151
|
Jeanvoine A, Richard M, Meunier A, Chassagne S, Cholley P, Gbaguidi-Haore H, Sauget M, Bertrand X, Hocquet D. Persistent contamination of a hospital hot water network by Legionellapneumophila. Int J Hyg Environ Health 2023; 250:114143. [PMID: 36907106 DOI: 10.1016/j.ijheh.2023.114143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/20/2023] [Accepted: 02/20/2023] [Indexed: 03/12/2023]
Abstract
OBJECTIVES We assessed the contamination with Legionella pneumophila (Lp) of the hot water network (HWN) of a hospital, mapped the risk of contamination, and evaluated the relatedness of isolates. We further validated phenotypically the biological features that could account for the contamination of the network. METHODS We collected 360 water samples from October 2017 to September 2018 in 36 sampling points of a HWN of a building from a hospital in France. Lp were quantified and identified with culture-based methods and serotyping. Lp concentrations were correlated with water temperature, date and location of isolation. Lp isolates were genotyped by pulsed-field gel electrophoresis and compared to a collection of isolates retrieved in the same HWN two years later, or in other HWN from the same hospital. RESULTS 207/360 (57.5%) samples were positive with Lp. In the hot water production system, Lp concentration was negatively associated with water temperature. In the distribution system, the risk of recovering Lp decreased when temperature was >55 °C (p < 10-3), the proportion of samples with Lp increased with distance from the production network (p < 10-3), and the risk of finding high loads of Lp increased 7.96 times in summer (p = 0.001). All Lp isolates (n = 135) were of serotype 3, and 134 (99.3%) shared the same pulsotype which is found two years later (Lp G). In vitro competition experiments showed that a 3-day culture of Lp G on agar inhibited the growth of a different pulsotype of Lp (Lp O) contaminating another HWN of the same hospital (p = 0.050). We also found that only Lp G survived to a 24h-incubation in water at 55 °C (p = 0.014). CONCLUSION We report here a persistent contamination with Lp of a hospital HWN. Lp concentrations were correlated with water temperature, season, and distance from the production system. Such persistent contamination could be due to biotic parameters such as intra-Legionella inhibition and tolerance to high temperature, but also to the non-optimal configuration of the HWN that prevented the maintenance of high temperature and optimal water circulation.
Collapse
|
152
|
Matiašovic J, Bzdil J, Papežíková I, Čejková D, Vasina E, Bizos J, Navrátil S, Šedivá M, Klaudiny J, Pikula J. Genomic analysis of Paenibacillus larvae isolates from the Czech Republic and the neighbouring regions of Slovakia. Res Vet Sci 2023; 158:34-40. [PMID: 36913910 DOI: 10.1016/j.rvsc.2023.03.007] [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: 05/10/2022] [Revised: 01/16/2023] [Accepted: 03/05/2023] [Indexed: 03/10/2023]
Abstract
Paenibacillus larvae is the causative agent of American foulbrood (AFB), a devastating disease of honeybee larvae. In the Czech Republic, two large infested regions were recognised. This study aimed to analyse P. larvae strains occurring in the Czech Republic in the years 2016-2017 and to characterise the genetic structure of their population with the use of Enterobacterial Repetitive Intergenic Consensus genotyping (ERIC), multilocus sequence typing (MLST) and whole genome sequence (WGS) analysis. The results were complemented by the analysis of isolates collected in the year 2018 in areas of Slovakia located near the Czechia-Slovakia border. ERIC genotyping revealed that 78.9% of tested isolates belonged to the ERIC II genotype and 21.1% to ERIC I genotype. MLST showed six sequence types with ST10 and ST11 being the most frequent among isolates. Within six isolates we found discrepancies in correlations between MLST and ERIC genotypes. The use of MLST and WGS analysis of isolates revealed that each of the large infested geographic regions had its own dominating P. larvae strains. We assume that these strains represented primary sources of infection in the affected areas. In addition, the sporadic presence of strains identified by core genome analysis as genetically related was unveiled in geographically distant regions suggesting possible human-mediated transmission of AFB.
Collapse
Affiliation(s)
- Ján Matiašovic
- Veterinary Research Institute, Hudcova 296/70, 62100 Brno, Czech Republic.
| | - Jaroslav Bzdil
- Ptácy s.r.o., Valašská Bystřice 194, 756 27 Valašská Bystřice, Czech Republic
| | - Ivana Papežíková
- Department of Ecology and Diseases of Zoo Animals, Game, Fish and Bees, University of Veterinary Sciences Brno, Palackého tř. 1946/1, 612 42 Brno, Czech Republic
| | - Darina Čejková
- Veterinary Research Institute, Hudcova 296/70, 62100 Brno, Czech Republic; Department of Biomedical Engineering, Brno University of Technology, Technická 12, 616 00 Brno, Czech Republic
| | - Evgeniya Vasina
- Department of Ecology and Diseases of Zoo Animals, Game, Fish and Bees, University of Veterinary Sciences Brno, Palackého tř. 1946/1, 612 42 Brno, Czech Republic
| | - Jiří Bizos
- Veterinary Research Institute, Hudcova 296/70, 62100 Brno, Czech Republic
| | - Stanislav Navrátil
- Department of Ecology and Diseases of Zoo Animals, Game, Fish and Bees, University of Veterinary Sciences Brno, Palackého tř. 1946/1, 612 42 Brno, Czech Republic
| | - Mária Šedivá
- Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 84538 Bratislava, Slovakia
| | - Jaroslav Klaudiny
- Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 84538 Bratislava, Slovakia
| | - Jiří Pikula
- Department of Ecology and Diseases of Zoo Animals, Game, Fish and Bees, University of Veterinary Sciences Brno, Palackého tř. 1946/1, 612 42 Brno, Czech Republic
| |
Collapse
|
153
|
Afrasiabi V, Ghojoghi R, Hosseini SY, Sarvari J, Nekooei F, Joharinia N, Hadian S, Gholami M, Nejabat M. The molecular epidemiology, genotyping, and clinical manifestation of prevalent adenovirus infection during the epidemic keratoconjunctivitis, South of Iran. Eur J Med Res 2023; 28:108. [PMID: 36859343 PMCID: PMC9979477 DOI: 10.1186/s40001-022-00928-0] [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: 09/16/2022] [Accepted: 12/02/2022] [Indexed: 03/03/2023] Open
Abstract
PURPOSE Adenoviral-mediated keratoconjunctivitis is among the emergency diseases of ophthalmology with long-term sequels. The role of adenovirus infection, ocular-related genotypes, and association with ocular symptoms need to be investigated for epidemiological as well as clinical purposes. METHODS The affected patients from two close keratoconjunctivitis epidemics were included in the study. The swab samples were taken from patients; the total DNA was extracted and then used as a template for in-house Real-time PCR. Besides, partial Hexon genes of 11 adenovirus positive samples were amplified and submitted to sanger sequencing. Moreover, they were finally evaluated by phylogenetic analysis. RESULTS Of 153 patients, 92 (60.1%) were males and 47 cases (30.7%) had a history of eye infection in the family or colleagues. Real-time PCR tests of 126 samples (82.4%) were positive for adenovirus, and all eleven cases that underwent sequencing analysis were determined to be group 8 (HAdV-D8). Adenovirus infection has a significant relationship with infection among family or colleagues (p = 0.048), membrane formation (p = 0.047), conjunctival bleeding (p = 0.046), tearing, and pain(p < 0.05). CONCLUSIONS The results indicated that Adenovirus is the major cause of keratoconjunctivitis, and HAdV-D8 was the most common genotype in the area. There were some clinical manifestations associated with Adenovirus infection of the conjunctiva.
Collapse
Affiliation(s)
- Vahidreza Afrasiabi
- grid.412571.40000 0000 8819 4698Poostchi Ophtalmalogy Research Center, Department of Ophtalmology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Rozita Ghojoghi
- grid.412571.40000 0000 8819 4698Department of Bacteriology & Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyed Younes Hosseini
- grid.412571.40000 0000 8819 4698Department of Bacteriology & Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Jamal Sarvari
- grid.412571.40000 0000 8819 4698Department of Bacteriology & Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran ,grid.412571.40000 0000 8819 4698Gastroenterohepatology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Fatemeh Nekooei
- grid.412571.40000 0000 8819 4698Department of Bacteriology & Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Negar Joharinia
- grid.412571.40000 0000 8819 4698Department of Bacteriology & Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Sahar Hadian
- grid.412571.40000 0000 8819 4698Poostchi Ophtalmalogy Research Center, Department of Ophtalmology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Gholami
- grid.412571.40000 0000 8819 4698Poostchi Ophtalmalogy Research Center, Department of Ophtalmology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mahmood Nejabat
- Poostchi Ophtalmalogy Research Center, Department of Ophtalmology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran.
| |
Collapse
|
154
|
Arnuphapprasert A, Nugraheni YR, Poofery J, Aung A, Kaewlamun W, Chankeaw W, Tasanaganjanakorn T, Wattanamethanont J, Kaewthamasorn M. Genetic characterization of genes encoding the major surface proteins of Anaplasma marginale from cattle isolates in Thailand reveals multiple novel variants. Ticks Tick Borne Dis 2023; 14:102110. [PMID: 36577307 DOI: 10.1016/j.ttbdis.2022.102110] [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: 06/28/2022] [Revised: 12/14/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022]
Abstract
Bovine anaplasmosis is a serious tick-borne disease that is responsible for economic loss worldwide. The major surface proteins (MSPs), encoded by msp1 to msp5 genes of Anaplasma marginale, play an important role in host-pathogen and tick-pathogen interactions. These markers have been used for genetic characterization and phylogenetic studies. Despite domestic reports concerning suspected outbreaks of anaplasmosis in Thailand, genetic analysis of A. marginale in the country remains largely limited. Therefore, we aim to investigate the infection rate of the rickettsia organism in the Anaplasmataceae family throughout five regions of Thailand and to further characterize the key genetic markers: msp1a, msp2, and msp5 of A. marginale. From 2016 to 2021, we collected a total of 384 cattle blood samples across 18 provinces. Overall, the infection rate of the rickettsia organism in the Anaplasmataceae family was 46.1%. Over 65% of the positive samples were confirmed as A. marginale. We successfully obtained a total of 138 A. marginale msp1a (38), msp2 (79), and msp5 (21) sequences from all regions of the country. The msp1a and msp2 genes exhibit a high degree of genetic diversity, while the msp5 gene is highly conserved among the Thai isolates. Our findings regarding msp1a corroborated the genetic heterogeneity of A. marginale strains in endemic regions worldwide. Additionally, we found multiple novel variants for the first time in the current nationwide survey. We found 45 tandem repeat characters of the msp1a sequence. Among them, 24 characters were not shared with other countries. Collectively, we expanded the extent of genetic diversity in key markers; msp1a and msp2 genes, and further confirmed the previous finding that msp5 was highly conserved. The msp1a and msp2 genes could be useful for the surveillance of newly introduced strains. The current data may also be useful in designing a vaccine containing potential epitopes of different antigens in the future.
Collapse
Affiliation(s)
- Apinya Arnuphapprasert
- Veterinary Parasitology Research Unit, Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand; Veterinary Pathobiology Graduate Program, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Yudhi Ratna Nugraheni
- The International Graduate Program of Veterinary Science and Technology (VST), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand; Department of Parasitology, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Indonesia
| | - Juthathip Poofery
- Veterinary Parasitology Research Unit, Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Aung Aung
- The International Graduate Program of Veterinary Science and Technology (VST), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Winai Kaewlamun
- School of Agricultural Resources, Chulalongkorn University, Bangkok, Thailand
| | - Wiruntita Chankeaw
- Faculty of Veterinary Science, Rajamangala University of Technology Srivijaya, Nakhon Si Thammarat, Thailand
| | - Tanuwong Tasanaganjanakorn
- Farmed Animal Hospital, Faculty of Veterinary Science, Chulalongkorn University, Nakorn Pathom, Thailand
| | - Juntra Wattanamethanont
- Department of Livestock Development, Parasitology Section, National Institute of Animal Health, Bangkok, Thailand
| | - Morakot Kaewthamasorn
- Veterinary Parasitology Research Unit, Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.
| |
Collapse
|
155
|
Balog K, Mizeranschi AE, Wanjala G, Sipos B, Kusza S, Bagi Z. Application potential of chicken DNA chip in domestic pigeon species - Preliminary results. Saudi J Biol Sci 2023; 30:103594. [PMID: 36874200 PMCID: PMC9975693 DOI: 10.1016/j.sjbs.2023.103594] [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: 09/21/2022] [Revised: 01/12/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
Introducing the SNP technology to pigeon breeding will enhance the competitiveness of a sector that produces one of the healthiest and best quality meats. The present study aimed to test the applicability of the Illumina Chicken_50K_CobbCons array on 24 domestic pigeon individuals from the Mirthys hybrids and Racing pigeon breeds. A total of 53,313 SNPs were genotyped. Principal component analysis shows a significant overlap between the two groups. The chip performed poorly in this data set, with a call rate per sample of 0.474 (49%). The low call rate was likely due to an increase in the evolutionary distance. A total of 356 SNPs were retained after a relatively strict quality control. We have demonstrated that it is technically feasible to use a chicken microarray chip on pigeon samples. Presumably, with a larger sample size and by assigning phenotypic data, efficiency would be improved, allowing more thorough analyses, such as genome-wide association studies.
Collapse
Affiliation(s)
- Katalin Balog
- University of Debrecen, Doctoral School of Animal Science, Böszörményi út 138, 4032, Debrecen, Hungary.,Centre for Agricultural Genomics and Biotechnology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, 4002 Debrecen, Hungary
| | | | - George Wanjala
- University of Debrecen, Doctoral School of Animal Science, Böszörményi út 138, 4032, Debrecen, Hungary.,Centre for Agricultural Genomics and Biotechnology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, 4002 Debrecen, Hungary
| | - Bíborka Sipos
- University of Debrecen, Faculty of Agricultural and Food Sciences and Environmental Management, Böszörményi út 138, 4032, Debrecen, Hungary
| | - Szilvia Kusza
- Centre for Agricultural Genomics and Biotechnology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, 4002 Debrecen, Hungary
| | - Zoltán Bagi
- Centre for Agricultural Genomics and Biotechnology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, 4002 Debrecen, Hungary
| |
Collapse
|
156
|
Busatto C, Possuelo LG, Bierhals D, de Oliveira CL, de Souza MQ, Fanfa D, Barreto É, Schwarzbold P, Von Groll A, Portugal I, Perdigão J, Croda J, Andrews JR, da Silva PA, Ramis IB. Spread of Mycobacterium tuberculosis in Southern Brazilian persons deprived of liberty: a molecular epidemiology study. Eur J Clin Microbiol Infect Dis 2023; 42:297-304. [PMID: 36701032 DOI: 10.1007/s10096-023-04546-4] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 01/10/2023] [Indexed: 01/27/2023]
Abstract
To evaluate the genetic diversity and clustering rates of M. tuberculosis strains to better understand transmission among persons deprived of liberty (PDL) in Rio Grande do Sul (RS), southern Brazil. This is a cross-sectional study, including strains of M. tuberculosis isolated from PDL, stored at the Central Laboratory of RS, in the period from 2013 to 2018. The molecular characterization was performed using the MIRU-VNTR 15 loci method. A total of 598 M. tuberculosis strains were genotyped, and 37.5% were grouped into 53 clusters. Cluster sizes ranged from 2 to 34 strains. The largest cluster of the study had strains from 34 PDL, and 58.8% of the PDL of this cluster were in P01. Among the clusters formed, in 60.3%, there was at least one strain from P01. The most common strains in RS were LAM (53.2%) and Haarlem (31.1%). The LAM strain was the most likely to form clusters, and Haarlem was associated with anti-TB drug resistance. This was translational research, and the results can collaborate with the TB control programs, leading to improved strategies that allow the reduction of the TB burden in prisons.
