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Zhu Y, Lin Y, Gong B, Zhang Y, Su G, Yu Y. Dual toeholds regulated CRISPR-Cas12a sensing platform for ApoE single nucleotide polymorphisms genotyping. Biosens Bioelectron 2024; 255:116255. [PMID: 38565025 DOI: 10.1016/j.bios.2024.116255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 03/13/2024] [Accepted: 03/26/2024] [Indexed: 04/04/2024]
Abstract
Single nucleotide polymorphisms (SNPs) are closely associated with many biological processes, including genetic disease, tumorigenesis, and drug metabolism. Accurate and efficient SNP determination has been proved pivotal in pharmacogenomics and diagnostics. Herein, a universal and high-fidelity genotyping platform is established based on the dual toeholds regulated Cas12a sensing methodology. Different from the conventional single stranded or double stranded activation mode, the dual toeholds regulated mode overcomes protospacer adjacent motif (PAM) limitation via cascade toehold mediated strand displacement reaction, which is highly universal and ultra-specific. To enhance the sensitivity for biological samples analysis, a modified isothermal recombinant polymerase amplification (RPA) strategy is developed via utilizing deoxythymidine substituted primer and uracil-DNA glycosylase (UDG) treatment, designated as RPA-UDG. The dsDNA products containing single stranded toehold domain generated in the RPA-UDG allow further incorporation with dual toeholds regulated Cas12a platform for high-fidelity human sample genotyping. We discriminate all the single-nucleotide polymorphisms of ApoE gene at rs429358 and rs7412 loci with human buccal swab samples with 100% accuracy. Furthermore, we engineer visual readout of genotyping results by exploiting commercial lateral flow strips, which opens new possibilities for field deployable implementation.
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Affiliation(s)
- Yuedong Zhu
- School of Pharmacy, Nantong University, Nantong, Jiangsu, 226001, China
| | - Yanan Lin
- School of Pharmacy, Nantong University, Nantong, Jiangsu, 226001, China
| | - Bin Gong
- School of Pharmacy, Nantong University, Nantong, Jiangsu, 226001, China
| | - Yan Zhang
- School of Pharmacy, Nantong University, Nantong, Jiangsu, 226001, China
| | - Gaoxing Su
- School of Pharmacy, Nantong University, Nantong, Jiangsu, 226001, China.
| | - Yanyan Yu
- School of Pharmacy, Nantong University, Nantong, Jiangsu, 226001, China.
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Cohen-Gihon I, Israeli O, Bilinsky G, Vasker B, Lazar S, Beth-Din A, Zvi A, Ghanem-Zoubi N, Atiya-Nasagi Y. Insights from genomic analysis of a novel Coxiella burnetii strain isolated in Israel. New Microbes New Infect 2024; 59:101242. [PMID: 38577384 PMCID: PMC10993178 DOI: 10.1016/j.nmni.2024.101242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 03/25/2024] [Accepted: 03/25/2024] [Indexed: 04/06/2024] Open
Abstract
The diagnosis of Q fever is challenging due to nonspecific symptoms and negative standard blood culture results. Serological testing through immunofluorescence assay (IFA) is the most commonly used method for diagnosing this disease. Polymerase chain reaction (PCR) tests can also be used to detect bacterial DNA if taken at an appropriate time. Once the presence of bacteria is confirmed in a sample, an enrichment step is required before characterizing it through sequencing. Cultivating C. burnetii is challenging as it can only be isolated by inoculation into cell culture, embryonated eggs, or animals. In this article, we describe the isolation of C. burnetii from a valve specimen in Vero cells. We conducted genome sequencing and taxonomy profiling of this isolate and were able to determine its taxonomic affiliation. Furthermore, Multispacer sequence typing (MST) analysis suggests that the infection originated from a local strain of C. burnetii found around northern Israel and Lebanon. This novel strain belongs to a previously described genotype MST6, harboring the QpRS plasmid, never reported in Israel.
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Affiliation(s)
- Inbar Cohen-Gihon
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Ofir Israeli
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Gal Bilinsky
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Barak Vasker
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Shirley Lazar
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Adi Beth-Din
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Anat Zvi
- Department of Biochemistry and Molecular Genetics, Israel Institute for Biological Research, Ness Ziona, Israel
| | | | - Yafit Atiya-Nasagi
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
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Jiang S, Yu S, Feng Y, Zhang L, Santin M, Xiao L, Li W. Widespread distribution of human-infective Enterocytozoon bieneusi genotypes in small rodents in northeast China and phylogeny and zoonotic implications revisited. Acta Trop 2024; 253:107160. [PMID: 38408590 DOI: 10.1016/j.actatropica.2024.107160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/20/2024] [Accepted: 02/23/2024] [Indexed: 02/28/2024]
Abstract
Enterocytozoon bieneusi features high genetic diversity among host species and environmental sources and over 500 genotypes in 11 phylogenetic groups have been defined. Here we investigated 291 small rodents in Heilongjiang province, northeast China, for the presence of E. bieneusi by PCR of the ribosomal internal transcribed spacer (ITS). Nine of 60 (15.0 %) gray squirrels from a park in Harbin, 120 of 201 (59.7 %) guinea pigs from a pet shop in Harbin, and two of 30 (6.7 %) peridomestic rats from a pasture in Qiqihar were positive for the parasite. Six known genotypes (EbpB, SCC-1, SCC-2, D, S7 and HLJ-CP1) and two novel genotypes (NESQ1 and NEGP1) were identified by sequence analysis of the ITS, with EbpB, SCC-1, SCC-2 and NESQ1 found in squirrels, D, S7 and NEGP1 in guinea pigs, and EbpB and HLJ-CP1 in rats. Widespread distribution of human-infective Group 10 genotype S7 and Group 1 genotype D in guinea pigs raised our concerns about the importance of pet animals as zoonotic reservoirs of microsporidiosis. Co-occurrence of Group 1 genotypes D and HLJ-CP1 in cancer patients and rodents in Heilongjiang indicated a possibility of zoonotic transmission. The host range of Group 1 genotype EbpB previously considered pig-adapted was extended. A potential variant of genotype S7, namely NESQ1, went into the existing Group 10 in phylogenetic analysis. The other new genotype, NEGP1, was clustered in an undefined clade we proposed as Group 15. With the emerging epidemiologic evidence, the host specificity of existing E. bieneusi genotypes is now being challenged.
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Affiliation(s)
- Shuning Jiang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Shui Yu
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, China
| | - Yaoyu Feng
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, China
| | - Longxian Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, China
| | - Monica Santin
- Environmental Microbial and Food Safety Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, AR, USA
| | - Lihua Xiao
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong, China.
| | - Wei Li
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, Heilongjiang, China.
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Jahanshahi S, Nejad HR, Kazemi B, Saeedi P. Cytokines signatures and susceptibility to cutaneous leishmaniasis in patients from Sistan and Baluchestan province of Iran. Gene 2024; 903:148224. [PMID: 38286270 DOI: 10.1016/j.gene.2024.148224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 01/20/2024] [Accepted: 01/26/2024] [Indexed: 01/31/2024]
Abstract
BACKGROUND Cutaneous leishmaniasis (CL) is a complex, multifactorial disease that results from environmental factors such as parasite polymorphism, phlebotomine vectors, and host genetic factors. Some studies have identified specific genetic factors that may be associated with cutaneous leishmaniasis. The objective of this research was to resolve the association of 8 cytokine polymorphisms, including TNF-α -308 A/G (rs 1800629), TNF-α -238 A/G (rs 361525), TGF-β1 -509 T/C (rs 1800469), TGF-β1+ 915 G/C (rs 1800471), IFN-γ -874 T/A (rs 2430561), IFN-γ -179 G/A (rs 2069709), IL-10 -819 C/T (rs 1800871), and IL-10 -592 A/C (rs 1800872) with susceptibility to CL. METHODS A total of 152 patients with designated CL and 100 healthy controls were selected from those referred to Sistan and Baluchestan hospitals. CL was diagnosed by microscopic examination of Giemsa-stained samples and culture. Leishmania species were identified using ITS2 gene PCR amplification with universal primers. Genetic polymorphism was determined by the ARMS PCR method on extracted genomic DNA of individuals. Eight SNPs cytokines were genotyped. RESULTS Most of the Genotypic and allelic frequency comparisons between patients with CL and healthy subjects showed no difference, except 3. Individual SNP analysis showed highest association of TGF-β1 -509 (rs1800469) -CC genotype (P = 0.03, OR = 7.05, 95 % CI = 3.3-15) with 5.7-fold increase, IFN-γ -874 (rs 2430561) -AA genotype (P = 0.04, OR = 4.72, 95 % CI = 1.6-14) with 4.2-fold increase, and IL10 -819 (rs1800871) -CC genotype (P = 0.05, OR = 3.63, 95 % CI = 2.5-5.3) with 1.9-fold increase, with CL. Odds ratios (ORs) and 95 % confidence intervals (CIs) were evaluated to assess the association power. CONCLUSION Our results conclude that rs1800469 (TGF-β1), rs2430561 (INF-γ), and rs1800872 (IL10) polymorphisms are associated with CL in southeastern Iranian people.
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Affiliation(s)
- Saeideh Jahanshahi
- Department of Biotechnology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Hamideh Rouhani Nejad
- Faculty of Science, Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran.
| | - Bahram Kazemi
- Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Pardis Saeedi
- Faculty of Science, Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
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Narang G, Jakhan J, Tamang S, Yadav K, Singh V. Characterization of drug resistance genes in Indian Plasmodium falciparum and Plasmodium vivax field isolates. Acta Trop 2024:107218. [PMID: 38636585 DOI: 10.1016/j.actatropica.2024.107218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 03/21/2024] [Accepted: 04/15/2024] [Indexed: 04/20/2024]
Abstract
One of the major challenges for malaria control and elimination is the spread and emergence of antimalarial drug resistance. Mutations in Plasmodium falciparum (Pf) and Plasmodium vivax (Pv) field isolates for five drug resistance genes viz. crt, mdr1, dhps, dhfr and kelch known to confer resistance to choloroquine (CQ), sulfadoxine-pyrimethamine (SP) and artemisinin (ART) and its derivatives were analyzed. A total of 342 symptomatic isolates of P. falciparum (Pf) and P. vivax (Pv) from 1993 to 2014 were retrieved from malaria parasite repository at National Institute of Malaria Research (NIMR). Sample DNA was extracted from dried blood spots and various targeted single nucleotide polymorphisms (SNPs) associated with antimalarial drug resistance were analysed for these isolates. C72S (67.7%) and K76T (83.8%) mutations along with SVMNT haplotype (67.7%) predominated the study population for Pfcrt. The most prevalent SNPs were S108N (73.2%) and A437G (24.8%) and the most prevalent haplotypes were ACNRNI (51.9%) and SAKAA (74.5%) in Pfdhfr and Pfdhps respectively. Only two mutations in Pfmdr1, N86Y (26.31%) and Y184F (56.26%), were seen frequently in our study population. No mutations associated with Pfk13 were observed. For Pv, all the studied isolates showed two Pvdhps mutations, A383G and A553G, and two Pfdhfr mutations, S58R and S117N. Similarly, three mutations, viz. T958M, M908L and F1076L were found in Pvmdr1. No variations were observed in Pvcrt-o and Pvk12 genes. Overall, our study demonstrates an increase in mutations associated with SP resistance in both Pf and Pv, however, no single nucleotide polymorphisms (SNPs) associated with ART resistance have been observed for either species. Various SNPs associated with CQ resistance were seen in Pf; whereas only Pvmdr1 associated resistant SNPs were observed in Pv. Therefore, molecular characterization of drug resistance genes is essential for timely monitoring and prevention of malaria by identifying the circulating drug resistant parasites in the country.
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Affiliation(s)
- Geetika Narang
- ICMR-National Institute of Malaria Research (NIMR), Sector-8, Dwarka, New Delhi 110077; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Jahnvi Jakhan
- ICMR-National Institute of Malaria Research (NIMR), Sector-8, Dwarka, New Delhi 110077; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Suman Tamang
- ICMR-National Institute of Malaria Research (NIMR), Sector-8, Dwarka, New Delhi 110077; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Karmveer Yadav
- ICMR-National Institute of Malaria Research (NIMR), Sector-8, Dwarka, New Delhi 110077
| | - Vineeta Singh
- ICMR-National Institute of Malaria Research (NIMR), Sector-8, Dwarka, New Delhi 110077; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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Dipta B, Sood S, Mangal V, Bhardwaj V, Thakur AK, Kumar V, Singh B. KASP: a high-throughput genotyping system and its applications in major crop plants for biotic and abiotic stress tolerance. Mol Biol Rep 2024; 51:508. [PMID: 38622474 DOI: 10.1007/s11033-024-09455-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 03/18/2024] [Indexed: 04/17/2024]
Abstract
Advances in plant molecular breeding have resulted in the development of new varieties with superior traits, thus improving the crop germplasm. Breeders can screen a large number of accessions without rigorous and time-consuming phenotyping by marker-assisted selection (MAS). Molecular markers are one of the most imperative tools in plant breeding programmes for MAS to develop new cultivars possessing multiple superior traits. Single nucleotide polymorphisms (SNPs) are ideal for MAS due to their low cost, low genotyping error rates, and reproducibility. Kompetitive Allele Specific PCR (KASP) is a globally recognized technology for SNP genotyping. KASP is an allele-specific oligo extension-based PCR assay that uses fluorescence resonance energy transfer (FRET) to detect genetic variations such as SNPs and insertions/deletions (InDels) at a specific locus. Additionally, KASP allows greater flexibility in assay design, which leads to a higher success rate and the capability to genotype a large population. Its versatility and ease of use make it a valuable tool in various fields, including genetics, agriculture, and medical research. KASP has been extensively used in various plant-breeding applications, such as the identification of germplasm resources, quality control (QC) analysis, allele mining, linkage mapping, quantitative trait locus (QTL) mapping, genetic map construction, trait-specific marker development, and MAS. This review provides an overview of the KASP assay and emphasizes its validation in crop improvement related to various biotic and abiotic stress tolerance and quality traits.
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Affiliation(s)
- Bhawna Dipta
- ICAR-Central Potato Research Institute, Bemloe, Shimla, Himachal Pradesh, 171001, India
| | - Salej Sood
- ICAR-Central Potato Research Institute, Bemloe, Shimla, Himachal Pradesh, 171001, India.
| | - Vikas Mangal
- ICAR-Central Potato Research Institute, Bemloe, Shimla, Himachal Pradesh, 171001, India
| | - Vinay Bhardwaj
- ICAR-National Research Centre on Seed Spices, Tabiji, Ajmer, Rajasthan, 305206, India
| | - Ajay Kumar Thakur
- ICAR-Central Potato Research Institute, Bemloe, Shimla, Himachal Pradesh, 171001, India
| | - Vinod Kumar
- ICAR-Central Potato Research Institute, Bemloe, Shimla, Himachal Pradesh, 171001, India
| | - Brajesh Singh
- ICAR-Central Potato Research Institute, Bemloe, Shimla, Himachal Pradesh, 171001, India
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Farrag MA, Aziz IM, Alsaleh AN, Almajhdi FN. Human bocavirus in Saudi Arabia: Molecular epidemiology and Co-infections among children with acute respiratory tract infections during 2014-2016. Heliyon 2024; 10:e28350. [PMID: 38560213 PMCID: PMC10981067 DOI: 10.1016/j.heliyon.2024.e28350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 03/14/2024] [Accepted: 03/17/2024] [Indexed: 04/04/2024] Open
Abstract
Respiratory tract infections due to a variety of viruses continue to threaten the human population worldwide, particularly in developing countries. Among the responsible viruses, Human Bocavirus (HBoV), a novel discovered virus, causes respiratory tract and gastroenteritis disorders in young children. In Saudi Arabia, data regarding virus molecular epidemiology and evolution and its implication in respiratory tract infection are scarce. In the current study, genetic diversity and circulation pattern of HBoV-1 among hospitalized children due to acute respiratory tract infection (ARTI) during two consecutive years were charted. We found that 3.44% (2014/2015) and 11.25% (2015/2016) of children hospitalized due to ARTI were infected by HBoV-1. We have shown that HBoV was detected year-round without a marked seasonal peak. HBoV-1 also was co-detected with one or multiple other respiratory viruses. The multisequence analysis showed high sequence identity (∼99%) (few point mutation sites) between strains of each genotype and high sequence variation (∼79%) between HBoV-1 and the other 3 genotypes. Phylogenetic analysis showed the clustering of the study's isolates in the HBoV-1 subclade. Our data reveal that genetically conserved HBoV-1 was circulating among admitted children during the course of the study. Further epidemiological and molecular characterization of multiple HBoV-1 strains for different years and from all regions of Saudi Arabia are required to understand and monitor the virus evolution.
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Affiliation(s)
- Mohamed A. Farrag
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Ibrahim M. Aziz
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Asma N. Alsaleh
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Fahad N. Almajhdi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
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Salemane K, Coetzee LZ, Pocock G, Genthe B, Taylor MB, Mans J. Water-Based Epidemiological Investigation of Hepatitis E Virus in South Africa. Food Environ Virol 2024:10.1007/s12560-024-09596-1. [PMID: 38613652 DOI: 10.1007/s12560-024-09596-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 03/08/2024] [Indexed: 04/15/2024]
Abstract
Hepatitis E virus (HEV) is an emerging zoonotic pathogen that exhibits great host diversity. The primary means of transmission of the virus in low- and middle-income countries is contaminated water, often due to a lack of access to proper sanitation, which leads to faecal contamination of water sources. Environmental surveillance is an important tool that can be used to monitor virus circulation and as an early warning system for outbreaks. This study was conducted to determine the prevalence and genetic diversity of HEV in wastewater, surface water (rivers and standpipe/ablution water), and effluent from a piggery in South Africa. A total of 536 water samples were screened for HEV using real-time reverse transcription-polymerase chain reaction. Overall, 21.8% (117/536) of the wastewater, river, and ablution water samples tested positive for HEV, whereas 74.4% (29/39) of the samples from the piggery tested positive. Genotyping revealed sequences belonging to HEV genotypes 3 (98%, 53/54) and 4 (2%, 1/54), with subtypes 3c, 3f, and 4b being identified.
