Genotypic Profiles Research Articles

Transcriptome-Wide Association Study Reveals Potentially Candidate Genes Responsible for Milk Production Traits in Buffalo.

Identifying key causal genes is critical for unraveling the genetic basis of complex economic traits, yet it remains a formidable challenge. The advent of large-scale sequencing data and computational algorithms, such as transcriptome-wide association studies (TWASs), offers a promising avenue for identifying potential causal genes. In this study, we harnessed the power of TWAS to identify genes potentially responsible for milk production traits, including daily milk yield (MY), fat percentage (FP), and protein percentage (PP), within a cohort of 100 buffaloes. Our approach began by generating the genotype and expression profiles for these 100 buffaloes through whole-genome resequencing and RNA sequencing, respectively. Through comprehensive genome-wide association studies (GWAS), we pinpointed a total of seven and four single nucleotide polymorphisms (SNPs) significantly associated with MY and FP traits, respectively. By using TWAS, we identified 55, 71, and 101 genes as significant signals for MY, FP, and PP traits, respectively. To delve deeper, we conducted protein-protein interaction (PPI) analysis, revealing the categorization of these genes into distinct PPI networks. Interestingly, several TWAS-identified genes within the PPI network played a vital role in milk performance. These findings open new avenues for identifying potentially causal genes underlying important traits, thereby offering invaluable insights for genomics and breeding in buffalo populations.

Metabolic profiling of highland barley (Hordeum vulgare var. nudum) genotypes

Highland barley (HB), a valuable crop thriving in challenging conditions on the Qinghai-Tibet Plateau, possesses rich nutrient contents. This study aims to investigate the nutrient profile of HB genotypes and compare the metabolic profiles of three representative genotypes exhibiting high, medium, and low quality. The screening of HB genotypes reveals significant genotype-dependent differences in starch content, protein content, amino acid content, flavonoid content, antioxidant capacity, β-glucan, and γ-aminobutyric acid. The selected genotypes, namely KKDM2021005, ZJDM012, and DCDM2020017, exemplify high, average, and low quality, respectively. Utilizing LC–MS/MS for metabolic profiling, 617 metabolites from 12 major classes, with flavonoids being the most abundant, are identified. Distinct metabolic profiles are observed among the three genotypes, with 262 DAMs for KKDM2021005 versus DCDM2020017, 261 DAMs for KKDM2021005 versus ZJDM012, and 298 DAMs for ZJDM012 versus DCDM2020017. Enrichment analysis of DAMs highlights pathways associated with anthocyanin, phenylpropanoid, flavone and flavonol, and isoflavonoid biosynthesis. Specific DAMs such as l-valine, l-isoleucine, l-leucine, trifolin, spiraeoside, ferulic acid, betanin, cyanidin-3-O-galactoside, and cyanidin-3-O-glucoside, along with others, contribute to the observed quality differences among the genotypes. These findings provide a foundation for further exploration of genotype-specific metabolic profiles to manipulate the quality aspects of HB utilizing the existing gene pool. By enhancing its nutritional value, functional properties, and potential health benefits, HB can receive significant value addition.

Phenotypic variants of occupational bronchial asthma (immune profile, cytokines, diagnosis and prognosis)

