Predominant Genotype Research Articles

Morphological Characterization and Genotyping of Acanthamoeba Isolates From Oral and Nasal Samples of Cancer Patients in Kashan, Iran

Background: Acanthamoeba​ species are recognized as the most prevalent free‐living amoebae (FLA). They can cause granulomatous amebic encephalitis (GAE) and pulmonary and ocular infections. The present study aimed to isolate and identify Acanthamoeba genotypes in cancer patients referred to Kashan’s hospitals in Central Iran.Methods: This cross‐sectional study was conducted with oral and nasal swab samples collected from a hundred cancer patients referred to Kashan’s Beheshti and Yasrebi hospitals during 2019–2020. The samples were cultured in 1.5% non‐nutrient agar (NNA) with heat‐killed Escherichia coli and examined for “FLA.” A polymerase chain reaction (PCR) assay amplifying the 18S rRNA gene was performed, and Acanthamoeba‐positive isolates were subjected to nucleotide sequencing to identify their genotypes.Results: The prevalence of Acanthamoeba infection was 51% in the oral cavity and 38% in the nasal samples of cancer patients. The most frequent Acanthamoeba cysts were (51.3%) wrinkled polygonal and sized 9.55‐11.5 μm (Group II). Acanthamoeba genotypes T4, T11, and T5 were identified in the oral cavity samples, whereas T4 and T11 were detected in the nasal samples.Conclusion: The prevalence of Acanthamoeba infection in oral and nasal cancer patients was higher in Kashan, Iran, compared to other countries. Due to the high rate of oral Acanthamoeba contamination, oral sampling is recommended for better detection of this protozoan. Since T4 is the predominant genotype that can cause serious diseases in high‐risk groups, increasing physicians’ awareness of infections associated with Acanthamoeba and preventive and control measures are strongly suggested.

Children and adolescents with sickle cell disease: characteristics and use of medicinal plants.

The aim of this study was to describe the epidemiological characteristics of pediatric patients with sickle cell disease (SCD) and evaluate the use of medicinal plants in these patients concomitantly with their drug treatment. This is a review of the medical records of pediatric patients at a public institution with tertiary care. The selection criterion was to be a child or adolescent with SCD undergoing pediatric follow-up at this outpatient clinic. In the medical records of the patients selected, records of the use of plants for medicinal purposes were sought. In total, 154 records (100% of total active patients followed in this clinic) were reviewed: 99 children and 55 adolescents. The predominant genotype was SS (58.4%), followed by SC (29.2%). The use of at least one medication for SCD was reported in 95.5% of the medical records. The use of medicinal plants was reported by 70.1% of patients, with 276 citations in the medical records referring to 64 different types of plants. Six plants were used for the treatment of SCD, the main one being Lemonvine/Ora-pro-nóbis (Pereskia aculeata). The use of medicinal plants was reported for flu-like symptoms and/or COVID-19 (both for prevention and treatment) by 60.5% of the citations, with 35 different plants reported for this use, exclusively or not. This use was followed by pain symptoms (14.2% of citations). The majority of patients in this study use both conventional and traditional/complementary/alternative medicine, highlighting the need for more studies in the area, with a special focus on patient safety.

Genótipos de Circovírus Suíno Tipo 2 e PCV3 em Amostras Clínicas de Suínos no Brasil

Abstract Porcine circovirus type 2 (PCV2), an important pathogen in swine, causes PCV disease (PCVD). Although PCVD is effectively controlled using commercial vaccines, its clinical presentation is changing. Moreover, PCV2 is genetically evolving, with new genotypes emerging in vaccinated or unvaccinated pigs. In this study, we aimed to verify the presence of the PCV2a, PCV2b, and PCV2d genotypes in PCV-positive porcine samples. Furthermore, to identify coinfections between the PCV2 genotypes and/or PCV3, which can also induce disease in pigs, we employed a quick, effective, and low-cost PCR diagnostic test. In this study, 333 PCV2 PCR and clinically positive samples from various production stages and herds across Brazil were analyzed. Among these, 266 samples were genotyped, with PCV2b emerging as the most predominant genotype (56.77% of the positive samples), mainly observed in nursery pigs. PCV2d was also identified in 33.10% of the samples, primarily from finishing pigs and breeding sows. The employed PCR test was compared with a commercial kit, proving effective in PCV2 genotyping. This study demonstrates the significance of PCV2 genotyping, showing PCV2b as the most predominant genotype responsible for disease in pig farms in Brazil. PCV2a, the prevalent genotype used in commercial vaccines, was not detected in any of the analyzed samples. While pigs infected with other PCV2 genotypes may receive some heterologous protection from PCV2a vaccines, adequate diagnosis and vaccine monitoring for updates must be considered.