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Affiliation(s)
- Karabo Salemane
- Department of Medical Virology, School of Medicine, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Gezina, Pretoria, 0031, South Africa
| | - Leanne Z Coetzee
- , Waterlab, Techno Park, 23B De Havilland Cres, Persequor, Pretoria, 0020, South Africa
| | - Gina Pocock
- , Waterlab, Techno Park, 23B De Havilland Cres, Persequor, Pretoria, 0020, South Africa
| | - Bettina Genthe
- Stellenbosch University, Private Bag X1, Matieland, Stellenbosch, 7602, South Africa
| | - Maureen B Taylor
- Department of Medical Virology, School of Medicine, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Gezina, Pretoria, 0031, South Africa
| | - Janet Mans
- Department of Medical Virology, School of Medicine, Faculty of Health Sciences, University of Pretoria, Private Bag X323, Gezina, Pretoria, 0031, South Africa.
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Aziz T, Hangyu H, Naveed M, Shabbir MA, Sarwar A, Nasbeeb J, Zhennai Y, Alharbi M. Genotypic Profiling, Functional Analysis, Cholesterol-Lowering Ability, and Angiotensin I-Converting Enzyme (ACE) Inhibitory Activity of Probiotic Lactiplantibacillus plantarum K25 via Different Approaches. Probiotics Antimicrob Proteins 2024:10.1007/s12602-024-10258-8. [PMID: 38613617 DOI: 10.1007/s12602-024-10258-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/07/2024] [Indexed: 04/15/2024]
Abstract
Due to its alleged health advantages, several uses in biotechnology and food safety, the well-known probiotic strain Lactiplantibacillus plantarum K25 has drawn interest. This in-depth investigation explores the genetic diversity, makeup, and security characteristics of the microbial genome of L. plantarum K25, providing insightful knowledge about its genotypic profile and functional characteristics. Utilizing cutting-edge bioinformatics techniques like comparative genomics, pan-genomics, and genotypic profiling was carried out to reveal the strain's multidimensional potential in various fields. The results not only add to our understanding of the genetic makeup of L. plantarum K25 but also show off its acceptability in various fields, notably in biotechnology and food safety. The explanation of evolutionary links, which highlights L. plantarum K25's aptitude as a probiotic, is one notable finding from this research. Its safety profile, which is emphasized by the absence of genes linked to antibiotic resistance, is crucial and supports its status as a promising probiotic option.
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Affiliation(s)
- Tariq Aziz
- Key Laboratory of Geriatric Nutrition and Health Ministry of Education, Engineering and Technology Research Center of Food Additives, Beijing Advanced Innovation Center for Food Nutrition and Human Health Beijing Technology and Business University Haidian District, No. 11 Fucheng Road, Beijing, 100048, China
| | - Hu Hangyu
- Key Laboratory of Geriatric Nutrition and Health Ministry of Education, Engineering and Technology Research Center of Food Additives, Beijing Advanced Innovation Center for Food Nutrition and Human Health Beijing Technology and Business University Haidian District, No. 11 Fucheng Road, Beijing, 100048, China
| | - Muhammad Naveed
- Department of Biotechnology, Faculty of Biological Sciences, Lahore University of Biological & Applied Sciences, Lahore, Punjab, 54800, Pakistan
| | - Muhammad Aqib Shabbir
- Department of Biotechnology, Faculty of Biological Sciences, Lahore University of Biological & Applied Sciences, Lahore, Punjab, 54800, Pakistan
- Department of Biotechnology, Faculty of Science & Technology, University of Central Punjab, Lahore , Punjab, 54590, Pakistan
| | - Abid Sarwar
- Key Laboratory of Geriatric Nutrition and Health Ministry of Education, Engineering and Technology Research Center of Food Additives, Beijing Advanced Innovation Center for Food Nutrition and Human Health Beijing Technology and Business University Haidian District, No. 11 Fucheng Road, Beijing, 100048, China
| | - Jasra Nasbeeb
- Key Laboratory of Geriatric Nutrition and Health Ministry of Education, Engineering and Technology Research Center of Food Additives, Beijing Advanced Innovation Center for Food Nutrition and Human Health Beijing Technology and Business University Haidian District, No. 11 Fucheng Road, Beijing, 100048, China
| | - Yang Zhennai
- Key Laboratory of Geriatric Nutrition and Health Ministry of Education, Engineering and Technology Research Center of Food Additives, Beijing Advanced Innovation Center for Food Nutrition and Human Health Beijing Technology and Business University Haidian District, No. 11 Fucheng Road, Beijing, 100048, China.
| | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O. Box 2455, 11451, Riyadh, Saudi Arabia
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Mehra R, Patra V, Dhillan R, Sharma A, Kashyap S, Rastogi G, Gupta L, Singh R, Chopra C, Sharma V. Replication study identified EFEMP1 association with varicose vein predisposition among Indians. Eur J Med Res 2024; 29:232. [PMID: 38609985 PMCID: PMC11015598 DOI: 10.1186/s40001-024-01786-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 03/11/2024] [Indexed: 04/14/2024] Open
Abstract
BACKGROUND Varicose vein is a chronic condition that affects the lower extremities of the human body. Several factors have been implicated in the development of this disease, viz age, gender, weight, height and prolonged standing. Recently, genome-wide studies have identified genetic biomarkers that are associated with varicose veins in different ethnic groups. Such genetic studies are lacking in South Asians specifically in Indians where the prevalence of varicose veins is high, and it is important to replicate these variants in the stated population. The study aimed to replicate the association of genetic variants associated with varicose veins in this target population, which were found to be associated with the other ethnic groups. METHODOLOGY The studied cohort is of the Indian population comprising unrelated 104 varicose veins cases and 448 non-varicose vein controls. The samples were genotyped using the Illumina Global Screening Array. Using the genomic data from UK BioBank and 23andMe studied cohorts; eight genetic variants were selected to replicate in our dataset. The allelic association was performed to identify the effective allele and risk was estimated using odds ratio and p-value as level of significance. Multifactor Dimensionality Reduction was used to estimate the cumulative effect of variants in Indians. RESULT Variant rs3791679 of EFEMP1 was found to be associated with varicose veins in Indians. After observing the association of the EFEMP1 with varicose veins, we further ensued to identify all genetic variants within EFEMP1 to uncover the additional variants associated with this trait. Interestingly, we identified six new variants of EFEMP1 gene that have shown association. Moreover, the cumulative effect of all associated variations was estimated and the risk was 2.7 times higher in cases than controls whereas independently their effect ranges from 0.37-1.58. CONCLUSION This study identifies EFEMP1 as a potential gene related to the risk of varicose veins in Indians. It also highlights that evaluating the maximum number of variants of a gene rather than focusing solely on replicating single variations offers a more comprehensive and nuanced understanding of the genetic factors contributing to a complex trait like varicose veins.
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Affiliation(s)
- Rohit Mehra
- Department of Vascular and Endovascular Surgery, Command Hospital (Southern Command), Pune, India.
| | - Vikram Patra
- Department of Vascular and Endovascular Surgery, Command Hospital (Northern Command), Udhampur, India
| | - Rishi Dhillan
- Department of Vascular and Endovascular Surgery, Army Hospital (Research and Referral), Delhi, India
| | - Anuka Sharma
- NMC Genetics India Pvt. Ltd. Gurugram, Haryana, 122001, India
| | - Sonal Kashyap
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Garima Rastogi
- NMC Genetics India Pvt. Ltd. Gurugram, Haryana, 122001, India
| | - Love Gupta
- NMC Genetics India Pvt. Ltd. Gurugram, Haryana, 122001, India
| | - Reena Singh
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Chirag Chopra
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Varun Sharma
- NMC Genetics India Pvt. Ltd. Gurugram, Haryana, 122001, India.
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11
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Du ZZ, He JB, Jiao WB. A comprehensive benchmark of graph-based genetic variant genotyping algorithms on plant genomes for creating an accurate ensemble pipeline. Genome Biol 2024; 25:91. [PMID: 38589937 PMCID: PMC11003132 DOI: 10.1186/s13059-024-03239-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 04/04/2024] [Indexed: 04/10/2024] Open
Abstract
BACKGROUND Although sequencing technologies have boosted the measurement of the genomic diversity of plant crops, it remains challenging to accurately genotype millions of genetic variants, especially structural variations, with only short reads. In recent years, many graph-based variation genotyping methods have been developed to address this issue and tested for human genomes. However, their performance in plant genomes remains largely elusive. Furthermore, pipelines integrating the advantages of current genotyping methods might be required, considering the different complexity of plant genomes. RESULTS Here we comprehensively evaluate eight such genotypers in different scenarios in terms of variant type and size, sequencing parameters, genomic context, and complexity, as well as graph size, using both simulated and real data sets from representative plant genomes. Our evaluation reveals that there are still great challenges to applying existing methods to plants, such as excessive repeats and variants or high resource consumption. Therefore, we propose a pipeline called Ensemble Variant Genotyper (EVG) that can achieve better genotyping performance in almost all experimental scenarios and comparably higher genotyping recall and precision even using 5× reads. Furthermore, we demonstrate that EVG is more robust with an increasing number of graphed genomes, especially for insertions and deletions. CONCLUSIONS Our study will provide new insights into the development and application of graph-based genotyping algorithms. We conclude that EVG provides an accurate, unbiased, and cost-effective way for genotyping both small and large variations and will be potentially used in population-scale genotyping for large, repetitive, and heterozygous plant genomes.
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Affiliation(s)
- Ze-Zhen Du
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Jia-Bao He
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Wen-Biao Jiao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, China.
- Hubei Hongshan Laboratory, Wuhan, China.
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12
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Karakavuk M, Can H, Çeltik A, Karakavuk T, Gül C, Erdem HA, Pullukçu H, Taşbakan M, Taşbakan MS, Gürüz AY, Döşkaya M, Değirmenci Döşkaya A. Genetic characterization of Toxoplasma gondii strains isolated from humans living in İzmir, Türkiye. Indian J Med Microbiol 2024; 49:100571. [PMID: 38554777 DOI: 10.1016/j.ijmmb.2024.100571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 02/22/2024] [Accepted: 03/24/2024] [Indexed: 04/02/2024]
Abstract
PURPOSE Toxoplasma gondii is an obligate intracellular zoonotic parasite that can infect all warm-blooded animals, including humans. Currently, clinical findings of toxoplasmosis are being related to T. gondii strains such as Type I genotype may cause high pathogenicity and Type II genotype causes a milder clinical presentation. We have showed in our previous that Type II genotype is the most frequent strain detected in stray cats and wild birds living in natural life of İzmir. The aim of this study was to assess toxoplasmosis seroprevalence in immunocompromised patients, investigate the presence of T. gondii DNA in their blood samples, and genotype the PCR positive ones. METHODS The 42 buffy-coat and serum samples were collected from immunocompromised patients who were from various clinics. Thereafter, Real-Time PCR targeting RE gene of T. gondii was performed with DNA samples obtained from buffy-coat samples. Genotyping was performed by sequencing of GRA6 and GRA7 gene regions of positive DNA samples obtained from tissues of bioassay and PCR positive samples. RESULTS According to Real-Time PCR results, T. gondii DNA was detected in 23.8% (10/42) samples. Among these 10 samples, two samples were determined as T. gondii Type II genotype. Anti-Toxoplasma IgG antibodies were detected in 28.57% (12/42) samples. CONCLUSIONS Overall, the detection of Type II genotype in humans in İzmir province suggested that T. gondii infection in humans, stray cats, and wild animals may be associated to each other in terms of transmission.
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Affiliation(s)
- Muhammet Karakavuk
- Ege University, Odemis Vocational School, Ödemiş, İzmir, Türkiye; Ege University, Vaccine Development Application and Research Center, Bornova, İzmir, Türkiye
| | - Hüseyin Can
- Ege University, Vaccine Development Application and Research Center, Bornova, İzmir, Türkiye; Ege University, Faculty of Science, Department of Biology, Molecular Biology Section, Bornova, İzmir, Türkiye
| | - Aygül Çeltik
- Ege University, Faculty of Medicine, Department of Internal Medicine, Division of Nephrology, Bornova, İzmir, Türkiye
| | - Tuğba Karakavuk
- Ege University, Vaccine Development Application and Research Center, Bornova, İzmir, Türkiye
| | - Ceren Gül
- Ege University, Vaccine Development Application and Research Center, Bornova, İzmir, Türkiye
| | - Hüseyin Aytaç Erdem
- Ege University, Faculty of Medicine, Department of Infectious Diseases, Bornova, İzmir, Türkiye
| | - Hüsnü Pullukçu
- Ege University, Faculty of Medicine, Department of Infectious Diseases, Bornova, İzmir, Türkiye
| | - Meltem Taşbakan
- Ege University, Faculty of Medicine, Department of Infectious Diseases, Bornova, İzmir, Türkiye
| | - Mehmet Sezai Taşbakan
- Ege University, Faculty of Medicine, Department of Chest Diseases, Bornova, İzmir, Türkiye
| | - Adnan Yüksel Gürüz
- Ege University, Vaccine Development Application and Research Center, Bornova, İzmir, Türkiye; Ege University, Faculty of Medicine, Department of Parasitology, Bornova, İzmir, Türkiye
| | - Mert Döşkaya
- Ege University, Vaccine Development Application and Research Center, Bornova, İzmir, Türkiye; Ege University, Faculty of Medicine, Department of Parasitology, Bornova, İzmir, Türkiye
| | - Aysu Değirmenci Döşkaya
- Ege University, Vaccine Development Application and Research Center, Bornova, İzmir, Türkiye; Ege University, Faculty of Medicine, Department of Parasitology, Bornova, İzmir, Türkiye.
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13
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Suksard K, Luangtrakool K, Rungroung T, Chamsai S, Saetam P, Kittisares K, Permpikul P, Kittivorapart J. Two Cases of Anti-D Alloimmunization in D-Negative Thai Patients as a Result of the Asian-Type DEL on Transfused Red Cells. Transfus Med Hemother 2024; 51:122-125. [PMID: 38584693 PMCID: PMC10996056 DOI: 10.1159/000533625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 08/13/2023] [Indexed: 04/09/2024] Open
Abstract
Introduction DEL is known to be one of the weakest D variants, which can be detected by the adsorption-elution technique or by molecular study. Currently, in Thailand, we do not routinely test for DEL variants serologically or genetically among serologic RhD-negative blood donors. Case Presentation We reported 2 cases of alloimmunization after transfused with Rh DEL, RHD*DEL1 allele, in the Thai population. The first case was a 73-year-old male with anemia who presented with post-cardiac arrest and septic shock. The patient was group B, RhD-negative, and was transfused with RhD-negative red blood cells (RBCs). Antibody screening and identification found that the patient developed anti-D and anti-Mia during the admission course. The second case was a 38-year-old woman with pseudomyxoma peritonei who developed anti-D after receiving four units of RhD-negative RBCs during cytoreductive surgery with hyperthermic intraperitoneal chemotherapy. Both patients did not receive anti-D immunoglobulin and had no previous history of anti-D detection. We retrospectively investigated and found two units of RHD*DEL1 among the RBCs transfused to these patients. Discussion Previous reports of several cases of anti-D alloimmunization in RhD-negative recipients transfused by RHD*DEL1, an Asian-type DEL, are limited only to East Asia. We first identified 2 patients with anti-D alloimmunization after receiving the RHD*DEL1 RBCs in the Thai population. This raises concern about Rh DEL screening among D-negative Thai blood donors and whether to remove DEL units from the D-negative inventory to improve patient safety.
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Affiliation(s)
- Kanyapon Suksard
- Department of Transfusion Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Komon Luangtrakool
- Department of Transfusion Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Thongbai Rungroung
- Department of Transfusion Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Sutthisak Chamsai
- Department of Transfusion Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Pradermchai Saetam
- Department of Transfusion Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Kulvara Kittisares
- Department of Transfusion Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Parichart Permpikul
- Department of Transfusion Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Janejira Kittivorapart
- Department of Transfusion Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
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14
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Suzuki Y, Ishitsuka T, Takagi M, Sasaki Y, Kakuda T, Kobayashi K, Kubota H, Ono HK, Kabeya H, Irie T, Andoh M, Asakura H, Takai S. Isolation and genetic characterization of Staphylococcus aureus from wild animal feces and game meats. Folia Microbiol (Praha) 2024; 69:347-360. [PMID: 37405631 DOI: 10.1007/s12223-023-01071-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 06/12/2023] [Indexed: 07/06/2023]
Abstract
The populations of Japanese deer and boar have increased dramatically and have a serious impact on farming and mountain villages. Although the Japanese government promotes the use of captured wild animals, game meat is not subject to sanitary control considering that it is not subject to meat inspection or quality control. Here, we have attempted to isolate Staphylococcus aureus, a typical foodborne pathogen, as a part of an investigation of contamination in the meats of wild animals and their processing stages. We examined 390 samples of deer feces, 117 samples of wild boar feces, and 75 samples of disemboweled deer meat for isolation of S. aureus; ultimately, 30 (positive rate: 7.7%), 2 (1.7%), and 21 (28.0%) strains were isolated, respectively, from the samples. The genome sequences of these isolates were analyzed and were subjected to multilocus sequence typing. We identified 12 new sequence types (STs) and a dominant population of S. aureus with a characteristic genetic background in wild animals, namely, the ST groups derived from CC121 (number of strains = 39). These strains did not harbor the enterotoxin gene or only harbored egc-related enterotoxin, which is of low involvement in Staphylococcal food poisoning. However, one ST2449 strain, which produces causative enterotoxins, was isolated from a deer's feces. Since there are several common STs isolated from feces and dismembered meat and because fecal contamination during dismemberment is suspected, continuous monitoring and guidance for improving sanitary management conditions during processing and handling of the meat are highly warranted with immediate effect.
