Search Results (354)

This study sought to quantify and characterize diverse rootstock scion interactions in cacao around graft compatibility, disease resistance, nutrient use efficiency, vigor traits, and translocation of nonstructural carbohydrates. In total, 106 grafts were performed with three scion cultivars (Matina 1/6, Criollo 22, Pound 7) and nine diverse open-pollinated seedling populations (BYNC, EQX 3348, GNV 360, IMC 14, PA 107, SCA 6, T 294, T 384, T 484). We found evidence for both local and translocated graft incompatibility. Cross sections and Micro-XCT imaging revealed anatomical anomalies, including necrosis and cavitation at the junction and accumulation of starch in the rootstock directly below the graft junction. Scion genetics were a significant factor in explaining differences in graft take, and graft take varied from 47% (Criollo 22) to 72% (Pound 7). Rootstock and scion identity both accounted for differences in survival over the course of the 30-month greenhouse study, with a low of 28.5% survival of Criollo 22 scions and a high of 72% for Pound 7 scions. Survival by rootstocks varied from 14.3% on GNV 360 to 100% survival on T 294 rootstock. A positive correlation of 0.34 (p = 0.098) was found between the graft success of different rootstock–scion combinations and their kinship coefficient, suggesting that relatedness of stock and scion could be a driver of incompatibility. Significant rootstock–scion effects were also observed for nutrient use efficiency, plant vigor, and resistance to Phytophthora palmivora. These findings, while preliminary in nature, highlight the potential of rootstock breeding to improve plant nutrition, resilience, and disease resistance in cacao. Full article

The improvement in yield in cultivar mixtures has been well established. Despite increasing knowledge of the improvement involving within-species diversification and resource use efficiency, little is known about the benefits arising from relatedness-mediated intraspecific interactions in cultivar mixtures. This study used a relatedness gradient of rice cultivars to test whether neighbor relatedness contributes to improvements in grain yields in cultivar mixtures. We experimentally demonstrated the grain yield of rice cultivar mixtures with varying genetic relatedness under both field and controlled conditions. As a result, a closely related cultivar mixture had increased grain yield compared to monoculture and distantly related mixtures by optimizing the root-to-shoot ratio and accelerating flowering. The benefits over monoculture were most pronounced when compared to the significant yield reductions observed in distantly related mixtures. The relatedness-mediated improvement in yields depended on soil volume and nitrogen use level, with effects attenuating under larger soil volumes or nitrogen deficiency. Furthermore, neighbor relatedness enhanced the richness and diversity of both bacterial and fungal communities in the rhizosphere soil, leading to a significant restructuring of the microbial community composition. These findings suggest that neighbor relatedness may improve the grain yield of rice cultivar mixtures. Beneficial plant–plant interactions may be generated by manipulating cultivar kinship within a crop species. A thorough understanding of kinship strategies in cultivar mixtures offers promising prospects for increasing crop production. Full article

Host genetic variability is relevant to understanding how parasites modulate natural selection in wild fish populations. Coastal lagoons are transitional ecosystems where knowledge lacks on relationships between genotypic diversity with parasitism. The aim of this study was to assess the effect of genetic diversity on host health and parasitological traits in fish inhabiting a Mediterranean lagoon. Black-striped pipefish Syngnathus abaster were collected in August 2023 and 2024 from the Mar Menor (Iberian lagoon, SE Spain). Genetic diversity was measured as Internal Relatedness (IR: a homozygosity index from microsatellite markers). Population frequency was lower for the medium IR level. For this same category, both health indices (external body condition and internal organs) indicated a worse status. Parasite prevalence, abundance and an index of life-cycle complexity (heteroxenous species) were greater for the medium level of genetic diversity. Such results are explained under a scenario of parasite-mediated disruptive selection: a higher disease pressure against the phenotypically intermediate individuals. Two contrasting strategies were detected to better control parasitism at the host genotypic level: (1) high homozygosity, and (2) high heterozygosity, which probably reflects better immuno-competence as a phenotypic trait. From an evolutionary perspective, parasites play a crucial role in shaping genetic diversity within host populations. Full article