Collapse
Affiliation(s)
- Caroline Busatto
- Núcleo de Pesquisa Em Microbiologia Medica, Faculdade de Medicina, Universidade Federal Do Rio Grande, Rio Grande, Rio Grande Do Sul, Brazil
| | - Lia Gonçalves Possuelo
- Programa de Pós-Graduação Em Promoção da Saúde, Universidade de Santa Cruz Do Sul, Santa Cruz Do Sul, Rio Grande Do Sul, Brazil
| | - Dienefer Bierhals
- Núcleo de Pesquisa Em Microbiologia Medica, Faculdade de Medicina, Universidade Federal Do Rio Grande, Rio Grande, Rio Grande Do Sul, Brazil
| | - Carolina Larrosa de Oliveira
- Núcleo de Pesquisa Em Microbiologia Medica, Faculdade de Medicina, Universidade Federal Do Rio Grande, Rio Grande, Rio Grande Do Sul, Brazil
| | - Mariana Quaresma de Souza
- Núcleo de Pesquisa Em Microbiologia Medica, Faculdade de Medicina, Universidade Federal Do Rio Grande, Rio Grande, Rio Grande Do Sul, Brazil
| | - Dandara Fanfa
- Programa de Pós-Graduação Em Promoção da Saúde, Universidade de Santa Cruz Do Sul, Santa Cruz Do Sul, Rio Grande Do Sul, Brazil
| | - Érika Barreto
- Programa de Pós-Graduação Em Promoção da Saúde, Universidade de Santa Cruz Do Sul, Santa Cruz Do Sul, Rio Grande Do Sul, Brazil
| | - Pauline Schwarzbold
- 8ª Delegacia Penitenciária Regional, Superintendência Dos Serviços Penitenciários, Santa Cruz Do Sul, RS, Brazil
| | - Andrea Von Groll
- Núcleo de Pesquisa Em Microbiologia Medica, Faculdade de Medicina, Universidade Federal Do Rio Grande, Rio Grande, Rio Grande Do Sul, Brazil
| | - Isabel Portugal
- Research Institute for Medicines - iMed.ULisboa, Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal
| | - João Perdigão
- Research Institute for Medicines - iMed.ULisboa, Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal
| | - Julio Croda
- Faculdade de Medicina, Universidade Federal Do Mato Grosso Do Sul, Campo Grande, Mato Grosso Do Sul, Brazil
| | - Jason R Andrews
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, Palo Alto, CA, US
| | - Pedro Almeida da Silva
- Núcleo de Pesquisa Em Microbiologia Medica, Faculdade de Medicina, Universidade Federal Do Rio Grande, Rio Grande, Rio Grande Do Sul, Brazil.
- Rua General Osório S/N, Centro, Rio Grande Do Sul, Rio Grande, 96200190, Brazil.
| | - Ivy Bastos Ramis
- Núcleo de Pesquisa Em Microbiologia Medica, Faculdade de Medicina, Universidade Federal Do Rio Grande, Rio Grande, Rio Grande Do Sul, Brazil
| |
Collapse
|
157
|
Etienne-Grimaldi MC, Pallet N, Boige V, Ciccolini J, Chouchana L, Barin-Le Guellec C, Zaanan A, Narjoz C, Taieb J, Thomas F, Loriot MA. Current diagnostic and clinical issues of screening for dihydropyrimidine dehydrogenase deficiency. Eur J Cancer 2023; 181:3-17. [PMID: 36621118 DOI: 10.1016/j.ejca.2022.11.028] [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: 06/13/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/13/2022]
Abstract
Fluoropyrimidine drugs (FP) are the backbone of many chemotherapy protocols for treating solid tumours. The rate-limiting step of fluoropyrimidine catabolism is dihydropyrimidine dehydrogenase (DPD), and deficiency in DPD activity can result in severe and even fatal toxicity. In this review, we survey the evidence-based pharmacogenetics and therapeutic recommendations regarding DPYD (the gene encoding DPD) genotyping and DPD phenotyping to prevent toxicity and optimize dosing adaptation before FP administration. The French experience of mandatory DPD-deficiency screening prior to initiating FP is discussed.
Collapse
Affiliation(s)
| | - Nicolas Pallet
- Department of Clinical Chemistry, Hôpital Européen Georges Pompidou, Assistance Publique-Hôpitaux de Paris, Paris, France; Université de Paris, INSERM UMRS1138, Centre de Recherche des Cordeliers, F-75006 Paris, France
| | - Valérie Boige
- Université de Paris, INSERM UMRS1138, Centre de Recherche des Cordeliers, F-75006 Paris, France; Department of Cancer Medicine, Institut Gustave Roussy, Villejuif, France
| | - Joseph Ciccolini
- SMARTc, CRCM INSERM U1068, Université Aix-Marseille, Marseille, France; Laboratory of Pharmacokinetics and Toxicology, Hôpital Universitaire La Timone, F-13385 Marseille, France; COMPO, CRCM INSERM U1068-Inria, Université Aix-Marseille, Marseille, France
| | - Laurent Chouchana
- Regional Center of Pharmacovigilance, Department of Pharmacology, Hôpital Cochin, Assistance Publique-Hopitaux de Paris, Université de Paris, Paris, France; French Pharmacovigilance Network, France
| | - Chantal Barin-Le Guellec
- Laboratory of Biochemistry and Molecular Biology, Centre Hospitalo-uinversitaire de Tours, Tours, France; INSERM U1248, IPPRITT, University of Limoges, Limoges, France
| | - Aziz Zaanan
- Department of Gastroenterology and Digestive Oncology, Hôpital Européen Georges Pompidou, Paris University; Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Céline Narjoz
- Department of Clinical Chemistry, Hôpital Européen Georges Pompidou, Assistance Publique-Hôpitaux de Paris, Paris, France; Université de Paris, INSERM UMRS1138, Centre de Recherche des Cordeliers, F-75006 Paris, France
| | - Julien Taieb
- SIRIC CARPEM, Université de Paris; Fédération Francophone de Cancérologie Digestive (FFCD), Assistance Publique-Hôpitaux de Paris, Department of Gastroenterology and Digestive Oncology, Hôpital Européen Georges Pompidou, Paris, France
| | - Fabienne Thomas
- Laboratory of Pharmacology, Institut Claudius Regaud, IUCT-Oncopole and CRCT, INSERM UMR1037, Université Paul Sabatier, Toulouse, France
| | - Marie-Anne Loriot
- Department of Clinical Chemistry, Hôpital Européen Georges Pompidou, Assistance Publique-Hôpitaux de Paris, Paris, France; Université de Paris, INSERM UMRS1138, Centre de Recherche des Cordeliers, F-75006 Paris, France.
| | | |
Collapse
|
158
|
Kong N, Shu S, Zhang C, Li C, Luo Y, Fang S, Bi S. Intergenic region polymorphism analysis: a novel genotyping method for Klebsiella pneumoniae. J Appl Microbiol 2023; 134:7044773. [PMID: 36801995 DOI: 10.1093/jambio/lxad030] [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: 12/21/2022] [Revised: 02/07/2023] [Accepted: 02/16/2023] [Indexed: 02/19/2023]
Abstract
AIMS The ability to distinguish between Klebsiella pneumoniae strains is critical for outbreak investigations. A new typing method, intergenic region polymorphism analysis (IRPA), was developed, validated, and the discriminatory power was determined by comparison with multiple-locus variable-number tandem repeat analysis (MLVA) in this study. METHODS AND RESULTS This method is based on the idea that every IRPA locus (polymorphic fragment of intergenic regions present in one strain but not in other strains or different fragment sizes in other strains) could divide strains into different genotypes. A 9-loci IRPA scheme was designed to type 64 K. pneumoniae isolates. Five IRPA loci were identified that conferred the same level of discrimination as the 9-loci initially examined. Among these K. pneumoniae isolates, 7.81% (5/64), 6.25% (4/64), 4.96% (3/64), 9.38% (6/64), and 1.56% (1/64) were capsular serotypes K1, K2, K5, K20, and K54, respectively. The discriminatory power of the IRPA method was better than that of MLVA expressed in Simpson's index of diversity (SI) at 0.997 and 0.988, respectively. The congruent analysis of the IRPA method and MLVA showed moderate congruence between the two methods (AR = 0.378). The AW indicated that if IRPA data are availabl, one can accurately predict the MLVA cluster. CONCLUSION The IRPA method was found to have higher discriminatory power than MLVA and allowed for simpler band profile interpretation. The IRPA method is a rapid, simple, and high-resolution technique for molecular typing of K. pneumoniae.
Collapse
Affiliation(s)
- Nianqing Kong
- College of Food Science, Guangdong Pharmaceutical University, Zhongshan, Guangdong Province 528458, China.,College of Public Health, Guangdong Pharmaceutical University, Guangzhou, Guangdong Province 510220, China
| | - Shenghuang Shu
- College of Food Science, Guangdong Pharmaceutical University, Zhongshan, Guangdong Province 528458, China
| | - Cangyun Zhang
- College of Food Science, Guangdong Pharmaceutical University, Zhongshan, Guangdong Province 528458, China
| | - Chuyi Li
- College of Food Science, Guangdong Pharmaceutical University, Zhongshan, Guangdong Province 528458, China
| | - Yongwen Luo
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, Guangdong Province 510642, China
| | - Shuying Fang
- College of Food Science, Guangdong Pharmaceutical University, Zhongshan, Guangdong Province 528458, China
| | - Shuilian Bi
- College of Food Science, Guangdong Pharmaceutical University, Zhongshan, Guangdong Province 528458, China
| |
Collapse
|
159
|
Hanafusa T, Arikawa K, Tanimoto Y. Prevalence of sapovirus and astrovirus in pediatric infectious gastroenteritis surveillance in Kobe City, Japan, during 2016-2019. Jpn J Infect Dis 2023. [PMID: 36858597 DOI: 10.7883/yoken.jjid.2023.037] [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] [Indexed: 03/03/2023]
Abstract
Sapovirus (SaV) and astrovirus (AstV) are important viral agents causing acute gastroenteritis. In this study, to determine the percentage of SaV and AstV as causative viruses of infectious gastroenteritis, we examined 53 samples of unknown cause from pediatric clinics in Kobe, Japan, where sentinel surveillance for infectious gastroenteritis was conducted from 2016 to 2019. SaV and AstV were screened for their presence by real-time PCR. Positive samples were genotyped by sequencing and genetic analysis of the partial regions of capsid and RdRp. Ninteen SaV and 3 AstV were detected, and the detection rate per unknown case and total case were follows; SaV: 35.8%, 11.0%, AstV: 5.7%, 1.7%. The most frequently detected genotype of SaV was GI.1, followed by GII.3. AstV genotypes were MAstV1.1 and MAstV1.4. This study indicates that SaV and AstV are important causative viruses of pediatric infectious gastroenteritis.
Collapse
Affiliation(s)
- Takeshi Hanafusa
- Department of Infectious Diseases, Kobe Institute of Health, Japan
| | - Kentaro Arikawa
- Department of Infectious Diseases, Kobe Institute of Health, Japan
| | | |
Collapse
|
160
|
Solnæs JV, Njor SH, Tranberg M. Does full HPV genotyping perform similarly well in clinician-collected cervical samples and self-collected vaginal samples when using the CLART HPV4S assay? BMC Womens Health 2023; 23:78. [PMID: 36823528 PMCID: PMC9948442 DOI: 10.1186/s12905-023-02215-4] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 02/07/2023] [Indexed: 02/25/2023] Open
Abstract
BACKGROUND Studies comparing self-collected vaginal samples with clinician-collected cervical samples with respect to high-risk human papillomavirus (HPV) detection and genotype agreement based on clinically validated full HPV genotype assays (e.g. the CLART HPV4S) are limited. This study compared the two types of samples using the CLART assay with respect to HPV detection and genotype agreement in a referral population. METHODS A total of 212 women aged 30-59 years and diagnosed with atypical squamous cells of undetermined significance (ASC-US) within the Danish cervical cancer screening programme had a cervical sample taken at their general practitioner. Afterwards, the women took a vaginal sample with the Evalyn Brush device at home. The paired samples were HPV-tested with the full genotyping CLART HPV4S assay. Histological results, i.e. cervical intraepithelial neoplasia of grade 2 or worse (CIN2+) were available for 14 women with HPV-positive clinician-collected samples. RESULTS The study found the same HPV prevalence in self-collected vaginal samples compared to clinician-collected cervical samples (19.3%, 95% CI 14.3-25.3% vs 18.4%, 95% CI 13.4-24.3%). The CLART HPV4S assay detected approximately the same number of CIN2+ cases in the self-collected vaginal samples compared to the clinician-collected cervical samples (13 vs 11 cases). Exactly the same genotypes were detected in 75% (21/28) of the HPV-positive paired samples, while at least one identical genotype was found in the remaining 25% (7/28) of the paired samples. CONCLUSIONS The CLART HPV4S assay performed similarly well in self-collected vaginal samples as in clinician-collected cervical samples with respect to both HPV detection and genotype agreement when using the Evalyn Brush and the CLART HPV4S assay in a referral population. Although further evaluation is needed, the findings suggest that full HPV genotyping based on the CLART assay can be useful when establishing HPV genotype-specific referral strategies for women tested HPV-positive by self-sampling.