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Affiliation(s)
- Yasunori Suzuki
- Laboratory of Animal Hygiene, Kitasato University School of Veterinary Medicine, Higashi 23-35-1, Towada, Aomori, 034-8628, Japan.
| | - Toko Ishitsuka
- Laboratory of Animal Hygiene, Kitasato University School of Veterinary Medicine, Higashi 23-35-1, Towada, Aomori, 034-8628, Japan
| | - Miu Takagi
- Laboratory of Animal Hygiene, Kitasato University School of Veterinary Medicine, Higashi 23-35-1, Towada, Aomori, 034-8628, Japan
| | - Yukako Sasaki
- Laboratory of Animal Hygiene, Kitasato University School of Veterinary Medicine, Higashi 23-35-1, Towada, Aomori, 034-8628, Japan
| | - Tsutomu Kakuda
- Laboratory of Animal Hygiene, Kitasato University School of Veterinary Medicine, Higashi 23-35-1, Towada, Aomori, 034-8628, Japan
| | - Kai Kobayashi
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, 3-24-1 Hyakunin-Cho, Shinjuku-Ku, Tokyo, 169-0073, Japan
| | - Hiroaki Kubota
- Department of Microbiology, Tokyo Metropolitan Institute of Public Health, 3-24-1 Hyakunin-Cho, Shinjuku-Ku, Tokyo, 169-0073, Japan
| | - Hisaya K Ono
- Laboratory of Zoonoses, Kitasato University School of Veterinary Medicine, Higashi 23-35-1, Towada, Aomori, 034-8628, Japan
| | - Hidenori Kabeya
- Laboratory of Veterinary Food Hygiene, Department of Veterinary Medicine, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa, 252-0880, Japan
| | - Takao Irie
- Laboratory of Veterinary Parasitic Diseases, Department of Veterinary Sciences, Faculty of Agriculture, University of Miyazaki, 1-1 Gakuen-Kibanadai-Nishi, Miyazaki, 889-2192, Japan
| | - Masako Andoh
- Department of Pathogenetic and Preventive Veterinary Science, Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima, Kagoshima, 890-0065, Japan
| | - Hiroshi Asakura
- Division of Biomedical Food Research, National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki-Ku, Kawasaki, Kanagawa, 210-9501, Japan
| | - Shinji Takai
- Laboratory of Animal Hygiene, Kitasato University School of Veterinary Medicine, Higashi 23-35-1, Towada, Aomori, 034-8628, Japan
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15
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Vorimore F, Aaziz R, Al Qaysi L, Wernery U, Borel N, Sachse K, Laroucau K. Detection of a novel genotype of Chlamydia buteonis in falcons from the Emirates. Vet Microbiol 2024; 291:110027. [PMID: 38430716 DOI: 10.1016/j.vetmic.2024.110027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 03/05/2024]
Abstract
Chlamydiaceae are a family of obligate intracellular bacterial pathogens that affect both humans and animals. Recently, a new species named Chlamydia (C.) buteonis was isolated from hawks. In this study, we aimed to investigate the prevalence of Chlamydiaceae in 60 falcons that underwent a routine health check at a specialized clinic in Dubai, United Arab Emirates. Using real-time PCR, we analyzed cloacal and tracheal swabs from these birds and found that 39 of them tested positive for Chlamydiaceae. Subsequent real-time PCR assays specific for C. psittaci, C. abortus, C. avium, and C. gallinacea yielded negative results, while testing positive for C. buteonis. Analysis of ompA and MLST sequences indicated a highly conserved group of strains within this set of samples, but with sequences distinct from the C. buteonis RSHA reference strains and other C. buteonis strains isolated from hawks in the United States. Two strains were further isolated by cell culture and sequenced using whole-genome sequencing, confirming the clustering of these falcon strains within the C. buteonis species, but in a separate clade from the previously identified hawk strains. We also developed a SNP-based PCR-HRM assay to distinguish between these different genotypes. Overall, our findings suggest a high prevalence of C. buteonis in falcons in Dubai and highlight the importance of monitoring this pathogen in birds of prey.
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Affiliation(s)
- F Vorimore
- Anses, Animal Health Laboratory, Bacterial Zoonoses Unit, Maisons-Alfort, France; Anses, Identhypath, Maisons-Alfort, France
| | - R Aaziz
- Anses, Identhypath, Maisons-Alfort, France
| | - L Al Qaysi
- Lehbab Clinic, Dubai, United Arab Emirates
| | | | - N Borel
- Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - K Sachse
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University, Jena, Germany
| | - K Laroucau
- Anses, Animal Health Laboratory, Bacterial Zoonoses Unit, Maisons-Alfort, France.
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16
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Viana MC, Alves-Pereira A, Oliveira MAP, Valença-Barbosa C, Folly-Ramos E, Souza AP, Takiya DM, Almeida CE. Population genetics and genomics of Triatoma brasiliensis (Hemiptera, Reduviidae) in an area of high pressure of domiciliary infestation in Northeastern Brazil. Acta Trop 2024; 252:107144. [PMID: 38336343 DOI: 10.1016/j.actatropica.2024.107144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/12/2024]
Abstract
Understanding the population dynamics of vectors is crucial for effective control of vector-borne diseases. In the Northeastern Brazilian semi-arid region, Triatoma brasiliensis persists as the most significant Chagas disease vector, frequently displaying recurrent domiciliary infestations. This situation raises relevant public health concerns in the municipality of Currais Novos in the state of Rio Grande do Norte. This area has experienced a high prevalence of peridomiciliary re-infestations by T. brasiliensis, coupled with elevated rates of Trypanosoma cruzi infection. Therefore, we assessed the distribution of genetic variation via mitochondrial Cytochrome b gene (MT-CYB) sequencing (n = 109) and single nucleotide polymorphisms (SNPs, n = 86) to assess the gene flow among distinct populations distributed in varied geographic spots and environments, mainly sylvatic and peridomiciliary. Insects were collected from rural communities at Currais Novos, enclosed within a 16 km radius. Sampling included 13 populations: one intradomiciliary, eight peridomiciliary, and four sylvatic. Furthermore, an external population located 220 km from Currais Novos was also included in the study. The method employed to obtain SNP information relied on ddRAD-seq genotyping-by-sequencing (GBS), enabling a genome-wide analysis to infer genetic variation. Through AMOVA analysis of MT-CYB gene variation, we identified four distinct population groups with statistical significance (FCT= 0.42; p<0.05). We identified a total of 3,013 SNPs through GBS, with 11 loci showing putative signs of being under selection. The variation based on 3,002 neutral loci evidenced low genetic structuration based on low FST values (p>0.05), indicating local panmixia. However, resampling algorithms pointed out that three samples from the external population were assigned (>98 %) in a cluster contrasting from the ones putatively under local panmixia - validating the newly applied genome-wide marker for studies on the population genetics at finer-scale resolution for T. brasiliensis. The presence of population structuring in some of the sampled points, as suggested by the mitochondrial marker, leads us to assume that infestations were probably initiated by small populations of females - demographic event poses a risk for rapid re-infestations. The local panmictic pattern revealed by the GBS marker poses a challenge for vector control measures, as re-infestation foci may be distributed over a wide geographical and ecological range. In such instances, vectors exhibit reduced susceptibility to conventional insecticide spraying operations since sylvatic populations are beyond the reach of these interventions. The pattern of infestation exhibited by T. brasiliensis necessitates integrating innovative strategies into the existing control framework, holding the potential to create a more resilient and adaptive vector control program. In our dataset, the results demonstrated that the genetic signals from both markers were complementary. Therefore, it is essential to consider the nature and inheritance pattern of each marker when inferring the pattern of re-infestations.
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Affiliation(s)
- Maria Carolina Viana
- Instituto de Biologia (IB), Universidade de Campinas - UNICAMP, Campinas, Brazil; Programa de Pós-Graduação em Genética e Biologia Molecular, IB, UNICAMP; Coordenação de Prevenção e Vigilância do Câncer (CONPREV), Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | | | - Marcelo A P Oliveira
- Programa de Pós-Graduação em Genética- IB, Universidade Federal do Rio de Janeiro - UFRJ, Rio de Janeiro, Brazil
| | - Carolina Valença-Barbosa
- Instituto de Biologia (IB), Universidade de Campinas - UNICAMP, Campinas, Brazil; Grupo Triatomíneos, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Fiocruz, Brazil
| | | | | | | | - Carlos E Almeida
- Instituto de Biologia (IB), Universidade de Campinas - UNICAMP, Campinas, Brazil; Programa de Pós-Graduação em Genética e Biologia Molecular, IB, UNICAMP; Laboratorio de Entomologia, Instituto de Biologia, UFRJ.
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17
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Kawamura H, Imuta N, Ooka T, Shigemi A, Nakamura M, Mougi K, Obama Y, Fukuyama R, Arimura S, Murata N, Tominaga H, Sasaki H, Nagano S, Taniguchi N, Nishi J. Impact of control measures including decolonization and hand hygiene for orthopaedic surgical site infection caused by MRSA at a Japanese tertiary-care hospital. J Hosp Infect 2024; 146:151-159. [PMID: 37516280 DOI: 10.1016/j.jhin.2023.07.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 06/16/2023] [Accepted: 07/01/2023] [Indexed: 07/31/2023]
Abstract
BACKGROUND Meticillin-resistant Staphylococcus aureus (MRSA) is the most common pathogen in orthopaedic surgical site infections (SSIs). However, few studies have investigated the transmission process of orthopaedic MRSA SSI. AIM To investigate the transmission process of orthopaedic MRSA SSI using epidemiological and molecular analyses and to determine a method to prevent MRSA SSI in nosocomial orthopaedic surgery. METHODS Active MRSA surveillance, preoperative decolonization and contact precautions for MRSA-positive cases was performed at our institution. Changes in epidemic strains were evaluated and the possibility of transmission from patients in an orthopaedic ward of a Japanese tertiary-care hospital was assessed by genotyping stored MRSA strains. In addition, data on the prevalence of MRSA SSI, MRSA colonization, and use of an alcohol antiseptic agent (mL/patient-days) during 2005-2022 were retrospectively assessed. FINDINGS SCCmec type II strain in the SSI group decreased over time, associated with fewer outbreaks. Even during a period of high infection rates, no cases of transmission-induced SSI from nasal MRSA carriers were identified. The infection rate correlated negatively with the use of an alcohol antiseptic agent (r = -0.82; P < 0.0001). Two cases among five nasal carriers developed MRSA SSI caused by strains different from those related to nasal colonization. CONCLUSION The infection control measures for transmission from the hospital reservoirs including strict adherence to hand hygiene and decolonization of carriers is likely to be important for the prevention of orthopaedic MRSA SSI. However, the need for contact precautions for decolonized nasal carriers might be low.
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Affiliation(s)
- H Kawamura
- Department of Infection Control and Prevention, Kagoshima University Hospital, Kagoshima, Japan; Department of Orthopaedic Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan.
| | - N Imuta
- Department of Microbiology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - T Ooka
- Department of Microbiology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - A Shigemi
- Department of Infection Control and Prevention, Kagoshima University Hospital, Kagoshima, Japan
| | - M Nakamura
- Department of Infection Control and Prevention, Kagoshima University Hospital, Kagoshima, Japan; Clinical Laboratory, Kagoshima University Hospital, Kagoshima, Japan
| | - K Mougi
- Department of Infection Control and Prevention, Kagoshima University Hospital, Kagoshima, Japan; Clinical Laboratory, Kagoshima University Hospital, Kagoshima, Japan
| | - Y Obama
- Clinical Laboratory, Kagoshima University Hospital, Kagoshima, Japan
| | - R Fukuyama
- Clinical Laboratory, Kagoshima University Hospital, Kagoshima, Japan
| | - S Arimura
- Department of Infection Control and Prevention, Kagoshima University Hospital, Kagoshima, Japan
| | - N Murata
- Department of Infection Control and Prevention, Kagoshima University Hospital, Kagoshima, Japan
| | - H Tominaga
- Department of Orthopaedic Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - H Sasaki
- Department of Orthopaedic Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - S Nagano
- Department of Orthopaedic Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - N Taniguchi
- Department of Orthopaedic Surgery, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - J Nishi
- Department of Infection Control and Prevention, Kagoshima University Hospital, Kagoshima, Japan; Department of Microbiology, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
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18
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Gurbel PA, Bliden K, Sherwood M, Taheri H, Tehrani B, Akbari M, Yazdani S, Asgar JA, Chaudhary R, Tantry US. Development of a routine bedside CYP2C19 genotype assessment program for antiplatelet therapy guidance in a community hospital catheterization laboratory. J Thromb Thrombolysis 2024; 57:566-575. [PMID: 38480590 PMCID: PMC11031274 DOI: 10.1007/s11239-024-02953-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/19/2024] [Indexed: 04/19/2024]
Abstract
Genotype based personalized antiplatelet therapy in the setting of percutaneous coronary intervention (PCI) has been studied in clinical trials. Despite the demonstrated risk associated with CYP2C19 loss-of-function (LoF) carriage in clopidogrel-treated PCI patients, real-world implementation of genotyping for PCI has been low. The goal of the current study was to provide CYP2C19 genotype information to the interventionalist prior to the completion of the catheterization to facilitate immediate personalized antiplatelet therapy. Routine personalization of P2Y12 inhibitor therapy for PCI in a community hospital cardiac catheterization laboratory by POC genotyping with the SpartanRx system was first offered in February 2017. A best practice advisory (BPA) based on the Clinical Pharmacogenetics Implementation Consortium Guideline for CYP2C19 genotype and clopidogrel therapy was placed in the electronic health record prescription medication ordering system. By December 2019, 1,052 patients had CYP2C19 genotype testing, 429 patients underwent PCI with genotype guided antiplatelet therapy, and 250 patients underwent PCI without genotype testing and received antiplatelet therapy at the discretion of the treating physician. BPA compliance was 93. 87% of LoF allele carriers were prescribed ticagrelor or prasugrel whereas 96% of non-LoF allele carriers were prescribed clopidogrel. The genotyping results were available within 1 h and made immediately available for decision making by the interventional cardiologist. POC CYP2C19 genotyping is feasible in a community hospital catheterization laboratory and is associated with high rate of best practice compliance.Clinical Trial Registration: https://clinicaltrials.gov/ct2/show/NCT03040622.
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Affiliation(s)
- Paul A Gurbel
- Sinai Center for Thrombosis Research, Sinai Hospital of Baltimore, Baltimore, MD, 21215, USA.
- Inova Center for Thrombosis Research and Drug Development, Inova Heart and Vascular Institute, Fairfax, VA, USA.
| | - Kevin Bliden
- Sinai Center for Thrombosis Research, Sinai Hospital of Baltimore, Baltimore, MD, 21215, USA
- Inova Center for Thrombosis Research and Drug Development, Inova Heart and Vascular Institute, Fairfax, VA, USA
| | - Matthew Sherwood
- Inova Center for Thrombosis Research and Drug Development, Inova Heart and Vascular Institute, Fairfax, VA, USA
| | - Hamid Taheri
- Inova Center for Thrombosis Research and Drug Development, Inova Heart and Vascular Institute, Fairfax, VA, USA
| | - Behnam Tehrani
- Inova Center for Thrombosis Research and Drug Development, Inova Heart and Vascular Institute, Fairfax, VA, USA
| | - Marjaneh Akbari
- Inova Center for Thrombosis Research and Drug Development, Inova Heart and Vascular Institute, Fairfax, VA, USA
| | - Shahram Yazdani
- Inova Center for Thrombosis Research and Drug Development, Inova Heart and Vascular Institute, Fairfax, VA, USA
| | - Juzer Ali Asgar
- Sinai Center for Thrombosis Research, Sinai Hospital of Baltimore, Baltimore, MD, 21215, USA
| | - Rahul Chaudhary
- Heart and Vascular Institute, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
- Artificial Intelligence for Holistic Evaluation and Advancement of Cardiovascular Thrombosis (AI-HEART) Lab, Pittsburgh, PA, USA
| | - Udaya S Tantry
- Sinai Center for Thrombosis Research, Sinai Hospital of Baltimore, Baltimore, MD, 21215, USA
- Inova Center for Thrombosis Research and Drug Development, Inova Heart and Vascular Institute, Fairfax, VA, USA
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19
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Scholz T, Kuchta R, Barčák D, Cech G, Oros M. Small intestinal flukes of the genus Metagonimus (Digenea: Heterophyidae) in Europe and the Middle East: A review of parasites with zoonotic potential. Parasite 2024; 31:20. [PMID: 38551578 PMCID: PMC10979786 DOI: 10.1051/parasite/2024016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 02/28/2024] [Indexed: 04/01/2024] Open
Abstract
The heterophyid trematode Metagonimus romanicus (Ciurea, 1915) (Digenea) is redescribed on the basis of type material from domestic dogs (Canis familiaris) in Romania, vouchers from experimentally infected cats (Felis catus) and adults recovered from golden hamsters (Mesocricetus auratus) infected with metacercariae from scales of chub (Squalius cephalus) and common nase (Chondrostoma nasus) (Cypriniformes: Leuciscidae) in Hungary. This trematode, endemic to Europe and neighbouring regions (northwestern Türkiye), was previously misidentified as M. yokogawai (Katsurada, 1912), a zoonotic parasite of humans in East Asia. However, the two species differ considerably both genetically and morphologically, e.g., in the position of the ventral sucker, the presence of the prepharynx, the anterior extent of the vitelline follicles and the posterior extent of the uterus. Metagonimus ciureanus (Witenberg, 1929) (syn. Dexiogonimus ciureanus Witenberg, 1929), described from domestic cats and dogs in Israel, is a valid species distributed in the Middle East and Transcaucasia, which is also confirmed by molecular data. It differs from all Metagonimus species, including M. romanicus, in having symmetrical testes instead of the oblique testes of the other congeners. The zoonotic significance of M. romanicus and M. ciureanus is unclear, but appears to be low in Europe, mainly because raw or undercooked, whole fish with scales are generally not consumed. Accidental infection of fishermen by metacercariae in the scales when cleaning fish is more likely, but has never been reported. Remains of cyprinoids with scales infected with metacercariae of Metagonimus spp. can be an important natural source of infection for dogs, cats, and other carnivores, which can serve as a reservoir for these parasites.