Effect of DGAT1 gene polymorphisms in coarse-haired fat-tailed lambs of different genotypes.

The aim of this study was to investigate the DGAT1 gene polymorphism and its effects on lamb weight in kazakh and tajik sheep breeds. A total of 97 blood samples were collected from purebred (еdilbay х еdilbay) and crossbred lambs (еdilbay x gissar) breеd by the Baiserke Agro Scientific and Production Center in the Talgar District of the Almaty Region of Kazakhstan. Animals were genotyped for DGAT1-AluI polymorphism using the polymerase chain reaction-restriction length polymorphism (PCR-RFLP) method. The result of PCR-RFLP showed that purebred (еdilbay х еdilbay) sheep had three genotypes (CC, CT and TT) and crossbred sheep had two genotypes (CC and CT). The predominant genotype was CC with a frequency of 0.70 and 0.58 in purebred sheep and crossbred sheep breeds, respectively. The DGAT1 gene showed no significant association with live weight of lambs at different times in both breeds studied. However, the study showed that the CC genotype produced higher live weight at day 60 in purebred sheep (CC: 33,668 kg and CT: 32,444) and at day 120 (CC: 41,487 and CT: 40,929) in crossbred lambs. The present study was the first to investigate the polymorphism and relationships between genotypes and lamb live weights for DGAT1 gene in sheep breeds, purebred and crossbred. We conclude that further comprehensive investigations should be done for the exact evidence of the effects of DGAT1/Aluı polymorphism on lamb live weights.

Morphological changes of cerebral gray matter in spinocerebellar ataxia type 3 using fractal dimension analysis.

Spinocerebellar ataxia type 3 (SCA3), or Machado-Joseph disease, presents as a cerebellar cognitive affective syndrome (CCAS) and represents the predominant SCA genotype in Taiwan. Beyond cerebellar involvement, SCA3 patients exhibit cerebral atrophy. While prior neurodegenerative disease studies relied on voxel-based morphometry (VBM) for brain atrophy assessment, its qualitative nature limits individual and region-specific evaluations. To address this, we employed fractal dimension (FD) analysis to quantify cortical complexity changes in SCA3 patients. We examined 50 SCA3 patients and 50 age- and sex-matched healthy controls (HC), dividing MRI cerebral gray matter (GM) into 68 auto-anatomical subregions. Using three-dimensional FD analysis, we identified GM atrophy manifestations in SCA3 patients. Results revealed lateral atrophy symptoms in the left frontal, parietal, and occipital lobes, and fewer symptoms in the right hemisphere's parietal and occipital lobes. Focal areas of atrophy included regions previously identified in SCA3 studies, alongside additional regions with decreased FD values. Bilateral postcentral gyrus and inferior parietal gyrus exhibited pronounced atrophy, correlating with Scale for the Assessment and Rating of Ataxia (SARA) scores and disease duration. Notably, the most notable focal areas were the bilateral postcentral gyrus and the left superior temporal gyrus, serving as imaging biomarkers for SCA3. Our study enhances understanding of regional brain atrophy in SCA3, corroborating known clinical features while offering new insights into disease progression.

Predominant genotypes of human papillomavirus in Korean men

Predominant genotypes of human papillomavirus in Korean men

Clinical and Bacterial Characteristics of Bloodstream Infections Caused by Listeria monocytogenes in Western China.

Bloodstream infections (BSIs) caused by Listeria monocytogenes are linked to high mortality of the patients. Case-specific details related to this disease and causative strains in different districts remain to be characterized. In this study, medical data of BSIs admitted to West China Hospital from October 2017 to March 2023 were retrieved from the hospital information system. The in vitro antimicrobial susceptibility testing and whole-genome sequencing were performed for L. monocytogenes strains isolated from blood specimens. The genetic relationship of these strains with those in public databases was also analyzed. The in-hospital mortality of L. monocytogenes BSIs was 25.7% (9/35). The changes in consciousness and elevated serum C-reactive protein (CRP) level were found to be the differential factors of L. monocytogenes BSIs (P < 0.05). All the 27 strains studied were susceptible to ampicillin, meropenem, and erythromycin. Only 22.2% of them were susceptible to trimethoprim-sulfamethoxazole. The Listeria pathogenicity islands 1 (LIPI-1), truncated LIPI-2, and multiple virulence-related genes outside the LIPIs were determined from these strains. Also, 12 sequence types (STs) and 12 clonal complexes (CCs) were identified and classified into clonal lineages I (9/27, 33.3%) and lineages II (18/27, 66.7%), demonstrating genetic differences with the strains in the database. ST451/CC11 (5/27, 18.5%) and ST8/CC8 (4/27, 14.8%) were the common genotypes. The consciousness change and elevated serum CRP level were found to be the differential factors of L. monocytogenes BSIs. Considering the high virulence of the strains, it is needed to pay more attention to the dissemination of the predominant genotype.