Currently, occupational bronchial asthma is considered as a phenotypically and genotypically heterogeneous disease. The assessment of immunological characteristics opens up new opportunities in assessing the disease development, predicting the characteristics of the course, and establishing a personalized approach to pharmacotherapy of occupational asthma, as well as in developing an individual strategy for its prevention. The purpose of the study is to determine immunological markers of the risk of developing occupational bronchial asthma under conditions of exposure to sensitizing substances for various phenotypes of this disease. Materials and methods. The study included 170 patients with various phenotypes of occupational asthma and 50 participants in the control group. The levels of immunoglobulins A, M, and G in serum were determined by the Mancini technique (radial immunodiffusion). The determination of the levels of cytokines IL-1β, IL-4, IL-6, IL-8, IL-10, IL-17, TNF-α, MCP- 1, and IFN-γ, total IgE, C-reactive protein, and fibronectin in blood serum was carried out by enzyme-linked immunosorbent assay using kits and reagents (OOO Proteinovy Kontur, Vektor-Best, Diateks-E, DIA-plus, Pharmacia diagnostika). To study the content of vascular endothelial growth factor (VEGF) in blood serum, we used a sandwich-type enzyme-linked immunosorbent assay with a set of reagents from eBioscience. Genotyping was performed by real-time polymerase chain reaction using primers and probes developed with the PrimerQuest program (Integrated DNA Technologies, Inc.). Results. For the first time, the study has established the features of immunological manifestations in allergic and non-allergic phenotypes of occupational bronchial asthma, as well as the phenotypes of the combination of occupational asthma with occupational chronic obstructive pulmonary disease and metabolic syndrome. The features of the formation, pathogenesis, and prognosis of various phenotypes of occupational bronchial asthma have been identified. This allows recommending the determination of these immunological parameters during in-depth periodic medical examinations of workers exposed to sensitizing and irritating substances for differential diagnosis of various occupational asthma phenotypes in a specialized inpatient examination. Limitations of the study. The study has regional (Samara Region) and professional (in terms of detailing working conditions in the studied comparison groups) limitations. Conclusion. The identified immunological features in various phenotypes of occupational bronchial asthma and the established profiles of occupational asthma genotypes can optimize the approach to early diagnosis, prognosis, prevention, and pharmacotherapy of this disease, as well as expand the list of immunological research indicators used during preliminary and periodic medical examinations, in-depth examination of patients with occupational asthma in occupational disease clinics and occupational pathology centers, and the use of new reliable criteria for predicting the course of the disease.

Clinical and microbiological features of host-bacterial interplay in chronic venous ulcers versus other types of chronic skin ulcers.

Chronic venous ulcers of the lower limbs develop in the context of advanced venous disease and have a significant impact on the patient's quality of life, being associated with depression and worrisome suicide rates, as well as with an economic burden caused by increased medical care costs and high epidemiological risks of healthcare associated infections and emergence of strains resistant to multiple classes of antibiotics and/ or antiseptics. Although numerous studies have investigated the composition of the chronic wounds microbiome, either by culture-dependent or independent methods, there are no data on the association between virulence and resistance profiles of strains isolated from venous ulcers and the clinical picture of this pathology. The elucidation of pathogenic mechanisms, at both phenotypic and molecular level, is crucial in the fight against these important human microbial agents, in order to develop novel biomarkers and discover new therapeutic targets. In this study we aimed to characterize the phenotypic virulence profiles (including the ability to develop biofilms) of microorganisms isolated from chronic skin wounds and to correlate them with the clinical symptomatology. Considering the high incidence of Staphylococcus aureus infections in chronic ulcers, but also the ability of this species to develop multi-drug resistance, we performed an more in-depth study of the phenotypic and genotypic virulence profiles of methicillin-resistant Staphylococcus. The study revealed important differences regarding the clinical evolution and virulence profiles of microorganisms isolated from lower limb wounds, as well as between patients diagnosed with chronic venous ulcers and those with lesions of different etiology.

Multi-drug Resistant Acinetobacter baumannii: Phenotypic and Genotypic Resistance Profiles and the Associated Risk Factors in Teaching Hospital in Jordan

BackgroundThis study aimed to determine the prevalence of Antimicrobial Resistance Genes (ARGs), with a focus on colistin resistance in clinical A. baumannii, as well as the risk factors associated with A. baumannii infection in Jordanian patients. MethodsIn total, 150 A. baumannii isolates were obtained from patients at a teaching hospital. The isolates were tested for antimicrobial susceptibility using disc diffusion and microdilution methods. PCR amplification was used to detect ARGs, and statistical analysis was conducted to evaluate the influence of identified risk factors on the ARGs acquisition. ResultsMore than 90% of A. baumannii isolates were resistant to monobactam, carbapenem, cephalosporins, Fluoroquinolones, penicillin, and β-lactam agents. Moreover, 20.6% of the isolates (n = 31) were colistin-resistant. Several ARGs were also detected in A. baumannii isolates. Univariate analysis indicated that risk factors and the carriage of ARGs were significantly associated P ≤ (0.05) with gender, invasive devices, immunodeficiency, systemic diseases, tumors, and covid-19. Logistic regression analysis indicated seven risk factors, and three protective factors were associated with the ARGs (armA, strA, and strB) P ≤ (0.05). In contrast, tetB and TEM were associated with 2 risk factors each P ≤ (0.05). ConclusionOur study indicates a high prevalence of MDR A. baumannii infections in ICU patients, as well as describing the case of colistin-resistant A. baumannii for the first time in Jordan. Additionally, the risk factors associated with ARGs-producing A. baumannii infections among ICU patients suggest a rapid emergence and spread of MDR A. baumannii without adequate surveillance and control measures.