Collapse
Affiliation(s)
- Jannie Villekjær Solnæs
- grid.7048.b0000 0001 1956 2722Faculty of Health, Aarhus University, Vennelyst Boulevard 4, 8000 Aarhus C, Denmark ,grid.415677.60000 0004 0646 8878University Research Clinic for Cancer Screening, Department of Public Health Programmes, Randers Regional Hospital, Skovlyvej 15, 8930 Randers NØ, Denmark
| | - Sisse Helle Njor
- grid.415677.60000 0004 0646 8878University Research Clinic for Cancer Screening, Department of Public Health Programmes, Randers Regional Hospital, Skovlyvej 15, 8930 Randers NØ, Denmark ,grid.7048.b0000 0001 1956 2722Department of Clinical Medicine, Aarhus University, Incuba Skejby, Building 2, Palle Juul-Jensens Boulevard 82, 8200 Aarhus N, Denmark
| | - Mette Tranberg
- University Research Clinic for Cancer Screening, Department of Public Health Programmes, Randers Regional Hospital, Skovlyvej 15, 8930, Randers NØ, Denmark.
| |
Collapse
|
161
|
El-Ghamrawy M, El-Gharbawi N, Shahin G, Abdelhady A, Sayed R, Diaa N, Bishai I. Combined tumor necrosis factor-α (-308 G/A) and tumor necrosis factor-β (+ 252 A/G) nucleotide polymorphisms and chronicity in Egyptian children with immune thrombocytopenia. Int J Hematol 2023; 117:856-862. [PMID: 36802017 DOI: 10.1007/s12185-023-03551-9] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/25/2023] [Accepted: 01/25/2023] [Indexed: 02/21/2023]
Abstract
BACKGROUND Primary immune thrombocytopenia (ITP) is a common autoimmune disorder. Secretion of TNF-α, TNF-β and IFN-γ plays a major role in the pathogenesis of ITP. OBJECTIVE This cross-sectional study aimed to detect TNF-α (-308 G/A) and TNF-β (+ 252 A/G) gene polymorphism in a cohort of Egyptian children with chronic ITP (cITP) to clarify their possible association with progression to chronic disease. METHODS The study included 80 Egyptian cITP patients and 100 unrelated age- and sex-matched controls. Genotyping was performed using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). RESULTS Patients with TNF-α homozygous (A/A) genotype had significantly higher mean age, longer disease duration and lower platelet counts (p values 0.005, 0.024 and 0.008, respectively). TNF-α wild (G/G) genotype was significantly more frequent among responders (p = 0.049). Complete response was more frequent among wild (A/A) TNF-β genotype patients (p = 0.011), and platelet count was significantly lower among homozygous (G/G) genotype (p = 0.018) patients. Combined polymorphisms were strongly associated with susceptibility to chronic ITP. CONCLUSION Homozygosity in either gene might contribute to a worse course of disease, increased severity and poor response to therapy. Patients expressing combined polymorphisms are more prone to progression to chronic disease, severe thrombocytopenia and longer disease duration.
Collapse
Affiliation(s)
- Mona El-Ghamrawy
- Pediatric Hematology & BMT Unit, Pediatrics Department, Faculty of Medicine, Cairo University, Cairo, Egypt.
| | - Nesrine El-Gharbawi
- Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Gehan Shahin
- Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Alaa Abdelhady
- Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Rasha Sayed
- Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Nehal Diaa
- Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Irene Bishai
- Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, Cairo, Egypt
| |
Collapse
|
162
|
Richins T, Sapp SG, Ketzis JK, Willingham AL, Mukaratirwa S, Qvarnstrom Y, Barratt JL. Genetic characterization of Strongyloides fuelleborni infecting free-roaming African vervets ( Chlorocebus aethiops sabaeus) on the Caribbean island of St. Kitts. Int J Parasitol Parasites Wildl 2023; 20:153-161. [PMID: 36860205 PMCID: PMC9969202 DOI: 10.1016/j.ijppaw.2023.02.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 01/24/2023] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 02/17/2023]
Abstract
Human strongyloidiasis is an important neglected tropical disease primarily caused by the nematode Strongyloides stercoralis, and to a lesser extent Strongyloides fuelleborni which mainly infects non-human primates. Zoonotic sources of infection have important implications for control and prevention of morbidity and mortality caused by strongyloidiasis. Recent molecular evidence suggests that for S. fuelleborni, primate host specificity is variable among genotypes across the Old World, and consequently that these types likely vary in their capacity for human spillover infections. Populations of free-roaming vervet monkeys (Chlorocebus aethiops sabaeus), introduced to the Caribbean Island of Staint Kitts from Africa, live in close contact with humans, and concern has arisen regarding their potential to serve as reservoirs of zoonotic infections. In this study, we sought to determine the genotypes of S. fuelleborni infecting St. Kitts vervets to explore whether they are potential reservoirs for human-infecting S. fuelleborni types. Fecal specimens were collected from St. Kitts vervets and S. fuelleborni infections were confirmed microscopically and by PCR. Strongyloides fuelleborni genotypes were determined from positive fecal specimens using an Illumina amplicon sequencing-based genotyping approach targeting the mitochondrial cox1 locus and 18S rDNA hypervariable regions I and IV of Strongyloides species. Phylogenetic analysis of resultant genotypes supported that S. fuelleborni from St. Kitts vervets is of an exclusively African variety, falling within the same monophyletic group as an isolate which has been detected previously in a naturally infected human from Guinea-Bissau. This observation highlights that St. Kitts vervets may serve as potential reservoirs for zoonotic S. fuelleborni infection, which warrants further exploration.
Collapse
Affiliation(s)
- Travis Richins
- Centers for Disease Control and Prevention, Division of Parasitic Diseases and Malaria, Parasitic Diseases Branch, USA,Oak Ridge Associated Universities, Oak Ridge, TN, USA
| | | | - Jennifer K. Ketzis
- Biomedical Sciences, One Health Center for Zoonoses & Tropical Veterinary Medicine, Ross University School of Veterinary Medicine, Saint Kitts and Nevis
| | - Arve Lee Willingham
- Department of Veterinary Medicine, College of Agriculture & Veterinary Medicine, United Arab Emirates
| | - Samson Mukaratirwa
- Biomedical Sciences, One Health Center for Zoonoses & Tropical Veterinary Medicine, Ross University School of Veterinary Medicine, Saint Kitts and Nevis
| | - Yvonne Qvarnstrom
- Centers for Disease Control and Prevention, Division of Parasitic Diseases and Malaria, Parasitic Diseases Branch, USA
| | - Joel L.N. Barratt
- Centers for Disease Control and Prevention, Division of Parasitic Diseases and Malaria, Parasitic Diseases Branch, USA,Corresponding author.
| |
Collapse
|
163
|
Jiang L, Du Y, Hao K, Mei M, Li Y, Chen B, Xie Y. Transfusion support for a patient with alloanti-D and the RHD*DV.1 allele. Clin Chim Acta 2023; 541:117268. [PMID: 36841426 DOI: 10.1016/j.cca.2023.117268] [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: 11/18/2022] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 02/27/2023]
Abstract
BACKGROUND Safe blood transfusion is significantly affected by the complex antigen polymorphism and a high proportion of autoantibodies of the Rh blood group system. THE PATIENT AND METHODS A male Chinese patient with primary biliary cirrhosis, esophageal and gastric rupture, and bleeding was admitted to our hospital. Blood typing identified that he had serological O and D+ blood groups. Because autoantibody was not detected using routine immediate spin (IS) and indirect antiglobulin test (IAT), he was treated by transfusing D+ red blood cells (RBCs). However, this treatment was ineffective. Thus, manual polybrene test (MPT) and low ionic salt solution indirect antiglobulin test (LISS-IAT) were performed, followed by exon sequencing of the RHD gene. RESULTS The patient was confirmed as a DV Type 1 individual by gene sequencing, and had 4+ RhD antigen agglutination. The anti-D in serum and elution could only be detected by MPT (2+ agglutination) and LISS-IAT methods (1+/3+ agglutination). It was presumed that attenuated alloantibody contributed to ineffective RBC transfusion, causing a transient increase in hemoglobin (HGB) before falling back to 50 g/L or even lower within four days. CONCLUSION Genotyping helps to support the specificity of detecting autoantibodies and alloantibodies. Combining more serological methods with molecular technology in blood typing is beneficial to improve the safety and effectiveness of blood transfusion.
Collapse
Affiliation(s)
- Luxi Jiang
- Laboratory Medicine Center, Department of Transfusion Medicine, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Yaoqiang Du
- Laboratory Medicine Center, Department of Transfusion Medicine, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Ke Hao
- Laboratory Medicine Center, Department of Transfusion Medicine, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Menghan Mei
- Laboratory Medicine Center, Department of Transfusion Medicine, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Yu Li
- Laboratory Medicine Center, Department of Transfusion Medicine, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Bingyu Chen
- Laboratory Medicine Center, Department of Transfusion Medicine, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China.
| | - Yiwei Xie
- Laboratory Medicine Center, Department of Transfusion Medicine, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China.
| |
Collapse
|
164
|
Alvarado-Sizzo H, Alcántara-Ayala O, Espinosa D, Rivas G, Oyama K, Luna-Vega I. Genomic-based microsatellite development for Ternstroemia (Pentaphylacaceae) and transferability to other Ericales. Mol Biol Rep 2023. [PMID: 36787057 DOI: 10.1007/s11033-023-08258-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 01/06/2023] [Indexed: 02/15/2023]
Abstract
BACKGROUND The genus Ternstroemia is associated with the vulnerable tropical montane cloud forest in Mexico and with other relevant vegetation types worldwide. It contains threatened and pharmacologically important species and has taxonomic issues regarding its species limits. This study describes 38 microsatellite markers generated using a genomic-based approach. METHODS AND RESULTS We tested 23 of these markers in a natural population of Ternstroemia lineata. These markers are highly polymorphic (all loci polymorphic with 3-14 alleles per locus and expected heterozygosity between 0.202 and 0.908), most of them (19 out of 23) are in Hardy-Weinberg Equilibrium and free of null alleles (18 out of 23). Also we found no evidence of linkage among them. Finally, we tested the transferability to six other American species of Ternstroemia, two other Pentaphylacaceae species, and four species from different families within the order Ericales. CONCLUSIONS These molecular resources are promising tools to investigate genetic diversity loss and as barcodes for ethnopharmacological applications and species delimitation in the family Pentaphylacaceae and some Ericales, among other applications.
Collapse
|
165
|
Mukherjee A, Chattopadhyay T. Tetra-Primer Amplification Refractory Mutation System (T-ARMS). Methods Mol Biol 2023; 2638:315-325. [PMID: 36781652 DOI: 10.1007/978-1-0716-3024-2_22] [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] [Indexed: 02/15/2023]
Abstract
Single-nucleotide polymorphisms (SNPs), the most abundant genetic variation in the population, have become the molecular marker of choice. Generally, the efficient detection of SNPs requires specialized costly equipment. Although there are a few strategies for detecting SNPs through polymerase chain reaction, followed by restriction enzyme digestion and agarose gel electrophoresis, these methods are time-consuming and might be less diagnostic. Interestingly, the tetra primer amplification refractory mutation system (T-ARMS) strategy utilizes a pair of allele-specific primers in a single PCR for the diagnostic detection of SNPs in a codominant manner through standard agarose gel electrophoresis. The simplicity and robustness of the strategy have inspired the researchers to adopt this low-cost method of SNP detection in different crop plants. Here, we have described the principle, methods, and conditions for the T-ARMS strategy. The described methodology starts from the isolation of genomic DNA and ends with the post-PCR analysis of refractory amplicons in standard agarose gel electrophoresis. The limitations and future perspectives are also discussed. Taken together, T-ARMS evolves as a method of choice for low-cost SNP detection in plants.
Collapse
Affiliation(s)
- Arnab Mukherjee
- Department of Plant Breeding and Genetics, Bihar Agricultural College, Bihar Agricultural University, Sabour, Bhagalpur, Bihar, India
| | - Tirthartha Chattopadhyay
- Department of Plant Breeding and Genetics, Bihar Agricultural College, Bihar Agricultural University, Sabour, Bhagalpur, Bihar, India
| |
Collapse
|
166
|
da Costa Lima Moraes A, Sforça DA, Mancini MC, Vigna BBZ, de Souza AP. Polyploid SNP Genotyping Using the MassARRAY System. Methods Mol Biol 2023; 2638:93-113. [PMID: 36781637 DOI: 10.1007/978-1-0716-3024-2_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Molecular marker discovery and genotyping are major challenges in polyploid breeding programs incorporating molecular biology tools. In this context, this work describes a method for single nucleotide polymorphism (SNP) genotyping in polyploid crops using matrix-assisted laser desorption ionization (MALDI) time-of-flight (TOF) mass spectrometry, the MassARRAY System.
Collapse
|
167
|
Khassanova G, Khalbayeva S, Serikbay D, Mazkirat S, Bulatova K, Utebayev M, Shavrukov Y. SNP Genotyping with Amplifluor-Like Method. Methods Mol Biol 2023; 2638:201-219. [PMID: 36781644 DOI: 10.1007/978-1-0716-3024-2_14] [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] [Indexed: 02/15/2023]
Abstract
For SNP genotyping, amplification of fluorescence (Amplifluor) is a popular and actively developing method in the plant sciences. The "Amplifluor-like" is a "home-made" modification of the original commercial Amplifluor method. Amplifluor-like genotyping requires two essential components: (1) two allele-specific forward primers targeting the SNP site with one common reverse primer; and (2) a universal part with two non-allele-specific molecular probes containing one of the two used fluorophores and a quencher. Allele discrimination is based on the fluorescence score, where the dominance of one dye over the other confirms the presence of each specific SNP allele. The Amplifluor-like method is similar to commercial KASP and original Amplifluor methods but is much cheaper because all components can be ordered as regular and modified oligos. The easily adaptable Amplifluor-like method can be modified by any researcher to make it suitable for available instruments, reagents and conditions in low-budget laboratories for SNP genotyping of any plant species with identified genetic polymorphism.
Collapse
Affiliation(s)
- Gulmira Khassanova
- A.I. Barayev Research and Production Centre of Grain Farming, Shortandy, Kazakhstan
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Astana, Kazakhstan
| | - Sholpan Khalbayeva
- Kazakh Research Institute of Agriculture and Plant Production, Almalybak, Almaty, Kazakhstan
| | - Dauren Serikbay
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi, China
| | - Shynar Mazkirat
- Kazakh Research Institute of Agriculture and Plant Production, Almalybak, Almaty, Kazakhstan
| | - Kulpash Bulatova
- Kazakh Research Institute of Agriculture and Plant Production, Almalybak, Almaty, Kazakhstan
| | - Maral Utebayev
- A.I. Barayev Research and Production Centre of Grain Farming, Shortandy, Kazakhstan
| | - Yuri Shavrukov
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA, Australia.
| |
Collapse
|
168
|
Ruff TM, Marlowe K, Hooker MA, Liu Y, See DR. Genotyping by Multiplexed Sequencing (GMS) Using SNP Markers. Methods Mol Biol 2023; 2638:9-21. [PMID: 36781632 DOI: 10.1007/978-1-0716-3024-2_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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
SNP-based genotyping has become the most effective approach to generate target-specific data for use in genetic studies. In this chapter, we will describe a high-throughput genotyping method that multiplexes hundreds to thousands of SNP markers in a two-step PCR protocol that can be customized to fit the specific needs of a study.