Genotype Variation of HIV/HCV Co-infections in Karachi, Pakistan

Human Immunodeficiency Virus (HIV) and Hepatitis C Virus (HCV) are among major health issues that affect a large section of the world's population. While HCV affects around 170 million people worldwide, HIV affects 3% of the global population, with 10 million HCV cases documented in Pakistan alone. Co-infection with HIV and HCV results in a variety of genotypic patterns, with significant global heterogeneity in the incidence of spontaneous resolution of hepatitis C and the distribution of HCV genotypes among co-infected individuals. Co-infection is usually transmitted by sexual contact, contaminated blood supplies, and mother-to-child transmission, with high-risk populations like intravenous drug users (IDUs), and men who have sex with men (MSM) having increased vulnerability. This study, conducted in Karachi, Pakistan, aimed to explore the predominant genotypes and viral load of HIV and HCV. The genetic features of the HIV Gag and HCV NS5b genes were examined using genotyping techniques and phylogenetic methodology. The study revealed that out of the 150 individuals examined, 70 were diagnosed with HIV alone, 55 with HCV only, and 25 had both HIV and HCV infections concurrently. Furthermore, genetic analysis demonstrated that HIV-1 subtype A1 was the predominant genotype, with subtype C closely following. In the case of HCV, genotype 3a was the most prevalent in both mono- and co-infected individuals. Notably, individuals with dual infections exhibited limited genotypic variability for each virus. In the case of HIV co-infection, there was an elevation in viral load, while HCV demonstrated lower viremia relative to mono-infection. In conclusion, the study revealed the predominance of HIV-1 subtype A1 and HCV genotype 3a, as well as an elevated level of HIV and a lowered level of HCV in co-infection.

Prevalence of hepatitis D virus infection among patients with chronic hepatitis B infection in a tertiary care centre in Thailand

Knowledge about the epidemiology of hepatitis D virus (HDV) is essential for effective screening and management. Our study aimed to update the prevalence of HDV infection among patients with hepatitis B virus (HBV) infection at hepatology clinics in Thailand. We enrolled HBV-infected patients from hepatology clinics at King Chulalongkorn Memorial Hospital, Bangkok, Thailand, between June 2022 and November 2023. Demographic, biochemical characteristics, and liver-related complications (LRC), including cirrhosis and hepatocellular carcinoma, were reviewed. The competitive enzyme and chemiluminescence immunoassays were used to detect anti-HDV antibodies. Real-time polymerase chain reaction (RT-PCR) was used to test for HDV RNA in anti-HDV-positive patients. The HDV genotype was identified in detectable HDV RNA samples. Of the 702 enrolled patients, four (0.6%) had positive and equivocal for both anti-HDV tests. Two (50.0%) of the four patients tested positive for HDV RNA and genotype 1 was identified; one had multiple risk factors. Anti-HDV seroprevalence was not significantly different between patients with and without LRC. In conclusion, HDV co-infection is less common in Thailand than globally. Additionally, our study identified genotype 1, the predominant HDV genotype worldwide, and observed co-infection even without LRC.

Echinococcus granulosus sheep strain (G1) as the predominant genotype in definitive host (dogs) isolates in northeastern Iran

Echinococcus granulosus sensu lato (E. granulosus s.l.) is a zoonotic parasite, causing cystic echinococcosis in humans. In the present study, prevalence and genotypes of E. granulosus s.l. was assessed in stools collected from 244 dogs including 138 stray and 106 domestic animals using high resolution melting curve (HRM) method. Initially, to detect taeniid eggs in feces, all samples were examined using the formalin-ether techniques. Genomic DNA was extracted from the positive samples and E. granulosus s.l. was differentiated from other Taeniidae parasites using SSU-rDNA gene and E. granulosus s.l. was analyzed for genotyping using HRM based on the cox1 gene. In total, 12.7% (31/244) of the samples were positive for Taeniidae eggs. In addition, among the positive samples, 77.4% (24/31) were positive for E. granulosus s.l.. In details, 11.3% (12/106) of the domestic dogs and 8.7% (12/138) of the stray dogs were positive for E. granulosus s.l.. The results of HRM analysis showed that all E. granulosus s.l. isolates were G1 strain. Findings of the present study indicated a considerable prevalence of E. granulosus G1 among dogs in the northeast of Iran and imply a serious risk of transmitting to humans and livestock.