Linezolid Resistance Genes and Mutations among Linezolid-Susceptible Enterococcus spp.-A Loose Cannon?

The National Reference Centre for Enterococci receives an increasing number of linezolid-resistant Enterococcus isolates. Linezolid (LIN) resistance is mediated by G2576T 23S rDNA gene mutations and/or acquisition of resistance genes (cfr, optrA, poxtA). There are anecdotal reports that those resistance traits may be present in phenotypically linezolid-susceptible isolates. We aimed to determine the prevalence of LIN resistance genes and mutations in enterococci with a LIN MIC of 4 mg/L in broth microdilution (EUCAST = susceptible) isolated from German hospital patients 2019-2021. LIN MICs were additionally determined by ETEST® and VITEK2. Selected strains were subjected to LIN selective pressure and growth was monitored with increasing antibiotic concentrations. We received 195 isolates (LIN MIC = 4 mg/L). In total, 78/195 (40%) isolates contained either a putative resistance gene, the G2576T mutation, or a combination thereof. Very major error was high for broth microdilution. The ability to predict phenotypic resistance from genotypic profile was highest for G2576T-mediated resistance. Selection experiments revealed that, in particular, E. faecium isolates with resistance gene mutations or poxtA rapidly adapt to MICs above the clinical breakpoint. In conclusion, LIN resistance genes and mutations can be observed in phenotypically linezolid-susceptible enterococci. Those isolates may rapidly develop resistance under LIN selective pressure potentially leading to treatment failure.

Serotype and genotyping of <i>Salmonella</i> sp. isolated from street foods in N’Djaména, Chad

Group foodborne illness infections with Salmonella are often caused by the simultaneous consumption by several people of heavily contaminated food. The objective of this work was to determine the phylogenetic relationships between dietary strains of Salmonella sp. isolated from our samples and confirmed clinical strains. A total of 447 samples were collected and analyzed using standard food microbiology methods. Enterobacterial Repetitive Intergenic Consensus-Polymerase chain Reaction (ERIC-PCR) technique allowed confirmation that all our strains belong to the genus Salmonella. From ten (10) strains characterized, eight (8) different genotype profiles were identified. The different DNA fragments of the isolates were generated by ERIC-PCR and then revealed on the agarose gel and had bands ranging from 2 to 6 bands with sizes between 150 and 1500 bp. The two food strains of S. Mbadaka (1 and 2) presented identical profiles. However, it is noted that two (2) strains of S. Anatum had different ERIC-PCR profiles. There is also a very high resemblance between the strain of S. Anatum (strain 5) and the confirmed clinical strains (H5: Salmonella Typhi). The presence of risky germs in the food analyzed poses a public health problem and should call on the competent authorities and prompt the taking of corrective measures.

Antibiotic resistance profile in sediments and bacterial isolates from a human-impacted mangrove from Bahía Magdalena, Mexico

Abstract Antibiotic-resistant bacteria (ARB) and antibiotic-resistance genes (ARGs) in the environment are considered emerging contaminants. One of the ecosystems that can harbor resistant bacteria and genes is mangroves. This report aims to assess ARB and ARG's presence at two mangrove locations in Bahia Magdalena, Mexico. Bacterial isolates were selected based on their phenotypic profiles of antibiotic resistance. DNA from mangrove sediments and bacterial isolates was tested for int1 and antibiotic resistance genes by final point PCR. From 90 ARB isolates, the phenotypic profile showed resistance to ciprofloxacin (90%), cefotaxime (85.7%), and ampicillin (78.6%), while the beta-lactamase gene (blaCTX-M) was present in 72.9% of the isolates. Antibiotic resistance genes identified in sediments were found even at 30–50 cm depth, but the integron Class gen (int1) was found mainly in shallow samples. Principal component analysis showed a close relationship between the integron gene, vancomycin, and sulfonamides resistance genes. No correlation was found between the phenotypic and genotypic profiles of the bacterial isolates. Also, no differences were observed between the two mangrove ecosystems studied. The impact of anthropogenic activities was equally significant on both sites. The role of mangrove ecosystems in the dispersion of antibiotic resistance needs to be further explored.