Collapse
Affiliation(s)
- Travis M Ruff
- USDA-ARS Wheat Health, Genetics and Quality Research Unit, Pullman, WA, USA
| | - Karol Marlowe
- USDA-ARS Wheat Health, Genetics and Quality Research Unit, Pullman, WA, USA
| | - Marcus A Hooker
- Department of Plant Pathology, Washington State University, Pullman, WA, USA
| | - Yan Liu
- Department of Plant Pathology, Washington State University, Pullman, WA, USA
| | - Deven R See
- USDA-ARS Wheat Health, Genetics and Quality Research Unit, Pullman, WA, USA. .,Department of Plant Pathology, Washington State University, Pullman, WA, USA.
| |
Collapse
|
169
|
Saito Y, Tada F, Takashina T, Ikegami H. Allele-Specific Mutation Genotyping with Mismatches in Primer Design. Methods Mol Biol 2023; 2638:249-262. [PMID: 36781647 DOI: 10.1007/978-1-0716-3024-2_17] [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] [Indexed: 02/15/2023]
Abstract
Genotyping technologies for single nucleotide polymorphisms (SNPs) and other mutation types have evolved to become essential tools in various fields. Although high-throughput genotyping technologies occupy a key position in handling large amounts of SNP data, simple, low-cost, and conventional genotyping technologies remain in demand. Allele-specific (AS) polymerase chain reaction (PCR) and its related improved methods can effectively identify target SNPs and allele types using AS primers that introduce instability through mismatched bases at and around the SNP site. In this chapter, we present what is known from the literature on primer design with mismatches for AS-PCR and describe three cases of mutation detection (SNPs and insertions/deletions) associated with functional genes of crop species, which could be useful to guide future AS-PCR experiments.
Collapse
Affiliation(s)
- Yutaro Saito
- Yamagata Integrated Agricultural Research Center, Horticultural Research Institute, Yamagata, Japan
| | - Fumito Tada
- Yamagata Integrated Agricultural Research Center, Horticultural Research Institute, Yamagata, Japan
| | - Tadashi Takashina
- Yamagata Integrated Agricultural Research Center, Horticultural Research Institute, Yamagata, Japan
| | - Hidetoshi Ikegami
- Fukuoka Agriculture and Forestry Research Center, Buzen Branch, Yukuhashi, Japan.
| |
Collapse
|
170
|
Kaundun SS, Hutchings SJ, Downes J, Baker K. Derived Polymorphic Amplified Cleaved Sequence (dPACS) Assay. Methods Mol Biol 2023; 2638:373-85. [PMID: 36781657 DOI: 10.1007/978-1-0716-3024-2_27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
The derived polymorphic amplified cleaved sequence (dPACS) assay is a simple polymerase chain reaction/restriction fragment length polymorphism (PCR-RFLP)-based procedure for detecting known single-nucleotide polymorphisms (SNPs) and deletion-insertion polymorphisms (DIPs). It is relatively straightforward to carry out using basic and commonly available molecular biology kits. The method differs from other PCR-RFLP assays in that it employs 35-55 bp primer pairs that encompass the entire targeted DNA region except for a few diagnostic nucleotides being examined. In so doing, it allows for the introduction of nucleotide mismatches in one or both primers for differentiating wild from mutant sequences following polymerase chain reaction, restriction digestion and MetaPhor gel electrophoresis. Primer design and the selection of discriminating enzymes are achieved with the help of the dPACS 1.0 program. The method is exemplified here with the positive detection of serine 264-psbA, a key determinant for the effective binding of some photosystem II inhibitors to their target. A serine-to-glycine mutation at codon 264 of psbA causes resistance to serine-binding photosystem II herbicides in several grasses and broad-leaf weeds, including Amaranthus retroflexus, which is employed in this study.
Collapse
|
171
|
Zhou Y, Pan H. Specific-Locus Amplified Fragment Sequencing (SLAF-Seq). Methods Mol Biol 2023; 2638:165-171. [PMID: 36781641 DOI: 10.1007/978-1-0716-3024-2_11] [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] [Indexed: 02/15/2023]
Abstract
Specific length amplified fragment sequencing (SLAF-seq) technology is a simplified genome sequencing technology based on next-generation sequencing. SLAF-seq technology has several distinguishing characteristics: 1. Deep sequencing to ensure accuracy of genotyping; 2. Effectively reduce sequencing costs; 3. Pre-designed simplified representation scheme to optimize marker efficiency; 4. Doubled barcode system for large populations. The advantages and technical process of SLAF-seq are described briefly with summarized results for the application of SLAF-seq in development of molecular markers, construction of high-density genetic map and gene mapping in ornamental plants. Finally, the difficulties and prospects of this method are discussed in application.
Collapse
Affiliation(s)
- Yang Zhou
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, College of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Huitang Pan
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, College of Landscape Architecture, Beijing Forestry University, Beijing, China.
| |
Collapse
|
172
|
Hardinge P. Molecular Beacons - Loop-Mediated Amplification (MB-LAMP). Methods Mol Biol 2023; 2638:289-299. [PMID: 36781650 DOI: 10.1007/978-1-0716-3024-2_20] [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] [Indexed: 02/15/2023]
Abstract
High specificity has been demonstrated in polymerase chain reaction (PCR) with the use of molecular beacons (MBs) to detect amplified sequences containing mutations or single-nucleotide polymorphisms (SNPs). MBs have been adapted for use with the isothermal nucleic acid amplification technology loop-mediated amplification (LAMP) by targeting single-stranded loop sequences under optimized conditions to enable applications such as plant genotyping. LAMP has several benefits over PCR, such as rapid amplification, single-temperature reaction conditions enabling low-cost equipment, and robustness to certain PCR inhibitors. However, and despite the increased number of primers required, the specificity of LAMP is limited, and false positive results can be problematic. In this chapter, design considerations for molecular beacons in LAMP assays are described, as well as a method for MB-LAMP amplification and detection, with an example of gene sequences in genetically modified (GM) maize samples.
Collapse
|
173
|
Adonina I. Fluorescence In Situ Hybridization (FISH) for the Genotyping of Triticeae Tribe Species and Hybrids. Methods Mol Biol 2023; 2638:437-49. [PMID: 36781661 DOI: 10.1007/978-1-0716-3024-2_31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
This chapter is dedicated to using fluorescence in situ hybridization (FISH) for the genotyping of Triticeae tribe species and hybrids. The basic method of FISH on metaphase chromosomes is presented with a discussion on its modifications, and deoxyribonucleic acid (DNA) probes that can be useful for genotyping are proposed.
Collapse
|
174
|
Amangeldiyeva A, Baidyussen A, Kuzbakova M, Yerzhebayeva R, Jatayev S, Shavrukov Y. Modified Allele-Specific qPCR (ASQ) Genotyping. Methods Mol Biol 2023; 2638:231-47. [PMID: 36781646 DOI: 10.1007/978-1-0716-3024-2_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
The allele-specific qPCR (ASQ) method for SNP (single nucleotide polymorphism) detection is based on the FRET (fluorescence resonance energy transfer) system, a system using position-dependent fluorescent dyes and quenches. The modified ASQ method requires two separate components: (1) the allele-specific part, two AS primers targeting the SNP with identity in the penultimate positions at the 3'-end and specific tags in the 5'-end, and (2) the universal part, two universal probes (UPs) with corresponding tags and different fluorescent dyes in the 5'-end and a single common universal probe with a quencher in the 3'-ends (Uni-Q), complementary to all UP tags. There are two major variations of the ASQ method, with either short 4-bp tags (variant A) or longer 6-bp tags (variant B), both of which have been successfully used for SNP genotyping in plants. The modified ASQ method is much cheaper compared to other similar FRET-based methods because the most expensive parts, the universal probes, have a short and linear structure, where fluorophores and quenchers are located in the ends but not incorporated inside of the sequences.
Collapse
|
175
|
Wang H, Dang J, Guo Q, Liang G. qPCR Genotyping of Polyploid Species. Methods Mol Biol 2023; 2638:115-122. [PMID: 36781638 DOI: 10.1007/978-1-0716-3024-2_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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
A simple and cost-effective method for genotyping polyploid plants using quantitative PCR (qPCR) is described in this chapter. There is no additional operation, only simultaneous amplification of alleles and reference sequences with constant copy number in the genome. The qPCR genotyping can detect the genotypes of important traits in polyploid plants without whole genome sequencing data.
Collapse
Affiliation(s)
- Haiyan Wang
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, China
| | - Jiangbo Dang
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, China
| | - Qigao Guo
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, China
| | - Guolu Liang
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Beibei, Chongqing, China.
| |
Collapse
|
176
|
Kobayashi R, Horii T, Hatada I. Efficient Detection of Flox Mice Using In Vitro Cre Recombination. Methods Mol Biol 2023; 2637:149-159. [PMID: 36773145 DOI: 10.1007/978-1-0716-3016-7_12] [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] [Indexed: 02/12/2023]
Abstract
Advances in CRISPR/Cas9 genome editing technologies have allowed for the rapid generation of Cre-loxP conditional knockout mice. However, current strategies for genotyping flox mice, typically based on Sanger sequencing following cloning of target sequences from dozens of pups, are time-consuming. Here, we describe a rapid screening method for flox mice, using in vitro Cre recombination that can be performed using simple enzymatic reactions and enables detection of functional flox mouse within 1 day. In addition, we introduce an efficient strategy for subsequent sequence analysis by cloning of floxed regions using the In-Fusion system. Our genotyping pipeline reduces laborious tasks and thus contributes to the rapid selection of accurately edited flox mice.
Collapse
Affiliation(s)
- Ryosuke Kobayashi
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Gunma, Japan
| | - Takuro Horii
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Gunma, Japan
| | - Izuho Hatada
- Laboratory of Genome Science, Biosignal Genome Resource Center, Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Gunma, Japan.
| |
Collapse
|
177
|
Franzo G, Segalés J. Porcine circovirus 3 (PCV-3) variability: Is it in the virus or in the classification criteria? Virol J 2023; 20:26. [PMID: 36759848 PMCID: PMC9909946 DOI: 10.1186/s12985-023-01984-6] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 02/05/2023] [Indexed: 02/11/2023] Open
Abstract
The continuous discovery of new viruses during the last decades has increased the need for new classification approaches and rules. Currently, the International Committee on Taxonomy of Viruses classifies viruses up to the species level. However, because of the higher variability of most of these infectious agents, a below-species categorization is often required for proper epidemiological investigations. Unfortunately, variable criteria are typically proposed by different research groups, leading to misleading and poorly reproducible results. This scenario occurred for the recently identified Porcine circovirus 3. Although genotype definition standards had been defined by a group of experts in the field, recent articles have been published introducing new genotypes, whose classification rules are not reported. We therefore would like to stress the usefulness of defining and maintaining a common language to allow proper results comparison among groups. We consider the consensus opinion of a heterogeneous expert team as the most valuable approach. Nevertheless, if other approaches are proposed, the disclosure of the criteria and the comparison with previous literature should be deemed mandatory to allow effective results reproducibility, interpretation and sharing.
Collapse
Affiliation(s)
- Giovanni Franzo
- Department of Animal Medicine, Production and Health (MAPS), Padua University, 35020, Legnaro, Italy.
| | - Joaquim Segalés
- Departament de Sanitat i Anatomia Animals, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain. .,Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193, Bellaterra, Spain. .,OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), 08193, Bellaterra, Spain.
| |
Collapse
|
178
|
Ali MI, Wahab WMAE, Hassan A, Ryan U, Xiao L, Arafa WM, Hamdy DA. Detection of unusual Cryptosporidium parvum subtype in patients with gastrointestinal cancer in Egypt. Parasitol Res 2023; 122:597-606. [PMID: 36539638 DOI: 10.1007/s00436-022-07761-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022]
Abstract
While the importance of cryptosporidiosis in immunocompromised persons is well known, the prevalence of Cryptosporidium spp. in cancer patients is not clear. The current study was designed to assess the occurrence and genetic characteristics of Cryptosporidium spp. in patients with gastrointestinal (GI) cancer in Egypt. Stool samples were collected from 100 patients with GI malignancies and 20 healthy individuals without any GI manifestations (control group). They were screened by microscopy and the immunochromatographic RIDA®QUICK Cryptosporidium kit. Subtyping of Cryptosporidium spp. was conducted by sequence analysis of the glycoprotein 60 (gp60) locus. Sociodemographic, environmental data and information on GI symptoms, cancer types, and clinical treatment were obtained via a questionnaire. By microscopy and RIDA®QUICK, only 7% (7/100) of GI cancer patients were positive for Cryptosporidium, compared with 40% (40/100) by gp60 nPCR. No positives were obtained from the control group. Male sex (P = 0.02) and younger age (P = 0.004) were major Cryptosporidium risk factors for infection. The occurrence of Cryptosporidium was also significantly more frequent (P = 0.003) in watery stool samples. Sequence analysis of the gp60 amplicons (~ 400 bp) identified a novel C. parvum subtype with nine TCA repeats and eleven ACATCA repeats. A formal subtype designation could not be made due to the short sequence length. More studies should be conducted to verify the common occurrence of this unusual C. parvum subtype and establish its genetic identity.
Collapse
|
179
|
Parida P, N S, E R S, Jagadesh A, Marate S, Govindakaranavar A. The emergence of human metapneumovirus G gene duplication in hospitalized patients with respiratory tract infection, India, 2016-2018. Mol Biol Rep 2023; 50:1109-1116. [PMID: 36399244 PMCID: PMC9889522 DOI: 10.1007/s11033-022-08092-8] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 11/04/2022] [Indexed: 11/19/2022]
Abstract
BACKGROUND Human metapneumovirus (HMPV) belongs to the family Pneumoviridae. It is one of the emerging respiratory viruses causing both upper and lower respiratory tract illnesses. HMPV has two genotypes: A and B. These genotypes are classified into lineage A1, A2, B1 and B2. Lineage-A2 is further classified as A2a, A2b and A2c. Similarly, B2 is classified as B2a and B2b. Studies have shown the circulation of A2b, B1 and B2 lineages in India. However, a limited amount of data is available on the current circulating genotypes of HMPV in India. METHODS Throat swab samples positive for HMPV by real-time RT- PCR, archived at Manipal Institute of Virology as a part of a hospital-based acute febrile illness surveillance study, was used from April 2016 to August 2018 by purposive sampling method. We performed the conventional reverse transcriptase-polymerase chain reaction for twenty samples targeting the G gene and then subjected them to sequencing. Phylogenetic analysis was done using MEGA X software by the Maximum Likelihood method. RESULTS All the twenty sequences belonged to the A2c subgroup. Phylogenetic analysis showed that strains from the study have genetic relation with circulating strains in Japan, China and Croatia. Seven out of the twenty sequences showed 180-nucleotide duplication and eleven sequences showed 111-nucleotide duplication. Two sequences did not show any duplications. CONCLUSION In the current study, we report that A2c is the sub-lineage in India from April 2016 to August 2018. This study is the first retrospective study reporting the circulation of the A2c sub-lineage among adults in India with 180- and 111-nucleotide duplications in the G gene of human metapneumovirus.