Immediate histologic correlation in patients with different HPV genotypes and ages: a single center analysis in China

BackgroundHuman papillomavirus (HPV) has been confirmed as a major causative factor for malignant transformation of cervical epithelial cells and for the development of cervical intraepithelial neoplasia (CIN) and invasive cervical cancer. We carried out this study to investigate the association of different HPV genotypes and ages with immediate histological cervical lesions in opportunistic screening patients in a single center.MethodsA total of 1,661 samples with biopsy-confirmed histologic findings were collected from the gynecological clinic of our hospital between October 2017 and May 2020 for analysis. The distribution of single-type HPV genotypes in CIN of different severities and the age-dependent prevalence for single-type HPV infection were analyzed.ResultsIn both CIN2 and CIN3 group, HPV16, 58, 52, 33 and 31/18 were detected as top 5 high-risk human papillomavirus (hrHPV) types, which accounts for 89.25% and 88.54% of single HPV infection incidence respectively. Besides, not a single case of HPV45 was found in CIN2 and CIN3. HPV16 was the dominant genotype in both CIN2 and CIN3, accounted for 46.24% and 55.21%, respectively. The prevalence of HPV16 was the most frequent in all the age groups, except ≥ 65 years group in CIN3, and almost one in three HPV16-positive patients were diagnosed with high grade CIN. The peak of the incidence of CIN3 was observed at 25 ~ 34 years (33.68%), followed by 35 ~ 44 years (31.58%).ConclusionHigh grade CIN peak at 25 ~ 44 years, women of this age are recommended for normative screening if conditions permit. HPV16-positive patients should be given high priority in opportunistic screening, while the single-center data suggesting a low risk of CIN2/3 in HPV45-positive patients. For women ≥ 65 years old, patients infected with other HPV types should be also taken seriously. In general, HPV16, 58, 52, 33, 31 and 18 were the most common genotypes in CIN2/3, and a vaccine including these predominant genotypes might be of great significance for cervical cancer prevention in China.

Genotype distribution of hepatitis C virus in the province of Gaziantep, a 10-year evaluation

AbstractHepatitis C virus (HCV) can cause both acute and chronic hepatitis infections. Gaziantep is located southeast part of Turkey and has a border with Syria. More than 400,000 Syrian refugees live in Gaziantep. The aim of this study was to evaluate distribution of HCV genotypes among Syrian patients and in people who inject drugs.Serum samples form 1,628 individuals (786 female, 842 male) which were sent to our laboratory for genotyping between January 2013 and December 2022, were analyzed retrospectively. Three different HCV genotyping assays (Qiagen, RTA and Abbott) were used during the 10-year study period.Out of the 1,628 patients, genotype 1 was detected in 51.5%, genotype 3 in 21.4%, genotype 4 in 20%, genotype 5 in 4.6%, genotype 2 in 1.3%. Mixed genotype was found in 20 patients. Of the patients, 1,143 were Turkish patients and among those patients genotype 1 (66.8%) was the most common genotype followed by genotype 3 (29%). Among Syrian patients (n = 477), genotype 4 (64.2%) was predominant genotype followed by genotype 1 and genotype 5. Genotype 3 was detected in 277 (79.6%) prisoners. All of them were male and probably the main source of HCV infection was intravenous drug abuse. While genotypes 1 and 4 were common in females, genotypes 1 and 3 were common in males.In the future genotype 3 may become an increasing problem due to the persons who inject drugs. Less frequent genotypes such as 4 and 5 may become more frequent due to Syrian patients.