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Affiliation(s)
- Tomáš Scholz
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences Branišovská 31 370 05 České Budějovice Czech Republic
| | - Roman Kuchta
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences Branišovská 31 370 05 České Budějovice Czech Republic
| | - Daniel Barčák
- Institute of Parasitology, Slovak Academy of Sciences Hlinkova 3 040 01 Košice Slovakia
| | - Gábor Cech
- HUN-REN Veterinary Medical Research Institute Hungária krt. 21 1143 Budapest Hungary
| | - Mikuláš Oros
- Institute of Parasitology, Slovak Academy of Sciences Hlinkova 3 040 01 Košice Slovakia
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20
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Hung CC, Moi SH, Huang HI, Hsiao TH, Huang CC. Polygenic risk score-based prediction of breast cancer risk in Taiwanese women with dense breast using a retrospective cohort study. Sci Rep 2024; 14:6324. [PMID: 38491043 PMCID: PMC10943108 DOI: 10.1038/s41598-024-55976-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 02/29/2024] [Indexed: 03/18/2024] Open
Abstract
Mammographic screening has contributed to a significant reduction in breast cancer mortality. Several studies have highlighted the correlation between breast density, as detected through mammography, and a higher likelihood of developing breast cancer. A polygenic risk score (PRS) is a numerical score that is calculated based on an individual's genetic information. This study aims to explore the potential roles of PRS as candidate markers for breast cancer development and investigate the genetic profiles associated with clinical characteristics in Asian females with dense breasts. This is a retrospective cohort study integrated breast cancer screening, population genotyping, and cancer registry database. The PRSs of the study cohort were estimated using genotyping data of 77 single nucleotide polymorphisms based on the PGS000001 Catalog. A subgroup analysis was conducted for females without breast symptoms. Breast cancer patients constituted a higher proportion of individuals in PRS Q4 (37.8% vs. 24.8% in controls). Among dense breast patients with no symptoms, the high PRS group (Q4) consistently showed a significantly elevated breast cancer risk compared to the low PRS group (Q1-Q3) in both univariate (OR = 2.25, 95% CI 1.43-3.50, P < 0.001) and multivariate analyses (OR: 2.23; 95% CI 1.41-3.48, P < 0.001). The study was extended to predict breast cancer risk using common low-penetrance risk variants in a PRS model, which could be integrated into personalized screening strategies for Taiwanese females with dense breasts without prominent symptoms.
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Affiliation(s)
- Chih-Chiang Hung
- Division of Breast Surgery, Department of Surgery, Taichung Veterans General Hospital, Taichung, 407, Taiwan
- Department of Applied Cosmetology, College of Human Science and Social Innovation, Hung Kuang University, Taichung, 433, Taiwan
- College of Life Sciences, National Chung Hsing University, Taichung, 402, Taiwan
| | - Sin-Hua Moi
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
- Research Center for Precision Environmental Medicine, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, 807, Taiwan
| | - Hsin-I Huang
- Department of Information Management, National Sun Yat-Sen University, Kaohsiung, 804, Taiwan
- International Integrated Systems, INC, Kaohsiung, 806, Taiwan
| | - Tzu-Hung Hsiao
- Department of Medical Research, Taichung Veterans General Hospital, 1650 Taiwan Boulevard Sect. 4, Taichung, 407219, Taiwan.
- Department of Public Health, Fu Jen Catholic University, New Taipei City, 242, Taiwan.
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, 402, Taiwan.
| | - Chi-Cheng Huang
- Division of Breast Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, 112, Taiwan.
- Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, No.17, Xuzhou Rd., Taipei City, 100, Taiwan.
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21
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Wei SM, Gregory MD, Nash T, de Abreu e Gouvêa A, Mervis CB, Cole KM, Garvey MH, Kippenhan JS, Eisenberg DP, Kolachana B, Schmidt PJ, Berman KF. Altered pubertal timing in 7q11.23 copy number variations and associated genetic mechanisms. iScience 2024; 27:109113. [PMID: 38375233 PMCID: PMC10875153 DOI: 10.1016/j.isci.2024.109113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/20/2023] [Accepted: 01/31/2024] [Indexed: 02/21/2024] Open
Abstract
Pubertal timing, including age at menarche (AAM), is a heritable trait linked to lifetime health outcomes. Here, we investigate genetic mechanisms underlying AAM by combining genome-wide association study (GWAS) data with investigations of two rare genetic conditions clinically associated with altered AAM: Williams syndrome (WS), a 7q11.23 hemideletion characterized by early puberty; and duplication of the same genes (7q11.23 Duplication syndrome [Dup7]) characterized by delayed puberty. First, we confirm that AAM-derived polygenic scores in typically developing children (TD) explain a modest amount of variance in AAM (R2 = 0.09; p = 0.04). Next, we demonstrate that 7q11.23 copy number impacts AAM (WS < TD < Dup7; p = 1.2x10-8, η2 = 0.45) and pituitary volume (WS < TD < Dup7; p = 3x10-5, ηp2 = 0.2) with greater effect sizes. Finally, we relate an AAM-GWAS signal in 7q11.23 to altered expression in postmortem brains of STAG3L2 (p = 1.7x10-17), a gene we also find differentially expressed with 7q11.23 copy number (p = 0.03). Collectively, these data explicate the role of 7q11.23 in pubertal onset, with STAG3L2 and pituitary development as potential mediators.
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Affiliation(s)
- Shau-Ming Wei
- Behavioral Endocrinology Branch, National Institute of Mental Health, Intramural Research Program, National Institutes of Health, Bethesda, MD, USA
- Section on Integrative Neuroimaging, Clinical and Translational Neuroscience Branch, National Institute of Mental Health, Intramural Research Program, National Institutes of Health, Bethesda, MD, USA
| | - Michael D. Gregory
- Section on Integrative Neuroimaging, Clinical and Translational Neuroscience Branch, National Institute of Mental Health, Intramural Research Program, National Institutes of Health, Bethesda, MD, USA
| | - Tiffany Nash
- Section on Integrative Neuroimaging, Clinical and Translational Neuroscience Branch, National Institute of Mental Health, Intramural Research Program, National Institutes of Health, Bethesda, MD, USA
| | - Andrea de Abreu e Gouvêa
- Section on Integrative Neuroimaging, Clinical and Translational Neuroscience Branch, National Institute of Mental Health, Intramural Research Program, National Institutes of Health, Bethesda, MD, USA
| | - Carolyn B. Mervis
- Neurodevelopmental Sciences Laboratory, Department of Psychological and Brain Sciences, University of Louisville, Louisville, KY, USA
| | - Katherine M. Cole
- Behavioral Endocrinology Branch, National Institute of Mental Health, Intramural Research Program, National Institutes of Health, Bethesda, MD, USA
- Section on Integrative Neuroimaging, Clinical and Translational Neuroscience Branch, National Institute of Mental Health, Intramural Research Program, National Institutes of Health, Bethesda, MD, USA
| | - Madeline H. Garvey
- Section on Integrative Neuroimaging, Clinical and Translational Neuroscience Branch, National Institute of Mental Health, Intramural Research Program, National Institutes of Health, Bethesda, MD, USA
| | - J. Shane Kippenhan
- Section on Integrative Neuroimaging, Clinical and Translational Neuroscience Branch, National Institute of Mental Health, Intramural Research Program, National Institutes of Health, Bethesda, MD, USA
| | - Daniel P. Eisenberg
- Section on Integrative Neuroimaging, Clinical and Translational Neuroscience Branch, National Institute of Mental Health, Intramural Research Program, National Institutes of Health, Bethesda, MD, USA
| | - Bhaskar Kolachana
- Human Brain Collection Core, National Institute of Mental Health, Intramural Research Program, National Institutes of Health, Bethesda, MD, USA
| | - Peter J. Schmidt
- Behavioral Endocrinology Branch, National Institute of Mental Health, Intramural Research Program, National Institutes of Health, Bethesda, MD, USA
| | - Karen F. Berman
- Section on Integrative Neuroimaging, Clinical and Translational Neuroscience Branch, National Institute of Mental Health, Intramural Research Program, National Institutes of Health, Bethesda, MD, USA
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22
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Islam A, Manjarrez-González JC, Song X, Gore T, Draviam VM. Search for chromosomal instability aiding variants reveal naturally occurring kinetochore gene variants that perturb chromosome segregation. iScience 2024; 27:109007. [PMID: 38361632 PMCID: PMC10867425 DOI: 10.1016/j.isci.2024.109007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/15/2023] [Accepted: 01/19/2024] [Indexed: 02/17/2024] Open
Abstract
Chromosomal instability (CIN) is a hallmark of cancers, and CIN-promoting mutations are not fully understood. Here, we report 141 chromosomal instability aiding variant (CIVa) candidates by assessing the prevalence of loss-of-function (LoF) variants in 135 chromosome segregation genes from over 150,000 humans. Unexpectedly, we observe both heterozygous and homozygous CIVa in Astrin and SKA3, two evolutionarily conserved kinetochore and microtubule-associated proteins essential for chromosome segregation. To stratify harmful versus harmless variants, we combine live-cell microscopy and controlled protein expression. We find the naturally occurring Astrin p.Q1012∗ variant is harmful as it fails to localize normally and induces chromosome misalignment and missegregation, in a dominant negative manner. In contrast, the Astrin p.L7Qfs∗21 variant generates a shorter isoform that localizes and functions normally, and the SKA3 p.Q70Kfs∗7 variant allows wild-type SKA complex localisation and function, revealing distinct resilience mechanisms that render these variants harmless. Thus, we present a scalable framework to predict and stratify naturally occurring CIVa, and provide insight into resilience mechanisms that compensate for naturally occurring CIVa.
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Affiliation(s)
- Asifa Islam
- School of Biological and Chemical Sciences, Queen Mary, University of London, London E1 4NS, UK
| | | | - Xinhong Song
- School of Biological and Chemical Sciences, Queen Mary, University of London, London E1 4NS, UK
| | - Trupti Gore
- School of Biological and Chemical Sciences, Queen Mary, University of London, London E1 4NS, UK
- London Interdisciplinary Doctoral Program, University College London, London, UK
| | - Viji M. Draviam
- School of Biological and Chemical Sciences, Queen Mary, University of London, London E1 4NS, UK
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23
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Cho EH, Park MS, Woo HY, Park H, Kwon MJ. Evaluation of clinical usefulness of HPV-16 and HPV-18 genotyping for cervical cancer screening. J Gynecol Oncol 2024; 35:35.e72. [PMID: 38522949 DOI: 10.3802/jgo.2024.35.e72] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 12/12/2023] [Accepted: 02/25/2024] [Indexed: 03/26/2024] Open
Abstract
OBJECTIVE High-risk human papillomavirus (HR-HPV) infection is a leading cause of cervical cancer, of which human papillomavirus (HPV)-16 and HPV-18 account for about 70% of cases. Since HPV infection is common, it is important to focus on the HPV genotypes that pose the highest risk for effective cervical cancer screening. In this study, we evaluated the clinical usefulness of HPV-16/HPV-18 genotyping for cervical cancer screening. METHODS A total of 86,022 women aged 25 years or older was analyzed in this study. Sensitivity, specificity, positive predictive value, and negative predictive value of HPV genotyping and cytology were analyzed. In addition, we subdivided participants into two groups according to cytology results, negative for intraepithelial lesion of malignancy (NILM) and atypical squamous cells of undetermined significance (ASC-US), and analyzed absolute risk (AR) and relative risk (RR) of cervical intraepithelial neoplasia (CIN) 3 or worse according to HPV genotype. RESULTS The AR of CIN 3 or worse was 77.0 times higher in HR-HPV-positive compared to HR-HPV-negative. Compared to 12 other HR-HPV-positive, the AR of CIN 3 or worse was 4.2 times higher in HPV-16 and/or HPV-18 positive. This finding was more evident in women with NILM than in women with ASC-US. The RR of CIN 3 or worse was 7.0 in women with NILM and 4.5 in women with ASC-US. CONCLUSION Regardless of the cytology results, the risk of CIN 3 or worse was higher in HPV-16/HPV-18 than in other HR-HPV. HPV-16/HPV-18 genotyping is recommended to screen women with a high risk of cervical cancer.
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Affiliation(s)
- Eun Hye Cho
- Department of Laboratory Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Min-Seung Park
- Department of Laboratory Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hee-Yeon Woo
- Department of Laboratory Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hyosoon Park
- Department of Laboratory Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Min-Jung Kwon
- Department of Laboratory Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Korea.
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24
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Voogd L, Drittij AM, Dingenouts CK, Franken KL, Unen VV, van Meijgaarden KE, Ruibal P, Hagedoorn RS, Leitner JA, Steinberger P, Heemskerk MH, Davis MM, Scriba TJ, Ottenhoff TH, Joosten SA. Mtb HLA-E-tetramer-sorted CD8 + T cells have a diverse TCR repertoire. iScience 2024; 27:109233. [PMID: 38439958 PMCID: PMC10909886 DOI: 10.1016/j.isci.2024.109233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/05/2024] [Accepted: 02/09/2024] [Indexed: 03/06/2024] Open
Abstract
HLA-E molecules can present self- and pathogen-derived peptides to both natural killer (NK) cells and T cells. T cells that recognize HLA-E peptides via their T cell receptor (TCR) are termed donor-unrestricted T cells due to restricted allelic variation of HLA-E. The composition and repertoire of HLA-E TCRs is not known so far. We performed TCR sequencing on CD8+ T cells from 21 individuals recognizing HLA-E tetramers (TMs) folded with two Mtb-HLA-E-restricted peptides. We sorted HLA-E Mtb TM+ and TM- CD8+ T cells directly ex vivo and performed bulk RNA-sequencing and single-cell TCR sequencing. The identified TCR repertoire was diverse and showed no conservation between and within individuals. TCRs selected from our single-cell TCR sequencing data could be activated upon HLA-E/peptide stimulation, although not robust, reflecting potentially weak interactions between HLA-E peptide complexes and TCRs. Thus, HLA-E-Mtb-specific T cells have a highly diverse TCR repertoire.
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Affiliation(s)
- Linda Voogd
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | - Anne M.H.F. Drittij
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | - Calinda K.E. Dingenouts
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | - Kees L.M.C. Franken
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | - Vincent van Unen
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Palo Alto, CA, USA
| | | | - Paula Ruibal
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | - Renate S. Hagedoorn
- Department of Hematology, Leiden University Medical Center, Leiden, the Netherlands
| | - Judith A. Leitner
- Centre for Pathophysiology, Infectiology and Immunology, Institute of Immunology, Medical University of Vienna, Vienna, Austria
| | - Peter Steinberger
- Centre for Pathophysiology, Infectiology and Immunology, Institute of Immunology, Medical University of Vienna, Vienna, Austria
| | | | - Mark M. Davis
- Institute of Immunity, Transplantation and Infection, Stanford University School of Medicine, Palo Alto, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Thomas J. Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Tom H.M. Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | - Simone A. Joosten
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
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25
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Wittwer CT, Hemmert AC, Kent JO, Rejali NA. DNA melting analysis. Mol Aspects Med 2024; 97:101268. [PMID: 38489863 DOI: 10.1016/j.mam.2024.101268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 02/19/2024] [Accepted: 03/11/2024] [Indexed: 03/17/2024]
Abstract
Melting is a fundamental property of DNA that can be monitored by absorbance or fluorescence. PCR conveniently produces enough DNA to be directly monitored on real-time instruments with fluorescently labeled probes or dyes. Dyes monitor the entire PCR product, while probes focus on a specific locus within the amplicon. Advances in amplicon melting include high resolution instruments, saturating DNA dyes that better reveal multiple products, prediction programs for domain melting, barcode taxonomic identification, high speed microfluidic melting, and highly parallel digital melting. Most single base variants and small insertions or deletions can be genotyped by high resolution amplicon melting. High resolution melting also enables heterozygote scanning for any variant within a PCR product. A web application (uMelt, http://www.dna-utah.org) predicts amplicon melting curves with multiple domains, a useful tool for verifying intended products. Additional applications include methylation assessment, copy number determination and verification of sequence identity. When amplicon melting does not provide sufficient detail, unlabeled probes or snapback primers can be used instead of covalently labeled probes. DNA melting is a simple, inexpensive, and powerful tool with many research applications that is beginning to make its mark in clinical diagnostics.
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Affiliation(s)
- Carl T Wittwer
- Department of Pathology, University of Utah, Salt Lake City, UT, USA.
| | | | - Jana O Kent
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Nick A Rejali
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
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26
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Holubová N, Zikmundová V, Kicia M, Zajączkowska Ż, Rajský M, Konečný R, Rost M, Mravcová K, Sak B, Kváč M. Genetic diversity of Cryptosporidium spp., Encephalitozoon spp. and Enterocytozoon bieneusi in feral and captive pigeons in Central Europe. Parasitol Res 2024; 123:158. [PMID: 38460006 DOI: 10.1007/s00436-024-08169-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 02/22/2024] [Indexed: 03/11/2024]
Abstract
Cryptosporidium spp., Enterocytozoon bieneusi and Encephalitozoon spp. are the most common protistan parasites of vertebrates. The results show that pigeon populations in Central Europe are parasitised by different species of Cryptosporidium and genotypes of microsporidia of the genera Enterocytozoon and Encephalitozoon. A total of 634 and 306 faecal samples of captive and feral pigeons (Columba livia f. domestica) from 44 locations in the Czech Republic, Slovakia and Poland were analysed for the presence of parasites by microscopy and PCR/sequence analysis of small subunit ribosomal RNA (18S rDNA), 60 kDa glycoprotein (gp60) and internal transcribed spacer (ITS) of SSU rDNA. Phylogenetic analyses revealed the presence of C. meleagridis, C. baileyi, C. parvum, C. andersoni, C. muris, C. galli and C. ornithophilus, E. hellem genotype 1A and 2B, E. cuniculi genotype I and II and E. bieneusi genotype Peru 6, CHN-F1, D, Peru 8, Type IV, ZY37, E, CHN4, SCF2 and WR4. Captive pigeons were significantly more frequently parasitised with screened parasite than feral pigeons. Cryptosporidium meleagridis IIIa and a new subtype IIIl have been described, the oocysts of which are not infectious to immunodeficient mice, whereas chickens are susceptible. This investigation demonstrates that pigeons can be hosts to numerous species, genotypes and subtypes of the studied parasites. Consequently, they represent a potential source of infection for both livestock and humans.