Vibrio parahaemolyticus is the leading bacterial cause of gastroenteritis associated with aquatic food consumption globally. This study aimed to determine the prevalence of V. parahaemolyticus in aquatic foods from Huzhou and to identify the serotypes, antimicrobial resistance, virulence factors, and genetic relatedness of the strains. A total of 306 isolates were detected from 1314 aquatic food samples from 2022 to 2024. The results indicated that the most prevalent serotypes were O1:KUT (17.0%), O2:K28 (13.7%), and O2:KUT (13.1%). Multilocus sequence typing analysis divided the 306 isolates into 175 sequence types (STs), and the predominant sequence type was ST864 (3.3%). Antimicrobial susceptibility tests showed that 2.6% of isolates were multidrug resistant. High resistance was observed to ampicillin (64.7%) and streptomycin (44.4%). A total of seven antimicrobial categories of resistance genes were identified, and the resistance gene bla_CARB was detected in all isolates. The virulence genes tdh and trh were found in 16 (5.2%) and 12 (3.9%) isolates, respectively. In addition, we observed that all the 306 V. parahaemolyticus isolates encode type III secretion systems 1. The phylogenomic analysis based on the whole-genome sequence revealed that the 306 isolates were divided into four clusters. Our findings broaden perspectives on V. parahaemolyticus genetic diversity and enhance our ability to assess the potential risks of its spread. Full article

Staphylococcus aureus (S. aureus) is a major cause of opportunistic infections in humans and animals, leading to severe systemic diseases. The rise of MDR strains associated with animal carriage poses significant health challenges, underscoring the need to investigate animal-derived S. aureus. Objectives: This study examined the genotypic relatedness and phenotypic profiles of antimicrobial resistance in S. aureus, previously sampled from nostril swabs of healthy horses from two geographically distant Brazilian states (Northeast and South), separated by over 3700 km. The study also sought to confirm the presence of methicillin-resistant (MRSA) and borderline oxacillin-resistant (BORSA) strains and to characterize the isolates through molecular typing using PCR. Methods: Among 123 screened staphylococci, 21 isolates were confirmed as S. aureus via biochemical tests and PCR targeting species-specific genes (femA, nuc, coa). Results: REP-PCR analysis generated genotypic profiles, revealing four antimicrobial resistance patterns, with MDR observed in ten isolates. Six isolates exhibited cefoxitin resistance, suggesting methicillin resistance, despite the absence of the mecA gene. REP-PCR demonstrated high discriminatory power, grouping the isolates into five major clusters. Conclusions: The genotyping indicated no clustering by geographical origin, highlighting significant genetic diversity among S. aureus strains colonizing horses’ nostrils in Brazil. These findings highlight the widespread and varied nature of S. aureus among horses, contributing to a deeper understanding of its epidemiology and resistance profiles in animals across diverse regions. Ultimately, this genetic diversity can pose a public health risk that the epidemiological surveillance services must investigate. Full article

Background/Objectives: Clostridioides difficile is a “One Health” pathogen and a cause of antibiotics-associated diarrhea and pseudomembranous colitis. Mobile genetic elements (MGEs) have been documented in the genomes of clinical C. difficile strains; however, the presence of MGEs in environmental strains remains poorly characterized. Thus, the present study was conducted with the objective of identifying the prevalence of MGEs, including mobilizable transposons (MTns), conjugative transposons (CTns), plasmids, and insertion sequences, in whole genome sequences (WGSs) of environmental C. difficile isolates. Methods: The analysis of MGEs was conducted using 166 WGSs obtained from C. difficile strains isolated from various environmental sources contaminated with feces. The MGEs were identified using bioinformatic tools. Results: A total of 48.2% (80/166) of the studied genomes were identified to harbor nine transposons, including Tn916, Tn6194-like, Tn5397, Tn6215, Tn4001, Tn6073, Tn6110, Tn6107, or Tn5801-like. The majority of MTns and CTns could be found within C. difficile sequence types ST11, ST3, and ST35. The results demonstrated close genetic relatedness among the studied genomes, the array of antimicrobial resistance (AMR) genes, such as tetM, ermB, and aac(6′)-aph(2″), and the presence of CTns. Furthermore, the analysis revealed that 24.7% (41/166) of the genome sequences of isolates were associated with various predominant plasmid groups, including pCD6, pCD-ECE4-6, pCD-WTSI1-4, pCDBI1, and pCd1_3, which belonged to 16 different sequence types. Furthermore, several plasmids were identified as harboring the prophage phiCDHM19. Conclusions: The results of the current study suggest that the identified plasmids are abundant and may encode functions that are relevant to C. difficile physiology. The genomes of C. difficile strains examined contain closely related CTns, suggesting that horizontal transfer of AMR is important in this species or other bacterial species. Further research is required to ascertain the effect of these genetic elements and their transferability on the biology of C. difficile. Full article