Molecular detection of bornavirus in parrots imported to China in 2022

BackgroundAvian bornavirus (ABV) is a neurotropic virus, it has been established as the primary causative agent of proventricular dilatation disease (PDD). However, substantial international trade and transnational trafficking of wild birds occur, potentially enabling these birds to harbor and transmit pathogens to domestic poultry, adversely affecting their well-being. Real-time RT-PCR was employed to detect the presence of PaBV-4 in parrots imported to China in 2022.ResultsIn 2022, a total of 47 cloacal swabs from 9 distinct species of parrots were collected at the Wildlife Rescue Monitoring Center in Guangdong, China. The purpose of this collection was to detect the presence of PaBV-4. Using real-time PCR techniques, it was determined that the positive rate of PaBV-4 was 2.12% (1 out of 47) in parrots. The PaBV-4 virus was detected in a Amazona aestiva that had been adopted for one month. Conversely, all other species tested negative for the virus. Subsequently, the whole genome of the PaBV-4 GD2207 strains was sequenced, and the homology and genetic evolution between these strains and previously published PaBV-4 strains on GenBank were analyzed using DNAStar and MEGA7.0 software. The findings revealed that the full-length genome of PaBV-4 consisted of 8915 nucleotides and encoded six proteins. Additionally, it exhibited the highest nucleotide similarity (99.9%) to the GZ2019 strain, which causes death and severe clinical symptoms in Aratinga solstitialis. Furthermore, when compared to other strains of PaBV-4, the GD2207 strain demonstrated the highest amino acid homology with GZ2019. The phylogenetic analysis demonstrated that the GD2207 strain clustered with various strains found in Japanese, American, and German parrots, indicating a close genetic relationship with PaBV-4, but it revealed a distant relationship with PaBV-5 Cockg5 from America. Notably, the GD2207 was closely associated with the GZ2019 strain from Aratinga solstitialis in China.ConclusionThis study presents the preliminary identification of PaBV-4 in Amazona aestiva parrots, emphasizing its importance as the predominant viral genotype linked to parrot infections resulting from trade into China. Through genetic evolution analysis, it was determined that the GD2207 strain of PaBV-4 exhibits the closest genetic relationship with GZ 2019 (Aratinga solstitialis, China), M14 (Ara macao, USA), AG5 (Psittacus erithacus, USA) and 6758 (Ara ararauna, Germany) suggesting a shared ancestry.

Whole-genome analysis and evolutionary characterization of cervical and oral human papillomavirus 16.

High-throughput genome-wide sequencing has revealed high genomic variability of HPV16 in different geographic regions which is the most predominant genotype in human papillomavirus (HPV)-associated malignancies. Analysis of the HPV16 by whole-genome sequence (WGS) is an advanced method for the identification of mutations in the genome. There is limited information about HPV16 diversity in Pakistan, especially at the genomic level. Till now, WGS for HPV16 has not been previously reported in Pakistan. The current study has sequenced three HPV16 viral genomes, from two cervical and one oral cavity positive sample of women presented with general gynecological problems without any evidence of precancerous or cancerous lesions using an ion ampliseq customized panel. Sequencing analysis detected 38 variations, including single-nucleotide polymorphisms (SNPs) and two Indels, across three samples with the highest number of SNPs present in E1, E2, and L2, respectively. A total of 20 non-synonymous and 11 synonymous mutations with amino acid substitutions (T1421C, G1515A, T2223C, T1389C, G1483A, and T2191C) were identified. The phylogenetic analysis revealed the genomes of HPV16 are closely associated with those reported from Thailand and the United States. These are the first HPV16 WGS from Pakistan. However, more research is needed with a large sample size from diversified areas to assess the carcinogenic consequences and impact of HPV vaccinations.

Genetic characterisation of Cryptosporidium parvum in dairy cattle and calves during the early stages of a calving season

Cryptosporidium parvum is a causative agent of cryptosporidiosis, an infectious gastroenteritis in neonatal ruminants, which can be fatal in severe cases. The aim of this study was to determine the prevalence of infections in dairy cattle/calves during the early stages of a calving season and the species/genotypes of the Cryptosporidium present. Faecal samples collected from pre- and post-partum dams (n = 224) as well as calves from age ∼1 day onwards (n = 312) were examined. Oocysts were concentrated, DNA extracted and tested by Cryptosporidium 18S rRNA gene PCR and sequencing, while genotypes of C. parvum were determined by gp60 and VNTR analysis. Results showed that 31.3% and 30.4% of pre- and post-partum dams tested positive for Cryptosporidium, respectively. In the adults, C. parvum (n = 52), C. bovis (n = 4) and C. andersoni (n = 19) were identified, while in the calves 248 out of 312 (79.5%) were PCR-positive for C. parvum. The proportion of positive calf samples was significantly higher (P < 0.0001) than the proportion of positive adult cattle during the first seven weeks of the calving season. In adult cattle, three distinct gp60 genotypes were identified, a predominant genotype IIaA15G2R1 (n = 36) and genotypes IIaA15R1 (n = 2) and IIaA14G2R1 (n = 1). In the calves, only genotype IIaA15G2R1 was detected (n = 125). Although C. parvum was observed in adult cattle two weeks after the start of the calving season, the predominant genotypes were not detected until Week 4 in both adults and calves, meaning it is still unclear whether adult cattle are the initial source of C. parvum infections on the farm. Historically calves on this dairy farm demonstrated the IIaA19G2R1 genotype, which, has now clearly been replaced with the IIaA15G2R1 genotype that is now found in both adults and calves. During the study season, significantly higher levels of neonatal calf mortality were observed compared to the seasons before (P = 0.046) and after (P = 0.0002). This study has shown comparable levels of C. parvum infection in both pre- and post-partum dams but higher levels of infection in neonatal calves.