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Affiliation(s)
- Nikola Holubová
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic.
| | - Veronika Zikmundová
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Agriculture and Technology, University of South Bohemia in České Budějovice, České Budějovice, Czech Republic
| | - Marta Kicia
- Department of Biology and Medical Parasitology, Wrocław Medical University, Wrocław, Poland
| | - Żaneta Zajączkowska
- Department of Biology and Medical Parasitology, Wrocław Medical University, Wrocław, Poland
| | - Matúš Rajský
- Research Institute for Animal Production Nitra, National Agricultural and Food Centre, Lužianky, Slovakia
| | - Roman Konečný
- Faculty of Agriculture and Technology, University of South Bohemia in České Budějovice, České Budějovice, Czech Republic
| | - Michael Rost
- Faculty of Agriculture and Technology, University of South Bohemia in České Budějovice, České Budějovice, Czech Republic
| | - Kristina Mravcová
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Bohumil Sak
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Martin Kváč
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
- Faculty of Agriculture and Technology, University of South Bohemia in České Budějovice, České Budějovice, Czech Republic
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Kapritchkoff RTI, Okino CH, Niciura SCM, Bello HJS, Matos RS, Melito GR, Bressani FA, Esteves SN, Chagas ACDS. Association of β-globin polymorphisms and tolerance to haemonchosis in ewes and lambs of different sheep breeds. Vet Parasitol 2024; 328:110163. [PMID: 38513446 DOI: 10.1016/j.vetpar.2024.110163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/06/2024] [Accepted: 03/05/2024] [Indexed: 03/23/2024]
Abstract
Gastrointestinal nematodes (GIN), especially Haemonchus contortus, represent a significant challenge for sheep production. Given the global concern about GIN anthelmintic resistance, alternative control methods able to reduce the dependence on these drugs are highly advisable. Since previous studies have shown that sheep carrying the Hb-A allele of β-globin are more resistant to H. contortus, this study aimed to investigate the relationship between the different haplotypes (Hb-AA, Hb-AB and Hb-BB) and phenotypes in Santa Inês (SI), Texel (TX) and White Dorper (DO) breeds infected with H. contortus. Blood samples were collected from 180 ewes and 123 lambs of the three breeds for DNA extraction followed by qPCR using a hydrolysis probe to identify the β-globin haplotypes. Phenotypic data, including fecal egg count (FEC), packed cell volume (PCV), FAMACHA score and body condition score for ewes and lambs, as well as weight gain for lambs, were collected. The genotypic frequencies of β-globin for ewes and lambs were, respectively: 21.7% and 21.4% Hb-AA, 50% and 50% Hb-AB and 28.3% and 28.6% Hb-BB in SI; 0% and 0% Hb-AA, 18.6% and 9.4% Hb-AB and 81.4% and 90.6% Hb-BB in TX; and 0% and 0% Hb-AA, 13.1% and 0% Hb-AB and 86.9% and 100% Hb-BB in DO. In ewes, mean PCV differed (p<0.05) between the three haplotypes, with higher PCV in Hb-AA animals, followed by Hb-AB and Hb-BB. When considering each breed separately, SI Hb-AA ewes presented higher PCV (p<0.05), highlighting that even in a breed already considered resistant, animals with Hb-AA haplotype showed superior performance. Lambs with the Hb-AA haplotype exhibited a higher (p<0.05) mean PCV compared to those with Hb-AB and Hb-BB. The same pattern was found in SI when analyzing each breed separately. No significant association was found between β-globin haplotypes and FEC, FAMACHA score, body condition score, or weight gain. Nevertheless, given that anemia is the major clinical sign of haemonchosis, our findings on PCV reinforce that sheep carrying the Hb-A allele of β-globin are more tolerant to haemonchosis. This study may support the development of a valuable tool, targeting genetic selection for GIN control, reducing the dependence on anthelmintics and boosting sheep production worldwide.
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Affiliation(s)
- Rafaela Tami Ikeda Kapritchkoff
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Via de Acesso Prof. Paulo Donato Castellane, s/n, Jaboticabal, São Paulo 14884-900, Brazil.
| | - Cintia Hiromi Okino
- Embrapa Pecuária Sudeste, Rodovia Washington Luiz, Km 234 s/n, Fazenda Canchim, P.O. Box 339, São Carlos, São Paulo 13560-970, Brazil
| | - Simone Cristina Méo Niciura
- Embrapa Pecuária Sudeste, Rodovia Washington Luiz, Km 234 s/n, Fazenda Canchim, P.O. Box 339, São Carlos, São Paulo 13560-970, Brazil
| | - Hornblenda Joaquina Silva Bello
- Embrapa Pecuária Sudeste, Rodovia Washington Luiz, Km 234 s/n, Fazenda Canchim, P.O. Box 339, São Carlos, São Paulo 13560-970, Brazil
| | - Renata Silva Matos
- Embrapa Pecuária Sudeste, Rodovia Washington Luiz, Km 234 s/n, Fazenda Canchim, P.O. Box 339, São Carlos, São Paulo 13560-970, Brazil
| | - Glaucia Roberta Melito
- Embrapa Pecuária Sudeste, Rodovia Washington Luiz, Km 234 s/n, Fazenda Canchim, P.O. Box 339, São Carlos, São Paulo 13560-970, Brazil
| | - Flavia Aline Bressani
- Embrapa Pecuária Sudeste, Rodovia Washington Luiz, Km 234 s/n, Fazenda Canchim, P.O. Box 339, São Carlos, São Paulo 13560-970, Brazil
| | - Sérgio Novita Esteves
- Embrapa Pecuária Sudeste, Rodovia Washington Luiz, Km 234 s/n, Fazenda Canchim, P.O. Box 339, São Carlos, São Paulo 13560-970, Brazil
| | - Ana Carolina de Souza Chagas
- Embrapa Pecuária Sudeste, Rodovia Washington Luiz, Km 234 s/n, Fazenda Canchim, P.O. Box 339, São Carlos, São Paulo 13560-970, Brazil
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Ali M, Polgári D, Sepsi A, Kontra L, Dalmadi Á, Havelda Z, Sági L, Kis A. Rapid and cost-effective molecular karyotyping in wheat, barley, and their cross-progeny by chromosome-specific multiplex PCR. Plant Methods 2024; 20:37. [PMID: 38444026 PMCID: PMC10913579 DOI: 10.1186/s13007-024-01162-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 02/20/2024] [Indexed: 03/07/2024]
Abstract
BACKGROUND Interspecific hybridisation is a powerful tool for increasing genetic diversity in plant breeding programmes. Hexaploid wheat (Triticum aestivum, 2n = 42) × barley (Hordeum vulgare, 2n = 14) intergeneric hybrids can contribute to the transfer of agronomically useful traits by creating chromosome addition or translocation lines as well as full hybrids. Information on the karyotype of hybrid progenies possessing various combinations of wheat and barley chromosomes is thus essential for the subsequent breeding steps. Since the standard technique of chromosome in situ hybridisation is labour-intensive and requires specific skills. a routine, cost-efficient, and technically less demanding approach is beneficial both for research and breeding. RESULTS We developed a Multiplex Polymerase Chain Reaction (MPCR) method to identify individual wheat and barley chromosomes. Chromosome-specific primer pairs were designed based on the whole genome sequences of 'Chinese Spring' wheat and 'Golden Promise' barley as reference cultivars. A pool of potential primers was generated by applying a 20-nucleotide sliding window with consecutive one-nucleotide shifts on the reference genomes. After filtering for optimal primer properties and defined amplicon sizes to produce an ordered ladder-like pattern, the primer pool was manually curated and sorted into four MPCR primer sets for the wheat A, B, and D sub-genomes, and for the barley genome. The designed MPCR primer sets showed high chromosome specificity in silico for the genome sequences of all 18 wheat and barley cultivars tested. The MPCR primers proved experimentally also chromosome-specific for the reference cultivars as well as for 13 additional wheat and four barley genotypes. Analyses of 16 wheat × barley F1 hybrid plants demonstrated that the MPCR primer sets enable the fast and one-step detection of all wheat and barley chromosomes. Finally, the established genotyping system was fully corroborated with the standard genomic in situ hybridisation (GISH) technique. CONCLUSIONS Wheat and barley chromosome-specific MPCR offers a fast, labour-friendly, and versatile alternative to molecular cytogenetic detection of individual chromosomes. This method is also suitable for the high-throughput analysis of distinct (sub)genomes, and, in contrast to GISH, can be performed with any tissue type. The designed primer sets proved to be highly chromosome-specific over a wide range of wheat and barley genotypes as well as in wheat × barley hybrids. The described primer design strategy can be extended to many species with precise genome sequence information.
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Affiliation(s)
- Mohammad Ali
- Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllő, 2100, Hungary
- Doctoral School of Plant Sciences, Hungarian University of Agriculture and Life Sciences, Gödöllő, 2100, Hungary
| | - Dávid Polgári
- Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllő, 2100, Hungary
- Centre for Agricultural Research, Hungarian Research Network, Martonvásár, 2462, Hungary
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Plant Biotechnology Section, Centre for Agricultural Research, Martonvásár, 2462, Hungary
| | - Adél Sepsi
- Centre for Agricultural Research, Hungarian Research Network, Martonvásár, 2462, Hungary
| | - Levente Kontra
- Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllő, 2100, Hungary
- Institute of Experimental Medicine, Bioinformatics Core Facility, Hungarian Research Network, Budapest, 1083, Hungary
| | - Ágnes Dalmadi
- Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllő, 2100, Hungary
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Plant Biotechnology Section, Hungarian University of Agriculture and Life Sciences, Gödöllő, 2100, Hungary
| | - Zoltán Havelda
- Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllő, 2100, Hungary
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Plant Biotechnology Section, Hungarian University of Agriculture and Life Sciences, Gödöllő, 2100, Hungary
| | - László Sági
- Centre for Agricultural Research, Hungarian Research Network, Martonvásár, 2462, Hungary.
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Plant Biotechnology Section, Centre for Agricultural Research, Martonvásár, 2462, Hungary.
| | - András Kis
- Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllő, 2100, Hungary.
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Gentile A, Fulgione A, Auzino B, Iovane V, Gallo D, Garramone R, Iaccarino N, Randazzo A, Iovane G, Cuomo P, Capparelli R, Iannelli D. In vivo biological validation of in silico analysis: A novel approach for predicting the effects of TLR4 exon 3 polymorphisms on brucellosis. Infect Genet Evol 2024; 118:105552. [PMID: 38218390 DOI: 10.1016/j.meegid.2024.105552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/15/2024]
Abstract
The role of the Toll-like receptor 4 (TLR4) is of recognising intracellular and extracellular pathogens and of activating the immune response. This process can be compromised by single nucleotide polymorphisms (SNPs) which might affect the activity of several TLRs. The aim of this study is of ascertaining whether SNPs in the TLR4 of Bubalus bubalis infected by Brucella abortus, compromise the protein functionality. For this purpose, a computational analysis was performed. Next, computational predictions were confirmed by performing genotyping analysis. Finally, NMR-based metabolomics analysis was performed to identify potential biomarkers for brucellosis. The results indicate two SNPs (c. 672 A > C and c. 902 G > C) as risk factor for brucellosis in Bubalus bubalis, and three metabolites (lactate, 3-hydroxybutyrate and acetate) as biological markers for predicting the risk of developing the disease. These metabolites, together with TLR4 structural modifications in the MD2 interaction domain, are a clear signature of the immune system alteration during diverse Gram-negative bacterial infections. This suggests the possibility to extend this study to other pathogens, including Mycobacterium tuberculosis. In conclusion, this study combines multidisciplinary approaches to evaluate the biological and structural effects of SNPs on protein function.
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Affiliation(s)
- Antonio Gentile
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Naples 80055, Italy
| | - Andrea Fulgione
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Naples 80055, Italy
| | - Barbara Auzino
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Naples 80055, Italy
| | - Valentina Iovane
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Naples 80055, Italy
| | - Daniela Gallo
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Naples 80055, Italy
| | - Raffaele Garramone
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Naples 80055, Italy
| | - Nunzia Iaccarino
- Department of Pharmacy, University of Naples Federico II, Naples 80131, Italy
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, Naples 80131, Italy
| | - Giuseppe Iovane
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples 80137, Italy
| | - Paola Cuomo
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Naples 80055, Italy
| | - Rosanna Capparelli
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Naples 80055, Italy.
| | - Domenico Iannelli
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Naples 80055, Italy
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Herrmann B, Aaziz R, Kaden R, Riedel HM, Spörndly-Nees E, Sandelin LL, Laroucau K. SNP-based high-resolution typing of Chlamydia psittaci from humans and wild birds in Sweden: circulation of the Mat116 genotype reveals the transmission mode to humans. Microbes Infect 2024; 26:105251. [PMID: 37952689 DOI: 10.1016/j.micinf.2023.105251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/29/2023] [Accepted: 11/07/2023] [Indexed: 11/14/2023]
Abstract
The incidence of Chlamydia psittaci respiratory tract infections in humans has increased in Sweden in recent years. This study aimed to identify the transmission route by genotyping C. psittaci from infected humans and birds. 42 human C. psittaci samples and 5 samples from C. psittaci-infected birds were collected. Genotyping was performed using ompA sequencing, Multi-locus sequence typing, and/or SNP-based high-resolution melting-PCR. Epidemiological data was also collected, and a phylogenetic analysis was conducted. Analysis of ompA provided limited resolution, while the SNP-based PCR analysis successfully detected the Mat116 genotype in 3/5 passerine birds and in 26/29 human cases, indicating a high prevalence of this genotype in the human population. These cases were associated with contact with wild birds, mainly through bird feeding during winter or other outdoor exposure. Human cases caused by other genotypes (psittacine and pigeon) were less common and were linked to exposure to caged birds or pigeons. The SNP-genotype Mat116 is rare, but predominated in this study. The use of SNP-based PCR provided a better understanding of the C. psittaci transmission from birds to humans compared to ompA analysis. In Sweden, human psittacosis appears mainly to be transmitted from garden birds during bird feeding in the winter season.
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Affiliation(s)
- Björn Herrmann
- Department of Clinical Microbiology, Uppsala University Hospital, SE-751 85 Uppsala, Sweden; Department of Medical Sciences, Clinical Microbiology, Uppsala University, SE-751 85 Uppsala, Sweden.
| | - Rachid Aaziz
- Anses, Laboratory for Animal Health, Bacterial Zoonosis Unit, Paris-Est University, F-94706 Maisons-Alfort, France
| | - Rene Kaden
- Department of Clinical Microbiology, Uppsala University Hospital, SE-751 85 Uppsala, Sweden; Science for Life Laboratory, Clinical Genomics Uppsala, SE-751 85 Uppsala, Sweden
| | - Hilde M Riedel
- Department of Clinical Microbiology, Uppsala University Hospital, SE-751 85 Uppsala, Sweden; Department of Medical Sciences, Clinical Microbiology, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Ellinor Spörndly-Nees
- Department of Pathology and Wildlife Diseases, National Veterinary Institute (SVA), SE-751 89 Uppsala, Sweden
| | - Lisa Labbé Sandelin
- Department of Communicable Diseases and Disease Control, Region Kalmar County, SE- 391 26 Kalmar, Sweden; Department of Biology and Environmental Science, Linnaeus University, SE-391 82 Kalmar, Sweden
| | - Karine Laroucau
- Anses, Laboratory for Animal Health, Bacterial Zoonosis Unit, Paris-Est University, F-94706 Maisons-Alfort, France
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Fernandez NB, Spruijtenburg B, Tiraboschi IN, Meis JF, Lugo A, López Joffre MC, Meijer EF. Genotyping and clonal origin of Sporothrix brasiliensis in human sporotrichosis cases in Argentina. Med Mycol Case Rep 2024; 43:100633. [PMID: 38420181 PMCID: PMC10899009 DOI: 10.1016/j.mmcr.2024.100633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/15/2024] [Accepted: 02/15/2024] [Indexed: 03/02/2024] Open
Abstract
Sporothrix brasiliensis is considered a highly virulent emerging pathogen that causes sporotrichosis in humans, mainly after zoonotic transmission from infected cats. The epidemic of this zoonosis that originated from Brazil has spread in the last decades, generating hyperendemic regions in Latin America. We present two cases of human sporotrichosis causes by S. brasiliensis in Buenos Aires, Argentina, with good clinical response to differing treatments after contact with sick cats. Using Short tandem repeat (STR) genotyping, the two S. brasiliensis cases appear to be introduced from Brazil and likely originate from the same source.
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Affiliation(s)
- Norma B. Fernandez
- Sección Micología, División Infectología, Hospital de Clínicas “José de San Martín”, Universidad de Buenos Aires, Av. Córdoba 2351, Ciudad Autónoma de Buenos Aires, C1121ABJ, Argentina
| | - Bram Spruijtenburg
- Radboudumc-CWZ Center of Expertise for Mycology, Nijmegen, the Netherlands
- Canisius-Wilhelmina Hospital (CWZ)/Dicoon, Nijmegen, the Netherlands
| | - Iris N. Tiraboschi
- División Infectología, Hospital de Clínicas “José de San Martín”, Universidad de Buenos Aires, Av. Córdoba 2351, Ciudad Autónoma de Buenos Aires, C1121ABJ, Argentina
| | - Jacques F. Meis
- Radboudumc-CWZ Center of Expertise for Mycology, Nijmegen, the Netherlands
- Institute of Translational Research, Cologne Excellence Cluster on Cellular Stress Response in Aging-Associated Diseases (CECAD), Excellence Center for Medical Mycology (ECMM), University of Cologne, Cologne, Germany
| | - Ana Lugo
- División Infectología, Hospital de Clínicas “José de San Martín”, Universidad de Buenos Aires, Av. Córdoba 2351, Ciudad Autónoma de Buenos Aires, C1121ABJ, Argentina
| | - María Cecilia López Joffre
- Departamento Micología, Instituto Nacional de Enfermedades Infecciosas INEI-ANLIS “Dr. Carlos G. Malbrán” Av. VélezSarsfield563, Ciudad Autónoma de Buenos Aires, C1282AFF, Argentina
| | - Eelco F.J. Meijer
- Radboudumc-CWZ Center of Expertise for Mycology, Nijmegen, the Netherlands
- Canisius-Wilhelmina Hospital (CWZ)/Dicoon, Nijmegen, the Netherlands
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Cenko E, Manfrini O, Bugiardini R. Net adverse clinical events with P2Y 12 inhibitor therapy in older patients after percutaneous coronary interventions. Atherosclerosis 2024; 390:117434. [PMID: 38233328 DOI: 10.1016/j.atherosclerosis.2023.117434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 12/20/2023] [Indexed: 01/19/2024]
Affiliation(s)
- Edina Cenko
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy.
| | - Olivia Manfrini
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy; IRCCS Azienda Ospedaliero-Universitaria di Bologna Sant'Orsola Hospital, Bologna, Italy
| | - Raffaele Bugiardini
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
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Bartosch C, Nadal A, Braga AC, Salerno A, Rougemont AL, Van Rompuy AS, Fitzgerald B, Joyce C, Allias F, Maher GJ, Turowski G, Tille JC, Alsibai KD, Van de Vijver K, McMahon L, Sunde L, Pyzlak M, Downey P, Wessman S, Patrier S, Kaur B, Fisher R. Practical guidelines of the EOTTD for pathological and genetic diagnosis of hydatidiform moles. Virchows Arch 2024; 484:401-422. [PMID: 37857997 DOI: 10.1007/s00428-023-03658-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/30/2023] [Accepted: 09/15/2023] [Indexed: 10/21/2023]
Abstract
Hydatidiform moles are rare and thus most pathologists and geneticists have little experience with their diagnosis. It is important to promptly and correctly identify hydatidiform moles given that they are premalignant disorders associated with a risk of persistent gestational trophoblastic disease and gestational trophoblastic neoplasia. Improvement in diagnosis can be achieved with uniformization of diagnostic criteria and establishment of algorithms. To this aim, the Pathology and Genetics Working Party of the European Organisation for Treatment of Trophoblastic Diseases has developed guidelines that describe the pathological criteria and ancillary techniques that can be used in the differential diagnosis of hydatidiform moles. These guidelines are based on the best available evidence in the literature, professional experience and consensus of the experts' group involved in its development.