Collapse
Affiliation(s)
- Preetiparna Parida
- Manipal Institute of Virology (MIV), Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India
| | - Sudheesh N
- Manipal Institute of Virology (MIV), Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India.
| | - Sanjay E R
- Manipal Institute of Virology (MIV), Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India
| | - Anitha Jagadesh
- Manipal Institute of Virology (MIV), Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India
| | - Srilatha Marate
- Manipal Institute of Virology (MIV), Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India
| | - Arunkumar Govindakaranavar
- Manipal Institute of Virology (MIV), Manipal Academy of Higher Education (MAHE), Manipal, Karnataka, 576104, India.
- , 2-49, Vaikathu, Maratithota Road, MooduAthradi, Athradi PO, Udupi, Karnataka, 576107, India.
| |
Collapse
|
180
|
Prodromidou A, Dimitroulia E, Mavrogianni D, Kathopoulis N, Pappa KI, Loutradis D. The Effect of the Allelics of Ser680Asn Polymorphisms of Follicle-Stimulating Hormone Receptor Gene in IVF/ICSI Cycles: a Systematic Review and Meta-analysis. Reprod Sci 2023; 30:428-441. [PMID: 35680725 DOI: 10.1007/s43032-022-00996-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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 06/02/2022] [Indexed: 10/18/2022]
Abstract
A significant number of single-nucleotide polymorphisms (SNPs) of the follicle-stimulating hormone receptor (FSHr) can modify the response to exogenous FSH administration. A significant diversity in response to controlled ovarian stimulation (COS) in assisted reproductive technologies (ART) according to the type of allelic has been reported. We aimed to evaluate the relation between the Asn680Ser allelics and COS. A total of 4 electronic databases were searched for articles published up to August 2021. Prospective and retrospective comparative studies which reported outcomes after COS in patients who underwent genotyping for the detection of FSHr polymorphisms were considered eligible. A total of 11 studies including 4343 patients with Asn680Ser polymorphisms of the FSHr were included. Patients carrying the Asn/Asn allelic provide elevated E2 on the day of human chorionic gonadotropin (hCG) administration (1549 patients MD 262.39 pg/ml, p = 0.0007), but less transferrable embryos as compared with Ser/Ser genotype (283 patients MD - 0.11 embryos, p = 0.04). Ans/Ser versus Ser/Ser genotypes showed a higher E2 on the day of hCG administration (1799 patients, MD 207.86 pg/ml, p = 0.02). Pregnancy rates were similar in all combination of genotypes. There is currently no strong evidence suggesting that the examination of one gene in relation to genotypes can be effectively used as single tool to improve COS. However, polygenic analysis of different polymorphisms by analyzing the genetic profile of each individual could be useful. Further research is warranted to develop an algorithm that will enable simultaneous analysis of many genes, which combined with hormonal profile could promote treatment individualization.
Collapse
Affiliation(s)
- Anastasia Prodromidou
- Department of Obstetrics and Gynecology, National and Kapodistrian University of Athens School of Medicine, Athens, Greece.
| | - Evangelia Dimitroulia
- Department of Microbiology, Medical School, Biopathology University of Athens, Athens, Greece
| | - Depy Mavrogianni
- Department of Obstetrics and Gynecology, National and Kapodistrian University of Athens School of Medicine, Athens, Greece
| | - Nikolaos Kathopoulis
- Department of Obstetrics and Gynecology, National and Kapodistrian University of Athens School of Medicine, Athens, Greece
| | - Kalliopi I Pappa
- Department of Obstetrics and Gynecology, National and Kapodistrian University of Athens School of Medicine, Athens, Greece
| | - Dimitrios Loutradis
- Athens Medical School, Kapodistrian University of Athens, Fertility Institute, Athens, Greece
| |
Collapse
|
181
|
Stimac R, Tomicic M, Bingulac-Popovic J, Kundid R, Babic I, Hecimovic A, Vuk T, Jukic I. Human neutrophil antigen-1, -3, -4, and -5 allele and genotype frequencies in the Croatian blood donor population and their clinical significance. Transfus Clin Biol 2023; 30:111-5. [PMID: 36243306 DOI: 10.1016/j.tracli.2022.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/05/2022] [Accepted: 10/06/2022] [Indexed: 11/11/2022]
Abstract
OBJECTIVES Human neutrophil antigens (HNAs) and antibodies play an important role in allo- and autoimmunity associated with immune neutropenia and transfusion reactions. The aim of this study was to determine the HNA-1, -3, -4 and -5 allele and genotype frequencies in the Croatian blood donor population to assess the role of HNA-1, -3, -4, and -5 alleles in the development of neonatal alloimmune neutropenia and antibody-mediated transfusion-related acute lung injury. MATERIAL AND METHODS A total of 371 blood samples from unselected healthy blood donors were analyzed. Samples from all 371 donors were genotyped for HNA-1, samples from 160 donors were genotyped for HNA-3, and samples from 142 donors were genotyped for HNA-4 and HNA-5 using the polymerase chain reaction with sequence-specific primers (PCR-SSP) method. RESULTS The frequencies of the FCGR3B*01, FCGR3B*02 and FCGR3B*03 HNA-1 alleles were 0.393, 0.607 and 0.022, and of the SLC44A2*01 and SLC44A2*02 HNA-3 alleles 0.781 and 0.219, respectively. The frequencies of the ITGAM*01 and ITGAM*02 HNA-4 alleles were 0.796 and 0.204, and of the ITGAL*01 and ITGAL*02 HNA-5 alleles 0.718 and 0.282, respectively. CONCLUSION These are the first results on the HNA allele and genotype frequencies in the Croatian blood donor population. We observed no deviations from previous reports on Caucasian populations. Determination of the HNA antigen frequencies in the population is important to estimate the risk of alloimmunization to HNA, especially the risk of fetal-maternal incompatibility and alloantibody production by transfusion of the HNA incompatible blood components.
Collapse
|
182
|
Torres G, Vargas K, Reyes-Vélez J, Jiménez N, Blanchard A, Olivera-Angel M. High genetic diversity and zoonotic potential of Staphylococcus aureus strains recovered from bovine intramammary infections in Colombians dairy herds. Comp Immunol Microbiol Infect Dis 2023; 93:101940. [PMID: 36603241 DOI: 10.1016/j.cimid.2022.101940] [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: 09/06/2022] [Revised: 12/28/2022] [Accepted: 12/30/2022] [Indexed: 01/02/2023]
Abstract
Genotyping of Staphylococcus aureus isolated from mastitis has become a fundamental tool to understand its complex epidemiology and to evaluate spillover events. The aim of this study was to describe the frequency of genotypes of the S. aureus strains isolated from intramammary infections by spa typing technique, and to evaluate the association between genotypes and the ability to form biofilm under in vitro conditions. Sixty-six strains of S. aureus recovered from bovines intramammary infections on 56 dairy herds located in 14 municipalities of the department of Antioquia were characterized. The majority of strains (65/66) were isolated from milk samples collected from dairy cows with subclinical intramammary infections. Nineteen different spa types were found in this study, t521 (19.70%), t267 (15.15%), and t605 (12.12%) being the most frequent. The strains from the t605 spa type showed the highest biofilm production. The high frequency of spa types with zoonotic potential found in this study, identified cattle as an important reservoir of theses clones for people in close proximity, such as milkers and consumers of unpasteurized dairy products.
Collapse
Affiliation(s)
- G Torres
- Biogenesis Research Group, Department of Agricultural Sciences, University of Antioquia, Cra. 75 No. 65-87, Medellín, Antioquia, Colombia; Instituto Colombiano de Medicina Tropical - Universidad CES, Cra. 43A No. 52 sur-99, Sabaneta, Antioquia, Colombia.
| | - K Vargas
- Biogenesis Research Group, Department of Agricultural Sciences, University of Antioquia, Cra. 75 No. 65-87, Medellín, Antioquia, Colombia
| | - J Reyes-Vélez
- Biogenesis Research Group, Department of Agricultural Sciences, University of Antioquia, Cra. 75 No. 65-87, Medellín, Antioquia, Colombia; Instituto Colombiano de Medicina Tropical - Universidad CES, Cra. 43A No. 52 sur-99, Sabaneta, Antioquia, Colombia
| | - N Jiménez
- Basic and Applied Microbiology Research Group, School of Microbiology, University of Antioquia, Cl. 67 No. 53-108, Medellín, Antioquia, Colombia
| | - A Blanchard
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, United Kingdom
| | - M Olivera-Angel
- Biogenesis Research Group, Department of Agricultural Sciences, University of Antioquia, Cra. 75 No. 65-87, Medellín, Antioquia, Colombia
| |
Collapse
|
183
|
Het Lam J, Derkman THJ, van Garderen E, Dijkman R, van Engelen E. Distinct Mannheimia haemolytica serotypes isolated from fatal infections in veal calves and dairy cows. Vet J 2023; 292:105940. [PMID: 36543311 DOI: 10.1016/j.tvjl.2022.105940] [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: 03/26/2022] [Revised: 12/08/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022]
Abstract
Fatal Mannheimia haemolytica (M. haemolytica) infections in cattle, which emerged in the Netherlands between 2004 and 2018, showed two distinct disease presentations: acute fibrinous polyserositis (FPS) in veal calves, and acute fibrinous pleuro-pneumonia (FPP) in adult dairy cattle. To determine whether these presentations were caused by different M. haemolytica genotypes, whole genome sequencing was performed on 96 isolates cultured after necropsy from inflamed sites of veal calves that died of M. haemolytica-associated FPS (n = 49) or with FPP lesions (n = 2), and from dairy cows that died of M. haemolytica-associated FPP (n = 45). Among the 96 M. haemolytica isolates, 93 were shown to belong to either of two large clusters, with 48/51 calf isolates belonging to one, and 43/45 cow isolates and two calf isolates from cases of FPP to the other. All M. haemolytica isolates from veal calves with FPS were of serotype A2, whereas the isolates from dairy cows and two calves with FPP were predominantly of serotypes A1 and A6. Most serotype A2 isolates from veal calves with FPS (95.6 %) contained multiple antibiotic resistance genes (ARGs) against three to five antimicrobial classes (phenicols, sulphonamides, tetracyclines, aminoglycosides or beta-lactams). In contrast, these ARGs were only present in 10.8 % of M. haemolytica A1 and A6 isolates from pneumonic adult cattle and absent in isolates from the two calves with FPP. These two disease presentations appear to be caused by genetically distinct strains with different antimicrobial resistance gene patterns. While M. haemolytica serotype A2 is generally considered to be a commensal microorganism of cattle, it was clearly associated with fatal FPS in veal calves in the Netherlands.
Collapse
Affiliation(s)
- J Het Lam
- Ruminant Health Department, Royal GD (Animal Health Service), Arnsbergstraat 7, 7418 EZ Deventer, the Netherlands.
| | - T H J Derkman
- Ruminant Health Department, Royal GD (Animal Health Service), Arnsbergstraat 7, 7418 EZ Deventer, the Netherlands
| | - E van Garderen
- Laboratory for Pathology and Histology, Royal GD, Arnsbergstraat 7, 7418 EZ Deventer, the Netherlands
| | - R Dijkman
- Research and Development, Molecular Biology Department, Royal GD, Arnsbergstraat 7, 7418 EZ Deventer, the Netherlands
| | - E van Engelen
- Research and Development, Bacteriology Department, Royal GD, Arnsbergstraat 7, 7418 EZ Deventer, the Netherlands
| |
Collapse
|
184
|
Rennert W, Hindiyeh M, Allahham M, Mercer LD, Hamad KI, Ghuneim NI, A. M. Eljaro Z, Abu-Awwad F, Bozya Y, Hjaija D, Bhat N, Leader T, Ramlawi A, Marzouqa H. Introducing ROTAVAC® to the occupied Palestinian Territories: Impact on diarrhea incidence, rotavirus prevalence and genotype composition. Vaccine 2023; 41:945-954. [PMID: 36585280 PMCID: PMC9880560 DOI: 10.1016/j.vaccine.2022.12.046] [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: 07/06/2022] [Revised: 12/16/2022] [Accepted: 12/19/2022] [Indexed: 12/29/2022]
Abstract
BACKGROUND Rotavirus infection remains an important cause of morbidity and mortality in children. The introduction of vaccination programs in more than 100 countries has contributed to a decrease in hospitalizations and mortality. This study investigates the epidemiological impact of the rotavirus vaccine ROTAVAC® in the Palestinian Territories, the first country to switch from ROTARIX® to this new vaccine. METHODS Clinical surveillance data was collected fromchildren younger than 5attendingoutpatient clinics throughout Gaza withdiarrhea between 2015 and 2020. The incidence of all-cause diarrhea was assessed using an interrupted time-series approach. Rotavirus prevalence was determined at the Caritas Baby Hospital in the West Bank usingELISA on stool specimen of children younger than 5with diarrhea. Genotyping was performed on 325 randomly selected rotavirus-positive samples from January 2015 through December 2020 using multiplex PCR analysis. RESULTS Average monthly diarrhea casesdropped by 16.7% annually fromintroduction of rotavirus vaccination in May 2016 to the beginning of the SARS-CoV-2 epidemic in March 2020 for a total of 53%. Case count declines were maintained afterthe switchto ROTAVAC® in October 2018. Rotavirus positivity in stool samples declined by 67.1% over the same period without change followingthe switch to ROTAVAC®. The distribution of predominant genotypes in rotavirus-positive stool samples changed from a pre-vaccination G1P [8] to G9P[8] and G12P[8] during the ROTARIX® period and G2P[4] after the introduction of ROTAVAC®. CONCLUSION ROTAVAC® has shown epidemiological impact on par with ROTARIX® after its introduction to the national immunization schedule in the Palestinian Territories. A molecular genotype shift from a pre-vaccination predominance of G1P[8] to a current predominance of G2P[4] requires more long-term surveillance.