Phenotypic and Genotypic Characterizations of Antimicrobial-Resistant Escherichia coli Isolates from Diverse Retail Meat Samples in North Carolina During 2018-2019.

Surveillance of antimicrobial-resistant pathogens in U.S. retail meats is conducted to identify potential risks of foodborne illness. In this study, we conducted a phenotypic and genotypic analysis of Escherichia coli recovered from a diverse range of retail meat types during 2018-2019 in North Carolina. The investigation was conducted as part of the National Antimicrobial Resistance Monitoring System (NARMS). Retail meat sampling and E. coli isolation were performed in accordance with NARMS retail meat isolation protocols. We used the Sensititre™ broth microdilution system to determine phenotypic resistance to 14 antimicrobial agents and the Illumina next-generation sequencing platform for genotypic resistance profiling. The highest prevalence of E. coli isolates was found in ground turkey (n = 57, 42.9%) and chicken (n = 27, 20.3%), followed by ground beef (n = 25, 18.9%) and pork (n = 24, 18%). The isolates were divided into seven different phylogroups using the Clermont typing tool, with B1 (n = 59, 44.4%) and A (n = 39, 29.3%) being the most dominant, followed by B2 (n = 14, 10.5%), D (n = 7, 5.3%), F (n = 6, 4.5%), E (n = 3, 2.3%), and C (n = 2, 1.5%). Using multilocus sequence typing (MLST), 128 Sequence types (STs) were identified indicating high diversity. Phenotypic and genotypic resistance was observed toward aminoglycosides, sulfonamides, beta-lactams, macrolides, tetracyclines, phenicols, and fluoroquinolones. Ground turkey samples were more resistant to the panel of tested antimicrobials than chicken, beef, or pork (p < 0.05). All isolates were found to be susceptible to meropenem. A high percentage of turkey isolates (n = 16, 28%) were multidrug-resistant (MDR) compared with 18.5% of chicken (n = 5), 8.4% of pork (n = 2), and 8% of beef isolates (n = 2). This study highlights the benefit of surveillance to identify MDR E. coli for epidemiologic tracking and is a comprehensive report of the phenotypic and genotypic characterization of E. coli isolated from retail meats in North Carolina.

Determination of antibiotic resistance patterns and genotypes of Escherichia coli isolated from wild birds

BackgroundCurbing the potential negative impact of antibiotic resistance, one of our era's growing global public health crises, requires regular monitoring of the resistance situations, including the reservoir of resistance genes. Wild birds, a possible bioindicator of antibiotic resistance, have been suggested to play a role in the dissemination of antibiotic-resistant bacteria. Therefore, this study was conducted with the objective of determining the phenotypic and genotypic antibiotic resistance profiles of 100 Escherichia coli isolates of gull and pigeon origin by using the Kirby-Bauer disk diffusion method and PCR. Furthermore, the genetic relationships of the isolates were determined by RAPD-PCR.ResultsPhenotypic antibiotic susceptibility testing revealed that 63% (63/100) and 29% (29/100) of E. coli isolates were resistant to at least one antibiotic and multidrug-resistant (MDR), respectively. With the exception of cephalothin, to which the E. coli isolates were 100% susceptible, tetracycline (52%), kanamycin (38%), streptomycin (37%), ampicillin (28%), chloramphenicol (21%), trimethoprim/sulfamethoxazole (19%), gentamicin (13%), enrofloxacin (12%) and ciprofloxacin (12%) resistances were detected at varying degrees. Among the investigated resistance genes, tet(B) (66%), tet(A) (63%), aphA1 (48%), sul3 (34%), sul2 (26%), strA/strB (24%) and sul1 (16%) were detected. Regarding the genetic diversity of the isolates, the RAPD-PCR-based dendrograms divided both pigeon and gull isolates into five different clusters based on a 70% similarity threshold. Dendrogram analysis revealed 47–100% similarities among pigeon-origin strains and 40–100% similarities among gull-origin E.coli strains.ConclusionsThis study revealed that gulls and pigeons carry MDR E. coli isolates, which may pose a risk to animal and human health by contaminating the environment with their feces. However, a large-scale epidemiological study investigating the genetic relationship of the strains from a "one health" point of view is warranted to determine the possible transmission patterns of antibiotic-resistant bacteria between wild birds, the environment, humans, and other hosts.3bRmtrrdv9vbDYjBBmhJ2hVideo