Understanding how urbanisation and habitat fragmentation influence wildlife is critical for biodiversity conservation. Fragmentation and population isolation can reduce genetic diversity, yet few studies have assessed these genetic impacts in urbanised environments. Eastern grey kangaroos (Macropus giganteus), widespread across eastern Australia, often inhabit landscapes shaped by urbanisation. Using single nucleotide polymorphism (SNP) data from scat and tissue samples, we compared genetic characteristics of kangaroo populations in urban and non-urban areas across three regions. We assessed the influence of habitat isolation on genetic diversity and relatedness at 18 study sites. Overall, urban populations did not show significantly lower genetic diversity than those in less developed areas (p > 0.05; Urban mean H_O = 0.196, Non-urban mean H_O = 0.188). However, populations fully isolated by roads, buildings, and fences exhibited reduced genetic diversity and increased inbreeding. Additionally, significant genetic differences were observed among regions. These findings suggest that while urbanisation alone may not always reduce genetic diversity, complete physical isolation poses greater risks to population genetic health. This study highlights how urban landscape features can shape the genetics of large terrestrial mammals and underscores the need for spatially informed urban planning and management strategies that maintain or restore habitat connectivity. Full article

Introduction: Genetic plasticity and adaptive camouflage in critical pathogens have contributed to the global surge in multidrug-resistant (MDR) infections, posing a serious threat to public health and therapeutic efficacy. Antimicrobial resistance, now a leading cause of global mortality, demands urgent action through diagnostics, vaccines, and therapeutics. In India, the Indian Council of Medical Research’s surveillance network identifies Escherichia coli as a major cause of urinary tract infections, with increasing prevalence in human gut microbiomes, highlighting its significance across One Health domains. Methods: Whole-genome sequencing of E. coli strain ECG015, isolated from a human gut sample, was performed using the Illumina NextSeq platform. Results: Genomic analysis revealed multiple antibiotic resistance genes, virulence factors, and efflux pump components. Phylogenomic comparisons showed close relatedness to pathovars from both human and animal origins. Notably the genome encoded protein tyrosine kinases (Etk/Ptk and Wzc) and displayed variations in the envelope stress-responsive CpxAR two-component system. Promoter analysis identified putative CpxR-binding sites upstream of genes involved in resistance, efflux, protein kinases, and the MazEF toxin–antitoxin module, suggesting a potential regulatory role of CpxAR in stress response and persistence. Conclusions: This study presents a comprehensive genomic profile of E. coli ECG015, a gut-derived isolate exhibiting clinically significant resistance traits. For the first time, it implicates the CpxAR two-component system as a potential central regulator coordinating antimicrobial resistance, stress kinase signaling, and programmed cell death. These findings lay the groundwork for future functional studies aimed at targeting stress-response pathways as novel intervention strategies against antimicrobial resistance. Full article

Identification and differentiation of Candida spp. yeasts, especially clinically relevant isolates, is of high importance with respect to their origin, pathogenic potential, colonization pattern, and resistance to antimycotics. Currently, numerous typing methods with varying or unknown discriminatory power are used. This study evaluated the utility of five methods—biotyping using the API system, ITS1 and ITS4 sequence analysis, ITS region polymorphism, multiplex PCR of ITS1, ITS3, and ITS4 regions, and karyotyping—for typing 42 strains differing in origin (24 clinical and 18 food-borne). The highest discriminatory power was obtained for ITS sequencing and karyotyping, both yielding a discrimination index of 1.000. The discrimination indices for other methods ranged from 0.957 for genotyping based on ITS region polymorphism to 0.997 for multiplex PCR-genotyping. Although biotyping showed relatively high discriminatory potential, its use led to misclassification of 64.3% of isolates compared to ITS sequencing. These findings emphasize the importance of applying a typing method with a discrimination index of 1.000 to ensure accurate interpretation of strain-relatedness and origin. Methods with lower indices may reflect methodological limitations rather than actual genetic relatedness. Determining the discrimination index is therefore essential when selecting appropriate tools for yeast typing, particularly in clinical and epidemiological contexts. Full article