Collapse
Affiliation(s)
- Wolfgang Rennert
- Rostropovich Vishnevskaya Foundation, 1776 K Street, NW, Washington, D.C. 20006, USA,MedStar Georgetown University, 4200 Wisconsin Ave NW, Suite 200, Washington D.C2. 200162, USA,Corresponding author.
| | - Musa Hindiyeh
- Caritas Baby Hospital, Caritas Street, Bethlehem, West Bank, Palestine
| | - Majd Allahham
- Caritas Baby Hospital, Caritas Street, Bethlehem, West Bank, Palestine
| | - Laina D. Mercer
- PATH, 2201 Westlake Avenue, Suite 200, Seattle, WA 98121, USA
| | - Khalil I. Hamad
- Health Department, UNRWA, Al-Azhar Road, Rimal Quarter, Gaza, Palestine
| | - Nedal I. Ghuneim
- Preventive Medicine Department, Ministry of Health, Tal-Sultan-190/82, Rafah, Gaza, Palestine
| | | | - Fakhr Abu-Awwad
- Rostropovich Vishnevskaya Foundation, 1776 K Street, NW, Washington, D.C. 20006, USA
| | - Yaser Bozya
- Public Health General Directorate, Ministry of Health, Ramallah, Palestine
| | - Diaa Hjaija
- Public Health General Directorate, Ministry of Health, Ramallah, Palestine
| | - Niranjan Bhat
- PATH, 2201 Westlake Avenue, Suite 200, Seattle, WA 98121, USA
| | - Troy Leader
- PATH, 2201 Westlake Avenue, Suite 200, Seattle, WA 98121, USA
| | - Asad Ramlawi
- Rostropovich Vishnevskaya Foundation, 1776 K Street, NW, Washington, D.C. 20006, USA
| | - Hiyam Marzouqa
- Caritas Baby Hospital, Caritas Street, Bethlehem, West Bank, Palestine
| |
Collapse
|
185
|
Pardo Gil M, Hegglin D, Briner T, Ruetten M, Müller N, Moré G, Frey CF, Deplazes P, Basso W. High prevalence rates of Toxoplasma gondii in cat-hunted small mammals - Evidence for parasite induced behavioural manipulation in the natural environment? Int J Parasitol Parasites Wildl 2023; 20:108-116. [PMID: 36747510 PMCID: PMC9898578 DOI: 10.1016/j.ijppaw.2023.01.007] [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: 12/22/2022] [Revised: 01/21/2023] [Accepted: 01/21/2023] [Indexed: 01/24/2023]
Abstract
Toxoplasma gondii causes one of the most frequent parasitic infections in vertebrates on earth. The present study aimed to assess the occurrence of T. gondii infection in cat-hunted wild small mammals, and to determine the circulating T. gondii genotypes in cat prey. There is evidence suggesting that T. gondii may manipulate rodents' behaviour enhancing transmission to their definitive feline host by facilitating predation. Given that most studies focusing on rodent behavior have been performed under laboratory conditions, we tested this hypothesis in the natural environment. We analysed 157 cat-hunted wild small mammals of six different species from Switzerland. Brain and skeletal muscle samples from each animal were tested for T. gondii DNA by PCR, and positive samples were genotyped using a multilocus sequence typing approach, including 10 genetic markers. Additionally, to evaluate exposure to cat faeces, the presence of Taenia taeniaeformis metacestodes was investigated at necropsy. The prevalence of T. gondii in cat-hunted Arvicola amphibius s.l. was 11.1% (7/63), 14.6% (7/48) in Apodemus spp., 13.6% (3/22) in Myodes glareolus, 6.7% (1/15) in Crocidura russula, and 0% in Microtus arvalis (0/8) and Sorex sp. (0/1). All completely genotyped T. gondii parasites, exhibited the ToxoDB #3 genotype, a Type II variant. We additionally analysed 48 trap-captured A. amphibius s.l., which all tested negative for T. gondii infection, contrasting with the higher prevalence in cat-hunted A. amphibius s.l. (0% vs. 11.1%; p = 0.0176). Furthermore, T. taeniaeformis was detected in both groups, indicating widespread contamination with cat faeces in the sampled areas. These results provide evidence that T. gondii infected rodents are at higher risk to be predated by cats and therewith support the behaviour manipulation hypothesis.
Collapse
Affiliation(s)
- Miguel Pardo Gil
- Institute of Parasitology, Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122, CH-3012, Bern, Switzerland
- Corresponding author.
| | - Daniel Hegglin
- Institute of Parasitology, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 266a, CH-8057, Zurich, Switzerland
- SWILD– Urban Ecology and Wildlife Research, Wuhrstrasse 12, CH-8003, Zürich, Switzerland
| | - Thomas Briner
- Naturmuseum Solothurn, Klosterplatz 2, CH-4500, Solothurn, Switzerland
| | - Maja Ruetten
- PathoVet AG, Buckstrasse 2, CH-8317, Tagelswangen, Switzerland
| | - Norbert Müller
- Institute of Parasitology, Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122, CH-3012, Bern, Switzerland
| | - Gastón Moré
- Institute of Parasitology, Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122, CH-3012, Bern, Switzerland
| | - Caroline F. Frey
- Institute of Parasitology, Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122, CH-3012, Bern, Switzerland
| | - Peter Deplazes
- Institute of Parasitology, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 266a, CH-8057, Zurich, Switzerland
| | - Walter Basso
- Institute of Parasitology, Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Länggassstrasse 122, CH-3012, Bern, Switzerland
- Corresponding author.
| |
Collapse
|
186
|
Fernandez N, Chua M, Villanueva J, Varela D, Bagli D, Shnorhavorian M. Neural network non-linear modeling to predict hypospadias genotype-phenotype correlation. J Pediatr Urol 2023:S1477-5131(23)00013-X. [PMID: 36709079 DOI: 10.1016/j.jpurol.2023.01.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 12/23/2022] [Accepted: 01/09/2023] [Indexed: 01/19/2023]
Abstract
INTRODUCTION Hypospadias is an abnormal development of the urethral, ventral skin and corporeal bodies. Urethral meatus and ventral curvature have been historically the landmarks to define clinical severity. Genotyping has never been explored as a clinical predictor. Available reports have demonstrated a correlation between genetic mutations and syndromic hypospadias with poor surgical outcomes. We hypothesize that inclusion of genotyping can serve at classifying all types of hypospadias. We present the use of neural network algorithm to evaluate phenotype/genotype correlations and propose its potential clinical applicability. METHODS A systematic review was performed from January 1974 to June 2022. Literature was retrieved from Medline, Embase, Web of Science and Google Scholar. Included manuscripts were those that had an explicit anatomical description of hypospadias phenotype (urethral meatus location following an anatomical description) and a defined genotype (genetic mutation) description. Cases with more than one variant/mutation were excluded. A comprehensive phenotype-genotype statistical analysis using neural network non-linear data modeling SPSS™ was performed. RESULTS Genotype-Phenotype analysis was performed on 1731 subjects. Of those, 959 (55%) were distal and 772 (45%) proximal. 49 genes with mutations were identified. Neural network clustering predicted better for coronal (90%) and glanular (80%), and lowest for midshaft (22%) and perineal (45%). Using genes as predictor factor only, the model was able to highly and more accurately predict the phenotype for coronal and glanular hypospadias. The following genotypes showed association to a specific phenotype: AR gene n.2058G > A for glanular (p<0.0001), n.480C > T for coronal (p = 0.034), R840C for perineal (p = 0.002), MAMLD1 gene c.2960C > T for coronal (p< 0.0001), p. G289S for glanular (p<0.0001), gene SRD5A2 607G > A for scrotal (p<0.0001), c16C > T for penoscrotal (p<0.0001), c59 T > c for perineal (p = 0.042), V89L for midshaft and scrotal (p<0.0001, p = 0.041; respectively). DISCUSSION Hypospadias phenotype has always been described from a purely anatomical perspective. Our results demonstrate that current phenotyping has poor correlation to the genotype. Higher genotype/phenotype correlation for distal hypospadias proves the clinical applicability of genotyping these cases. The concept and classification of differences in sexual development needs to be reconsidered given high positive yield reported for distal hypospadias. Given the better predictive value of genotyping in correlation to the phenotype, future efforts should be directed towards using the genotype. CONCLUSION Hypospadias has poor phenotype/genotype correlation. Sequencing all hypospadias phenotypes may add clinical value if used in association to other predictive variables. Neural network analysis may have the ability to combine all these variables for clinical prediction.
Collapse
Affiliation(s)
- Nicolas Fernandez
- Division of Pediatric Urology. Seattle Children's Hospital. University of Washington. Seattle USA.
| | - Michael Chua
- Division of Pediatric Urology. Hospital for Sick Kids. University of Toronto. Canada
| | - Juliana Villanueva
- Division of Urology. Hospital Universitario San Ignacio. Pontificia Universidad Javeriana. Bogota Colombia
| | - Daniela Varela
- Division of Urology. Hospital Universitario San Ignacio. Pontificia Universidad Javeriana. Bogota Colombia
| | - Darius Bagli
- Division of Pediatric Urology. Hospital for Sick Kids. University of Toronto. Canada
| | - Margarett Shnorhavorian
- Division of Pediatric Urology. Seattle Children's Hospital. University of Washington. Seattle USA
| |
Collapse
|
187
|
Abdulqadir MO, Rashid PMA, Hussain AH, Rahman HS, Ezzaddin SA. Genetic characterization of hepatitis B virus genotypes among patients with chronic infection in Sulaimaniyah city, Iraq. PeerJ 2023; 11:e14454. [PMID: 36655038 PMCID: PMC9841906 DOI: 10.7717/peerj.14454] [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: 05/09/2022] [Accepted: 11/02/2022] [Indexed: 01/15/2023] Open
Abstract
Background Hepatitis B virus (HBV) genotypes are distributed unevenly throughout the world's regions. The researchers' goal in this study was to find out which HBV genotypes are now prevalent in the blood of chronic HBV patients in Iraq's Kurdistan Region's Sulaimaniyah governorate. Methods Genotyping was carried out utilizing Polymerase Chain Reaction (PCR) type-specified primers. Thirty-three chronic HBV patients were included in the HBV genotyping assay. Phylogenic trees of Pre-S1/Pre S2/S genes' nucleotide sequences were constructed using 36 HBV isolates. Results All the patients had HBV genotype D. Additionally, two samples were further analyzed by sequencing and deposited in GenBank as HBV/Sul-1/2021 accession numbers MZ077051 and HBV/Sul-2/2021 accession numbers MZ077052. Phylogenic analysis indicated that the HBV isolates belong to sub-genotype D1/serotype ayw2. The HBV/Sul-2/2021 had two sequence deletion mutations from G61del-T87del, which accounted for 27 amino acid deletions, and ten other mutations were identified in the carboxylic terminus of the pre-S1 from Q104del-R113del. Accordingly, 37 amino acids were deleted in the S promoter region. Several other substitution mutations were recorded in both HBV isolates. Conclusion Patients with chronic HBV were found to have the HBV sub-genotype D1/subtype ayw2 with no mixed genotypes. HBV/Sul-1/2022, a new strain with a 37-amino acid mutation, was found to be distinct from any previously known HBV isolates.
Collapse
Affiliation(s)
- Mardin Othman Abdulqadir
- Medical Laboratory Department, Technical College of Health, Sulaimani Polytechnic University, Republic of Iraq, Sulaimaniyah, Iraq
| | - Peshnyar Muhammad Atta Rashid
- Department of Medical Laboratory Sciences, Komar University of Science and Technology, Sulaimaniyah, Republic of Iraq, Sulaimaniyah, Iraq
| | - Ali Hattem Hussain
- Nursing Department, Technical College of Health, Sulaimani Polytechnic University, Sulaimaniyah, Republic of Iraq, Sulaimaniyah, Iraq
| | - Heshu Sulaiman Rahman
- Department of Physiology, College of Medicine, Sulaimani University, Sulaimaniyah, Republic of Iraq, Sulaimaniyah, Iraq
| | - Shahow Abdulrehman Ezzaddin
- Family and Community Medicine Department, College of Medicine, Sulaimani University, Sulaimaniyah, Republic of Iraq, Sulaimaniyah, Iraq
| |
Collapse
|
188
|
Wang X, Bai Y, Xiang Z, Zeng W, Wu Y, Zhao H, Zhao W, Chen X, Duan M, Li X, Zhu W, Sun K, Wu Y, Zhang Y, Li X, Rosenthal BM, Cui L, Yang Z. Genetic diversity of Plasmodium vivax populations from the China-Myanmar border identified by genotyping merozoite surface protein markers. Trop Med Health 2023; 51:2. [PMID: 36631913 PMCID: PMC9832627 DOI: 10.1186/s41182-022-00492-7] [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: 09/23/2022] [Accepted: 12/20/2022] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Parasite diversity and population structure influence malaria control measures. Malaria transmission at international borders affects indigenous residents and migrants, defying management efforts and resulting in malaria re-introduction. Here we aimed to determine the extent and distribution of genetic variations in Plasmodium vivax populations and the complexity of infections along the China-Myanmar border. METHODS We collected clinical P. vivax samples from local and migrant malaria patients from Laiza and Myitsone, Kachin State, Myanmar, respectively. We characterized the polymorphisms in two P. vivax merozoite surface protein markers, Pvmsp-3α and Pvmsp-3β, by PCR-restriction fragment length polymorphism (PCR-RFLP) analysis. We sought to determine whether these genetic markers could differentiate these two neighboring parasite populations. RESULTS PCR revealed three major size variants for Pvmsp-3α and four for Pvmsp-3β among the 370 and 378 samples, respectively. PCR-RFLP resolved 26 fragment-size alleles by digesting Pvmsp-3α with Alu I and Hha I and 28 alleles by digesting Pvmsp-3β with Pst I. PCR-RFLP analysis of Pvmsp-3α found that infections in migrant laborers from Myitsone bore more alleles than did infections in residents of Laiza, while such difference was not evident from genotyping Pvmsp-3β. Infections originating from these two places contained distinct but overlapping subpopulations of P. vivax. Infections from Myitsone had a higher multiplicity of infection as judged by the size of the Pvmsp-3α amplicons and alleles after Alu I/Hha I digestion. CONCLUSIONS Migrant laborers from Myitsone and indigenous residents from Laiza harbored overlapping but genetically distinct P. vivax parasite populations. The results suggested a more diverse P. vivax population in Myitsone than in the border town of Laiza. PCR-RFLP of Pvmsp-3α offers a convenient method to determine the complexity of P. vivax infections and differentiate parasite populations.