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Affiliation(s)
- Carla Bartosch
- Department of Pathology, Cancer Biology & Epigenetics Group, Research Center of IPO Porto (CI-IPOP) / RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto) / Porto Comprehensive Cancer Center Raquel Seruca (Porto.CCC) and Centro Hospitalar Universitário S. João, Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal.
| | - Alfons Nadal
- Department of Pathology, Clínic Barcelona, Department of Basic Clinical Practice, Universitat de Barcelona, Institut d'Investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
| | - Ana C Braga
- Department of Pathology, University Hospital Centre of São João (CHUSJ) / Faculty of Medicine - University of Porto (FMUP) / School of Health (ESS) - Polytechnic Institute of Porto (P. PORTO), Alameda Prof. Hernâni Monteiro, 4200-319, Porto, Portugal
| | - Angela Salerno
- Anatomia Patologica, Ospedale Maggiore AUSL Bologna, Bologna, Italy
| | | | | | | | - Caroline Joyce
- Department of Clinical Biochemistry, Cork University Hospital, Ireland/ Pregnancy Loss Research Group, Department of Obstetrics & Gynaecology, University College Cork, Cork, Ireland
| | - Fabienne Allias
- Department of Pathology, Hospices Civils de Lyon, Centre Hospitalier Lyon Sud, Pierre Bénite, France
| | - Geoffrey J Maher
- Trophoblastic Tumour Screening & Treatment Centre, Imperial College NHS Trust, Charing Cross Hospital, Fulham Palace Road, London, W6 8RF, UK
| | - Gitta Turowski
- Department of Pathology, Oslo University Hospital, INNPATH Tirolkliniken, Innsbruck, Austria
| | | | - Kinan Drak Alsibai
- Department of Pathology and Center of Biological Resources (CRB Amazonie), Cayenne Hospital Center Andrée Rosemon, 97306, Cayenne, France
| | | | - Lesley McMahon
- Scottish Hydatidiform Mole Follow-Up Service, Ninewells Hospital and Medical School, Dundee, Scotland
| | - Lone Sunde
- Department of Clinical Genetics, Aalborg University Hospital, Denmark/Department of Biomedicine, Aarhus University, Aalborg, Aarhus, Denmark
| | - Michal Pyzlak
- Department of Pathology, Institute of Mother and Child, Warsaw, Poland
| | - Paul Downey
- Department of Pathology, National Maternity Hospital, Dublin, D02YH21, Ireland
| | - Sandra Wessman
- Department of Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
| | - Sophie Patrier
- Department of Pathology, Rouen University Hospital, Rouen, France
| | - Baljeet Kaur
- Department of Pathology, North West London Pathology, Imperial College NHS Trust, Fulham Palace Road, London, W6 8RF, UK
| | - Rosemary Fisher
- Department of Surgery and Cancer, Imperial College London, Charing Cross Hospital. Fulham Palace Road, London, W6 8RF, UK
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Hueppe K, Ortman J, Gauselmann H, Santibanez S, Mankertz A. Measles vaccination - An underestimated prevention measure: Analyzing a fatal case in Hildesheim, Germany. Int J Med Microbiol 2024; 314:151608. [PMID: 38335886 DOI: 10.1016/j.ijmm.2024.151608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/16/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
Measles and rubella are targeted for elimination in the WHO region Europe. To reach the elimination goal, vaccination coverage of 95% must be achieved and sustained, the genotype information has to be provided for 80% of all outbreaks and transmission chains of a certain variant must not be detected for >12 months. The latter information is collected at Germany's National Reference Center Measles, Mumps, Rubella (NRC MMR). We describe here an outbreak of measles occurring in Hildesheim. The outbreak comprised 43 cases and lasted 14 weeks. Surprisingly, a high number of vaccination failures was observed since 11 cases had received two doses of the MMR vaccine and 4 additional cases were vaccinated once. A 33-year-old woman passed away during the outbreak. She was the mother of 5 children between 4 and 16 years of age. Two schoolchildren contracted measles and passed it on to the rest of the family. Due to delivery bottlenecks, the vaccination of the mother was delayed. She developed measles-like symptoms 3 days after vaccination and was found dead on the morning of day 8 after vaccination. A post-mortem examination was done to identify the cause of death. Moreover, molecular characterization of the virus was performed to analyze whether she was infected by the wildtype virus circulating at that time in Hildesheim or whether the vaccine may have been a concomitant and aggravating feature of her death. The result showed that the samples taken from her at the time of death and during necropsy contained the wildtype measles virus variant corresponding to MVs/Gir Somnath.IND/42.16 (WHO Seq-ID D8-4683) that fueled the Hildesheim outbreak and circulated in Germany from March 2018 to March 2020. The vaccine virus was not detected. Moreover, two aspects uncovered by the post-mortem examination were remarkable; the woman died from giant cell pneumonia, which is a complication seen in immune-suppressed individuals and she was actively using cannabis. THC is known to influence the immune system, but literature reports describing the effects are limited.
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Affiliation(s)
- Katharina Hueppe
- Local Health Authority, Hildesheim, Ludolfingerstr. 2, 31137 Hildesheim, Germany
| | - Jan Ortman
- Institute for Forensic Medicine, Medizinische Hochschule Hannover, Hannover, Germany
| | - Hannah Gauselmann
- Brandenburgisches Landesinstitut für Rechtsmedizin, Potsdam, Germany
| | - Sabine Santibanez
- National Reference Center Measles, Mumps, Rubella; Robert Koch-Institute; Seestr. 10, 13353 Berlin, Germany
| | - Annette Mankertz
- National Reference Center Measles, Mumps, Rubella; Robert Koch-Institute; Seestr. 10, 13353 Berlin, Germany.
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Zhu N, Ren H, Yang L, Mao G, Li J, Su C, Yang Y. Direct evidence of cheetah (Acinonyx jubatus) as intermediate host of Toxoplasma gondii through isolation of viable strains. BMC Vet Res 2024; 20:71. [PMID: 38395812 PMCID: PMC10893619 DOI: 10.1186/s12917-024-03928-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
Toxoplasma gondii causes lifelong infection in most definitive and intermediate hosts. Clinical cases of toxoplasmosis in captive cheetahs have been reported. However, there are few reports of viable T. gondii strains isolated from cheetahs. Here, T. gondii infection was investigated using molecular and serological assays in cheetahs from China. Modified agglutination test (MAT) (cut-off: 1:25) indicated that all six examined cheetahs (n = 6) showed T. gondii antibodies. Toxoplasma gondii DNA was detected in three out of five cheetahs. Two viable T. gondii strains were isolated from the striated muscles of two cheetahs using mice bioassay. They were designated as TgCheetahCHn1 and TgCheetahCHn2. Genetic characterization of DNA derived from tachyzoites was performed using RFLP-PCR of 10 markers. Toxoplasma gondii TgCheetahCHn1 is ToxoDB PCR-RFLP genotype #319, and the alleles of ROP18/ROP5 types were 3/7. TgCheetahCHn2 is ToxoDB genotype #9, and the alleles of ROP18/ROP5 were 3/6. The average survival time of TgCheetahCHn1-infected Swiss mice was 22 ± 1 days (n = 23), and the mice did not have detectable T. gondii-specific antibodies until 117 ± 30 days post-inoculation (n = 8), therefore, TgCheetahCHn1 had intermediate virulence. TgCheetahCHn2 was avirulent for Swiss mice. Few brain tissue cysts (0-50) were observed in the mice inoculated with TgCheetahCHn1 or TgCheetahCHn2. The results provide direct evidence of cheetah as intermediate host of T. gondii.
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Affiliation(s)
- Niuping Zhu
- Veterinary Pathology, Henan Agricultural University, Zhengzhou, PR China
| | - Hongjie Ren
- Veterinary Pathology, Henan Agricultural University, Zhengzhou, PR China
| | - Liulu Yang
- Veterinary Pathology, Henan Agricultural University, Zhengzhou, PR China
| | - Gaohui Mao
- Veterinary Pathology, Henan Agricultural University, Zhengzhou, PR China
| | | | - Chunlei Su
- Department of Microbiology, University of Tennessee, Knoxville, USA
| | - Yurong Yang
- Veterinary Pathology, Henan Agricultural University, Zhengzhou, PR China.
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Koo YK, Kwon SS, Suh EJ, Kim NH, Kim HK, Cho YK, Choi SJ, Kim S, Lee KA. Evaluating the TaqMan Jr a- Genotyping Method for Rapidly Predicting the Presence of Anti-Jr a Antibodies. Ann Lab Med 2024:alm.2023.0325. [PMID: 38373791 DOI: 10.3343/alm.2023.0325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/14/2023] [Accepted: 02/06/2024] [Indexed: 02/21/2024] Open
Abstract
Background The Jra antigen is a high-prevalence red blood cell (RBC) antigen. Reports on cases of fatal hemolytic disease of the fetus and newborn and acute hemolytic transfusion reactions suggest that antibodies against Jra (anti-Jra) have potential clinical significance. Identifying anti-Jra is challenging owing to a lack of commercially available antisera. We developed an alternative approach to rapidly predict the presence of anti-Jra using the TaqMan single-nucleotide polymorphism (SNP)-genotyping method. Methods Residual peripheral blood samples from 10 patients suspected of having the anti-Jra were collected. Two samples with confirmed Jr(a-) RBCs and anti-Jra were used to validate the TaqMan genotyping assay by comparing the genotyping results with direct sequencing. The accuracy of the assay in predicting the presence of anti-Jra was verified through crossmatching with in-house Jr(a-) O+ RBCs. Results The TaqMan-genotyping method was validated with two Jr(a-) RBC- and anti-Jra-confirmed samples that showed concordant Jra genotyping and direct sequencing results. Jra genotyping for the remaining samples and crossmatching the serum samples with in-house Jr(a-) O+ RBCs showed consistent results. Conclusions We validated a rapid, simple, accurate, and cost-effective method for predicting the presence of anti-Jra using a TaqMan-based SNP-genotyping assay. Implementing this method in routine practice in clinical laboratories will assist in solving difficult problems regarding alloantibodies to high-prevalence RBC antigens and ultimately aid in providing safe and timely transfusions and proper patient care.
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Affiliation(s)
- Yu-Kyung Koo
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Soon Sung Kwon
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Eun Jung Suh
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Na Hyeong Kim
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Hyun Kyung Kim
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Youn Keong Cho
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Seung Jun Choi
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Sinyoung Kim
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Kyung-A Lee
- Department of Laboratory Medicine, Severance Hospital, Yonsei University College of Medicine, Seoul, Korea
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Pontes A, Paraíso F, Liu YC, Limtong S, Jindamorakot S, Jespersen L, Gonçalves C, Rosa CA, Tsai IJ, Rokas A, Hittinger CT, Gonçalves P, Sampaio JP. Tracking alternative versions of the galactose gene network in the genus Saccharomyces and their expansion after domestication. iScience 2024; 27:108987. [PMID: 38333711 PMCID: PMC10850751 DOI: 10.1016/j.isci.2024.108987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/27/2023] [Accepted: 01/17/2024] [Indexed: 02/10/2024] Open
Abstract
When Saccharomyces cerevisiae grows on mixtures of glucose and galactose, galactose utilization is repressed by glucose, and induction of the GAL gene network only occurs when glucose is exhausted. Contrary to reference GAL alleles, alternative alleles support faster growth on galactose, thus enabling distinct galactose utilization strategies maintained by balancing selection. Here, we report on new wild populations of Saccharomyces cerevisiae harboring alternative GAL versions and, for the first time, of Saccharomyces paradoxus alternative alleles. We also show that the non-functional GAL version found earlier in Saccharomyces kudriavzevii is phylogenetically related to the alternative versions, which constitutes a case of trans-specific maintenance of highly divergent alleles. Strains harboring the different GAL network variants show different levels of alleviation of glucose repression and growth proficiency on galactose. We propose that domestication involved specialization toward thriving in milk from a generalist ancestor partially adapted to galactose consumption in the plant niche.
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Affiliation(s)
- Ana Pontes
- UCIBIO, Department of Life Sciences, Nova School of Science and Technology, Caparica 2829-516, Portugal
- Associate Laboratory i4HB, Nova School of Science and Technology, Caparica 2829-516, Portugal
| | - Francisca Paraíso
- UCIBIO, Department of Life Sciences, Nova School of Science and Technology, Caparica 2829-516, Portugal
- Associate Laboratory i4HB, Nova School of Science and Technology, Caparica 2829-516, Portugal
| | - Yu-Ching Liu
- Biodiversity Research Center, Academia Sinica, Taipei 11529, Taiwan
| | - Savitree Limtong
- Department of Microbiology Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Biodiversity Center Kasetsart University, Bangkok 10900, Thailand
| | - Sasitorn Jindamorakot
- Microbial Diversity and Utilization Research Team, Thailand Bioresource Research Center, National Centre for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology, Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Lene Jespersen
- Department of Food Science, University of Copenhagen, 1958 Frederiksberg C, Denmark
| | - Carla Gonçalves
- UCIBIO, Department of Life Sciences, Nova School of Science and Technology, Caparica 2829-516, Portugal
- Associate Laboratory i4HB, Nova School of Science and Technology, Caparica 2829-516, Portugal
| | - Carlos A. Rosa
- Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | | | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
- Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA
| | - Chris Todd Hittinger
- Laboratory of Genetics, DOE Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Center for Genomic Science Innovation, J.F. Crow Institute for the Study of Evolution, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Paula Gonçalves
- UCIBIO, Department of Life Sciences, Nova School of Science and Technology, Caparica 2829-516, Portugal
- Associate Laboratory i4HB, Nova School of Science and Technology, Caparica 2829-516, Portugal
| | - José Paulo Sampaio
- UCIBIO, Department of Life Sciences, Nova School of Science and Technology, Caparica 2829-516, Portugal
- Associate Laboratory i4HB, Nova School of Science and Technology, Caparica 2829-516, Portugal
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Deng J, Lai G, Zhang C, Li K, Zhu W, Xie B, Zhong X. A robust primary liver cancer subtype related to prognosis and drug response based on a multiple combined classifying strategy. Heliyon 2024; 10:e25570. [PMID: 38352751 PMCID: PMC10861988 DOI: 10.1016/j.heliyon.2024.e25570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 01/13/2024] [Accepted: 01/29/2024] [Indexed: 02/16/2024] Open
Abstract
The recurrence or resistance to treatment of primary liver cancer (PLL) is significantly related to the heterogeneity present within the tumor. In this study, we integrated prognosis risk score, mRNAsi index, and immune characteristics clustering to classify patients. The four subtypes obtained from the combined classification are associated with PLC's prognosis and drug response. In these subtypes, we observed mRNAsiH_ICCA subtype, the intersection between high mRNAsi and immune characteristics clustering A, had the worst prognosis. Specifically, immune characteristics clustering B (ICC_B) had high drug sensitivity in most drugs regardless of the value of mRNAsi. On the other hand, patients with low mRNAsi responded better to ten drugs including KU-55933 and NU7441, while patients with high mRNAsi might benefit from drugs like Leflunomide. By matching the specific characteristics of each combined subtype with the drug-induced cell line expression profile, we identified a group of potential therapeutic drugs that might regulate the expression of disease signature genes. We developed a feasible multiple combined typing strategy, hoping to guide therapeutic selection and promote the development of precision medicine.
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Affiliation(s)
- Jielian Deng
- Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Chongqing, China
- Medical Department, Yidu Cloud (Beijing) Technology Co., Beijing, China
| | - Guichuan Lai
- Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Chongqing, China
| | - Cong Zhang
- Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Chongqing, China
| | - Kangjie Li
- Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Chongqing, China
| | - Wenyan Zhu
- Chongqing Engineering Research Center of Pharmaceutical Sciences, Chongqing Medical and Pharmaceutical College, Chongqing, China
- College of Pharmacy, Chongqing Medical University, Chongqing, China
- Medical Department, Yidu Cloud (Beijing) Technology Co., Beijing, China
| | - Biao Xie
- Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Chongqing, China
| | - Xiaoni Zhong
- Department of Epidemiology and Health Statistics, School of Public Health, Chongqing Medical University, Chongqing, China
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Abedian R, Esboei BR, Fakhar M, Rahmani Z, Montazeri M, Solaymani M, Hezarjaribi HZ. Is GRA6 Gene a Suitable Marker for Molecular Typing of Toxoplasma Gondii? A Scoping Systematic Review. Acta Parasitol 2024:10.1007/s11686-023-00790-y. [PMID: 38319447 DOI: 10.1007/s11686-023-00790-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 12/21/2023] [Indexed: 02/07/2024]
Abstract
Toxoplasmosis is a zoonotic disease with a worldwide prevalence that is caused by Toxoplasma gondii. This study aimed to summarize available data on genotyping T. gondii strains based on the GRA6 gene marker in different hosts around the world. We conducted a comprehensive literature search using five international databases (PubMed, Scopus, Science Direct, Web of Science, and Google Scholar) from inception until December 2021. We identified 32 papers eligible for inclusion in this systematic review. The majority of studies (50%) were carried out in Iran (n = 16) to identify T. gondii genotypes based on the GRA6 gene. Other countries with reported studies include China, Japan, Sweden, and Italy (n = 2 each). Out of 3,434 samples collected from various hosts, most studies (n = 11) focused on human samples (34.4%), followed by ovine (n = 7), pig (n = 4), goat (n = 3) and soil and cattle (n = 2).Using various molecular methods such as conventional PCR, nested-PCR, real-time PCR, microsatellite analysis, and Restriction Fragment Length Polymorphism (RFLP), we found DNA positive results in 805 out of 3,434 samples. Of these, 285 (35.40%), 207 (25.71%), 182 (22.60%), 65 (8.07%), and 18 (2.23%) were infected with types I, II, III, mix I, II, III, and mix II, III, respectively. Our data demonstrate that the GRA6 gene marker has sufficient polymorphism to detect three types of T. gondii genotypes in various hosts. Identifying the specific genotype could be valuable in developing new strategies for treatment, vaccination, diagnosis, control, and prevention of T. gondii infection.
