central highlands, a non-traditional/low risk malaria transmission zone where there have been anecdotal reports of emerging malaria infections.MethodsSampling of adult mosquitoes was done indoors, while larvae were sampled outdoors in June 2019. The malaria clinical study was an open label non-randomized clinical trial where the efficacy of one ACT drug, was evaluated in two health facilities. Microscopy was used at the facility while nested 18 s rRNA subunit gene PCR amplification and MSP-1 and MSP-2 family alleles genotyping was done in the laboratory. Anti-malarial resistance gene markers Pfk13 and Pfmdr1 were profiled.ResultsAnopheles funestus mosquitoes were the predominant vectors at 76.35% of all larvae collections (N = 148). Only two non-blood fed, parasites negative adult mosquitoes were collected from houses sampled. Parasitological analysis of the 838 patients screened resulted in 41 positives whose treatment outcome was 100% Adequate Clinical and Parasitological Response (ACPR). From the 35 positive samples genotyped, 29 (82.9%) were polyclonal. The overall mean MOI was 2.8 (95% CI 2.36–3.35). The MOI for msp-1 and msp-2 genes, was 2.02 (95% CI 0.72–2.27) and 2.9 (95% CI 2.22–3.55), and parasite strains range of 1–3 and 1–7, respectively. Polyclonal variation in the two genes was at 76.4% and 70.3%, respectively. The Pfk13 gene revealed no single nucleotide polymorphisms (SNP) associated with suspected artemisinin resistance nor was there any pfmdr1 N86 mutant allele detected.ConclusionThe Plasmodium infections positivity rate observed in the study site was very low but significant. A proportion of participants who tested positive did not report recent history of travel. This observation together with the finding of competent known vectors can probably suggest that several of the cases could have been acquired and transmitted locally. The observed genetic diversity and polyclonal variations was on the contrary and suggest that these are imported cases. This however does not rule out a likely changing malaria transmission scenario in this zone, thus the need for further investigations.

Prevalence of Uropathogenic E. Coli, Antimicrobial Susceptibility Profiles and Carriage of Extended-Spectrum Beta-Lactamases Genes at Mama Lucy Hospital, Kenya

Purpose: Urinary tract infection (UTI) is a common bacterial infection affecting millions worldwide. Escherichia coli (E. coli) is the most prevalent causative agent of UTIs. This study aimed to determine the prevalence, antimicrobial susceptibility profiles and carriage of ESβL resistance genes among uropathogenic E. coli recovered from adults at Mama Lucy Hospital. Methodology: A cross-sectional study was conducted. A purposive method was used to obtain 347 urine samples from patients who presented with symptoms suggestive of UTI and were cultured for E. coli using cysteine lactose electrolyte-deficient agar and eosin methylene blue agar. The collected urine samples were also subjected to dipstick analysis and microscopy. Questionnaires were used to collect sociodemographic data and possible risk factors for urinary tract infections. The recovered isolates were identified using conventional biochemical tests. Antimicrobial susceptibility profiles were determined using the Kirby diffusion disc method. The occurrence of ESβLs, including TEM, OXA, SHV, and CTX-M, was determined by polymerase chain reaction (PCR). Findings: The overall prevalence rate of UTIs was 23.7%, whereas the E. coli prevalence rate was 13.3%. The isolates presented high levels of resistance to trimethoprim-sulfamethoxazole (81.3%), amoxicillin-clavulanic acid (66.7%), ciprofloxacin (62.5%), tetracycline (60.4%), ceftriaxone (54.2%), and cefoxitin (54.2%), whereas they were more susceptible to meropenem (14.6%), chloramphenicol (12.5%), and nitrofurantoin (8.3%). A total of 25 of the 46 E. coli isolates were screened for ESβL genes. TEM was the most common gene21/25 (84%), SHV12/25 (48%), OXA 7/25 (28%), and CTX-M 18/25 (66.1%), which indicates a high frequency of β-lactamase gene production among UTIs causing E. coli. Unique Contribution to Theory, Practice and Policy: Based on these findings, current treatment guidelines should be revised to prevent increasing antimicrobial resistance through continuous surveillance, screening for extended-spectrum beta-lactamase genes, routine culture and antibiotic sensitivity testing. Additionally, the prevalence of UTIs should be continuously monitored to monitor trends that form a basis for preventive and treatment guidelines, such as policy development and prudent use of antibiotics, to reduce the increasing UTI burden in the population.

Response Mechanism of Plants to Cadmium Pollution in Soil

Cadmium (Cd), as a widespread heavy metal pollutant in soil, has become one of the globally recognized contaminants due to its high toxicity and bioaccumulative properties. Soil cadmium pollution not only hinders the normal growth of plants but also poses a threat to human health through the food chain. Microbe-plant combined remediation is an essential approach for the treatment of heavy metal contamination in soil. Plants primarily respond to cadmium stress through intrinsic physiological and biochemical adjustments, including inhibiting cadmium absorption, promoting cadmium compartmentalization in vacuoles, and facilitating cadmium efflux from cells. Moreover, plants enhance their tolerance to cadmium through mechanisms such as the regulation of plant hormones. Gene expression regulation is the molecular mechanism underlying plant cadmium tolerance. To date, multiple resistance genes, transcription factors, and microRNAs involved in cadmium tolerance have been identified. Exogenous additives mitigate the effects of cadmium stress on plants by chemical adsorption, enhancing plant cadmium tolerance, and improving the physical and chemical properties of the soil, as well as the structure of soil microbial communities. Investigating the mechanisms by which plants respond to cadmium stress and exploring remediation measures for cadmium pollution will provide a basis for developing effective pollution control and remediation strategies.

In Silico Exploration of Staphylococcal Cassette Chromosome mec (SCCmec) Evolution Based on Phylogenetic Relationship of ccrAB/C

As the mobile cassette carrier of the methicillin resistance gene mecA that is transported across staphylococci species, the evolution and origin of Staphylococcal Cassette Chromosome mec (SCCmec)—and in particular, the composition of mecA and SCCmec—have been extensively discussed in the scientific literature; however, information regarding its dissemination across geographical limits and evolution over decades remains limited. In addition, whole-genome sequencing-based macro-analysis was unable to provide sufficiently detailed evolutionary information on SCCmec. Herein, the cassette chromosome recombinase genes ccrAB/C, as essential components of SCCmec, were employed to explore the evolution of SCCmec. This work established the basic taxonomy of 33 staphylococci species. The CUB of mecA, ccrAB/C of 12 SCCmec types and core genome of 33 staphylococci species were subsequently compared; the phylogenetic relationship of ccrAB/C was observed via SCCmec typing on a temporal and geographical scale; and the duplicate appearance of ccrAB/C was illustrated by comparing SCCmec compositions. The results highlighted a deviation in the CUB of mecA and ccrAB/C, which evidenced their exogenous characteristics to staphylococci, and provided theological support for the phylogenetic analysis of ccrAB/C as representative of SCCmec. Importantly, the phylogenetic relationship of ccrAB/C did not exhibit centralization over time; instead, similarly to mecA, ccrAB/C with similar identities had close clades across decades and geographical limits and different SCCmec types, which enabled us to discriminate SCCmec based on the sequence identity of ccrAB/C. In addition, the duplicate appearance of ccrAB/C and fixed composition of the ccrAB/C complex among different strains were indicative of more complicated transmission mechanisms than targeting direct repeats of SCCmec.