Collapse
Affiliation(s)
- Xun Wang
- grid.285847.40000 0000 9588 0960Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, 650500 Yunnan China
| | - Yao Bai
- grid.285847.40000 0000 9588 0960Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, 650500 Yunnan China
| | - Zheng Xiang
- grid.285847.40000 0000 9588 0960Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, 650500 Yunnan China
| | - Weilin Zeng
- grid.285847.40000 0000 9588 0960Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, 650500 Yunnan China
| | - Yanrui Wu
- grid.285847.40000 0000 9588 0960Department of Cell Biology and Genetics, Kunming Medical University, Kunming, China
| | - Hui Zhao
- grid.285847.40000 0000 9588 0960Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, 650500 Yunnan China
| | - Wei Zhao
- grid.285847.40000 0000 9588 0960Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, 650500 Yunnan China
| | - Xi Chen
- grid.285847.40000 0000 9588 0960Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, 650500 Yunnan China
| | - Mengxi Duan
- grid.285847.40000 0000 9588 0960Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, 650500 Yunnan China
| | - Xiaosong Li
- grid.285847.40000 0000 9588 0960Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, 650500 Yunnan China
| | - Wenya Zhu
- grid.285847.40000 0000 9588 0960Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, 650500 Yunnan China
| | - Kemin Sun
- grid.285847.40000 0000 9588 0960Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, 650500 Yunnan China
| | - Yiman Wu
- grid.285847.40000 0000 9588 0960Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, 650500 Yunnan China
| | - Yanmei Zhang
- grid.285847.40000 0000 9588 0960Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, 650500 Yunnan China
| | - Xiaomei Li
- grid.285847.40000 0000 9588 0960Faculty of Public Health, Kunming Medical University, Kunming, Yunnan Province China
| | - Benjamin M. Rosenthal
- grid.508984.8Animal Parasitic Disease Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD USA
| | - Liwang Cui
- grid.170693.a0000 0001 2353 285XDepartment of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612 USA
| | - Zhaoqing Yang
- grid.285847.40000 0000 9588 0960Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, 650500 Yunnan China
| |
Collapse
|
189
|
Kashi P, Pakdel F, Barhaghi MHS, Rezaee MA, Taghizadeh S, Sadeghi J, Yousefi M, Ghotaslou R, Asgharzadeh M, Gholizadeh P, Kafil HS. Genetic diversity of Mycobacterium tuberculosis isolates from northwest of Iran during COVID-19 era. Egypt J Med Hum Genet 2023; 24:3. [PMID: 37519898 PMCID: PMC9829222 DOI: 10.1186/s43042-023-00383-4] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 12/31/2022] [Indexed: 01/11/2023] Open
Abstract
Background Tuberculosis (TB) is considered one of the most infectious diseases in the world. In this study, we intended to examine the epidemiology of tuberculosis by MIRU-VNTR to define the changes that occur in the transmission of tuberculosis in the region during the COVID-19 era. A total of 120 Mycobacterium tuberculosis isolates were collected from sputum samples of patients referred to East Azerbaijan Center TB from December 2020 to August 2021. Demographic information such as age, sex, place of birth, previous TB history, and relevant medical data was collected. The proportion method was performed for drug susceptibility testing, and the PCR-based MIRU-VNTR method was applied to identify molecular epidemiology relationships. Results The isolates were collected from 78 male (65%) and 39 female (32.5%) Iranian patients and 3 (2.5%) Azerbaijani patients. Ninety-three distinct patterns were identified including 15 clustered patterns and 36 unique patterns. The largest cluster was composed of seven isolates. Furthermore, one cluster with 5 members, four clusters with 3 members, and nine clusters with 2 members. In MIRU-VNTR typing, 75 clusters belonged to the Tabriz region and just 3 to the Republic of Azerbaijan. All isolates were sensitive to rifampin, isoniazid, and ethambutol. Conclusions Results of the current study showed COVID-19 pandemic had a direct effect on the transmission and diagnosis of tuberculosis. Less diagnosis and less clustering can indicate public controls and hygiene, and the use of masks had a direct effect on the transmission and diagnosis of tuberculosis. However, misidentification and less focus on other respiratory infections are expected during the pandemic. Studies on the co-infection of COVID-19 and tuberculosis and the role of mask and sanitization against TB are strongly recommended.
Collapse
Affiliation(s)
- Peyvand Kashi
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Farzaneh Pakdel
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | | | - Sepehr Taghizadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Javid Sadeghi
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mehdi Yousefi
- Research Center for Pharmaceutical Nanotechnology, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Reza Ghotaslou
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Asgharzadeh
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Pourya Gholizadeh
- Research Center for Pharmaceutical Nanotechnology, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| |
Collapse
|
190
|
Taverna CG, Arias BA, Firacative C, Vivot ME, Szusz W, Vivot W, Mazza M, Córdoba SB, Canteros CE. Genotypic Diversity and Antifungal Susceptibility of Clinical Isolates of Cryptococcus Gattii Species Complex from Argentina. Mycopathologia 2023; 188:51-61. [PMID: 36609823 DOI: 10.1007/s11046-022-00705-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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 12/24/2022] [Indexed: 01/09/2023]
Abstract
The aim of this study was to determine the genotypic diversity of 22 Cryptococcus gattii species complex clinical isolates from Argentina and to place these genotypes within the diversity of clinical, veterinary and environmental isolates from Latin America. Mating type and antifungal susceptibility of the isolates were also determined. By URA5-RFLP, nine isolates were identified as molecular type VGI, 10 as VGII, one as VGIII and two as VGIV. Multilocus sequence typing (MSLT), following the International Society for Human and Animal Mycology (ISHAM) consensus MLST scheme, was used to determine the genotypic diversity. Our results suggest that, in Argentina, VGI isolates have low genetic diversity, while VGII isolates have high genetic diversity. Both isolates identified as VGIV by URA5-RFLP were genotyped by MLST as belonging to the currently named VGVI clade. From all isolates, eight sequence types (STs) were unique for Argentina, while five STs have been reported already in other countries, being of high interest the genotypes ST20 and ST7 since they belong to the subtypes VGIIa and VGIIb, respectively, which are associated with hypervirulent strains responsible for outbreaks in North America. To note, geographical analysis showed that some genotypes may be associated with some regions in Argentina. Most isolates were MATα, but we are reporting one isolate MATa for the first time in the country. Antifungal susceptibility tests showed that itraconazole, voriconazole and posaconazole had high activity against all isolates, while amphotericin B, fluconazole and 5-fluorocytosine were the least active drugs against all studied isolates.
Collapse
Affiliation(s)
- Constanza Giselle Taverna
- Departamento Micología, Instituto Nacional de Enfermedades Infecciosas "Dr. Carlos G. Malbrán", Ciudad Autónoma de Buenos Aires, Argentina.
| | - Barbara Abigail Arias
- Departamento Micología, Instituto Nacional de Enfermedades Infecciosas "Dr. Carlos G. Malbrán", Ciudad Autónoma de Buenos Aires, Argentina
| | - Carolina Firacative
- Studies in Translational Microbiology and Emerging Diseases (MICROS) Research Group, School of Medicine and Health Sciences, Universidad de Rosario, Bogotá, Colombia
| | - Matías Ezequiel Vivot
- Departamento Micología, Instituto Nacional de Enfermedades Infecciosas "Dr. Carlos G. Malbrán", Ciudad Autónoma de Buenos Aires, Argentina
| | - Wanda Szusz
- Departamento Micología, Instituto Nacional de Enfermedades Infecciosas "Dr. Carlos G. Malbrán", Ciudad Autónoma de Buenos Aires, Argentina
| | - Walter Vivot
- Departamento Micología, Instituto Nacional de Enfermedades Infecciosas "Dr. Carlos G. Malbrán", Ciudad Autónoma de Buenos Aires, Argentina
| | - Mariana Mazza
- Departamento Micología, Instituto Nacional de Enfermedades Infecciosas "Dr. Carlos G. Malbrán", Ciudad Autónoma de Buenos Aires, Argentina
| | - Susana Beatriz Córdoba
- Departamento Micología, Instituto Nacional de Enfermedades Infecciosas "Dr. Carlos G. Malbrán", Ciudad Autónoma de Buenos Aires, Argentina
| | - Cristina Elena Canteros
- Departamento Micología, Instituto Nacional de Enfermedades Infecciosas "Dr. Carlos G. Malbrán", Ciudad Autónoma de Buenos Aires, Argentina
| |
Collapse
|
191
|
Liu JH, Lan CL, Yao GF, Kong NQ, Luo YW, Li CY, Bi SL. Comparison of pulsed-field gel electrophoresis and a novel amplified intergenic locus polymorphism method for molecular typing of Campylobacter jejuni. Arch Microbiol 2023; 205:49. [PMID: 36595076 DOI: 10.1007/s00203-022-03392-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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/25/2022] [Accepted: 12/27/2022] [Indexed: 01/04/2023]
Abstract
Campylobacter is regarded as the leading cause of zoonotic diseases and Campylobacter jejuni (C. jejuni) is one of the predominant pathogenic species. To track C. jejuni infections, various genotyping methods have been used. In this study, amplified intergenic locus polymorphism (AILP) was used to type C. jejuni for the first time. To confirm its feasibility, pulsed-field gel electrophoresis (PFGE) was performed as a control, and the results obtained by the AILP and PFGE methods were compared. Fifty-one isolates were resolved into 34 and 29 different genotypes with Simpson's indices of 0.976 and 0.967 using the AILP and PFGE methods, respectively. The adjusted Rand coefficient of the two approaches was as high as 0.845. In summary, the data showed that the two genotyping methods were similar for discriminating isolates and were both appropriate methods to distinguish whether two isolates were indistinguishable, but the AILP was faster and less costly than PFGE. Therefore, the AILP is a reliable, rapid, and highly discriminative method to genotype C. jejuni collected from poultry meat, which is helpful to effectively monitor C. jejuni.
Collapse
Affiliation(s)
- Jin-Hong Liu
- School of Food Science, Guangdong Pharmaceutical University, Zhongshan, 528458, People's Republic of China
| | - Cheng-Lu Lan
- School of Food Science, Guangdong Pharmaceutical University, Zhongshan, 528458, People's Republic of China
| | - Ge-Feng Yao
- School of Food Science, Guangdong Pharmaceutical University, Zhongshan, 528458, People's Republic of China
| | - Nian-Qing Kong
- School of Food Science, Guangdong Pharmaceutical University, Zhongshan, 528458, People's Republic of China
| | - Yong-Wen Luo
- School of South, China Agricultural University, Guangzhou, 510642, People's Republic of China
| | - Chu-Yi Li
- School of Food Science, Guangdong Pharmaceutical University, Zhongshan, 528458, People's Republic of China
| | - Shui-Lian Bi
- School of Food Science, Guangdong Pharmaceutical University, Zhongshan, 528458, People's Republic of China.
| |
Collapse
|
192
|
Gamaleldin MA, Imbaby SAE. Association of two ARID5B gene variant single nucleotide polymorphisms with acute lymphoblastic leukemia in the Egyptian population. Asian Pac J Cancer Prev 2023; 24:337-343. [PMID: 36708585 PMCID: PMC10152858 DOI: 10.31557/apjcp.2023.24.1.337] [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: 09/10/2022] [Indexed: 05/04/2023] Open
Abstract
BACKGROUND ARID5B SNPs have been linked to ALL in many research studies in which it was identified as a risk factor. From this context, we had great interest to investigate the relationship between ARID5B rs4948488 and ARID5B rs2893881 genotypes and ALL susceptibility and relapse in this study. MATERIALS AND METHODS Peripheral blood mononuclear cells were analyzed for ARID5B rs4948488 and rs2893881 gene polymorphisms by real-time quantitative polymerase chain reaction in 80 ALL patients and 80 controls. RESULTS Our results showed that the C/C genotype of ARID5B rs4948488 and A/G genotype and G-allele of rs2893881 were linked to higher ALL incidence. Regarding the relapse of ALL, rs4948488 C/C genotype and C-alleles were significantly associated with relapse of ALL. Meanwhile, rs4948488 C/C genotype and rs2893881 A/A genotype and A-allele are associated with T-ALL, while rs2893881 A/G genotype and G-allele are associated with B-ALL. CONCLUSION The results of our study suggested that ARID5B rs4948488 and rs2893881 SNPs might be used risk factors for genetic susceptibility for B-ALL and T-ALL, and that ARID5B s4948488 is related to relapse in ALL patients.<br />.
Collapse
|
193
|
Hernández-Castro C, Dashti A, Vusirikala A, Balasegaram S, Köster PC, Bailo B, Imaña E, López A, Llorente MT, González-Barrio D, Sánchez S, Carmena D. Prevalence and temporal dynamics of Cryptosporidium spp., Giardia duodenalis, and Blastocystis sp. among toddlers attending day-care centres in Spain. A prospective molecular-based longitudinal study. Eur J Pediatr 2023; 182:213-223. [PMID: 36282323 DOI: 10.1007/s00431-022-04662-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 09/26/2022] [Accepted: 10/13/2022] [Indexed: 01/12/2023]
Abstract
Giardia duodenalis, Cryptosporidium spp., and Blastocystis sp. are common intestinal eukaryotic parasites affecting children in developed and resource-limited countries. Lack of information on the epidemiology and long-term stability in asymptomatic children complicates interpretation of transmission and pathogenesis. To assess the occurrence, genetic diversity, and temporal dynamics of intestinal eukaryotic parasites in young children, 679 stool samples from 125 toddlers attending six public day-care centres in Central Spain were collected bimonthly within a 1-year period. Detection and identification of species/genotypes were based on PCR and Sanger sequencing methods. Four eukaryotic species were identified: G. duodenalis (2.5‒31.6%), Cryptosporidium spp. (0.0‒2.4%), Blastocystis sp. (2.5‒6.4%), and Entamoeba dispar (0.0‒0.9%). Entamoeba histolytica and Enterocytozoon bieneusi were undetected. Sequence analyses identified assemblage A (63.6%) and B (36.4%) within G. duodenalis (n = 11), C. hominis (40%), C. parvum (40%), and C. wrairi (20%) within Cryptosporidium spp. (n = 5), and ST1 (3.8%), ST2 (46.2%), ST3 (15.4%), and ST4 (34.6%) within Blastocystis sp. (n = 26). Giardia duodenalis sub-assemblage AII/AIII was detected in a toddler for 10 consecutive months. Stable carriage of Blastocystis ST2 allele 9, ST3 allele 34, and ST4 allele 42 was demonstrated in five toddlers for up to 1 year. Conclusions: Giardia duodenalis and Blastocystis sp. were common in toddlers attending day-care centres in Central Spain. Long-term infection/colonization periods by the same genetic variant were observed for G. duodenalis (up to 10 months) and Blastocystis sp. (up to 12 months). What is Known: • Asymptomatic carriage of G. duodenalis and Blastocystis sp. is frequent in toddlers. • The epidemiology and long-term stability of these eukaryotes in asymptomatic young children is poorly understood. What is New: • Long-term colonization/infection periods by the same genetic variant were described for Blastocystis sp. (up to 12 months) and G. duodenalis (up to 10 months).