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Affiliation(s)
- Rohallah Abedian
- Iranian National Registry Center for Lophomoniasis and Toxoplasmosis, Imam Khomeini Hospital, Mazandaran University of Medical Sciences, Sari, Iran
- Department of Parasitology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
- Student Research Committee, Mazandaran University of Medical Sciences, Sari, Iran
| | - Bahman Rahimi Esboei
- Iranian National Registry Center for Lophomoniasis and Toxoplasmosis, Imam Khomeini Hospital, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mahdi Fakhar
- Iranian National Registry Center for Lophomoniasis and Toxoplasmosis, Imam Khomeini Hospital, Mazandaran University of Medical Sciences, Sari, Iran
| | - Zahra Rahmani
- Department of Obstetrics and Gynecology, Imam Khomeini Hospital, Mazandaran University of Medical Sciences, Sari, Iran.
| | - Mahbobeh Montazeri
- Toxoplasmosis Research Center, Communicable Diseases Institute, Mazandaran University of Medical Sciences, Sari, Iran.
| | - Mostafa Solaymani
- Iranian National Registry Center for Lophomoniasis and Toxoplasmosis, Imam Khomeini Hospital, Mazandaran University of Medical Sciences, Sari, Iran
| | - Hajar Ziaei Hezarjaribi
- Iranian National Registry Center for Lophomoniasis and Toxoplasmosis, Imam Khomeini Hospital, Mazandaran University of Medical Sciences, Sari, Iran.
- Department of Parasitology, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran.
- Department of Parasitology, Sari Medical School, Mazandaran University of Medical Sciences, 48168-95475, Sari, PC, Iran.
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Mojžišová M, Weiperth A, Gebauer R, Laffitte M, Patoka J, Grandjean F, Kouba A, Petrusek A. Diversity and distribution of Aphanomyces astaci in a European hotspot of ornamental crayfish introductions. J Invertebr Pathol 2024; 202:108040. [PMID: 38081448 DOI: 10.1016/j.jip.2023.108040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 11/28/2023] [Accepted: 12/07/2023] [Indexed: 12/19/2023]
Abstract
Ornamental trade has become an important introduction pathway of non-native aquatic species worldwide. Correspondingly, there has been an alarming increase in the number of established crayfish of aquarium origin in Europe over the previous decade. The oomycete Aphanomyces astaci, the pathogen causing crayfish plague responsible for serious declines of European crayfish populations, is dispersed with introduced North American crayfish. The role of ornamental taxa in introducing and spreading different genotypes of this pathogen in open waters remains unclear. We investigated the distribution, prevalence, and diversity of A. astaci in Budapest, Hungary, which became a hotspot of aquarium crayfish introductions. Their establishment in this area was facilitated by locally abundant thermal waters. We screened for A. astaci in six host taxa from 18 sites sampled between 2018 and 2021: five cambarids (Cambarellus patzcuarensis, Faxonius limosus, Procambarus alleni, P. clarkii, P. virginalis) and one native astacid (Pontastacus leptodactylus). The pathogen was confirmed at five sampled sites in four host taxa: P. virginalis, P. clarkii, F. limosus, and for the first time in European open waters also in P. alleni. Genotyping was successful only in individuals from two different brooks where multiple host species coexisted but revealed unexpected patterns. Mitochondrial B-haplogroup of A. astaci, previously usually reported from Pacifastacus leniusculus or infected European species, was detected in P. virginalis at both sites, and in both F. limosus and P. virginalis sampled from a thermally stable tributary of Barát brook in 2018. In contrast, A-haplogroup of A. astaci was detected in coexisting F. limosus, P. virginalis and P. clarkii sampled in the same watercourse just a few hundred meters downstream in 2020. Additional genotyping methods indicated that a previously unknown A. astaci strain was associated with the latter haplogroup. One P. virginalis individual from 2020 was apparently co-infected by strains representing both mitochondrial haplogroups. The results indicated multiple sources of A. astaci in Budapest, likely directly associated with the introduction of ornamental species, interspecific transmission of this pathogen among ornamental hosts, and potential for a quick spatial or temporal turnover of dominant A. astaci strains at a certain locality. This highlights that in regions with high richness of potential A. astaci hosts, host taxon/pathogen genotype combinations become unpredictable, which might prevent reliable genotyping of pathogen sources in local crayfish mass mortalities.
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Affiliation(s)
- Michaela Mojžišová
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague 2, CZ-12800, Czechia.
| | - András Weiperth
- Department of Freshwater Fish Ecology, Institute of Aquaculture and Environmental Safety, Hungarian University of Agriculture and Life Sciences, Páter Károly utca 1, Gödöllő, HU-2100, Hungary.
| | - Radek Gebauer
- Faculty of Fisheries and Protection of Waters, CENAKVA, University of South Bohemia in České Budějovice, Zátiší 728/II, Vodňany, CZ-38925, Czechia.
| | - Maud Laffitte
- Laboratoire Ecologie et Biologie des Interactions, UMR CNRS 7267 Equipe Ecologie Evolution Symbiose, Université de Poitiers, 3 rue Jacques Fort, TSA 51106, Poitiers Cedex, FR-86073, France.
| | - Jiří Patoka
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Kamýcká 129, Prague - Suchdol, CZ-16500, Czechia.
| | - Frédéric Grandjean
- Laboratoire Ecologie et Biologie des Interactions, UMR CNRS 7267 Equipe Ecologie Evolution Symbiose, Université de Poitiers, 3 rue Jacques Fort, TSA 51106, Poitiers Cedex, FR-86073, France.
| | - Antonín Kouba
- Faculty of Fisheries and Protection of Waters, CENAKVA, University of South Bohemia in České Budějovice, Zátiší 728/II, Vodňany, CZ-38925, Czechia.
| | - Adam Petrusek
- Department of Ecology, Faculty of Science, Charles University, Viničná 7, Prague 2, CZ-12800, Czechia.
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Quan Z, Li M, Chen Y, Liang J, Takiff H, Gao Q. Performance evaluation of core genome multilocus sequence typing for genotyping of Mycobacterium tuberculosis strains in China: based on multicenter, population-based collection. Eur J Clin Microbiol Infect Dis 2024; 43:297-304. [PMID: 38041721 DOI: 10.1007/s10096-023-04720-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 11/16/2023] [Indexed: 12/03/2023]
Abstract
PURPOSE To evaluate the performance of core genome multilocus sequence typing (cgMLST) for genotyping Mycobacterium tuberculosis (M.tuberculosis) Strains in regions where the lineage 2 strains predominate. METHODS We compared clustering by whole-genome SNP typing with cgMLST clustering in the analysis of WGS data of 6240 strains from five regions of China. Using both the receiver operating characteristic (ROC) curve and epidemiological investigation to determine the optimal threshold for defining genomic clustering by cgMLST. The performance of cgMLST was evaluated by quantifying the sensitivity, specificity and concordance of clustering between two methods. Logistic regression was used to gauge the impact of strain genetic diversity and lineage on cgMLST clustering. RESULTS The optimal threshold for cgMLST to define genomic clustering was determined to be ≤ 10 allelic differences between strains. The overall sensitivity and specificity of cgMLST averaged 99.6% and 96.3%, respectively; the concordance of clustering between two methods averaged 97.1%. Concordance was significantly correlated with strain genetic diversity and was 3.99 times (95% CI, 2.94-5.42) higher in regions with high genetic diversity (π > 1.55 × 10-4) compared to regions with low genetic diversity. The difference missed statistical significance, while concordance for lineage 2 strains (96.8%) was less than that for lineage 4 strains (98.3%). CONCLUSION : cgMLST showed a discriminatory power comparable to whole-genome SNP typing and could be used to genotype clinical M.tuberculosis strains in different regions of China. The discriminative power of cgMLST was significantly correlated with strain genetic diversity and was slightly lower with strains from regions with low genetic diversity.
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Affiliation(s)
- Zhuo Quan
- Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Fudan University, 131 Dongan Road, Shanghai, 200032, China
| | - Meng Li
- Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Fudan University, 131 Dongan Road, Shanghai, 200032, China
| | - Yiwang Chen
- Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Fudan University, 131 Dongan Road, Shanghai, 200032, China
| | - Jialei Liang
- Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Fudan University, 131 Dongan Road, Shanghai, 200032, China
| | - Howard Takiff
- Laboratorio de Genética Molecular, CMBC, Instituto Venezolano de Investigaciones Científicas, IVIC, Caracas, Venezuela
| | - Qian Gao
- Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Fudan University, 131 Dongan Road, Shanghai, 200032, China.
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Petermann S, Mayer V, Carbol A, Opitz A, Flesch BK. Compound heterozygosity induces a rare Gerbich-negative phenotype in an immunized blood donor. Transfusion 2024; 64:406-411. [PMID: 38235836 DOI: 10.1111/trf.17711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/06/2023] [Accepted: 12/20/2023] [Indexed: 01/19/2024]
Abstract
BACKGROUND Antibodies to Gerbich blood group antigens are exceedingly rare and can cause moderate transfusion reactions. Several deletional variants of the GE-gene, that harbors long sequence repeats, enable alloimmunization and formation of naturally occurring antibodies. SUBJECT AND METHODS A female blood donor and soldier of the German Army without history of pregnancy or transfusion showed an antibody reactive with all test cells except for GE:-2-3 RBC. Thus, anti-Ge2 was suspected. Molecular analysis including fragment length specific PCR, Sanger sequencing and NGS should reveal the molecular background of the deficiency. Segregation of the variant alleles should be demonstrated by family analysis. RESULTS Compound heterozygosity for GYPC exon 2 (GE*01.-02) and exon 3 (GE*01.-03) deletion was detected in the donor and her sister. The mother had one exon 3 amplicon of reduced length, while the father heterozygously exhibited a truncated GYPC exon 2. NGS clearly demonstrated reduced coverages within the deletional fragments within each family member. The donor and her sister showed the complete absence of a 640 bp fragment. DISCUSSION AND CONCLUSION Rare GE deletion variants can induce naturally occurring anti-Ge2 in Caucasians. Because of an enhanced risk of injury as soldier autologous RBC of the donor were cryopreserved. The donor and her sibling can give blood for each other because of identical ABO, Rh, and K antigen blood types.
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Affiliation(s)
- Sarah Petermann
- Laboratory for Immunogenetics / HLA, German Red Cross Blood Service Rhineland-Palatinate and Saarland gGmbH, Bad Kreuznach, Germany
| | - Vanessa Mayer
- Laboratory for Immunogenetics / HLA, German Red Cross Blood Service Rhineland-Palatinate and Saarland gGmbH, Bad Kreuznach, Germany
| | - Alexander Carbol
- Laboratory for Immunogenetics / HLA, German Red Cross Blood Service Rhineland-Palatinate and Saarland gGmbH, Bad Kreuznach, Germany
| | - Andreas Opitz
- Laboratory for Immunogenetics / HLA, German Red Cross Blood Service Rhineland-Palatinate and Saarland gGmbH, Bad Kreuznach, Germany
| | - Brigitte K Flesch
- Laboratory for Immunogenetics / HLA, German Red Cross Blood Service Rhineland-Palatinate and Saarland gGmbH, Bad Kreuznach, Germany
- Laboratory for Immunogenetics / HLA, German Red Cross Blood Service West gGmbH, Hagen, Germany
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Gunasekera KT, Premaratne RG, Handunnetti SM, Weerasena J, Premawansa S, Fernando DS. msp1, msp2, and glurp genotyping to differentiate Plasmodium falciparum recrudescence from reinfections during prevention of reestablishment phase, Sri Lanka, 2014-2019. Malar J 2024; 23:35. [PMID: 38281044 PMCID: PMC10821543 DOI: 10.1186/s12936-024-04858-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 01/22/2024] [Indexed: 01/29/2024] Open
Abstract
BACKGROUND Sri Lanka after eliminating malaria in 2012, is in the prevention of re-establishment (POR) phase. Being a tropical country with high malariogenic potential, maintaining vigilance is important. All malaria cases are investigated epidemiologically and followed up by integrated drug efficacy surveillance (iDES). Occasionally, that alone is not adequate to differentiate Plasmodium falciparum reinfections from recrudescences. This study evaluated the World Health Organization and Medicines for Malaria Venture (MMV) recommended genotyping protocol for the merozoite surface proteins (msp1, msp2) and the glutamate-rich protein (glurp) to discriminate P. falciparum recrudescence from reinfection in POR phase. METHODS All P. falciparum patients detected from April 2014 to December 2019 were included in this study. Patients were treated and followed up by iDES up to 28 days and were advised to get tested if they develop fever at any time over the following year. Basic socio-demographic information including history of travel was obtained. Details of the malariogenic potential and reactive entomological and parasitological surveillance carried out by the Anti Malaria Campaign to exclude the possibility of local transmission were also collected. The msp1, msp2, and glurp genotyping was performed for initial and any recurrent infections. Classification of recurrent infections as recrudescence or reinfection was done based on epidemiological findings and was compared with the genotyping outcome. RESULTS Among 106 P. falciparum patients, six had recurrent infections. All the initial infections were imported, with a history of travel to malaria endemic countries. In all instances, the reactive entomological and parasitological surveillance had no evidence for local transmission. Five recurrences occurred within 28 days of follow-up and were classified as recrudescence. They have not travelled to malaria endemic countries between the initial and recurrent infections. The other had a recurrent infection after 105 days. It was assumed a reinfection, as he had travelled to the same malaria endemic country in between the two malaria attacks. Genotyping confirmed the recrudescence and the reinfection. CONCLUSIONS The msp1, msp2 and glurp genotyping method accurately differentiated reinfections from recrudescence. Since reinfection without a history of travel to a malaria endemic country would mean local transmission, combining genotyping outcome with epidemiological findings will assist classifying malaria cases without any ambiguity.
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Affiliation(s)
- Kumudunayana T Gunasekera
- Anti Malaria Campaign, Ministry of Health, 555/5 Public Health Complex, Elvitigala Mawatha, Colombo 5, Sri Lanka.
| | | | - Shiroma M Handunnetti
- Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, Colombo, Sri Lanka
| | - Jagathpriya Weerasena
- Institute of Biochemistry, Molecular Biology and Biotechnology, University of Colombo, Colombo, Sri Lanka
| | - Sunil Premawansa
- Department of Zoology and Environmental Science, University of Colombo, Colombo, Sri Lanka
| | - Deepika S Fernando
- Department of Parasitology, Faculty of Medicine, University of Colombo, Colombo, Sri Lanka
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Elnagdy MH, Magdy A, Eldars W, Elgamal M, El-Nagdy AH, Salem O, Elmowafy MM, Elborsh OA, Elshafey AW, Kesba MM, Abdulgalil AE, Sobh A. Genetic association of ACE2 and TMPRSS2 polymorphisms with COVID-19 severity; a single centre study from Egypt. Virol J 2024; 21:27. [PMID: 38263160 PMCID: PMC10807154 DOI: 10.1186/s12985-024-02298-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 01/16/2024] [Indexed: 01/25/2024] Open
Abstract
BACKGROUND Since the emergence of the COVID-19 infection in China, it has caused considerable morbidity, mortality, and economic burden. It causes the vast majority of clinical manifestations, ranging from mild or even no symptoms to severe respiratory failure. There are many risk factors for severe COVID-19, such as old age, male gender, and associated comorbidities. A major role for genetic factors may exist. The SARS-CoV-2 virus enters the cell primarily through ACE2 receptors. rs2285666 is one of many polymorphisms found in the ACE2 receptor gene. To enable endosome-independent entry into target cells, the transmembrane protease serine-type 2 (TMPRSS2) is necessary to cleave the virus' spike (S) glycoprotein. TMPRSS2 is characterized by an androgen receptor element. The rs12329760 polymorphism in TMPRSS2 may explain different genetic susceptibilities to COVID-19. METHOD This cross-sectional study was held in Mansoura University Hospitals during the period from June 2020 to April 2022 on patients who had mild and severe COVID-19. Demographic, clinical, and laboratory data were collected, and the TaqMan real-time polymerase chain was used for allelic discrimination in the genotyping of rs2285666 and rs12329760. RESULTS This study included 317 Egyptian patients, aged from 0.2 to 87 years. Males were 146, while females were 171. They were divided into mild and severe groups (91 and 226 patients, respectively) based on their clinical symptoms. There was a significant association between COVID-19 severity and male gender, hypertension, diabetes mellitus, and high CRP. The genotype and allele frequency distributions of the ACE2 rs2285666 polymorphism showed no significant association with the severity of COVID-19 in both. In contrast, in TMPRSS2 rs12329760 minor T allele and CT, TT genotypes were significantly associated with a reduced likelihood of developing severe COVID-19. CONCLUSION Our study indicates that the ACE2 rs2285666 polymorphism is not related to the severity of COVID-19, whether genotypes or alleles. In TMPRSS2 rs12329760, the dominant model and T allele showed significantly lower frequencies in severe cases, with a protective effect against severity. The discrepancies with previous results may be due to variations in other ACE2 receptor-related genes, inflammatory mediators, and coagulation indicators. Haplotype blocks and differences in racial makeup must be taken into consideration. Future research should be done to clarify how ethnicity affects these polymorphisms and how other comorbidities combine to have an additive effect.