Molecular detection of Hepatitis C virus (HCV) genotypes and viral loads in chronic hcv infected patients in Kirkuk, Iraq

Abstract Background: Hepatitis C is a disease that has a significant global impact. The World Health Organization estimates that over 150 million people are chronically infected with the hepatitis C virus (HCV). Objectives: The purpose of the study was to make a quantitative determination of the hepatitis C viral load and genotype using real-time polymerase chain reaction (RT-PCR) and to determine how these factors relate to the HCV chronicity. Materials and Methods: A cross-sectional hospital-based study was carried out in Kirkuk city, Iraq. A total of 50 patients with chronic hepatitis C whose ages ranged from 20 to 75 years were the subjects of the study. The control group consisted of 30 apparently healthy persons admitted to the blood bank for blood donation. Five milliliters of blood were drawn for the molecular detection of HCV load and genotype by RT-PCR, detection of hepatitis C antibodies by enzyme-linked immunosorbent assay (ELISA), and biochemical analysis of alanine aminotransferase (ALT), aspartate aminotransferase (AST), alkaline phosphatase (ALP), and total serum bilirubin (TSB). Results: According to the research, 86% of chronic hepatitis C patients with ELISA-detected anti-HCV obtained positive PCR results. Statistically significant (P = 0.01). According to the study, more chronic hepatitis C patients (31 out of 43) had genotype 4 HCV than genotype 1a (27.91%). According to the study, genotype 4 chronic hepatitis C patients exhibited significantly higher viral loads than genotype 1a patients (1901.3 vs. 1693.41 IU/mL; P = 0.01). About 41.94% of men and 58.06% of females with chronic hepatitis C had genotype 4, whereas 33.3% of males and 66.67% of females had genotype 1a. Chronic hepatitis C patients had higher ALT, AST, ALP, and TSB levels than the control group, and the difference was very significant. ALT values were 64.69, 54.8, 285.5, and 4.33 mg/dL. This study found a connection between chronic hepatitis C viral load and ALT, AST, ALP, and TSB levels. Viral load rose as fibrosis progressed, according to this study. Patients without fibrosis had the lowest mean viral load (1235.5 IU/mL), followed by those with stage 1 fibrosis, whereas cirrhosis (stage 4) had the highest (2088.1 IU/mL). Non-fibrotic patients had the lowest virus burden. Conclusions: Genotype 4 of HCV was the most predominant genotype in Kirkuk city and there was a strong positive correlations of ALT and viral load with stages of fibrosis in patients with chronic hepatitis C.

Histopathological study and molecular characterization of Infectious Bronchitis virus circulating in broilers in Basrah governorate, Iraq

The poultry industry plays an important role in the food economics and the food industry in both their layer and broiler chicken. Poultry diseases on the other way impact in the poultry industry especially diseases from virus sources since it does not have a specific treatment except for vaccines with routine prevention and control. This study was designed for the assessment of histopathological changes, molecular diagnosis and phylogenetic analyses of the Infectious Bronchitis virus circulating in broilers in Basrah province in the south of Iraq. The tissue samples were (trachea, lung and kidney). One hundred samples were studied with clinical signs and lesions related to IB. The histopathological changes caused by the virus were studied with hematoxylin and eosin stain, and the causative agent Infectious Bronchitis Virus (IBV) was identified using a polymerase chain reaction combined with explaining the phylogenetic analysis. The results of molecular diagnosis and identification showed the twelve Iraqi field strains of IBV were closely related and shared a high identity of 98.44 %- 99.69 % of each other. Variant 2(IS/1494 like) was a predominant genotype of IBV in the present study, and has high similarity with the variant 2(IS/1494) like a strain of IBV circulating in Iran and in the Kurdistan region north of Iraq. The histopathological findings were desquamation of the cilia of the mucosa layer of the trachea, infiltration of inflammatory cells, hyperplasia of goblet cells with thickening of mucosal layer in some areas infiltration of inflammatory exudate within capillaries and Para bronchus, where the microscopic results in kidney were showed interstitial hemorrhage, necrosis of the renal tubular epithelium, infiltration of inflammatory cell. The present results provided useful information on target organs damaged by IBV and the genetic epidemiology of such virus strains circulating in Basrah governorate Iraq during this year that would be helpful to develop a local vaccine.