Gene expression, proteomic, and metabolic profiles of Brazilian soybean genotypes reveal a possible mechanism of resistance to the velvet bean caterpillar Anticarsia gemmatalis

Gene expression, proteomic, and metabolic profiles of Brazilian soybean genotypes reveal a possible mechanism of resistance to the velvet bean caterpillar Anticarsia gemmatalis

Determination of the virulence status of Clostridium perfringens strains using a chicken intestinal ligated loop model is important for understanding the pathogenesis of necrotic

Necrotic enteritis (NE) is a poultry intestinal disease caused by virulent strains of the bacterium Clostridium perfringens (C. perfringens). This anaerobic bacterium produces a wide range of enzymes and toxins in the gut which leads to NE development. It is generally accepted by the poultry veterinarians that netB-positive C. perfringens strains are virulent and netB-negative strains do not cause NE. However, NE pathogenesis remains unclear as contradictory results have been reported. The use of experimental in vivo models is a valuable tool to understand the pathogenesis of a disease. In this study, a chicken ligated loop model was used to determine the virulence status of 79 C. perfringens strains from various geographical locations, sources, and genotype profiles. According to our model and based on histologic lesion scoring, 9 C. perfringens strains were classified as commensal, 35 as virulent, and 34 as highly virulent. The virulence of only 1 C. perfringens strain could not be classified as its lesion score was variable (from <10 to >15). In general, NE lesions were more severe in intestinal loops inoculated with netB-positive C. perfringens strains than those inoculated with netB-negative strains. The prevalence of netB among strains classified as commensal, virulent, and highly virulent was 56% (5/9), 54%, (19/35), and 59% (20/34). These results suggest that NetB is not required to cause NE lesions and that other factors are also involved. The classification of the virulence status of C. perfringens strains should not be based solely on the presence or absence of this toxin. Therefore, the use of an in vivo model is essential to distinguish commensal from virulent strains of C. perfringens.

Antimicrobial susceptibility profiles and genotyping of Neisseria meningitidis of serogroup C, Italy, 2000-2020.

In Italy the introduction of meningococcal C conjugate vaccine in 2005 has led to a significant reduction of invasive meningococcal disease (IMD) caused by Neisseria meningitidis of serogroup C (MenC). However, this serogroup is still responsible of sporadic cases, clusters and local outbreaks. The study aims to investigate the genotype and antimicrobial susceptibility profile of MenC isolates collected in Italy from 2000 to 2020. Bacterial isolates and biological samples (blood or cerebrospinal fluid) from invasive meningococcal cases are collected and characterized at the National Reference Laboratory for IMD of Istituto Superiore di Sanità. Antimicrobial susceptibility was determined by MIC Test Strip Method and interpreted according to the EUCAST breakpoints guideline. Genotypic characteristics, including multi locus sequence typing (MLST), finetype, and antimicrobial resistance target genes were performed and analyzed using the PubMLST database. Genomic comparison of core genome MLST (cgMLST) of MenC genomes was also carried out. From 2000 to 2020, a total of 665 MenC isolates were investigated for antimicrobial susceptibility and 301 for genotyping. Over two decades, almost all MenC isolates resulted susceptible to antimicrobials with few isolates resulting resistant to ciprofloxacin (N = 2), penicillin G (N = 13), and rifampicin (N = 9), respectively. Molecular typing of MenC obtained from isolates or clinical specimens identified mostly the genotype C:P1.5-1,10-8:F3-6:ST-11(cc11). However, phylogenetic analysis, performed on genomes from MenC isolates, identified two sub lineages, 11.1 and 11.2, among cc11, of which the sub lineage 11.2 was the predominant. Wider application of the genomic analysis and monitoring of antimicrobial susceptibility represent key aspects of IMD surveillance and to monitor the continued evolution of these hyperinvasive strains.