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Affiliation(s)
- Marwa H Elnagdy
- Department of Medical Biochemistry and Molecular Biology, Mansoura University Faculty of Medicine, Mansoura, Egypt
- Department of Basic Medical Sciences, Faculty of Medicine, New Mansoura University, Mansoura, Egypt
| | - Alshimaa Magdy
- Department of Medical Biochemistry and Molecular Biology, Mansoura University Faculty of Medicine, Mansoura, Egypt
| | - Waleed Eldars
- Department of Basic Medical Sciences, Faculty of Medicine, New Mansoura University, Mansoura, Egypt
- Department of Medical Microbiology and Immunology, Mansoura University Faculty of Medicine, Mansoura, Egypt
| | - Mohamed Elgamal
- Department of Chest Medicine, Mansoura University Faculty of Medicine, Mansoura, Egypt
| | - Ahmed Hazem El-Nagdy
- Department of Microbiology, Faculty of Dentistry, Horus University, Damietta El Gadeeda, Egypt
| | - Omnia Salem
- Department of Pediatrics, Mansoura University Children's Hospital, Mansoura University Faculty of Medicine, 60 El Gomhouria Street, Mansoura, 35516, Egypt
| | | | - Omar Ahmed Elborsh
- Intern, Mansoura University Hospitals, Mansoura University, Mansoura, Egypt
| | | | | | - Ahmed Elsaeed Abdulgalil
- Mansoura Nephrology and Dialysis Unit, Internal Medicine Department, Mansoura University Faculty of Medicine, Mansoura, Egypt
| | - Ali Sobh
- Department of Pediatrics, Mansoura University Children's Hospital, Mansoura University Faculty of Medicine, 60 El Gomhouria Street, Mansoura, 35516, Egypt.
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Bukic E, Dragovic G, Toljic B, Obradovic B, Jadzic J, Jevtovic D, Milasin JM. TERT single nucleotide polymorphism rs2736098 but not rs2736100 is associated with telomere length in HIV-infected patients on cART. Mol Biol Rep 2024; 51:147. [PMID: 38236501 DOI: 10.1007/s11033-023-08967-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 11/14/2023] [Indexed: 01/19/2024]
Abstract
BACKGROUND Continuous application of "combination antiretroviral therapy" (cART) has transformed Human immunodeficiency virus (HIV) infection into a manageable chronic disease; however, due to lasting inflammation and cumulative toxicity, progressive pathophysiological changes do occur and potentially lead to accelerated aging, among others, contributing to telomere shortening. The single nucleotide polymorphisms (SNP) rs2736100 and rs2736098 are particularly important for human telomerase (TERT) gene expression. The objective of this study was to evaluate the effects of clinical parameters and single nucleotide polymorphisms in TERT (rs2736100 and rs2736098) on telomere length in HIV-infected patients. METHODS AND RESULTS This cross-sectional study included 176 patients diagnosed with HIV infection. Relative telomere length (RTL) was determined by real-time polymerase chain reaction (qPCR), whereas genotyping was performed by polymerase chain reaction, followed by restriction fragment length polymorphism analysis (PCR-RFLP). The mean age of the patients (p = .904), time since HIV diagnosis (p = .220), therapy-related variables such as the cART regimen (0.761), and total cART duration (p = .096) did not significantly affect RTL. TERT rs2736100 genotype showed no association with RTL. However, TERT rs2736098 heterozygotes (GA) had significantly longer telomeres (P = .049) than both homozygotes (GG and AA). CONCLUSIONS Our findings support the fact that cellular aging in HIV-infected patients is influenced by the TERT rs2736098 polymorphism.
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Affiliation(s)
- Ena Bukic
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Gordana Dragovic
- Department of Pharmacology, Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Bosko Toljic
- Department of Human Genetics, School of Dental Medicine, University of Belgrade, Dr Subotica 8, Belgrade, 11000, Serbia
| | - Bozana Obradovic
- Department of Pharmacology, Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Jelena Jadzic
- Faculty of Medicine, Center of Bone Biology, University of Belgrade, Belgrade, Serbia
| | - Djordje Jevtovic
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia
- Infectious and Tropical Diseases Hospital, University Clinical Center Serbia, Belgrade, Serbia
| | - Jelena M Milasin
- Department of Human Genetics, School of Dental Medicine, University of Belgrade, Dr Subotica 8, Belgrade, 11000, Serbia.
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Zoqi H, Schmidt D, Sedlacek L, Rath PM, Steinmann J, Kirchhoff L. Establishment of a Novel Short Tandem Repeat Typing Method for Exophiala dermatitidis. Mycopathologia 2024; 189:5. [PMID: 38231292 PMCID: PMC10794339 DOI: 10.1007/s11046-023-00825-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 12/18/2023] [Indexed: 01/18/2024]
Abstract
The opportunistic black yeast-like fungus Exophiala dermatitidis frequently colonizes the respiratory tract of cystic fibroses (CF) patients. Additionally, it can cause superficial, systemic, and cerebral forms of phaeohyphomycoses. The objective of this study was to develop and apply a microsatellite or short tandem repeat (STR) genotyping scheme for E. dermatitidis. In total, 82 E. dermatitidis isolates from various geographic origins (environmental = 9, CF = 63, invasive isolates = 9, melanin-deficient mutant = 1) were included in this study. After next-generation sequencing of a reference strain and sequence filtering for microsatellites, six STR markers were selected and amplified in two multiplex PCR reactions. The included isolates were discriminated in a genetic cluster analysis using the Pearson algorithm to reveal the relatedness of the isolates. The E. dermatitidis isolates clustered on basis of both, their source and their origin. The invasive isolates from Asia were unrelated to isolates from CF. Nearly all environmental isolates were grouped separately from patients' isolates. The Simpson index was 0.94. In conclusion, we were able to establish a STR genotyping scheme for investigating population genomics of E. dermatitidis.
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Affiliation(s)
- Hamide Zoqi
- Institute of Medical Microbiology, ECMM Center of Excellence in Clinical and Laboratory Mycology and Clinical Studies (Diamond Status), University Hospital Essen, University of Duisburg-Essen, 45122, Essen, Germany
| | - Dirk Schmidt
- Institute of Medical Microbiology, ECMM Center of Excellence in Clinical and Laboratory Mycology and Clinical Studies (Diamond Status), University Hospital Essen, University of Duisburg-Essen, 45122, Essen, Germany
| | - Ludwig Sedlacek
- Institute of Medical Microbiology and Hospital Epidemiology, Medical School Hannover (MHH), Hannover, Germany
| | - Peter-Michael Rath
- Institute of Medical Microbiology, ECMM Center of Excellence in Clinical and Laboratory Mycology and Clinical Studies (Diamond Status), University Hospital Essen, University of Duisburg-Essen, 45122, Essen, Germany
| | - Joerg Steinmann
- Institute of Medical Microbiology, ECMM Center of Excellence in Clinical and Laboratory Mycology and Clinical Studies (Diamond Status), University Hospital Essen, University of Duisburg-Essen, 45122, Essen, Germany
- Institute of Clinical Microbiology, Infectious Diseases and Infection Control, Klinikum Nürnberg, Paracelsus Medical University, 90419, Nuremberg, Germany
| | - Lisa Kirchhoff
- Institute of Medical Microbiology, ECMM Center of Excellence in Clinical and Laboratory Mycology and Clinical Studies (Diamond Status), University Hospital Essen, University of Duisburg-Essen, 45122, Essen, Germany.
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Gholamzad A, Khakpour N, Hashemi M, Gholamzad M. Prevalence of high and low risk HPV genotypes among vaccinated and non-vaccinated people in Tehran. Virol J 2024; 21:9. [PMID: 38183101 PMCID: PMC10768147 DOI: 10.1186/s12985-023-02270-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 12/15/2023] [Indexed: 01/07/2024] Open
Abstract
BACKGROUND Human Papillomavirus (HPV) is a prevalent STI (Sexually Transmitted Infection) that is estimated almost all sexually active Patients at some stage of their life will be infected by the virus. Although most HPV infections resolve spontaneously, some can result in health complications, such as genital warts and several types of cancer. This study analyzed the variety of HPV genotypes in females and males among the infected population. METHODS Samples were obtained from the oral, vaginal, and genital sites of study participants and the samples underwent DNA extraction and subsequently amplified using Real-Time PCR. The recognition of high-risk (HR) and low-risk (LR) HPV genotypes was carried out using the HPV REALQUALITY RQ-Multi diagnostic kit and demographic information was analyzed alongside statistical virological data. RESULTS Out of 936 samples, 324 cases (34.6%) were found to be positive for HPV, while 612 cases (65.4%) were negative. Of our participants, 70 samples of males (27.5%) and 254 samples of females (37.3%) were HPV-positive. Common genotypes included 16, 6, 11, and 18, while genotypes 59, 56, 31, 45, and 52 were also detected. CONCLUSION According to the findings of this study, a significant prevalence of HPV infection was seen in males and females, and the incidence of high-risk genotypes was more diverse in males. While the vaccine was effective in preventing some types of HPV, such as 16, 18, 6, and 11, there seems to be an increase in infections caused by other genotypes, and precautions should be taken to prevent future health problems.
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Affiliation(s)
- Amir Gholamzad
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
- Department of Laboratory Medicine, Faculty of Paramedical Sciences, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Niloofar Khakpour
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
- Department of Bacteriology and Virology, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mehrdad Hashemi
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | - Mehrdad Gholamzad
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
- Department of Microbiology and Immunology, Faculty of Medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
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Marian L, Withoeft JA, Fornara MA, Pandolfo GW, D'ambroso Fernandes F, Vogel FSF, Zapala MP, Casagrande RA. Toxoplasmosis outbreak caused by north American genotypes in captive black-tufted marmosets in southern Brazil. Vet Parasitol Reg Stud Reports 2024; 47:100960. [PMID: 38199681 DOI: 10.1016/j.vprsr.2023.100960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 10/24/2023] [Accepted: 11/20/2023] [Indexed: 01/12/2024]
Abstract
In this study, we describe an outbreak of toxoplasmosis in an enclosure of five Callithrix penicillata in Southern Brazil. The marmosets were found dead and submitted to necropsy and histopathology. Liver, spleen, and lungs were frozen and sent for polymerase chain reaction (PCR) and nested-PCR-restriction fragment length polymorphism (RFLP) genotyping of Toxoplasma gondii. Necropsy revealed a liver with a lobular pattern, along with diffusely congested lungs, spleen, and kidneys, and hemorrhage in the mesenteric lymph nodes. Mild-to-moderate, multifocal, necrotic hepatitis and splenitis, multifocal lymphoplasmacytic myocarditis, and moderate, diffuse necrohemorrhagic lymphadenitis were observed. T. gondii tachyzoites were in all the organs mentioned. The detected strains were closely related with the isolates TgWtdUs10, TgSoUs39, and TgShUs2, which were originally found in non-primate species all in the United States of America. This is an unprecedented report of North American strains causing mortality in captive individuals of the species Callithrix penicillata in the Southern Brazil.
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Affiliation(s)
- Lucas Marian
- Laboratório de Patologia Animal, Centro de Ciências Agroveterinárias, Universidade do Estado de Santa Catarina, Av. Luís de Camões, 2090, Bairro Conta Dinheiro, Lages, Santa Catarina 88520-000, Brazil
| | - Jéssica Aline Withoeft
- Laboratório de Patologia Animal, Centro de Ciências Agroveterinárias, Universidade do Estado de Santa Catarina, Av. Luís de Camões, 2090, Bairro Conta Dinheiro, Lages, Santa Catarina 88520-000, Brazil
| | - Maria Augusta Fornara
- Laboratório de Patologia Animal, Centro de Ciências Agroveterinárias, Universidade do Estado de Santa Catarina, Av. Luís de Camões, 2090, Bairro Conta Dinheiro, Lages, Santa Catarina 88520-000, Brazil
| | - Gustavo Willian Pandolfo
- Laboratório de Patologia Animal, Centro de Ciências Agroveterinárias, Universidade do Estado de Santa Catarina, Av. Luís de Camões, 2090, Bairro Conta Dinheiro, Lages, Santa Catarina 88520-000, Brazil
| | - Fagner D'ambroso Fernandes
- Laboratório de Doenças Parasitárias, Departamento de Medicina Veterinária Preventiva, Centro de Ciências Rurais, Universidade Federal de Santa Maria, Av. Roraima, 1000, Prédio 63D, Bairro Camobi, Santa Maria, Rio Grande do Sul 97105-900, Brazil
| | - Fernanda Silveira Flores Vogel
- Laboratório de Doenças Parasitárias, Departamento de Medicina Veterinária Preventiva, Centro de Ciências Rurais, Universidade Federal de Santa Maria, Av. Roraima, 1000, Prédio 63D, Bairro Camobi, Santa Maria, Rio Grande do Sul 97105-900, Brazil
| | - Milene Pugliese Zapala
- Médica Veterinária, Prefeitura de Brusque, Praça das Bandeiras, 77, Centro 1, Brusque, Santa Catarina 88350-051, Brazil
| | - Renata Assis Casagrande
- Laboratório de Patologia Animal, Centro de Ciências Agroveterinárias, Universidade do Estado de Santa Catarina, Av. Luís de Camões, 2090, Bairro Conta Dinheiro, Lages, Santa Catarina 88520-000, Brazil.
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Al-hakami RG, Mashraqi AY, Shannaq RAA, Kaabi YA. Association of the GHRd3 polymorphism with adult height and type 2 diabetes in a Saudi Arabian population from Jazan Province: A case-control study. Pak J Med Sci 2024; 40:308-312. [PMID: 38356830 PMCID: PMC10862461 DOI: 10.12669/pjms.40.3.7686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/16/2023] [Accepted: 11/18/2023] [Indexed: 02/16/2024] Open
Abstract
Objectives This study investigated the association of the GHRd3 polymorphism with height and type-2 diabetes mellitus (T2DM) in Saudi Arabia. Methods This case-control study included a total of 284 participants, divided into healthy controls (n = 142) and patients with T2DM (n = 142), recruited from Jazan University Hospital, southwest of Saudi Arabia in the period between January to September 2022. The GHRd3 polymorphism was genotyped using multiplex PCR. The correlation between height and genotypes was analyzed using one-way analysis of variance. The association between GHRd3 polymorphism and T2DM was assessed using logistic regression analysis. Results The data showed a significant difference between the means of heights associated with each GHRd3 genotype, flfl, fld3, and d3d3. Logistic regression analysis showed no association between GHRd3 variants and T2DM. Conclusion Homozygous GHRd3 polymorphism carriers, d3d3 genotype, were taller than fld3 or flfl carriers in our population. None of the GHRd3 variants were associated with T2DM. Thus, the GHRd3 polymorphism has growth-related actions with a minor contribution to T2DM. However, more studies with a larger sample size are required to confirm these findings.
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Affiliation(s)
- Reham G. Al-hakami
- Reham Ghazi Al-hakami, BSc. Department of Medical Laboratory Technology, College of Applied Medical Sciences, Medical Research Center, Jazan University, Jazan, Saudi Arabia
| | - Alaa Y. Mashraqi
- Alaa Yahia Mashraqi, BSc. Department of Medical Laboratory Technology, College of Applied Medical Sciences, Medical Research Center, Jazan University, Jazan, Saudi Arabia
| | - Rola Ali Atiah Shannaq
- Rola Ali Atiah, BSc. Department of Medical Laboratory Technology, College of Applied Medical Sciences, Medical Research Center, Jazan University, Jazan, Saudi Arabia
| | - Yahia A. Kaabi
- Yahia Ali Kaabi, PhD. Department of Medical Laboratory Technology, College of Applied Medical Sciences, Medical Research Center, Jazan University, Jazan, Saudi Arabia
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Kumaraswamy J, Govindasamy P, Nagarajan LS, Gunasekaran K, Abhilash KPP, Prakash JAJ. Genotyping of Orientia tsutsugamushi circulating in and around Vellore (South India) using TSA 56 gene. Indian J Med Microbiol 2024; 47:100483. [PMID: 37890413 DOI: 10.1016/j.ijmmb.2023.100483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 08/05/2023] [Accepted: 09/20/2023] [Indexed: 10/29/2023]
Abstract
PURPOSE The immunodominant TSA 56 gene of Orientia tsutsugamushi, (scrub typhus agent) has four variable regions (VD-I to VD-IV) making it useful for genotyping. This study was undertaken to determine Orientia tsutsugamushi genotypes circulating in and around Vellore using complete and partial TSA 56 gene. METHODS Of the 162 patients positive by 47 kDa qPCR, on 21 samples PCR to amplify the complete TSA 56 gene (≈1605 bp: Long protocol) and the partial gene sequence using the Horinouchi (≈650bp) and the Furuya (≈480 bp) protocol was performed. Sanger and Nanopore sequencing was performed to obtain sequence data for assigning genotype. For 13 amplicons partial and complete gene data was obtained. RESULTS Phylogenetic analysis of the complete gene (Long protocol) which includes VD-I to VD-IV region and partial gene (Horinouchi) which amplifies the VD-I to VD-III regions showed identical genotypes. Twelve belonged to TA763 genotype and one belongs to Karp genotype. The Furuya sequence (in silico) correctly identified the Karp genotype and 10 of the TA763 genotypes. Two TA763 genotypes (identified by complete and 650 bp partial gene analysis) were misidentified by Furuya sequence analysis as Karp genotype. CONCLUSIONS Analysis of the 13 complete 56 kDa gene sequences suggests that TA763 is the commonest genotype in Vellore. Sanger sequencing of the 650 bp fragment gives similar results. However, these results need to be validated by larger prospective multi-centric studies.
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Affiliation(s)
- Janaki Kumaraswamy
- Department of Clinical Microbiology, Christian Medical College, Vellore, 632004, Tamil Nadu, India.
| | - Punitha Govindasamy
- Department of Clinical Microbiology, Christian Medical College, Vellore, 632004, Tamil Nadu, India.
| | - Lakshmi Surya Nagarajan
- Department of Clinical Microbiology, Christian Medical College, Vellore, 632004, Tamil Nadu, India.
| | - Karthik Gunasekaran
- Department of Medicine, Christian Medical College, Vellore, Tamil Nadu, India.
| | - K P P Abhilash
- Emergency Medicine, Christian Medical College, Vellore, 632004, Tamil Nadu, India.
| | - John Antony Jude Prakash
- Department of Clinical Microbiology, Christian Medical College, Vellore, 632004, Tamil Nadu, India.
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