2183. Porin Mutations Potentiate the in Vitro Synergy of Meropenem-Vaborbactam (MVB), but not Ceftazidime-Avibactam (CZA) in Combination with Other Antibiotics against KPC-producing Klebsiella Pneumoniae (KPC-Kp)

Abstract Background CZA and MVB are often used in combination with other antibiotics in clinical practice. Our objective was to assess their in vitro synergy stratified by predominant ompK36 genotype: wild-type (WT), or mutants that included an insertion sequence 5 (IS5) or GD duplication (GD). Methods 15 KPC-Kp clinical isolates were selected. Minimum inhibitory concentrations (MICs) were determined by broth microdilution in triplicate. Time-kill analyses were used to test CZA and MVB alone (1 and 4x MIC) and in combination with colistin (COL; 2 mg/L), fosfomycin (FOS; 100 mg/L + 25 mg/L G6P), gentamicin (GEN; 2 µg/mL), meropenem (MEM; 8 mg/L), and tigecycline (TGC; 2 mg/L) against 1x108 cFu/mL. 24 hour log-kill was calculated as log cFu/mL decrease from time 0. Results 5 isolates each had ompK36 WT, IS5, or GD. 27% and 73% were KPC-3 and KPC-2, respectively. 100% were susceptible to CZA and MVB. None were resistant to COL. 3 were non-susceptible to GEN, which were all IS5 (Table 1). In combination with CZA 1x MIC, each of COL, GEN, and MEM were bactericidal against all isolates; mean ± standard error (SE) log kills were -7.39 ± 0.3, -6.58 ± 0.93, and -5.81 ± 0.21, respectively (Figure 1). Mean log-kills did not vary for CZA + COL, GEN, or TGC against ompK36 mutants vs WT; however, log-kills were significantly lower for CZA + FOS (-3.78 vs -6.6; p &amp;lt; 0.05) or MEM (-5.4 vs -6.62; p &amp;lt; 0.01) against ompK36 mutants compared to WT. Synergy rates were reduced from 100% against WT to 80%, 60%, and 40% against mutant isolates for CZA + COL, MEM, and FOS, respectively (Figure 2). MVB 1x MIC in combination with COL, FOS, GEN, and TGC were bactericidal 67, 27, 80, and 47% of the time, with corresponding log kills of -3.96 ± 1.1, -1.56 ± 0.83, -5.05 ± 0.82, and -2.53 ± 0.28, respectively (Figure 1). Mean ± SE log kills were significantly greater against porin mutants compared to WT for MVB + COL (-5.57 vs -0.73; p = 0.03), FOS (-3.11 vs 1.54; p = 0.03), or TGC (-2.93 vs -1.73; p = 0.04). Rates of synergy were also higher against porin mutants vs WT for MVB + FOS or COL (Figure 2). Table 1 Characteristics and susceptibility data for fifteen KPC-Kp isolates chosen for analysis. CAZ = ceftazidime; COL = colistin; CZA = Ceftazidime-avibactam; FOS = fosfomycin; GD = GD duplication; GEN = gentamicin; IS5 = insertion sequence 5; KPC = Klebsiella pneumoniae carbapenemase; MEM = meropenem; MVB = meropenem-vaborbactam; TGC = tigecycline; WT = wild-type. Figure 1 24-hour log kills for antibiotic combinations with CZA (ceftazidime-avibactam) and MVB (meropenem-vaborbactam) at 1X MIC, stratified by ompk36 status: wild-type (WT) versus mutant (MUT). Bactericidal is defined as -3 log kill from time 0 at 24 hours and indicated by the dotted horizontal line. COL = colistin; FOS = fosfomycin; GEN = gentamicin; MEM = meropenem; MIC = minimum inhibitory concentration; TGC = tigecycline. Figure 2 Proportion of bactericidal, synergistic, and antagonistic outcomes for ompK36 wild-type (WT; n = 5) versus mutant (MUT; n = 10) KPC-Kp isolates tested against CZA (ceftazidime-avibactam) or MVB (meropenem-vaborbactam) at 1X MIC as single agents and in combination with colistin (COL), gentamicin (GEN), tigecycline (TGC), meropenem (MEM), or fosfomycin (FOS). Bactericidal activity was defined as -3 log kill from time 0 at 24 hours; synergy and antagonism were defined as -2 or +2 log kill at 24 hours compared to most active single agent, respectively. Conclusion Porin mutations negatively impact CZA synergy with other antibiotics compared to WT, though 24-hour log kills for COL, FOS, GEN, and MEM remained below the bactericidal threshold. Conversely, porin mutations potentiate synergy between MVB and COL, FOS, or TGC. Disclosures Ryan K. Shields, PharmD, MS, Allergan: Advisor/Consultant|Cidara: Advisor/Consultant|Entasis: Advisor/Consultant|GSK: Advisor/Consultant|Melinta: Advisor/Consultant|Melinta: Grant/Research Support|Menarini: Advisor/Consultant|Merck: Advisor/Consultant|Merck: Grant/Research Support|Pfizer: Advisor/Consultant|Roche: Grant/Research Support|Shionogi: Advisor/Consultant|Shionogi: Grant/Research Support|Utility: Advisor/Consultant|Venatorx: Advisor/Consultant|Venatorx: Grant/Research Support