Behavior Physiology of Workplace Bullying and It’s Role to Job Satisfaction and Psychologycal Distress among Workers at Water Supply Company

Individuals strive to fulfill their essential needs by working. Every company has different work environment. The work environment tends to have impact on each individual. One of the key issues that usually occur at workplace is bullying. Workplace bullying can happen to anyone while both bullies and their victims may experience psychological effects from bullying. This study aims to see the effect of workplace bullying on job satisfaction and psychological distress among water supply company employees. This research design is quantitative using cross sectional design. The results showed that the psychological distress variable played a significant role in workplace bullying (p. &lt;0.05). However, the job satisfaction variable does not contribute to workplace bullying (p. &gt; 0.05). The serotonin trasporter-linked promoter region (5-HTTLPR) polymorphism of the SLC6A4 gene consists of an insertion/deletion that creates a short (S) 14 repeat or a long (L) 16 repeat allele. Genotype profile on one’s serotonergic system is correlated by their dominance in the community. Individuals with allele LL type is more likely become bullies when they are encouraged by the environment. In contrast, individuals with SS allele type with in a characteristic of low transcription activity at transporter serotonin gene tend to become bullying victims in their workplace due to they more vulnerable to stress. Employee with amygdala which easily triggered and intimidated by the dominant individuals, more likely to experience workplace bullying. Those employee who work in supportive workplace show higher job satisfaction and they are not distress psychologically.

Advances in genomics and genome editing for improving strawberry (Fragaria ×ananassa).

The cultivated strawberry, Fragaria ×ananassa, is a recently domesticated fruit species of economic interest worldwide. As such, there is significant interest in continuous varietal improvement. Genomics-assisted improvement, including the use of DNA markers and genomic selection have facilitated significant improvements of numerous key traits during strawberry breeding. CRISPR/Cas-mediated genome editing allows targeted mutations and precision nucleotide substitutions in the target genome, revolutionizing functional genomics and crop improvement. Genome editing is beginning to gain traction in the more challenging polyploid crops, including allo-octoploid strawberry. The release of high-quality reference genomes and comprehensive subgenome-specific genotyping and gene expression profiling data in octoploid strawberry will lead to a surge in trait discovery and modification by using CRISPR/Cas. Genome editing has already been successfully applied for modification of several strawberry genes, including anthocyanin content, fruit firmness and tolerance to post-harvest disease. However, reports on many other important breeding characteristics associated with fruit quality and production are still lacking, indicating a need for streamlined genome editing approaches and tools in Fragaria ×ananassa. In this review, we present an overview of the latest advancements in knowledge and breeding efforts involving CRISPR/Cas genome editing for the enhancement of strawberry varieties. Furthermore, we explore potential applications of this technology for improving other Rosaceous plant species.

Genotypic and phenotypic profiling of 127 Legionella pneumophila strains: Insights into regional spread.

Given the recent global surge in Legionnaires' disease cases, the monitoring of Legionella pneumophila becomes increasingly crucial. Epidemiological cases often stem from local outbreaks rather than widespread dissemination, emphasizing the need to study the characteristics of this pathogen at a local level. This study focuses on isolates of L. pneumophila in the Italian region of Friuli Venezia Giulia to assess specific genotype and phenotype distribution over time and space. To this end, a total of 127 L. pneumophila strains isolated between 2005 and 2017 within national surveillance programs were analysed. Rep-PCR, RAPD, and Sau-PCR were used for genotypic characterization, while phenotypic characterization was conducted through fatty acids analysis. RAPD and Sau-PCR effectively assessed genetic characteristics, identifying different profiles for the isolates and excluding the presence of clones. Although Sau-PCR is rarely used to analyse this pathogen, it emerged as the most discriminatory technique. Phenotypically, hierarchical cluster analysis categorized strains into three groups based on varying membrane fatty acid percentages. However, both phenotypic and genotypic analyses revealed a ubiquitous profile distribution at a regional level. These results suggest an absence of correlations between strain profiles, geographical location, and isolation time, indicating instead high variability and strain dissemination within this region.