(1) Background: CRISPR-Cas systems provide adaptive immunity against mobile genetic elements (MGEs) carrying antimicrobial resistance (AMR) genes. Carbapenem-resistant (CR) Klebsiella pneumoniae is a major public health concern, and the role of CRISPR-Cas in its resistance is understudied. This study explored CRISPR-Cas associations with multidrug resistance in clinical K. pneumoniae. (2) Methods: 400 K. pneumoniae isolates (200 CR and 200 carbapenem susceptible (CS)) were analyzed. Carbapenemase genes (bla_OXA-48, bla_NDM-1, bla_KPC-2), cas1, rpoB, and CRISPR1-3 loci were identified by PCR, while only CRISPR loci were sequenced. Genetic relatedness was assessed via PFGE, MLST, and spacer analysis. Statistical analysis utilized chi-squared and Fisher’s exact tests. (3) Results: CRISPR-Cas was present in 15.8% of isolates, mainly subtypes I-E and I-E* (93.3%), with CRISPR3 loci showing the greatest spacer diversity. Clonal complexes ST14/15/101 (CR) and ST35 (CS) were identified. bla_OXA-48 was linked to CRISPR-Cas-negative strains, while bla_NDM-1 and bla_KPC-2 were more frequent in CRISPR-Cas-positive strains (p < 0.0001). Imipenem/relebactam resistance was higher in CRISPR-Cas-negative isolates. (4) Conclusions: K. pneumoniae CRISPR-Cas systems correlate with specific carbapenemase profiles, suggesting pressure against bla_OXA-48 acquisition. The coexistence of I-E and I-E* subtypes highlight synergies in targeting MGEs. CRISPR loci could be tools for subtyping organisms following MLST. Full article

Pseudomonas aeruginosa poses a significant global concern in human and veterinary medicine due to its resistance to multiple antimicrobials. Limited research has been carried out on rifampicin-resistant P. aeruginosa, particularly in food-producing animals such as camels. Therefore, the purpose of this study was to investigate the occurrence of rifampicin- and multidrug-resistant P. aeruginosa in apparently healthy camels. Nasal swabs and tissue samples were collected from one hundred apparently healthy slaughtered camels, and they were subjected to bacteriological isolation and identification of P. aeruginosa. Antimicrobial susceptibility testing was performed, followed by phenotypic and genotypic detection of ESBL-producing P. aeruginosa isolates. Twenty-two P. aeruginosa strains were investigated for the rpoB gene, including rifampicin-resistant isolates. P. aeruginosa was found in 16% (16/100) of the investigated apparently healthy slaughtered camels. P. aeruginosa was confirmed in sixteen and six isolates from nasal swabs and tissue samples, respectively, by pigment production on cetrimide agar. The most predominant beta-lactamase-encoding gene in twenty-two ESBL-producing isolates was bla_PER (40.9%), followed by bla_CTX-M (36.4%), bla_TEM (31.8%), and bla_SHV (27.3%). Multidrug resistance was identified in 54.5% (12/22) of P. aeruginosa isolates. The rpoB gene was detected in 11 (50%) out of 22 P. aeruginosa strains, with eleven positive isolates being regarded as rifampicin-resistant. Furthermore, phylogenetic analysis of a rifampicin- and multidrug-resistant P. aeruginosa rpoB gene sequence revealed a genetic relatedness to P. aeruginosa strains retrieved from human clinical cases. In conclusion, this study provides a snapshot on the occurrence of rifampicin- and multidrug-resistant P. aeruginosa among apparently healthy camels. In line with a possible risk of animal-to-human transfer, further molecular studies on rifampicin-resistant P. aeruginosa in animals are required to better understand and combat this serious zoonotic pathogen. Full article

Rhodopseudomonas is recognized for its versatile metabolic capabilities that enable it to effectively degrade pollutants and survive various environmental stresses. In this study, we conducted a genome analysis of Rhodopseudomonas sp. P1 to investigate its genetic potential for wastewater treatment processes. Phylogenetic and genome-relatedness analyses confirmed that strain P1 is genetically distinct from other species within the Rhodopseudomonas genus, establishing it as a novel species. The genome sequences obtained and analyzed focused on genes related to carbon and nutrient removal, photosynthetic capabilities, nitrate and nitrite reduction, and the biodegradation of common wastewater pollutants. The identification of wastewater treatment-related genes followed an extensive review of the existing literature that helped in selecting genes involved in various wastewater treatment mechanisms. The genome of Rhodopseudomonas sp. P1 contains a diverse array of genes involved in carbon and nutrient cycling, pollutant biodegradation, and metal resistance, all of which are crucial for its survival in the complex wastewater environment. Specifically, the strain contains genes responsible for the denitrification, nitrogen fixation, sulfur cycling, and detoxification of toxic metals such as copper and arsenic. These findings highlight the potential application of Rhodopseudomonas sp. P1 in wastewater treatment, particularly in environments contaminated with organic pollutants and heavy metals. However, while the genomic features indicate significant promise, the practical implementation of Rhodopseudomonas sp. P1 in real-world wastewater treatment systems will require further investigation, optimization, and validation to fully harness its potential for sustainable and efficient wastewater treatment. Full article

Methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of pediatric infections and has shown evolving molecular characteristics over time. This study aimed to investigate the phenotypic and genotypic features of MRSA isolates collected from pediatric patients at a tertiary medical center in northern Taiwan between 2011 and 2020. A total of 182 MRSA strains were analyzed for SCCmec types, PVL gene presence, antimicrobial susceptibility, multilocus sequence typing (MLST), and clonal relatedness using pulsed-field gel electrophoresis (PFGE). ST59/SCCmec Vt was the most prevalent genotype, followed by ST59/SCCmec IV and ST8/SCCmec IV. Most ST59/SCCmec Vt and ST8/SCCmec IV isolates clustered genetically. Clindamycin and erythromycin resistance remained high, whereas co-trimoxazole susceptibility ranged from 76% to 100%. These findings confirm ST59 as the dominant clone and highlight the emergence of ST8 and ST45 in community-associated MRSA (CA-MRSA) infections. Oral co-trimoxazole remains the most effective empirical option, while clindamycin and erythromycin should be avoided. Continuous molecular surveillance is warranted to monitor trends and guide treatment strategies in pediatric MRSA infections. Full article

Background/Objectives: Dense genetic marker panels are increasingly used in kinship analysis for the identification of distant relatives. As more markers are available, it is possible to pinpoint IBD segments more precisely and more reliably, ultimately approaching close to continuously observed IBD. This study investigates the evidential value obtained for discrimination between common pedigree relationships if IBD is observed continuously across the autosomal genome without error. In the continuous case, the evidential value is limited only by the pedigree relationship and the recombination rates. Methods: We conducted simulations to generate IBD segments across the autosomal genome for individuals with defined pedigree relationships. The evidential value for relationship discrimination was then calculated exactly from the underlying model, assuming no genotyping error and full genome coverage. Results: The simulations show that the ability to distinguish pedigree relationships quickly diminishes as relationships become more distant. First cousins can be distinguished from second cousins with 99.9% accuracy which drops to 94% when distinguishing second and third cousins. Relationships with the same expected degree of relatedness can be discriminated using continuously observed IBD, although the effectiveness decreases with more distant relationships. Conclusions: Continuous IBD observation establishes a theoretical upper bound on the power to distinguish relationships if a large but finite number of markers is used. The findings provide a benchmark for evaluating kinship analyses based on finite genetic marker panels. Full article

Background: Shigella flexneri is a major cause of shigellosis in developing regions and is known to cause outbreaks in institutional settings. Transmission occurs via the fecal–oral route. It invades intestinal epithelial cells, causing diarrhea, systemic symptoms, and complications such as hemolytic uremic syndrome. This study aimed to characterize the clinical presentation, administered treatment, infection outcomes, and infection control measures during a local S. flexneri outbreak at a rehabilitation center. Methods: This case series at King Saud University Medical City (Oct–Dec 2024) investigated S. flexneri infections from a rehabilitation center. Stool and blood samples were cultured and analyzed using microbiological methods. Molecular studies were used to verify the genetic linkage between the isolates and to study their virulence genes. Results: Four cases of S. flexneri were included, involving patients with various comorbidities, residing in a rehabilitation center, and presenting with symptoms like fever and diarrhea. Laboratory investigations revealed leukocytosis, electrolyte imbalances, and elevated inflammatory markers. Imaging studies showed findings consistent with colitis in two cases. Patients were managed with IV fluids and targeted antibiotics, leading to symptom resolution. Molecular studies confirmed the genetic relatedness between the S. flexneri isolates, with virulence genes indicating cellular invasion and inflammation as primary drivers of disease severity. Outbreak management comprised contact isolation, environmental disinfection, and education. Conclusions: S. flexneri outbreaks in long-term care facilities pose challenges among bedbound patients. Diapers may facilitate transmission, and infections may cause severe complications. Robust infection control, identifying outbreak sources, and strengthening prevention strategies are essential to protect vulnerable populations. Full article