Molecular Diversity of Mycobacterium avium subsp. paratuberculosis in Four Dairy Goat Herds from Thuringia (Germany).

This study investigated the intra- and inter-herd diversity of Mycobacterium avium subsp. paratuberculosis (MAP) isolates from four goat herds in Thuringia (Germany) that were affected by paratuberculosis for several years. The main focus was on the characterization and distribution of genotypes among animals and the environment of goat herd 1. This study included 196 isolates from the feces of 121 infected goats, various tissues from 13 clinically diseased goats, 29 environmental samples from herd 1, and additionally, 22 isolates of different origin from herds 2 to 4. The isolates, sampled between 2018 and 2022, were genotyped using short-sequence-repeat (SSR) analysis, mycobacterial-interspersed repetitive units-variable-number tandem repeat (MIRU-VNTR) analysis, and a single nucleotide polymorphism (SNP)-based assay for phylogenetic grouping. All the isolates belonged to the MAP-C group. In herd 1, one predominant genotype was determined, while two other genotypes were identified very rarely and only in fecal and environmental samples. One of three further genotypes was found in each of herds 2 to 4. The assignment of genotypes to different phylogenetic clades suggested six different infection strains. The results indicated no epidemiological links between the examined herds. Based on the current MAP genotyping data from Germany, possible sources of infection are MAP-contaminated barns previously used by infected cattle and the purchase of sub-clinically infected goats.

Genotype analysis of rotaviruses isolated from children during a phase III clinical trial with the hexavalent rotavirus vaccine in China

The oral hexavalent live human-bovine reassortant rotavirus vaccine (RV6) developed by Wuhan Institute of Biological Products Co., Ltd (WIBP) has finished a randomized, placebo-controlled phase III clinical trial in four provinces of China in 2021. The trail demonstrated that RV6 has a high vaccine efficacy against the prevalent strains and is safe for use in infants. During the phase III clinical trial (2019–2021), 200 rotavirus-positive fecal samples from children with RV gastroenteritis (RVGE) were further studied. Using reverse transcription-polymerase chain reaction and high-throughput sequencing, VP7 and VP4 sequences were obtained and their genetic characteristics, as well as the differences in antigenic epitopes of VP7, were analyzed in detail. Seven rotavirus genotypes were identified. The predominant rotavirus genotype was G9P [8] (77.0%), followed by prevalent strains G8P [8] (8.0%), G3P [8] (3.5%), G3P [9] (1.5%), G1P [8] (1.0%), G2P [4] (1.0%), and G4P [6] (1.0%). The amino acid sequence identities of G1, G2, G3, G4, G8, and G9 genotypes of isolates compared to the vaccine strains were 98.8%, 98.2%–99.7%, 88.4%–99.4%, 98.2%, 94.2%–100%, and 93.9%–100%, respectively. Notably, the vaccine strains exhibited high similarity in amino acid sequence, with only minor differences in antigenic epitopes compared to the Chinese endemic strains. This supports the potential application of the vaccine in preventing diseases caused by rotaviruses.