Phenotypic and Genotypic Identification of Antimicrobial Resistance amongst the Campylobacter jejuni and Campylobacter coli Strains Isolated from Raw Milk of Animal Species

Campylobacter jejuni and Campylobacter coli portion as an important food‐borne pathogen owing to the consumption of raw milk of animal species is unmoving unidentified. This survey appraised both phenotypic and genotypic patterns of antimicrobial resistance amongst the C. jejuni and C. coli strains isolated from raw milk samples. Totally, 850 raw milk samples were examined for C. jejuni and C. coli. After culture, species identification was done using PCR. Phenotypic and genotypic patterns of antimicrobial resistance were assessed using disk diffusion and PCR, respectively. One hundred and ten out of 850 (12.94%) raw milk samples were contaminated with Campylobacter spp (95% confidence interval). The highest contamination rate with Campylobacter spp. was observed in raw cow milk (18.18%). C. jejuni and C. coli species were detected in 45.45% and 32.72% of Campylobacter isolates, respectively (P &lt; 0.05). C. jejuni strains showed the highest resistance rate toward tetracycline (84%), gentamicin (80%), ampicillin (74%), and erythromycin (64%). Similarly, C. coli isolates showed the highest resistance rate toward tetracycline (63.88%), gentamicin (58.33%), and ampicillin (52.77%). The lowest resistance rate of C. jejuni and C. coli was observed against chloramphenicol (10% and 2.77%), nalidixic acid (22% and 8.33%), clindamycin (36% and 13.88%), and ciprofloxacin (38% and 16.66%), respectively. The most routinely identified antimicrobial resistance genes amongst the C. jejuni isolates were tetA (66%), blaOXA−61 (54%), tetO (46%), and tetB (40%), while those of C. coli isolates were blaOXA−61 (52.77%), tetA (41.66%), cmeA (27.77%), and tetO (27.77%). The prevalence of simultaneous resistance toward more than 4 antimicrobial agents amongst the C. jejuni and C. coli isolates was 46% and 16.66%, respectively. C. jejuni and C. coli average multiple antimicrobial resistance (MAR)‐indexes in the present research were 0.49 and 0.32, respectively. The simultaneous presence of phenotypic and genotypic profiles of antimicrobial resistance amongst the resistant C. jejuni and C. coli bacteria suggests an imperative threat rendering contaminated raw milk consumption and probable occurrence of campylobacteriosis.

Pre-treatment HIV-1 drug resistance in Cuban patients with late presentation to health care: 2009-2020.

Background: The presence of antiretroviral-resistant HIV-1 genetic variants in patients with late presentation to health care may impact the success of antiretroviral therapy, costs of care, and potential HIV transmission. Aim: To determine the prevalence of pre-treatment HIV-1 drug resistance to antiretrovirals (PDR) in Cuban patients classified as late presenters (LP). Methods: A retrospective cross-sectional study was carried out on 255 HIV-positive Cubans classified as LP (CD4+ T cell count ≤350 cells/mm3) and included in PDR surveillance studies in Cuba during the period 2009-2020. The viral subtype and the genotypic profile of antiretroviral resistance were analyzed. Some clinical and epidemiological variables were evaluated. Results: 83.2% of the patients were male and 65.9% were men who had sex with other men (MSM). The average age was 31 years. 40% of the individuals studied had advanced disease (CD4+ T cell count ≤200 cells/mm3). The predominant genetic variants were subtype B (29.4%); CRF20, 23, 24_BG (24.3%) and CRF19_cpx (22.4%). The prevalence of PDR was 21.2% (95%, CI 16.3-26.7). The prevalence was 8.2% (95%, CI 5.3-11.9) for any Nucleoside Reverse Transcriptase Inhibitor (NRTI), 15.1 % (95%, CI 11.2-19.7) for any Non-Nucleoside Reverse Transcriptase Inhibitor (NNRTI), 2.1 % (95%, CI 0.75-4.41) for any Protease Inhibitor (PI). 9.25% of the LPs with PDR died a year after diagnosis of the HIV infection. The most frequent mutations were K103N (6.7%), G190A (4.7%) and M184V (4.3%). The treatment will not be effective in 17.3 % of patients who start therapy with the NRTI+NNRTI combinations. Conclusion: The high PDR values in LPs show the need to enhance genotypic studies of HIV resistance in this population at the time of diagnosis of the infection, since the success of first-line antiretroviral therapy may be compromised and influence compliance with the global goals set forth by UNAIDS for the year 2030.