Collapse
Affiliation(s)
- Carolina Hernández-Castro
- Parasitology Reference and Research Laboratory, National Centre for Microbiology, 28220, Majadahonda, Madrid, Spain.,Parasitology Group, Faculty of Medicine, Academic Corporation for the Study of Tropical Pathologies, University of Antioquia, Medellín, Colombia
| | - Alejandro Dashti
- Parasitology Reference and Research Laboratory, National Centre for Microbiology, 28220, Majadahonda, Madrid, Spain
| | - Amoolya Vusirikala
- UK Field Epidemiology Training Programme, UK Health Security Agency, London, SE1 8UG, UK
| | | | - Pamela Carolina Köster
- Parasitology Reference and Research Laboratory, National Centre for Microbiology, 28220, Majadahonda, Madrid, Spain
| | - Begoña Bailo
- Parasitology Reference and Research Laboratory, National Centre for Microbiology, 28220, Majadahonda, Madrid, Spain
| | - Elena Imaña
- Parasitology Reference and Research Laboratory, National Centre for Microbiology, 28220, Majadahonda, Madrid, Spain
| | - Andrea López
- Food and Waterborne Bacterial Infections Reference and Research Laboratory, National Centre for Microbiology, 28220, Majadahonda, Madrid, Spain
| | - María Teresa Llorente
- Food and Waterborne Bacterial Infections Reference and Research Laboratory, National Centre for Microbiology, 28220, Majadahonda, Madrid, Spain
| | - David González-Barrio
- Parasitology Reference and Research Laboratory, National Centre for Microbiology, 28220, Majadahonda, Madrid, Spain
| | - Sergio Sánchez
- Food and Waterborne Bacterial Infections Reference and Research Laboratory, National Centre for Microbiology, 28220, Majadahonda, Madrid, Spain.
| | - David Carmena
- Parasitology Reference and Research Laboratory, National Centre for Microbiology, 28220, Majadahonda, Madrid, Spain. .,CIBER Infectious Diseases (CIBERINFEC), Health Institute Carlos III, Madrid, Spain.
| |
Collapse
|
194
|
Brusa A, Patterson E, Fleming M. Modifications of Kompetitive Allele-Specific PCR (KASP) Genotyping for Detection of Rare Alleles. Methods Mol Biol 2023; 2638:173-189. [PMID: 36781642 DOI: 10.1007/978-1-0716-3024-2_12] [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] [Indexed: 04/27/2023]
Abstract
KASP is commonly used to genotype bi-allelic SNPs and In/Dels, and the standard protocol works well when both alleles are nearly equally prevalent in the DNA template. To detect rare alleles in bulked samples or to distinguish more than three genotypes, such as tri-allelic loci or mutations across orthologous genes in polyploids, adjustments to the protocol and/or data analysis are required. In this chapter, we present modified protocols for these non-traditional applications, including reaction conditions that enhance the fluorophore signal from rare alleles, resulting in increased KASP assay sensitivity. We also describe alternative KASP data analysis approaches that increase statistical certainty of genotyping calls. Furthermore, this increased assay sensitivity enables high-throughput genotyping using KASP, as samples can be pooled and tested in a single reaction. For example, rare alleles can be detected in mixed seed pools when present in ratios as low as 1 in 200. The assay modifications presented here expand the options available for complex genotyping, and retain KASP's advantages of being cheap, fast, and accurate.
Collapse
Affiliation(s)
- Anthony Brusa
- Department of Agronomy and Plant Genetics, University of Minnesota, Minneapolis, MN, USA.
| | - Eric Patterson
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Margaret Fleming
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| |
Collapse
|
195
|
Lichtmannsperger K, Harl J, Roehl SR, Schoiswohl J, Eibl C, Wittek T, Hinney B, Wiedermann S, Joachim A. Enterocytozoon bieneusi in fecal samples from calves and cows in Austria. Parasitol Res 2023; 122:333-340. [PMID: 36394671 PMCID: PMC9669533 DOI: 10.1007/s00436-022-07733-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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 11/12/2022] [Indexed: 11/18/2022]
Abstract
Enterocytozoon bieneusi is an obligate intracellular pathogen that infects livestock, companion animals, and wildlife and has the potential to cause severe diarrhea especially in immunocompromised humans. In the underlying study, fecal samples from 177 calves with diarrhea and 174 adult cows originating from 70 and 18 farms, respectively, in Austria were examined for the presence of E. bieneusi by polymerase chain reaction targeting the Internal Transcribed Spacer 1 (ITS1) region. All positive samples were further sequenced for genotype determination. Overall, sixteen of the 351 (4.6%) samples were positive for E. bieneusi, two of the 174 samples from cows (1.2%) and 14 of the 177 samples from calves (7.9%). In total, four genotypes, J (n = 2), I (n = 12), BEB4 (n = 3), and BEB8 (n = 1), were identified. The uncorrected p-distance between the four ITS1 lineages (344 bp) ranges from 0.3% to 2.9%. The lineages differ by 1 bp (I and J), 2 bp (J and BEB4), and 3 bp (I and BEB4), respectively, and BEB8 differs by 7 to 10 bp from the latter three lineages. Two of the E. bieneusi-positive calves showed an infection with two different genotypes. E. bieneusi occurred significantly more often in calves > 3 weeks (8/59) than in calves ≤ 3 weeks (6/118), respectively (p = 0.049). Calves with a known history of antimicrobial treatment (50 of 177 calves) shed E. bieneusi significantly more often than untreated calves (p = 0.012). There was no statistically significant difference in E. bieneusi shedding in calves with or without a medical history of antiparasitic treatment (p = 0.881). Calves showing a co-infection with Eimeria spp. shed E. bieneusi significantly more often than uninfected calves (p = 0.003). To our knowledge, this is the first report of E. bieneusi in cattle in Austria. Cattle should be considered as a reservoir for human infection since potentially zoonotic E. bieneusi genotypes were detected.
Collapse
Affiliation(s)
- Katharina Lichtmannsperger
- Department for Farm Animals and Veterinary Public Health, University Clinic for Ruminants, University of Veterinary Medicine Vienna, Vienna, Austria.
| | - Josef Harl
- Institute of Pathology, Department of Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Sarah Rosa Roehl
- Department for Farm Animals and Veterinary Public Health, University Clinic for Ruminants, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Julia Schoiswohl
- Department for Farm Animals and Veterinary Public Health, University Clinic for Ruminants, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Cassandra Eibl
- Department for Farm Animals and Veterinary Public Health, University Clinic for Ruminants, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Thomas Wittek
- Department for Farm Animals and Veterinary Public Health, University Clinic for Ruminants, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Barbara Hinney
- Institute of Parasitology, Department of Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Sandra Wiedermann
- Institute of Parasitology, Department of Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Anja Joachim
- Institute of Parasitology, Department of Pathobiology, University of Veterinary Medicine Vienna, Vienna, Austria
| |
Collapse
|
196
|
Wang Y, He L, Huang J, Li J, Liu L, Xu Y, Peng T, Yang X, Zhao Y, Fu C, Huang S, Tang H, Xu K. Association of Nogo-A Gene Polymorphisms with Cerebral Palsy in Southern China: A Case-Control Study. Dev Neurosci 2023; 45:8-18. [PMID: 36323241 PMCID: PMC10129029 DOI: 10.1159/000527801] [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: 01/12/2022] [Accepted: 10/26/2022] [Indexed: 03/10/2023] Open
Abstract
Cerebral palsy (CP) is a motor and postural disorder syndrome caused by the nonprogressive dysfunction of the developing brain. Previous studies strongly indicated that the Nogo-A gene might be related to the pathogenesis of CP. The objective of this research was to explore the relationship between Nogo-A polymorphisms (rs1012603, rs12464595, and rs2864052) and CP in Southern China. The Hardy-Weinberg equilibrium (HWE) testing, allele and genotype frequencies analysis, and haplotype association analysis were applied to the genotyping of 592 CP children and 600 controls. The results showed that the allele and genotype frequencies of rs1012603 of CP group were significantly different from the control group. The haplotype "TTGGG" was significantly associated with an increased risk of CP. The allele frequencies of rs1012603 were significant differences between CP with spastic diplegia, female CP cases, and controls. Furthermore, significant differences in allele and genotype frequencies were also noticed between GMFCS I of CP and controls for rs1012603, and significant differences in allele and genotype frequencies were observed between the ADL (>9) of CP and controls for rs1012603 and rs12464595. This study showed that the SNPs rs1012603 of Nogo-A were significantly correlated with CP, and the correlations were also found in spastic diplegia, GMFCS I of CP, ADL (>9) of CP, and female subgroups, indicating that Nogo-A might mainly affect mild types of CP and there might be sex-related differences.
Collapse
Affiliation(s)
- Yuxin Wang
- Department of Rehabilitation, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Lu He
- Department of Rehabilitation, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Jingyu Huang
- Department of Rehabilitation, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Jinling Li
- Department of Rehabilitation, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Liru Liu
- Department of Rehabilitation, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Yunxian Xu
- Department of Rehabilitation, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Tingting Peng
- Department of Rehabilitation, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Xubo Yang
- Department of Rehabilitation, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Yiting Zhao
- Department of Rehabilitation, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Chaoqiong Fu
- Department of Rehabilitation, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Shiya Huang
- Department of Rehabilitation, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Hongmei Tang
- Department of Rehabilitation, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Kaishou Xu
- Department of Rehabilitation, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| |
Collapse
|
197
|
Mackenzie M, Fower A, Allan AJ, Codner GF, Bunton-Stasyshyn RK, Teboul L. Genotyping Genome-Edited Founders and Subsequent Generation. Methods Mol Biol 2023; 2631:103-134. [PMID: 36995665 DOI: 10.1007/978-1-0716-2990-1_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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Targeted nucleases allow the production of many types of genetic mutations directly in the early embryo. However, the outcome of their activity is a repair event of unpredictable nature, and the founder animals that are produced are generally of a mosaic nature. Here, we present the molecular assays and genotyping strategies that will support the screening of the first generation for potential founders and the validation of positive animals in the subsequent generation, according to the type of mutation generated.
Collapse
Affiliation(s)
| | - Alex Fower
- The Mary Lyon Centre, MRC Harwell, Didcot, Oxon, UK
| | | | | | | | - Lydia Teboul
- The Mary Lyon Centre, MRC Harwell, Didcot, Oxon, UK.
| |
Collapse
|
198
|
Johne R, Tausch SH, Schilling-Loeffler K, Ulrich RG. Genome sequence analysis of a novel rotavirus strain indicates a broad genetic diversity of rotavirus A in shrews. Infect Genet Evol 2023; 107:105392. [PMID: 36494067 DOI: 10.1016/j.meegid.2022.105392] [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: 09/26/2022] [Revised: 12/01/2022] [Accepted: 12/05/2022] [Indexed: 12/12/2022]
Abstract
Rotavirus A (RVA) is an etiologic agent of diarrhea in humans and animals. It shows a high degree of genetic heterogeneity. Although distinct associations of RVA genotypes with certain host species are common, interspecies-transmission has also been described. Recently, RVA strains, which are genetically distinct and cluster basally to all other RVA strains in phylogenetic trees, have been identified in common shrews (Sorex araneus). Here, the genome sequence analysis of another RVA strain (RVA/Common Shrew-wt/GER/KS11-0893/2010/G42P[58]) from a common shrew from Germany is described. Generally, the strain shows low sequence identities to established strains, which is reflected by the assessment of the novel genotypes G42-P[58]-I32-R28-C24-M24-A39-N28-T28-E32-H28 to its genome segments. Specifically, the strain is phylogenetically distant from previously described RVA strains of common shrews, whereas it is more closely related to other avian and mammalian RVA strains including those from Asian house shrews (Suncus murinus). The results indicate that a broad variety of diverse RVA strains can be found in shrews suggesting a significant role of these animals in rotavirus evolution.
Collapse
Affiliation(s)
- Reimar Johne
- Department of Biological Safety, German Federal Institute for Risk Assessment, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany.
| | - Simon H Tausch
- Department of Biological Safety, German Federal Institute for Risk Assessment, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Katja Schilling-Loeffler
- Department of Biological Safety, German Federal Institute for Risk Assessment, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Rainer G Ulrich
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493 Greifswald-Insel Riems, Germany; Partner site Hamburg-Lübeck-Borstel-Riems, German Centre for Infection Research (DZIF), Südufer 10, 17493 Greifswald-Insel Riems, Germany
| |
Collapse
|
199
|
Lintott LG, Nutter LMJ. Genetic and Molecular Quality Control of Genetically Engineered Mice. Methods Mol Biol 2023; 2631:53-101. [PMID: 36995664 DOI: 10.1007/978-1-0716-2990-1_3] [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] [Indexed: 03/31/2023]
Abstract
Genetically engineered mice are used as avatars to understand mammalian gene function and develop therapies for human disease. During genetic modification, unintended changes can occur, and these changes may result in misassigned gene-phenotype relationships leading to incorrect or incomplete experimental interpretations. The types of unintended changes that may occur depend on the allele type being made and the genetic engineering approach used. Here we broadly categorize allele types as deletions, insertions, base changes, and transgenes derived from engineered embryonic stem (ES) cells or edited mouse embryos. However, the methods we describe can be adapted to other allele types and engineering strategies. We describe the sources and consequ ences of common unintended changes and best practices for detecting both intended and unintended changes by screening and genetic and molecular quality control (QC) of chimeras, founders, and their progeny. Employing these practices, along with careful allele design and good colony management, will increase the chance that investigations using genetically engineered mice will produce high-quality reproducible results, to enable a robust understanding of gene function, human disease etiology, and therapeutic development.
Collapse
Affiliation(s)
- Lauri G Lintott
- The Centre for Phenogenomics, Toronto, ON, Canada
- The Hospital for Sick Children, Toronto, ON, Canada
| | - Lauryl M J Nutter
- The Centre for Phenogenomics, Toronto, ON, Canada.
- The Hospital for Sick Children, Toronto, ON, Canada.
| |
Collapse
|
200
|
Escamilla-Guerrero G, García-Rosales JC. [ Genotyping and its applications, a look to the future]. Rev Med Inst Mex Seguro Soc 2023; 61:S37-S45. [PMID: 36378105 PMCID: PMC10396029] [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] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/19/2022] [Indexed: 06/16/2023]
Abstract
The detection of the most significant erythrocyte antigens present in each one of the individuals is fundamental when carrying out a transfusion or a transplant. Detection to date is performed by conventional serological methods through the antigen-antibody reaction. But several drawbacks may arise depending on the pathology under study, limiting the availability of blood components. Molecular methods such as genotyping is a tool that complements sensitivity and specificity and has come to revolutionize immunohematology in the blood bank, allowing not only the detection of erythrocyte antigens but also platelet antigens. These methodologies are applicable in patients and in large-scale donors, starting from the allelic variants present in each of the genes that code for the antigens of clinical interest, using microarray systems or systems based on particles labeled with specific probes or their variants that allow an analysis from the immunohematological point of view.
Collapse
Affiliation(s)
- Guillermo Escamilla-Guerrero
- Limogen, Laboratorio de Innovación Molecular y Genética, Laboratorio de Biología Molecular e Inmunohematología. Tlalnepantla, Estado de México, MéxicoLimogenMéxico
| | - Juan Carlos García-Rosales
- Limogen, Laboratorio de Innovación Molecular y Genética, Laboratorio de Biología Molecular e Inmunohematología. Tlalnepantla, Estado de México, MéxicoLimogenMéxico
| |
Collapse
|