The relationship between Fc epsilon receptor-1α and β (FCER1A and FCER1B) gene polymorphisms in patients with chronic urticaria using omalizumab.

Chronic urticaria requires well-defined treatment strategies in order to achieve a maximum treatment response and maintain the quality of life. Since 2014, omalizumab has been used in chronic urticaria. However, many studies showed that some patients are resistant to omalizumab. To determine the effects of single nucleotide changes in the FCER1A and FCER1B genes, which are thought to be related to resistance mechanisms, in our population of patients who have not responded to omalizumab treatment. We included 100 patients with chronic urticaria who were treated with omalizumab and 50 healthy individuals. Frequently observed gene polymorphisms, FCER1A (rs2251746) and FCER1B (rs569108), were examined in peripheral blood samples. The regions of rs2251746 and rs569108 gene polymorphisms were amplified using fluorescently labelled probes through real-time polymerase chain reaction (PCR). The analysis was performed bioinformatically via the SNP genotype profiling program. There was no statistically significant relationship between FCER1A (rs2251746) and FCER1B (rs569108) gene polymorphisms in patients and their clinical, demographic characteristics, and the resistance to treatment (p > 0.05). In our study, the mean patient age was found to be higher in the CT group (44.71 ±12.5 years) compared to the TT group (37.34 ±11.5 years) only in the rs2251746 polymorphism (p < 0.05). In our study, there was no significant relationship between FCER1A and FCER1B gene polymorphisms and resistance to omalizumab therapy. Further, multicentre, large-scale studies are needed to support our results.

Genotypic Profiling of Virulence and Antibiotic Resistance Patterns of Staphylococci and Streptococci Isolates from Dairy Cattle with Clinical Mastitis Infection in Region IV-A, Philippines

Staphylococci and Streptococci spp. play a significant role as primary causal agents of bovine mastitis. Farmers commonly employ the use of antibiotics as a widespread strategy for the management of mastitis infections. However, the frequent use of antibiotics is directly correlated to the increase in antimicrobial-resistant (AMR) bacterial strains resulting in some challenges in managing subsequent infections. In this current study, the virulence and AMR profiles of previously isolated Staphylococci and Streptococci bacterial strains from dairy cattle with clinical mastitis were evaluated to provide an overview of their pathogenic and resistant genetic characteristics. The incidence of virulence genes among Staphylococci isolates revealed low detection rates, whereas 42.2% of the Streptococci isolates were found to express the surface-anchored rib gene. The laminin-binding lmb and toxin β-hemolysin cylE genes were also frequently detected among Streptococci isolates. These observations suggest a strong association between Streptococci spp. and severe infection among the tested animals. Meanwhile, 28% of Staphylococci and 12.2% of Streptococci were observed to be resistant to three or more drug classes, thus considered multidrug-resistant. The most frequently detected AMR genes among Staphylococci isolates were aphA-1 (33%), mecA (25%), and blaSPM-1 (21%). Meanwhile, among Streptococci isolates, tetB (35%), blaIMP (31%) and ermA/TR (31%) were most prevalent. Although the phenotypic resistance of some isolates was comparable with its associated genotypic resistance, some isolates did not exhibit a consistent phenotype-genotype AMR. Nevertheless, the presence of these virulence and AMR genes in mastitis-associated pathogens is still critical because these genes can migrate across microbial populations, thus posing a serious threat to animal and public health.